Biofelsefe — Biokimya Terimleri
NFA 2020 / Aziz Yardımlı

 

Biofelsefe — Terimler / BİOKİMYA

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SİTE İÇİ ARAMA       
 

📹 What is Biochemistry? (VİDEO)

📹 What is Biochemistry? (LINK)

What is Biochemistry, and what do biochemists study? What is covered in this field, as opposed to Molecular Biology or Cell Biology? The truth is, there’s a lot of overlap in these disciplines. But in general, biochemistry is the study of the chemistry of life.

What’s so special about the molecules of life? It’s a case of emergent properties. When biochemical molecules interact, unexpected complexities arise! Phospholipids form the bilayers found in cells. These compartments allow for high concentrations of chemical reactions to take place, leading to...life.

The four main types of biological molecules studied by biochemists are proteins, carbohydrates, lipids, and nucleic acids. This video briefly introduces these topics, and each one will be covered in more depth in their own videos.

Our series on Biology is aimed at the first-year college level, including pre-med students.

 



 
a
acide
An acid is a molecule or ion capable of donating a proton (hydrogen ion H+) (a Brønsted–Lowry acid), or, alternatively, capable of forming a covalent bond with an electron pair (a Lewis acid). (W)

Many biologically important molecules are acids. Nucleic acids, which contain acidic phosphate groups, include DNA and RNA. Nucleic acids contain the genetic code that determines many of an organism's characteristics, and is passed from parents to offspring. DNA contains the chemical blueprint for the synthesis of proteins which are made up of amino acid subunits. Cell membranes contain fatty acid esters such as phospholipids. (W)


Acetic acid, a weak acid, donates a proton (hydrogen ion, highlighted in green) to water in an equilibrium reaction to give the acetate ion and the hydronium ion. Red: oxygen, black: carbon, white: hydrogen.
 
acid, organic
An organic acid is an organic compound with acidic properties. The most common organic acids are the carboxylic acids, whose acidity is associated with their carboxyl group –COOH. Sulfonic acids, containing the group –SO2OH, are relatively stronger acids. Alcohols, with –OH, can act as acids but they are usually very weak. The relative stability of the conjugate base of the acid determines its acidity. Other groups can also confer acidity, usually weakly: the thiol group –SH, the enol group, and the phenol group. In biological systems, organic compounds containing these groups are generally referred to as organic acids. (W)



The general structure of a few weak organic acids. From left to right: phenol, enol, alcohol, thiol. The acidic hydrogen in each molecule is colored red.
The general structure of a few organic acids. From left to right: carboxylic acid, sulfonic acid. The acidic hydrogen in each molecule is colored red.

 
adenin

Adenine (A, Ade) is a nucleobase (a purine derivative). It is one of the four nucleobases in the nucleic acid of DNA that are represented by the letters G–C–A–T. The three others are guanine, cytosine and thymine. Its derivatives have a variety of roles in biochemistry including cellular respiration, in the form of both the energy-rich adenosine triphosphate (ATP) and the cofactors nicotinamide adenine dinucleotide (NAD) and flavin adenine dinucleotide (FAD). It also has functions in protein synthesis and as a chemical component of DNA and RNA. The shape of adenine is complementary to either thymine in DNA or uracil in RNA.

The adjacent image shows pure adenine, as an independent molecule. When connected into DNA, a covalent bond is formed between deoxyribose sugar and the bottom left nitrogen (thereby removing the existing hydrogen atom). The remaining structure is called an adenine residue, as part of a larger molecule. Adenosine is adenine reacted with ribose, as used in RNA and ATP; deoxyadenosine is adenine attached to deoxyribose, as used to form DNA. (W)


🛑 Adenine

  • DNA’daki dört nükleobazdan biri (G–C–A–T; adenin, guanin, cytosin, adenin ve thymin).
  • Protein sentezinde işlevsel.

 





Adenine structure, with standard numbering of positions in red..
 


3D balls - Adenine.


3D vdW - Adenine.

 

 
adenosine diphosphate

Adenosine diphosphate (ADP), also known as adenosine pyrophosphate (APP), is an important organic compound in metabolism and is essential to the flow of energy in living cells. ADP consists of three important structural components: a sugar backbone attached to adenine and two phosphate groups bonded to the 5 carbon atom of ribose. The diphosphate group of ADP is attached to the 5’ carbon of the sugar backbone, while the adenosine attaches to the 1’ carbon.


ADP can be interconverted to adenosine triphosphate (ATP) and adenosine monophosphate (AMP). ATP contains one more phosphate group than does ADP. AMP contains one fewer phosphate group. Energy transfer used by all living things is a result of dephosphorylation of ATP by enzymes known as ATPases. The cleavage of a phosphate group from ATP results in the coupling of energy to metabolic reactions and a by-product of ADP. ATP is continually reformed from lower-energy species ADP and AMP. The biosynthesis of ATP is achieved throughout processes such as substrate-level phosphorylation, oxidative phosphorylation, and photophosphorylation, all of which facilitate the addition of a phosphate group to ADP. (W)



Skeletal formula of ADP.
 


Ball-and-stick model of ADP (shown here as a 3- ion).
 
adenosine monophosphate

Adenosine monophosphate (AMP), also known as 5'-adenylic acid, is a nucleotide. AMP consists of a phosphate group, the sugar ribose, and the nucleobase adenine; it is an ester of phosphoric acid and the nucleoside adenosine. As a substituent it takes the form of the prefix adenylyl-.

AMP plays an important role in many cellular metabolic processes, being interconverted to ADP and/or ATP. AMP is also a component in the synthesis of RNA.(W)



Skeletal formula of AMP.
   


Ball-and-stick model of AMP.

 

 
adenosine triphosphate

Adenosine triphosphate (ATP) is an organic compound that provides energy to drive many processes in living cells, e.g. muscle contraction, nerve impulse propagation, and chemical synthesis. Found in all known forms of life, ATP is often referred to as the "molecular unit of currency" of intracellular energy transfer. When consumed in metabolic processes, it converts either to adenosine diphosphate (ADP) or to adenosine monophosphate (AMP). Other processes regenerate ATP so that the human body recycles its own body weight equivalent in ATP each day. It is also a precursor to DNA and RNA, and is used as a coenzyme.

From the perspective of biochemistry, ATP is classified as a nucleoside triphosphate, which indicates that it consists of three components: a nitrogenous base (adenine), the sugar ribose, and the triphosphate. (W)



Structure of adenosine triphosphate (ATP), protonated.


Structure of adenosine triphosphate (ATP), a central intermediate in energy metabolism.


Structure of adenosine triphosphate (ATP), protonated.

Animation (LINK)
 
alcohol

In chemistry, alcohol is an organic compound that carries at least one hydroxyl functional group (−OH) bound to a saturated carbon atom. The term alcohol originally referred to the primary alcohol ethanol (ethyl alcohol), which is used as a drug and is the main alcohol present in alcoholic beverages. An important class of alcohols, of which methanol and ethanol are the simplest members, includes all compounds for which the general formula is CnH2n+1OH. Simple monoalcohols that are the subject of this article include primary (RCH2OH), secondary (R2CHOH) and tertiary (R3COH) alcohols.

The suffix -ol appears in the IUPAC chemical name of all substances where the hydroxyl group is the functional group with the highest priority. When a higher priority group is present in the compound, the prefix hydroxy- is used in its IUPAC name. The suffix -ol in non-IUPAC names (such as paracetamol or cholesterol) also typically indicates that the substance is an alcohol. However, many substances that contain hydroxyl functional groups (particularly sugars, such as glucose and sucrose) have names which include neither the suffix -ol, nor the prefix hydroxy-. (W)



Ball-and-stick model of an alcohol molecule (R3COH). The red and grey balls represent the hydroxyl group (-OH). The three "R's" stand for carbon substituents or hydrogen atoms.


The bond angle between an hydroxyl group (-OH) and a chain of carbon atoms (R).
 
 
aldehyde

An aldehyde is a compound containing a functional group with the structure −CHO, consisting of a carbonyl center (a carbon double-bonded to oxygen) with the carbon atom also bonded to hydrogen and to an R group, which is any generic alkyl or side chain. The group—without R—is the aldehyde group, also known as the formyl group. Aldehydes are common in organic chemistry, and many fragrances are or contain aldehydes.(W)



These are the two-dimensional chemical structures of important aldehydes. The aldehyde group is colored red. The structures are labeled with numbers (1 through 8) as follows... formaldehyde formaldehyde's trimer, 1,3,5-trioxane [chair conformation] acetaldehyde acetaldehyde's enol, vinyl alcohol α-D-glucopyranose [chair conformation] cinnamaldehyde retinal pyridoxal.

📂 Examples of aldehydes

Examples of aldehydes

 



 
alkane
In organic chemistry, an alkane, or paraffin (a historical name that also has other meanings) , is an acyclic saturated hydrocarbon. In other words, an alkane consists of hydrogen and carbon atoms arranged in a tree structure in which all the carbon–carbon bonds are single. Alkanes have the general chemical formula CnH2n+2. The alkanes range in complexity from the simplest case of methane (CH4), where n = 1 (sometimes called the parent molecule), to arbitrarily large and complex molecules, like pentacontane (C50H102) or 6-ethyl-2-methyl-5-(1-methylethyl) octane, an isomer of tetradecane (C14H30). (W)

 
   
Chemical structure of methane, the simplest alkane.  

📹 Alkanes & Alkenes (VİDEO)

📹 Alkanes & Alkenes (LINK)

Learn the basics of alkanes and alkenes. After watching the covalent bonds video you should have sufficient knowledge to understand about how alkanes and alkenes are formed and the differences between them.

 



 
amide
In organic chemistry, an amide, also known as an organic amide or a carboxamide, is a compound with the general formula RC(=O)NR′R″, where R, R′, and R″ represent organic groups or hydrogen atoms. The amide group is called a peptide bond when it is part of the main chain of a protein, and isopeptide bond when it occurs in a side chain, such as in the amino acids asparagine and glutamine. It can be viewed as a derivative of a carboxylic acid RC(=O)OH with the hydroxyl group –OH replaced by an amine group –NR′R″; or, equivalently, an acyl (alkanoyl) group RC(=O)– joined to an amine group. (W)



General structure of an amide (specifically, a carboxamide).


Formamide, the simplest amide.

 
amine

In organic chemistry, amines are compounds and functional groups that contain a basic nitrogen atom with a lone pair. Amines are formally derivatives of ammonia, wherein one or more hydrogen atoms have been replaced by a substituent such as an alkyl or aryl group (these may respectively be called alkylamines and arylamines; amines in which both types of substituent are attached to one nitrogen atom may be called alkylarylamines). Important amines include amino acids, biogenic amines, trimethylamine, and aniline.


The substituent -NH2 is called an amino group.


Compounds with a nitrogen atom attached to a carbonyl group, thus having the structure R–CO–NR′R″, are called amides and have different chemical properties from amines. (W)

 
   
Primary (1°) amine.  
 
   
Secondary (2°) amine.  
 
   
Tertiary (3°) amine.  
 
amino acid
Amino acids are organic compounds that contain amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) specific to each amino acid. The key elements of an amino acid are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N), although other elements are found in the side chains of certain amino acids. About 500 naturally occurring amino acids are known (though only 20 appear in the genetic code) and can be classified in many ways. (W)

📂 Amino acids

Amino acids

Amino acids (W)

Amino acids contain both amino and carboxylic acid functional groups. (In biochemistry, the term amino acid is used when referring to those amino acids in which the amino and carboxylate functionalities are attached to the same carbon, plus proline which is not actually an amino acid).

Modified amino acids are sometimes observed in proteins; this is usually the result of enzymatic modification after translation (protein synthesis). For example, phosphorylation of serine by kinases and dephosphorylation by phosphatases is an important control mechanism in the cell cycle. Only two amino acids other than the standard twenty are known to be incorporated into proteins during translation, in certain organisms:

Besides those used in protein synthesis, other biologically important amino acids include carnitine (used in lipid transport within a cell), ornithine, GABA and taurine.

 

Protein structure

The particular series of amino acids that form a protein is known as that protein's primary structure. This sequence is determined by the genetic makeup of the individual. It specifies the order of side-chain groups along the linear polypeptide "backbone".

Proteins have two types of well-classified, frequently occurring elements of local structure defined by a particular pattern of hydrogen bonds along the backbone: alpha helix and beta sheet. Their number and arrangement is called the secondary structure of the protein. Alpha helices are regular spirals stabilized by hydrogen bonds between the backbone CO group (carbonyl) of one amino acid residue and the backbone NH group (amide) of the i+4 residue. The spiral has about 3.6 amino acids per turn, and the amino acid side chains stick out from the cylinder of the helix. Beta pleated sheets are formed by backbone hydrogen bonds between individual beta strands each of which is in an "extended", or fully stretched-out, conformation. The strands may lie parallel or antiparallel to each other, and the side-chain direction alternates above and below the sheet. Hemoglobin contains only helices, natural silk is formed of beta pleated sheets, and many enzymes have a pattern of alternating helices and beta-strands. The secondary-structure elements are connected by "loop" or "coil" regions of non-repetitive conformation, which are sometimes quite mobile or disordered but usually adopt a well-defined, stable arrangement.

The overall, compact, 3D structure of a protein is termed its tertiary structure or its "fold". It is formed as result of various attractive forces like hydrogen bonding, disulfide bridges, hydrophobic interactions, hydrophilic interactions, van der Waals force etc.

When two or more polypeptide chains (either of identical or of different sequence) cluster to form a protein, quaternary structure of protein is formed. Quaternary structure is an attribute of polymeric (same-sequence chains) or heteromeric (different-sequence chains) proteins like hemoglobin, which consists of two "alpha" and two "beta" polypeptide chains.

 

Apoenzymes

An apoenzyme (or, generally, an apoprotein) is the protein without any small-molecule cofactors, substrates, or inhibitors bound. It is often important as an inactive storage, transport, or secretory form of a protein. This is required, for instance, to protect the secretory cell from the activity of that protein. Apoenzymes become active enzymes on addition of a cofactor. Cofactors can be either inorganic (e.g., metal ions and iron-sulfur clusters) or organic compounds, (e.g., [Flavin group|flavin] and heme). Organic cofactors can be either prosthetic groups, which are tightly bound to an enzyme, or coenzymes, which are released from the enzyme's active site during the reaction.

 

Isoenzymes

Isoenzymes, or isozymes, are multiple forms of an enzyme, with slightly different protein sequence and closely similar but usually not identical functions. They are either products of different genes, or else different products of alternative splicing. They may either be produced in different organs or cell types to perform the same function, or several isoenzymes may be produced in the same cell type under differential regulation to suit the needs of changing development or environment. LDH (lactate dehydrogenase) has multiple isozymes, while fetal hemoglobin is an example of a developmentally regulated isoform of a non-enzymatic protein. The relative levels of isoenzymes in blood can be used to diagnose problems in the organ of secretion .

 





The condensation of two amino acids to form a dipeptide through a peptide bond.

📹 Amino Acids — Intro to Structure,— Charge, Classification and Reactions (VİDEO)

📹 Amino Acids — Intro to Structure, Charge, Classification and Reactions (LINK)

Introduction to Amino Acids on the MCAT including backbone and side chain classification

 



 
atomic number
The atomic number or proton number (symbol Z) of a chemical element is the number of protons found in the nucleus of every atom of that element. The atomic number uniquely identifies a chemical element. It is identical to the charge number of the nucleus. In an uncharged atom, the atomic number is also equal to the number of electrons. (W)
 
atomic orbital

In atomic theory and quantum mechanics, an atomic orbital is a mathematical function that describes the wave-like behavior of either one electron or a pair of electrons in an atom. This function can be used to calculate the probability of finding any electron of an atom in any specific region around the atom's nucleus. The term atomic orbital may also refer to the physical region or space where the electron can be calculated to be present, as predicted by the particular mathematical form of the orbital.


Each orbital in an atom is characterized by a unique set of values of the three quantum numbers n, ℓ, and m[dubiousdiscuss], which respectively correspond to the electron's energy, angular momentum, and an angular momentum vector component (the magnetic quantum number) . Each such orbital can be occupied by a maximum of two electrons, each with its own spin quantum number s. The simple names s orbital, p orbital, d orbital, and f orbital refer to orbitals with angular momentum quantum number = 0, 1, 2, and 3 respectively. These names, together with the value of n, are used to describe the electron configurations of atoms. They are derived from the description by early spectroscopists of certain series of alkali metal spectroscopic lines as sharp, principal, diffuse, and fundamental. Orbitals for ℓ > 3 continue alphabetically, omitting j (g, h, i, k, ...) because some languages do not distinguish between the letters "i" and "j".


Atomic orbitals are the basic building blocks of the atomic orbital model (alternatively known as the electron cloud or wave mechanics model), a modern framework for visualizing the submicroscopic behavior of electrons in matter. In this model the electron cloud of a multi-electron atom may be seen as being built up (in approximation) in an electron configuration that is a product of simpler hydrogen-like atomic orbitals. The repeating periodicity of the blocks of 2, 6, 10, and 14 elements within sections of the periodic table arises naturally from the total number of electrons that occupy a complete set of s, p, d, and f atomic orbitals, respectively, although for higher values of the quantum number n, particularly when the atom in question bears a positive charge, the energies of certain sub-shells become very similar and so the order in which they are said to be populated by electrons (e.g. Cr = [Ar]4s13d5 and Cr2+ = [Ar]3d4) can only be rationalized somewhat arbitrarily. (W)



The shapes of the first five atomic orbitals are: 1s, 2s, 2px, 2py, and 2pz. The two colors show the phase or sign of the wave function in each region. Each picture is domain coloring of a ψ(x, y, z) function which depend on the coordinates of one electron. To see the elongated shape of ψ(x, y, z)2 functions that show probability density more directly, see pictures of d-orbitals below.

📹 Orbitals, the Basics — Atomic Orbital Tutorial (VİDEO)

📹 Orbitals, the Basics — Atomic Orbital Tutorial (LINK)

A crash course tutorial on atomic orbitals, quantum numbers and electron configuration + practice problems explained.

 



 

 
b
base (chemistry)

In chemistry, bases are substances that, in aqueous solution, release hydroxide (OH) ions, are slippery to the touch, can taste bitter if an alkali, change the color of indicators (e.g., turn red litmus paper blue), react with acids to form salts, promote certain chemical reactions (base catalysis), accept protons from any proton donor or contain completely or partially displaceable OH ions. Examples of bases are the hydroxides of the alkali metals and the alkaline earth metals (NaOH, Ca(OH)2, etc.—see alkali hydroxide and alkaline earth hydroxide). (W)

📂 Base (chemistry)

Base (chemistry) (W)

In chemistry, bases are substances that, in aqueous solution, release hydroxide (OH) ions, are slippery to the touch, can taste bitter if an alkali, change the color of indicators (e.g., turn red litmus paper blue), react with acids to form salts, promote certain chemical reactions (base catalysis), accept protons from any proton donor or contain completely or partially displaceable OH ions. Examples of bases are the hydroxides of the alkali metals and the alkaline earth metals (NaOH, Ca(OH)2, etc.—see alkali hydroxide and alkaline earth hydroxide).

In water, by altering the autoionization equilibrium, bases yield solutions in which the hydrogen ion activity is lower than it is in pure water, i.e., the water has a pH higher than 7.0 at standard conditions. A soluble base is called an alkali if it contains and releases OH ions quantitatively. However, it is important to realize that basicity is not the same as alkalinity. Metal oxides, hydroxides, and especially alkoxides are basic, and conjugate bases of weak acids are weak bases.

Bases can be thought of as the chemical opposite of acids. However, some strong acids are able to act as bases. Bases and acids are seen as opposites because the effect of an acid is to increase the hydronium (H3O+) concentration in water, whereas bases reduce this concentration. A reaction between an acid and a base is called neutralization. In a neutralization reaction, an aqueous solution of a base reacts with an aqueous solution of an acid to produce a solution of water and salt in which the salt separates into its component ions. If the aqueous solution is saturated with a given salt solute, any additional such salt precipitates out of the solution.

 



 
base, organic

An organic base is an organic compound which acts as a base. Organic bases are usually, but not always, proton acceptors. They usually contain nitrogen atoms, which can easily be protonated. For example, amines or nitrogen-containing heterocyclic compounds have a lone pair of electrons on the nitrogen atom and can thus act as proton acceptors. Examples include:

 

 
biomolecule (List of biomolecules — W)
A biomolecule or biological molecule is a loosely used term for molecules and ions present in organisms that are essential to one or more typically biological processes, such as cell division, morphogenesis, or development. Biomolecules include large macromolecules (or polyanions) such as proteins, carbohydrates, lipids, and nucleic acids, as well as small molecules such as primary metabolites, secondary metabolites and natural products. (W)



Myoglobin 3D structure.

📂 Biomolecule

Biomolecule (W)

A biomolecule or biological molecule is a loosely used term for molecules and ions present in organisms that are essential to one or more typically biological processes, such as cell division, morphogenesis, or development. Biomolecules include large macromolecules (or polyanions) such as proteins, carbohydrates, lipids, and nucleic acids, as well as small molecules such as primary metabolites, secondary metabolites and natural products. A more general name for this class of material is biological materials. Biomolecules are usually[citation needed] endogenous, produced within the organism but organisms usually need exogenous biomolecules, for example certain nutrients, to survive.

Biology and its subfields of biochemistry and molecular biology study biomolecules and their reactions. Most biomolecules are organic compounds, and just four elements oxygen, carbon, hydrogen, and nitrogen — make up 96% of the human body’s mass. But many other elements, such as the various biometals, are present in small amounts.

The uniformity of both specific types of molecules (the biomolecules) and of certain metabolic pathways are invariant features among the wide diversity of life forms; thus these biomolecules and metabolic pathways are referred to as "biochemical universals" or "theory of material unity of the living beings", a unifying concept in biology, along with cell theory and evolution theory.


 



📹📹📹 Biological Molecules (VİDEO)

📹 Organic Molecules & Carbohydrates (VİDEO)

📹 Organic Molecules & Carbohydrates (LINK)

Topics:
- organic molecules
- bonding
- monomers and polymers
- carbohydrates
- monosaccharides and polysaccharides
- Dehydration synthesis
- Hydrolysis

 



📹 Biological Molecules / Bozeman Science (VİDEO)

📹 Biological Molecules / Bozeman Science (LINK)

Paul Andersen describes the four major biological molecules found in living things. He begins with a brief discussion of polymerization. Dehydration synthesis is used to connect monomers into polymers and hydrolysis breaks them down again. The major characteristics of nucleic acids are described as well as there directionality from 3' to 5' end. Protein structure is describes as well as the structure of its monomers; amino acids. The carboxyl and amino ends of a protein are described. The major groups of lipids are included with a brief discussion of saturated, unsaturated and trans fats. Finally carbohydrates and their sugar monomers are discussed.

 



📹 Biological Molecules — / FuseSchoo (VİDEO)

📹 Biological Molecules / FuseSchoo (LINK)

📂 Biological molecules

Molecules make you think of chemistry, right? Well, they also are very important in biology too. In this video we are going to look at carbohydrates, proteins and lipids. When I say lipids, I am talking about fats and oils.
Life processes depend on biological molecules, whose structure is related to their function.
Did you know that living organisms are actually made from quite a small group of molecules? What do you think the most common molecule in you is?
It is actually water. About 55 to 60% of a human adult’s body weight comes from water. And in some organisms it can be up to 90% of their body weight!! [could show jellyfish here]
Your muscles and kidneys are particularly ‘watery’ at 79%, but even your bones have 31% water. Bet you didn’t expect that! Does that mean we really can walk on water?!
Ok, I’m done with the water for now. Imagine I removed all of the water from your body. What would be left? Well it would pretty much just be proteins, lipids, carbohydrates and nucleic acids such as DNA.
So what are these all made of? Well both carbohydrates and lipids are really simple; they both just contain three elements… carbon, hydrogen and oxygen.
Protein is a little more complex with four or five elements… carbon, hydrogen, oxygen, nitrogen and sometimes sulphur.
Let’s start by looking at carbohydrates. There are 3 main types of carbohydrate: monosaccharides, disaccharides and polysaccharides.
Simple sugars, like glucose and fructose, are monosaccharides.
Sucrose, which is made of 2 simple sugars joined together, is a disaccharide.
And some carbohydrates are polymers that are made of lots of sugars joined together, and so are called polysaccharides. Starch, glycogen and cellulose are three important polysaccharides. Cellulose is found in plant walls, and starch is the storage unit for surplus glucose made in photosynthesis. Glycogen is the storage unit used by animals for surplus glucose, and is found in liver and muscle tissues.
Starch is tested for using iodine solution. If the solution turns blue-black, then starch is present.
Now onto proteins… proteins are also polymers. But whereas in carbohydrates the monomer (or repeating unit) was glucose, for proteins it is amino acids.
The protein then folds up into a complex 3D shape, which is held together by weak bonds. The function of each protein depends on its shape.
Because enzymes are proteins, and the bonds holding proteins together are weak, this is why enzymes denature above certain temperatures. The bonds are broken and the structure of the protein is changed.
There are 20 different amino acids that make up proteins. The order of amino acids varies in different proteins and so 20 different amino acids means an almost infinite number of different proteins can be made. It is estimated that there are about 50,000 different proteins in the human body alone.
You will come across proteins everywhere…
In cell membranes where they control the movement of substances during active transport, as enzymes - so in photosynthesis, respiration, DNA copying and digestion, as hormones like insulin, oestrogen and testosterone,
and as antibodies for fighting infection to name just a few examples.
So that’s proteins and carbohydrates. Let’s end with lipids. Many lipids are triglycerides. These have a single glycerol molecule with three fatty acid tails attached.

 



 



 



 
biopolymer
Biopolymers are natural polymers produced by living organisms; in other words, they are polymeric biomolecules derived from cellular or extracellular matter. Biopolymers contain monomeric units that are covalently bonded to form larger structures. There are three main classes of biopolymers, classified according to the monomeric units used and the structure of the biopolymer formed: polynucleotides, polypeptides, and polysaccharides. More specifically, polynucleotides, such as RNA and DNA, are long polymers composed of 13 or more nucleotide monomers. Polypeptides or proteins, are short polymers of amino acids and some major examples include collagen, actin, and fibrin. The last class, polysaccharides,are often linear bonded polymeric carbohydrate structures and some examples include cellulose and alginate. Other examples of biopolymers include rubber, suberin, melanin and lignin. (W)
 
bond, bonding → chemical bond

c
carbohyrate
A carbohydrate is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms, usually with a hydrogen-oxygen atom ratio of 2:1 (as in water) and thus with the empirical formula Cm(H2O)n (where m may be different from n). (W)

📂 Carbohydrate

Carbohydrate (W)

A carbohydrate is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms, usually with a hydrogen-oxygen atom ratio of 2:1 (as in water) and thus with the empirical formula Cm(H2O)n (where m may be different from n). This formula holds true for monosaccharides. Some exceptions exist; for example, deoxyribose, a sugar component of DNA, has the empirical formula C5H10O4. The carbohydrates are technically hydrates of carbon; structurally it is more accurate to view them as aldoses and ketoses.

The term is most common in biochemistry, where it is a synonym of saccharide, a group that includes sugars, starch, and cellulose. The saccharides are divided into four chemical groups: monosaccharides, disaccharides, oligosaccharides, and polysaccharides. Monosaccharides and disaccharides, the smallest (lower molecular weight) carbohydrates, are commonly referred to as sugars. The word saccharide comes from the Greek word σάκχαρον (sákkharon), meaning “sugar.” While the scientific nomenclature of carbohydrates is complex, the names of the monosaccharides and disaccharides very often end in the suffix -ose, as in the monosaccharides fructose (fruit sugar) and glucose (starch sugar) and the disaccharides sucrose (cane or beet sugar) and lactose (milk sugar).

Carbohydrates perform numerous roles in living organisms. Polysaccharides serve for the storage of energy(e.g. starch and glycogen) and as structural components (e.g. cellulose in plants and chitin in arthropods). The 5-carbon monosaccharide ribose is an important component of coenzymes (e.g. ATP, FAD and NAD) and the backbone of the genetic molecule known as RNA. The related deoxyribose is a component of DNA. Saccharides and their derivatives include many other important biomolecules that play key roles in the immune system, fertilization, preventing pathogenesis, blood clotting, and development.

They are found in a wide variety of natural and processed foods. Starch is a polysaccharide. It is abundant in cereals (wheat, maize, rice), potatoes, and processed food based on cereal flour, such as bread, pizza or pasta. Sugars appear in human diet mainly as table sugar (sucrose, extracted from sugarcane or sugar beets), lactose (abundant in milk), glucose and fructose, both of which occur naturally in honey, many fruits, and some vegetables. Table sugar, milk, or honey are often added to drinks and many prepared foods such as jam, biscuits and cakes.

Cellulose, a polysaccharide found in the cell walls of all plants, is one of the main components of insoluble dietary fiber. Although it is not digestible, insoluble dietary fiber helps to maintain a healthy digestive system by easing defecation. Other polysaccharides contained in dietary fiber include resistant starch and inulin, which feed some bacteria in the microbiota of the large intestine, and are metabolized by these bacteria to yield short-chain fatty acids.

📥 Carbohydrate

 




 





Lactose is a disaccharide found in animal milk. It consists of a molecule of D-galactose and a molecule of D-glucose bonded by beta-1-4 glycosidic linkage.

📹📹📹 CARBOHYDRATES / Armando Hasudungan (VİDEO)

📹 Biochemistry of Carbohydrates (VİDEO)

📹 Biochemistry of Carbohydrates (LINK)

 



📹 Carbohydrates / Bozeman Science (VİDEO)

📹 Carbohydrates / Bozeman Science (LINK)

Paul Andersen begins by explaining the structure and purpose of carbohydrates. He describes and gives examples of monosaccharides, disaccharides, oligosaccharide and polysaccharides. He explains how they grow through dehydration reactions and shrink through hydrolysis.

 



📹 Carbohydrates & sugars — Biochemistry / OSMOSIS (VİDEO)

📹 Carbohydrates & sugars — Biochemistry / OSMOSIS (LINK)

 



 



 
carbon
Carbon (from Latin: carbo "coal") is a chemical element with the symbol C and atomic number 6. It is nonmetallic and tetravalent — making four electrons available to form covalent chemical bonds. It belongs to group 14 of the periodic table. Three isotopes occur naturally, 12C and 13C being stable, while 14C is a radionuclide, decaying with a half-life of about 5,730 years. Carbon is one of the few elements known since antiquity.

Carbon is the 15th most abundant element in the Earth's crust, and the fourth most abundant element in the universe by mass after hydrogen, helium, and oxygen. Carbon's abundance, its unique diversity of organic compounds, and its unusual ability to form polymers at the temperatures commonly encountered on Earth enables this element to serve as a common element of all known life. It is the second most abundant element in the human body by mass (about 18.5%) after oxygen. (W)



Some allotropes of carbon: a) diamond; b) graphite; c) lonsdaleite; d–f) fullerenes (C60, C540, C70); g) amorphous carbon; h) carbon nanotube.



Correlation between the carbon cycle and formation of organic compounds. In plants, carbon dioxide formed by carbon fixation can join with water in photosynthesis (green) to form organic compounds, which can be used and further converted by both plants and animals.



Diagram of the carbon cycle. The black numbers indicate how much carbon is stored in various reservoirs, in billions tonnes ("GtC" stands for gigatonnes of carbon; figures are circa 2004). The purple numbers indicate how much carbon moves between reservoirs each year. The sediments, as defined in this diagram, do not include the ≈70 million GtC of carbonate rock and kerogen.

📹 Geometry of carbon bonds (VİDEO)

📹 Geometry of carbon bonds (LINK)

Tetrahedral and trigonal planar bond geometries, conformation and rotation.

 



 
carbonyl group

In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom: C=O. It is common to several classes of organic compounds, as part of many larger functional groups. A compound containing a carbonyl group is often referred to as a carbonyl compound.



A compound containing a carbonyl group (C=O).

📂Carbonyl compounds

Carbonyl compounds (W)

A carbonyl group characterizes the following types of compounds:

Compound Aldehyde Ketone Carboxylic acid Carboxylate Ester Amide
Structure Aldehyde Ketone Carboxylic acid Ester Amide
General formula RCHO RCOR' RCOOH RCOOR' RCONR'R''

Compound Enone Acyl halide Acid anhydride Imide
Structure Enone Acyl chloride Acid anhydride Imide
General formula RC(O)C(R')CR''R''' RCOX (RCO)2O RC(O)N(R')C(O)R''
 

 

 
carboxylic acid
A carboxylic acid is an organic compound that contains a carboxyl group (C(=O)OH) attached to an R-group. The general formula of a carboxylic acid is R–COOH, with R referring to the alkyl group. Carboxylic acids occur widely. Important examples include the amino acids and fatty acids. Deprotonation of a carboxylic acid gives a carboxylate anion. (W)



Structure of a carboxylic acid.


3D structure of a carboxylic acid.
 
catenation
In chemistry, catenation is the bonding of atoms of the same element into a series, called a chain. A chain or a ring shape may be open if its ends are not bonded to each other (an open-chain compound), or closed if they are bonded in a ring (a cyclic compound). (W)
chemical bond

A chemical bond is a lasting attraction between atoms, ions or molecules that enables the formation of chemical compounds. The bond may result from the electrostatic force of attraction between oppositely charged ions as in ionic bonds or through the sharing of electrons as in covalent bonds. (W)




Examples of Lewis dot-style representations of chemical bonds between carbon (C), hydrogen (H), and oxygen (O). Lewis dot diagrams were an early attempt to describe chemical bonding and are still widely used today..

📂 Chemical bond

Chemical bond (W)

A chemical bond is a lasting attraction between atoms, ions or molecules that enables the formation of chemical compounds. The bond may result from the electrostatic force of attraction between oppositely charged ions as in ionic bonds or through the sharing of electrons as in covalent bonds. The strength of chemical bonds varies considerably; there are "strong bonds" or "primary bonds" such as covalent, ionic and metallic bonds, and "weak bonds" or "secondary bonds" such as dipole–dipole interactions, the London dispersion force and hydrogen bonding.

Since opposite charges attract via a simple electromagnetic force, the negatively charged electrons that are orbiting the nucleus and the positively charged protons in the nucleus attract each other. An electron positioned between two nuclei will be attracted to both of them, and the nuclei will be attracted toward electrons in this position. This attraction constitutes the chemical bond. Due to the matter wave nature of electrons and their smaller mass, they must occupy a much larger amount of volume compared with the nuclei, and this volume occupied by the electrons keeps the atomic nuclei in a bond relatively far apart, as compared with the size of the nuclei themselves.

In general, strong chemical bonding is associated with the sharing or transfer of electrons between the participating atoms. The atoms in molecules, crystals, metals and diatomic gases—indeed most of the physical environment around us—are held together by chemical bonds, which dictate the structure and the bulk properties of matter.

Examples of Lewis dot-style representations of chemical bonds between carbon (C), hydrogen (H), and oxygen (O). Lewis dot diagrams were an early attempt to describe chemical bonding and are still widely used today.

All bonds can be explained by quantum theory, but, in practice, simplification rules allow chemists to predict the strength, directionality, and polarity of bonds. The octet rule and VSEPR theory are two examples. More sophisticated theories are valence bond theory, which includes orbital hybridization and resonance, and molecular orbital theory which includes linear combination of atomic orbitals and ligand field theory. Electrostatics are used to describe bond polarities and the effects they have on chemical substances.

 



📹 Ionic and Covalent Bonds, Hydrogen Bonds, van der Waals — 4 types of Chemical Bonds in Biology (VİDEO)

📹 Ionic and Covalent Bonds, Hydrogen Bonds, van der Waals — 4 types of Chemical Bonds in Biology (LINK)

There are four types of chemical bonds essential for life to exist: Ionic Bonds, Covalent Bonds, Hydrogen Bonds, and van der Waals interactions. We need all of these different kinds of bonds to play various roles in biochemical interactions.

These bonds vary in their strengths. In Chemistry, we think of Ionic Bonds and Covalent bonds as having an overlapping range of strengths. But remember, in biochemistry, everything is happening in the context of water. This means Ionic bonds tend to dissociate in water. Thus, we will think of these bonds in the following order (strongest to weakest): Covalent, Ionic, Hydrogen, and van der Waals. Also note that in Chemistry, the weakest bonds are more commonly referred to as “dispersion forces.”

 



📹 Ionic and Covalent Bonds Made Easy (VİDEO)

📹 Ionic and Covalent Bonds Made Easy (LINK)

Simple explanation of Ionic and Covalent Bonds.

 



chemical element

In chemistry an element is a species of atom having the same number of protons in its atomic nuclei (that is, the same atomic number, or Z). For example, the atomic number of oxygen is 8, so the element oxygen describes all atoms which have 8 protons.


In total, 118 elements have been identified. The first 94 occur naturally on Earth, and the remaining 24 are synthetic elements. There are 80 elements that have at least one stable isotope and 38 that have exclusively radionuclides, which decay over time into other elements. Iron is the most abundant element (by mass) making up Earth, while oxygen is the most common element in the Earth's crust. (W)



Abundance (atom fraction) of the chemical elements in Earth's upper continental crust as a function of atomic number. The rarest elements in the crust (shown in yellow) are rare due to a combination of factors: all but one are the densest siderophiles (iron-loving) elements in the Goldschmidt classification, meaning they have a tendency to mix well with metallic iron, depleting them by being relocated deeper into the Earth's core. Their abundance in meteoroids is higher. Additionally, tellurium has been depleted by preaccretional sorting in the nebula via formation of volatile hydrogen telluride.

📂Elements in our galaxy

Elements in our galaxy (W)

Elements in our galaxy Parts per million by mass
Hydrogen 739,000
Helium 240,000
Oxygen 10,400
Carbon 4,600
Neon 1,340
Iron 1,090
Nitrogen 960
Silicon 650
Magnesium 580
Sulfur 440
Potassium 210
Nickel 100

 



📂Nutritional elements in the periodic table

Nutritional elements in the periodic table (W)

Nutritional elements in the periodic table
H He
Li Be B C N O F Ne
Na Mg Al Si P S Cl Ar
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe
Cs Ba La * Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
Fr Ra Ac ** Rf Db Sg Bh Hs Mt Ds Rg Cn Nh Fl Mc Lv Ts Og
* Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu
** Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr

Legend
The four basic organic elements
Quantity elements
Essential trace elements
Deemed essential trace element by U.S., not by European Union
Suggested function from deprivation effects or active metabolic handling, but no clearly-identified biochemical function in humans
Limited circumstantial evidence for trace benefits or biological action in mammals
No evidence for biological action in mammals, but essential in some lower organisms.
(In the case of lanthanum, the definition of an essential nutrient as being indispensable and irreplaceable is not completely applicable due to the extreme similarity of the lanthanides. The stable early lanthanides up to Sm are known to stimulate the growth of various lanthanide-using organisms.)

 



📹 Periodic Trends of the Periodic Table (VİDEO)

📹 Periodic Trends of the Periodic Table (LINK)

The most important trends of the periodic table are: Electronegativity, Ionization Energy, Electron Affinity, Atomic Radius, and Metallic Character.

These periodic trends are all discussed in the video as well as easy ways to remember them!

 



📹 Chemistry: Introduction to the Periodic Table (VİDEO)

📹 Chemistry: Introduction to the Periodic Table (LINK)

The periodic table is the most powerful tool chemists have for organizing chemical information. Without it, chemistry would be a chaotic, confusing jumble of seemingly random observations. What makes the periodic table really invaluable is its use as a predictive tool. You can predict a lot about the chemical behavior of an element if you know where it is on the periodic table.

We give credit to Dmitri Mendeleev for the first Periodic Table. He organized the elements in his table in order of atomic mass. Henry Moseley modified the table, ordering the elements in terms of atomic number. This is the periodic table we use today.

 



 

chemical polarity


In chemistry, polarity is a separation of electric charge leading to a molecule or its chemical groups having an electric dipole moment, with a negatively charged end and a positively charged end.


Polar molecules must contain polar bonds due to a difference in electronegativity between the bonded atoms. A polar molecule with two or more polar bonds must have a geometry which is asymmetric in at least one direction, so that the bond dipoles do not cancel each other.


Polar molecules interact through dipole–dipole intermolecular forces and hydrogen bonds. Polarity underlies a number of physical properties including surface tension, solubility, and melting and boiling points. (W)

 
   
A water molecule, a commonly used example of polarity. Two charges are present with a negative charge in the middle (red shade), and a positive charge at the ends (blue shade).  
 

cholesterol


Cholesterol (from the Ancient Greek chole- (bile) and stereos (solid), followed by the chemical suffix -ol for an alcohol) is an organic molecule. It is a sterol (or modified steroid), a type of lipid. Cholesterol is biosynthesized by all animal cells and is an essential structural component of animal cell membranes.


Cholesterol also serves as a precursor for the biosynthesis of steroid hormones, bile acid and vitamin D. Cholesterol is the principal sterol synthesized by all animals. In vertebrates, hepatic cells typically produce the greatest amounts. It is absent among prokaryotes (bacteria and archaea), although there are some exceptions, such as Mycoplasma, which require cholesterol for growth.

François Poulletier de la Salle first identified cholesterol in solid form in gallstones in 1769. However, it was not until 1815 that chemist Michel Eugène Chevreul named the compound "cholesterine". (W)



Chemical structure of cholesterol.


Ball-and-stick model of cholesterol.
 
covalent bond (molecular bond)

A covalent bond, also called a molecular bond, is a chemical bond that involves the sharing of electron pairs between atoms. These electron pairs are known as shared pairs or bonding pairs, and the stable balance of attractive and repulsive forces between atoms, when they share electrons, is known as covalent bonding. For many molecules, the sharing of electrons allows each atom to attain the equivalent of a full outer shell, corresponding to a stable electronic configuration. In organic chemistry, covalent bonds are much more common than ionic bonds. (W)



A covalent bond forming H2 (right) where two hydrogen atoms share the two electrons.
 


Lewis and MO diagrams of an individual 2e bond and 3e bond.

📂 Covalent bond

Covalent bond (W)

A covalent bond, also called a molecular bond, is a chemical bond that involves the sharing of electron pairs between atoms. These electron pairs are known as shared pairs or bonding pairs, and the stable balance of attractive and repulsive forces between atoms, when they share electrons, is known as covalent bonding. For many molecules, the sharing of electrons allows each atom to attain the equivalent of a full outer shell, corresponding to a stable electronic configuration. In organic chemistry, covalent bonds are much more common than ionic bonds.

Covalent bonding includes many kinds of interactions, including σ-bonding, π-bonding, metal-to-metal bonding, agostic interactions, bent bonds, and three-center two-electron bonds. The term covalent bond dates from 1939. The prefix co- means jointly, associated in action, partnered to a lesser degree, etc.; thus a "co-valent bond", in essence, means that the atoms share "valence", such as is discussed in valence bond theory.

In the molecule H2, the hydrogen atoms share the two electrons via covalent bonding. Covalency is greatest between atoms of similar electronegativities. Thus, covalent bonding does not necessarily require that the two atoms be of the same elements, only that they be of comparable electronegativity. Covalent bonding that entails sharing of electrons over more than two atoms is said to be delocalized.

History

The term covalence in regard to bonding was first used in 1919 by Irving Langmuir in a Journal of the American Chemical Society article entitled "The Arrangement of Electrons in Atoms and Molecules". Langmuir wrote that "we shall denote by the term covalence the number of pairs of electrons that a given atom shares with its neighbors."

The idea of covalent bonding can be traced several years before 1919 to Gilbert N. Lewis, who in 1916 described the sharing of electron pairs between atoms. He introduced the Lewis notation or electron dot notation or Lewis dot structure, in which valence electrons (those in the outer shell) are represented as dots around the atomic symbols. Pairs of electrons located between atoms represent covalent bonds. Multiple pairs represent multiple bonds, such as double bonds and triple bonds. An alternative form of representation, not shown here, has bond-forming electron pairs represented as solid lines.




Early concepts in covalent bonding arose from this kind of image of the molecule of methane. Covalent bonding is implied in the Lewis structure by indicating electrons shared between atoms.


Lewis proposed that an atom forms enough covalent bonds to form a full (or closed) outer electron shell. In the diagram of methane shown here, the carbon atom has a valence of four and is, therefore, surrounded by eight electrons (the octet rule), four from the carbon itself and four from the hydrogens bonded to it. Each hydrogen has a valence of one and is surrounded by two electrons (a duet rule) – its own one electron plus one from the carbon. The numbers of electrons correspond to full shells in the quantum theory of the atom; the outer shell of a carbon atom is the n = 2 shell, which can hold eight electrons, whereas the outer (and only) shell of a hydrogen atom is the n = 1 shell, which can hold only two.

While the idea of shared electron pairs provides an effective qualitative picture of covalent bonding, quantum mechanics is needed to understand the nature of these bonds and predict the structures and properties of simple molecules. Walter Heitler and Fritz London are credited with the first successful quantum mechanical explanation of a chemical bond (molecular hydrogen) in 1927. Their work was based on the valence bond model, which assumes that a chemical bond is formed when there is good overlap between the atomic orbitals of participating atoms.

 



📹 Valence Shell Electron Pair Repulsion Theory (VSEPR Theory) (VİDEO)

📹 Valence Shell Electron Pair Repulsion Theory (VSEPR Theory) (LINK)

 




d
deoxyribose C5H10O4
Deoxyribose, or more precisely 2-deoxyribose, is a monosaccharide with idealized formula H−(C=O)−(CH2)−(CHOH)3−H. Its name indicates that it is a deoxy sugar, meaning that it is derived from the sugar ribose by loss of an oxygen atom. (W)

🛑 deoxyribose

  • Monosakkarid.
  • DNA’nın ön-bileşeni.
  • Bir DNA nükleotidi = deoxyriboz + organik baz (1′ riboz karbonuna bağlı adenin (A), thymin (T), guanin (G) ya da cytosine (C)).

 



Numbered ribose carbons on cytidine.

 

 





The structure of the chain form of 2-deoxy-Dribose as verified at CAS Common Chemistry.


A model of D-deoxyribose in chain form.


Chemical structure of D-deoxyribose.


A model of D-deoxyribose.

📂 Deoxyribose

Deoxyribose C5H10O4 (W)

Deoxyribose, or more precisely 2-deoxyribose, is a monosaccharide with idealized formula H−(C=O)−(CH2)−(CHOH)3−H. Its name indicates that it is a deoxy sugar, meaning that it is derived from the sugar ribose by loss of an oxygen atom. Since the pentose sugars arabinose and ribose only differ by the stereochemistry at C2′, 2-deoxyribose and 2-deoxyarabinose are equivalent, although the latter term is rarely used because ribose, not arabinose, is the precursor to deoxyribose.

History

Deoxyribose was discovered in 1929 by Phoebus Levene.

Structure

Several isomers exist with the formula H−(C=O)−(CH2)−(CHOH)3−H, but in deoxyribose all the hydroxyl groups are on the same side in the Fischer projection. The term "2-deoxyribose" may refer to either of two enantiomers: the biologically important d-2-deoxyribose and to the rarely encountered mirror image l-2-deoxyribose. d-2-deoxyribose is a precursor to the nucleic acid DNA. 2-deoxyribose is an aldopentose, that is, a monosaccharide with five carbon atoms and having an aldehyde functional group.

In aqueous solution, deoxyribose primarily exists as a mixture of three structures: the linear form H−(C=O)−(CH2)−(CHOH)3−H and two ring forms, deoxyribofuranose ("C3′-endo"), with a five-membered ring, and deoxyribopyranose ("C2′-endo"), with a six-membered ring. The latter form is predominant (whereas the C3′-endo form is favored for ribose).


Chemical equilibrium of deoxyribose in solution

 

Biological importance

As a component of DNA, 2-deoxyribose derivatives have an important role in biology. The DNA (deoxyribonucleic acid) molecule, which is the main repository of genetic information in life, consists of a long chain of deoxyribose-containing units called nucleotides, linked via phosphate groups. In the standard nucleic acid nomenclature, a DNA nucleotide consists of a deoxyribose molecule with an organic base (usually adenine, thymine, guanine or cytosine) attached to the 1′ ribose carbon. The 5′ hydroxyl of each deoxyribose unit is replaced by a phosphate (forming a nucleotide) that is attached to the 3′ carbon of the deoxyribose in the preceding unit.

The absence of the 2′ hydroxyl group in deoxyribose is apparently responsible for the increased mechanical flexibility of DNA compared to RNA, which allows it to assume the double-helix conformation, and also (in the eukaryotes) to be compactly coiled within the small cell nucleus. The double-stranded DNA molecules are also typically much longer than RNA molecules. The backbone of RNA and DNA are structurally similar, but RNA is single stranded, and made from ribose as opposed to deoxyribose.

Other biologically important derivatives of deoxyribose include mono-, di-, and triphosphates, as well as 3′-5′ cyclic monophosphates.

Biosynthesis

Deoxyribose is generated from ribose 5-phosphate by enzymes called ribonucleotide reductases. These enzymes catalyse the deoxygenation process.

 



 
DNA

Deoxyribonucleic acid (DNA) is a molecule composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses. DNA and ribonucleic acid (RNA) are nucleic acids. Alongside proteins, lipids and complex carbohydrates (polysaccharides), nucleic acids are one of the four major types of macromolecules that are essential for all known forms of life. (W)


The structure of the DNA double helix.
The atoms in the structure are colour-coded by element and the detailed structures of two base pairs are shown in the bottom right.
🔎


Ausschnitt aus einem Kalottenmodell eines DNA-Moleküls, mittels Pymol generiert.


Chemical structure of DNA.

📂 DNA

DNA (W)

Deoxyribonucleic acid (DNA) is a molecule composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses. DNA and ribonucleic acid (RNA) are nucleic acids. Alongside proteins, lipids and complex carbohydrates (polysaccharides), nucleic acids are one of the four major types of macromolecules that are essential for all known forms of life.

The two DNA strands are known as polynucleotides as they are composed of simpler monomeric units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleobases (cytosine [C], guanine [G], adenine [A] or thymine [T]), a sugar called deoxyribose, and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds (known as the phospho-diester linkage) between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. The nitrogenous bases of the two separate polynucleotide strands are bound together, according to base pairing rules (A with T and C with G), with hydrogen bonds to make double-stranded DNA. The complementary nitrogenous bases are divided into two groups, pyrimidines and purines. In DNA, the pyrimidines are thymine and cytosine; the purines are adenine and guanine.

Both strands of double-stranded DNA store the same biological information. This information is replicated as and when the two strands separate. A large part of DNA (more than 98% for humans) is non-coding, meaning that these sections do not serve as patterns for protein sequences. The two strands of DNA run in opposite directions to each other and are thus antiparallel. Attached to each sugar is one of four types of nucleobases (informally, bases). It is the sequence of these four nucleobases along the backbone that encodes genetic information. RNA strands are created using DNA strands as a template in a process called transcription, where DNA bases are exchanged for their corresponding bases except in the case of thymine (T), for which RNA substitutes uracil (U). Under the genetic code, these RNA strands specify the sequence of amino acids within proteins in a process called translation.

Within eukaryotic cells, DNA is organized into long structures called chromosomes. Before typical cell division, these chromosomes are duplicated in the process of DNA replication, providing a complete set of chromosomes for each daughter cell. Eukaryotic organisms (animals, plants, fungi and protists) store most of their DNA inside the cell nucleus as nuclear DNA, and some in the mitochondria as mitochondrial DNA or in chloroplasts as chloroplast DNA. In contrast, prokaryotes (bacteria and archaea) store their DNA only in the cytoplasm, in circular chromosomes. Within eukaryotic chromosomes, chromatin proteins, such as histones, compact and organize DNA. These compacting structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.

DNA was first isolated by Friedrich Miescher in 1869. Its molecular structure was first identified by Francis Crick and James Watson at the Cavendish Laboratory within the University of Cambridge in 1953, whose model-building efforts were guided by X-ray diffraction data acquired by Raymond Gosling, who was a post-graduate student of Rosalind Franklin at King's College London. DNA is used by researchers as a molecular tool to explore physical laws and theories, such as the ergodic theorem and the theory of elasticity. The unique material properties of DNA have made it an attractive molecule for material scientists and engineers interested in micro- and nano-fabrication. Among notable advances in this field are DNA origami and DNA-based hybrid materials.

 



📹 What is DNA Structure? (VİDEO)

📹 What is DNA Structure? (LINK)

DNA is a double-helix - it looks like a twisted ladder. Its backbone is made of sugars (deoxyribose) and phosphate groups, and the rungs of the ladder are made from 4 nitrogenous bases: Guanine, Adenine, Thymine, and Cytosine. The order of the “rungs,” or bases, is what determines what the DNA is coding for. Think of it like the order of letters in a word, and the order of words in a sentence. Except in the language of DNA, there are only 4 letters.

In this video, we discuss the structure of DNA — how big is it, how are the components attached to each other, and what is the spacing between the rungs. We’ll also learn about the major groove and minor groove, and other important details about DNA structure.

 



📹 DNA Deoxyribonucleic Acid (DNA) / Beverly (VİDEO)

📹 DNA Deoxyribonucleic Acid (DNA) / Beverly (LINK)

Topics:
- Nucleotides
- Sugar
- Phosphate
- Nitrogen Base
- James Watson
- Francis Crick
- Rosalind Franklin
- Double helix
- A/T and C/G
- DNA replication
- DNA helicase
- DNA polymerase

 



 

e
electron configuration

In atomic physics and quantum chemistry, the electron configuration is the distribution of electrons of an atom or molecule (or other physical structure) in atomic or molecular orbitals. For example, the electron configuration of the neon atom is 1s2 2s2 2p6, using the notation explained below.

Electronic configurations describe each electron as moving independently in an orbital, in an average field created by all other orbitals. Mathematically, configurations are described by Slater determinants or configuration state functions.


According to the laws of quantum mechanics, for systems with only one electron, a level of energy is associated with each electron configuration and in certain conditions, electrons are able to move from one configuration to another by the emission or absorption of a quantum of energy, in the form of a photon.

Knowledge of the electron configuration of different atoms is useful in understanding the structure of the periodic table of elements. This is also useful for describing the chemical bonds that hold atoms together. In bulk materials, this same idea helps explain the peculiar properties of lasers and semiconductors. (W)

 
elements → chemical element
 
enzyme

Enzymes are proteins that act as biological catalysts (biocatalysts). Catalysts accelerate chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. Almost all metabolic processes in the cell need enzyme catalysis in order to occur at rates fast enough to sustain life. Metabolic pathways depend upon enzymes to catalyze individual steps. The study of enzymes is called enzymology and a new field of pseudoenzyme analysis has recently grown up, recognising that during evolution, some enzymes have lost the ability to carry out biological catalysis, which is often reflected in their amino acid sequences and unusual 'pseudocatalytic' properties.


Enzymes are known to catalyze more than 5,000 biochemical reaction types. Other biocatalysts are catalytic RNA molecules, called ribozymes. Enzymes' specificity comes from their unique three-dimensional structures.

Like all catalysts, enzymes increase the reaction rate by lowering its activation energy. Some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example is orotidine 5'-phosphate decarboxylase, which allows a reaction that would otherwise take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, nor do they alter the equilibrium of a reaction. Enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules: inhibitors are molecules that decrease enzyme activity, and activators are molecules that increase activity. Many therapeutic drugs and poisons are enzyme inhibitors. An enzyme's activity decreases markedly outside its optimal temperature and pH, and many enzymes are (permanently) denatured when exposed to excessive heat, losing their structure and catalytic properties.

Some enzymes are used commercially, for example, in the synthesis of antibiotics. Some household products use enzymes to speed up chemical reactions: enzymes in biological washing powders break down protein, starch or fat stains on clothes, and enzymes in meat tenderizer break down proteins into smaller molecules, making the meat easier to chew. (W)



The enzyme glucosidase converts the sugar maltose into two glucose sugars. Active site residues in red, maltose substrate in black, and NAD cofactor in yellow. (PDB: 1OBB​).

📹 Enzymes / Bozeman Science (VİDEO)

📹 Enzymes / Bozeman Science (LINK)

Paul Andersen explains how enzymes are used to break down substrates. The correct shape of the active site allows a key/lock fit between the enzyme and the substrate. The enzyme catalase is used to break down hydrogen peroxide. The importance of cofactors and coenzymes is emphasized. Competitive and allosteric inhibition is also included.

 



📹 How Enzymes Work? (VİDEO)

📹 How Enzymes Work? (LINK)

Every second inside every living cell, thousands of chemical reactions are taking place. These reactions constitute the essential tasks of life such as metabolism, protein synthesis, cell renewal and growth. Learn how the proteins called enzymes work to maintain the rate of these reactions at a life-sustaining level.

 




f
fat

Fats are one of the three main macronutrients, along with carbohydrates and proteins. Fat molecules consist of primarily carbon and hydrogen atoms and are therefore hydrophobic and are soluble in organic solvents and insoluble in water. Examples include cholesterol, phospholipids, and triglycerides.


The terms lipidoil, and fat are often confused. Lipid is the general term, though a lipid is not necessarily a triglycerideOil normally refers to a lipid with short or unsaturated fatty acid chains that is liquid at room temperature, while fat (in the strict sense) specifically refers to lipids that are solids at room temperature – however, fat (in the broad sense) may be used in food science as a synonym for lipid. (W)


📂 Fat

Fat (W)

Fats are one of the three main macronutrients, along with carbohydrates and proteins. Fat molecules consist of primarily carbon and hydrogen atoms and are therefore hydrophobic and are soluble in organic solvents and insoluble in water. Examples include cholesterolphospholipids, and triglycerides.

The terms lipidoil, and fat are often confused. Lipid is the general term, though a lipid is not necessarily a triglycerideOil normally refers to a lipid with short or unsaturated fatty acid chains that is liquid at room temperature, while fat (in the strict sense) specifically refers to lipids that are solids at room temperature – however, fat (in the broad sense) may be used in food science as a synonym for lipid.

Fat is an important foodstuff for many forms of life, and fats serve both structural and metabolic functions. They are a necessary part of the diet of most heterotrophs (including humans) and are the most energy dense, thus the most efficient form of energy storage.

Some fatty acids that are set free by the digestion of fats are called essential because they cannot be synthesized in the body from simpler constituents. There are two essential fatty acids (EFAs) in human nutrition: alpha-linolenic acid (an omega-3 fatty acid) and linoleic acid (an omega-6 fatty acid). Other lipids needed by the body can be synthesized from these and other fats. Fats and other lipids are broken down in the body by enzymes called lipases produced in the pancreas.

Fats and oils are categorized according to the number and bonding of the carbon atoms in the aliphatic chain. Fats that are saturated fats have no double bonds between the carbons in the chain. Unsaturated fats have one or more double bonded carbons in the chain. The nomenclature is based on the non-acid (non-carbonyl) end of the chain. This end is called the omega end or the n-end. Thus alpha-linolenic acid is called an omega-3 fatty acid because the 3rd carbon from that end is the first double bonded carbon in the chain counting from that end. Some oils and fats have multiple double bonds and are therefore called polyunsaturated fats. Unsaturated fats can be further divided into cis fats, which are the most common in nature, and trans fats, which are rare in nature. Unsaturated fats can be altered by reaction with hydrogen effected by a catalyst. This action, called hydrogenation, tends to break all the double bonds and makes a fully saturated fat. To make vegetable shortening, then, liquid cis-unsaturated fats such as vegetable oils are hydrogenated to produce saturated fats, which have more desirable physical properties e.g., they melt at a desirable temperature (30–40 °C), and store well, whereas polyunsaturated oils go rancid when they react with oxygen in the air. However, trans fats are generated during hydrogenation as contaminants created by an unwanted side reaction on the catalyst during partial hydrogenation.

Saturated fats can stack themselves in a closely packed arrangement, so they can solidify easily and are typically solid at room temperature. For example, animal fats tallow and lard are high in saturated fatty acid content and are solids. Olive and linseed oils on the other hand are unsaturated and liquid. Fats serve both as energy sources for the body, and as stores for energy in excess of what the body needs immediately. Each gram of fat when burned or metabolized releases about 9 food calories (37 kJ = 8.8 kcal). Fats are broken down in the healthy body to release their constituents, glycerol and fatty acids. Glycerol itself can be converted to glucose by the liver and so become a source of energy.

 



 



Examples of fatty acids


Ball-and-stick model of the elaidic acid molecule, the trans isomer of oleic acid and the major trans fat found in hydrogenated vegetable oils.
Elaidic acid is the principal trans unsaturated fatty acid often found in partially hydrogenated vegetable oils.



Oleic-acid-3D-ball-&-stick.
Oleic acid is a cis unsaturated fatty acid making up 55–80% of olive oil.


Ball-and-stick model of the stearic acid molecule (also known as octadecanoic acid), a saturated fatty acid with 18 carbon atoms.
Stearic acid is a saturated fatty acid found in animal fats and is the intended product in full hydrogenation. Stearic acid is neither cis nor trans because it has no carbon-carbon double bonds.

 
fatty acid (chemistry)
In chemistry, particularly in biochemistry, a fatty acid is a carboxylic acid with a long aliphatic chain, which is either saturated or unsaturated. Most naturally occurring fatty acids have an unbranched chain of an even number of carbon atoms, from 4 to 28. Fatty acids are usually not found in organisms, but instead as three main classes of esters: triglycerides, phospholipids, and cholesteryl esters. In any of these forms, fatty acids are both important dietary sources of fuel for animals and they are important structural components for cells. (W)



Three-dimensional representations of several fatty acids. Saturated fatty acids have perfectly straight chain structure. Unsaturated ones are typically bent, unless they have a trans configuration.


Arachidic acid, a saturated fatty acid.

📹 Fat — “Free Fatty Acids and Triglycerides” (VİDEO)

📹 Fat — “Free Fatty Acids and Triglycerides” (LINK)

Describes the basic biochemistry of the energy storing molecule, the free fatty acid and it's storage form in plants and animals, the triglyceride.

 



 
functional group (moiety)
In organic chemistry, functional groups are specific substituents or moieties within molecules that are responsible for the characteristic chemical reactions of those molecules. The same functional group will undergo the same or similar chemical reaction(s) regardless of the size of the molecule it is a part of. (W)



Benzyl acetate has an ester functional group (in red), an acetyl moiety (circled with dark green) and a benzyloxy moiety (circled with light orange). Other divisions can be made.

📹 The Functional Group Concept Explained (VİDEO)

📹 The Functional Group Concept Explained (LINK)

This is the introduction to the Functional Group concept - giving an oversight about Organic Chemistry, the composition of Alkenes.

 




g
gene
In biology, a gene is a sequence of nucleotides in DNA or RNA that encodes the synthesis of a gene product, either RNA or protein. (W)



A gene is a region of DNA that encodes function. A chromosome consists of a long strand of DNA containing many genes. A human chromosome can have up to 500 million base pairs of DNA with thousands of genes.
 
gene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein-coding genes such as transfer RNA (tRNA) or small nuclear RNA (snRNA) genes, the product is a functional RNA. (W)



The extended Central Dogma of molecular Biology includes all the cellular processes involved in the flow of genetic information.
 


The process of transcription is carried out by RNA polymerase (RNAP), which uses DNA (black) as a template and produces RNA (blue).
 
gene product
A gene product is the biochemical material, either RNA or protein, resulting from expression of a gene. A measurement of the amount of gene product is sometimes used to infer how active a gene is. Abnormal amounts of gene product can be correlated with disease-causing alleles, such as the overactivity of oncogenes which can cause cancer. A gene is defined as "a hereditary unit of DNA that is required to produce a functional product." (W)



Transcription of DNA to RNA using the protein RNA polymerase II.
 
glucose
Glucose is a simple sugar with the molecular formula C6H12O6. Glucose is the most abundant monosaccharide, a subcategory of carbohydrates. Glucose is mainly made by plants and most algae during photosynthesis from water and carbon dioxide, using energy from sunlight, where it is used to make cellulose in cell walls, which is the most abundant carbohydrate. In energy metabolism, glucose is the most important source of energy in all organisms. (W)



Alpha-D-glucopyranose-2D-skeletal.


Alpha-D-glucopyranose-2D-skeletal.


D-glucose in the en:Fischer projection.

📂 Glucose

Glucose (W)

Glucose is a simple sugar with the molecular formula C6H12O6. Glucose is the most abundant monosaccharide, a subcategory of carbohydrates. Glucose is mainly made by plants and most algae during photosynthesis from water and carbon dioxide, using energy from sunlight, where it is used to make cellulose in cell walls, which is the most abundant carbohydrate. In energy metabolism, glucose is the most important source of energy in all organisms.
Glucose for metabolism is partially stored as a polymer, in plants mainly as starch and amylopectin and in animals as glycogen. Glucose circulates in the blood of animals as blood sugar.The naturally occurring form of glucose is d-glucose, while l-glucose is produced synthetically in comparatively small amounts and is of lesser importance. Glucose is a monosaccharide containing six carbon atoms, an aldehyde group and is therefore referred to as an aldohexose. The glucose molecule can exist in an open-chain (acyclic) as well as ring (cyclic) form, the latter being the result of an intramolecular reaction between the aldehyde C atom and the C-5 hydroxyl group to form an intramolecular hemiacetal. In water solution both forms are in equilibrium and at pH 7 the cyclic one is the predominant. It is naturally occurring and is found in fruits and other parts of plants in its free state. In animals glucose arises from the breakdown of glycogen in a process known as glycogenolysis.

 



📹 Molecular structure of glucose | Macromolecules | Biology | Khan Academy (VİDEO)

📹 Molecular structure of glucose | Macromolecules | Biology | Khan Academy (LINK)

Molecular structure of glucose. Monosaccharide structure. Linear and ring forms.

 




h
hydrate
In chemistry, a hydrate is a substance that contains water or its constituent elements. The chemical state of the water varies widely between different classes of hydrates, some of which were so labeled before their chemical structure was understood. (W)
 
hydrocarbon
In organic chemistry, a hydrocarbon is an organic compound consisting entirely of hydrogen and carbon. 620 Hydrocarbons are examples of group 14 hydrides. Hydrocarbons from which one hydrogen atom has been removed are functional groups called hydrocarbyls. Hydrocarbons are generally colorless and hydrophobic with only weak odors. Because of their diverse molecular structures, it is difficult to generalize further. (W)



Ball-and-stick model of the methane molecule, CH4. Methane is part of a homologous series known as the alkanes, which contain single bonds only.

 
hydroxy group

A hydroxy or hydroxyl group is the entity with the formula OH. It contains oxygen bonded to hydrogen. In organic chemistry, alcohols and carboxylic acids contain hydroxy groups. Both the negatively charged anion OH, called hydroxide, and the neutral radical ·OH, known as the hydroxyl radical, consist of an unbounded hydroxyl group.


According to IUPAC rules, the term hydroxyl refers to the hydroxyl radical (·OH) only, while the functional group −OH is called hydroxy group. (W)



Representation of an organic hydroxy group, where R represents a hydrocarbon or other organic moiety, the red and grey spheres represent oxygen and hydrogen atoms respectively, and the rod-like connections between these, covalent chemical bonds.
 


Sulfuric acid contains two hydroxyl groups.
 
hydroxyl radical

The hydroxyl radical, •OH, is the neutral form of the hydroxide ion (OH). Hydroxyl radicals are highly reactive (easily becoming hydroxy groups) and consequently short-lived; however, they form an important part of radical chemistry. Most notably hydroxyl radicals are produced from the decomposition of hydroperoxides (ROOH) or, in atmospheric chemistry, by the reaction of excited atomic oxygen with water. It is also an important radical formed in radiation chemistry, since it leads to the formation of hydrogen peroxide and oxygen, which can enhance corrosion and SCC in coolant systems subjected to radioactive environments. Hydroxyl radicals are also produced during UV-light dissociation of H2O2 (suggested in 1879) and likely in Fenton chemistry, where trace amounts of reduced transition metals catalyze peroxide-mediated oxidations of organic compounds. (W)



Stick model of the hydroxyl radical with molecular orbitals.
 


Comparison of a hydroxide ion and a hydroxyl radical.

📂Biological significance

Biological significance (W)

Hydroxyl radicals can occasionally be produced as a byproduct of immune action. Macrophages and microglia most frequently generate this compound when exposed to very specific pathogens, such as certain bacteria. The destructive action of hydroxyl radicals has been implicated in several neurological autoimmune diseases such as HAND when immune cells become over-activated and toxic to neighboring healthy cells.

The hydroxyl radical can damage virtually all types of macromolecules: carbohydrates, nucleic acids (mutations), lipids (lipid peroxidation), and amino acids (e.g. conversion of Phe to m-Tyrosine and o-Tyrosine). The hydroxyl radical has a very short in vivo half-life of approximately 10−9 seconds and a high reactivity. This makes it a very dangerous compound to the organism.

Unlike superoxide, which can be detoxified by superoxide dismutase, the hydroxyl radical cannot be eliminated by an enzymatic reaction.

 




i
induction → redox
 
ionic bonding
Ionic bonding is a type of chemical bonding that involves the electrostatic attraction between oppositely charged ions, and is the primary interaction occurring in ionic compounds. (W)



Sodium and fluorine atoms undergoing a redox reaction to form sodium fluoride. Sodium loses its outer electron to give it a stable electron configuration, and this electron enters the fluorine atom exothermically. The oppositely charged ions – typically a great many of them – are then attracted to each other to form a solid.

k
ketone



Ketone group.
 

In chemistry, a ketone is a functional group with the structure RC(=O)R', where R and R' can be a variety of carbon-containing substituents. Ketones contain a carbonyl group (a carbon-oxygen double bond). The simplest ketone is acetone (R = R' = methyl), with the formula CH3C(O)CH3. Many ketones are of great importance in industry and in biology. Examples include many sugars (ketoses), many steroids (e.g., testosterone), and the solvent acetone. (W)






Representative ketones, from the left: acetone, a common solvent; oxaloacetate, an intermediate in the metabolism of sugars; acetylacetone in its (mono) enol form (the enol highlighted in blue); cyclohexanone, precursor to nylon; muscone, an animal scent; and tetracycline, an antibiotic.

l
Lewis structure
Lewis structures, also known as Lewis dot diagrams, Lewis dot formulas, Lewis dot structures, electron dot structures, or Lewis electron dot structures (LEDS), are diagrams that show the bonding between atoms of a molecule and the lone pairs of electrons that may exist in the molecule. (W)



Two lewis structures of the canonical structures of the nitrite ion, NO2−.

📥 Lewis structure (W)

 





 
lignin

Lignin is a class of complex organic polymers that form key structural materials in the support tissues of vascular plants and some algae. Lignins are particularly important in the formation of cell walls, especially in wood and bark, because they lend rigidity and do not rot easily. Chemically, lignins are cross-linked phenolic polymers. (W)




An example of a possible lignin structure. The portion shown here (not counting the side chain denoted "Carbohydrate") has 28 monomers (mostly coniferyl alcohol), 278 carbon atoms, 407 hydrogen atoms, and 94 oxygen atoms (64% carbon, 8% hydrogen, and 29% oxygen by weight) which seems to be too high in hydrogen.

Lignin

Lignin (W)

Lignin is a complex polyphenolic macromolecule composed mainly of beta-O4-aryl linkages. After cellulose, lignin is the second most abundant biopolymer and is one of the primary structural components of most plants. It contains subunits derived from p-coumaryl alcohol, coniferyl alcohol, and sinapyl alcohol and is unusual among biomolecules in that it is racemic. The lack of optical activity is due to the polymerization of lignin which occurs via free radical coupling reactions in which there is no preference for either configuration at a chiral center.

 



 
lipid

In biology and biochemistry, a lipid is a macrobiomolecule that is soluble in nonpolar solvents. Non-polar solvents are typically hydrocarbons used to dissolve other naturally occurring hydrocarbon lipid molecules that do not (or do not easily) dissolve in water, including fatty acids, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E, and K), monoglycerides, diglycerides, triglycerides, and phospholipids.


The functions of lipids include storing energy, signaling, and acting as structural components of cell membranes. Lipids have applications in the cosmetic and food industries as well as in nanotechnology. (W)

Lipid

Lipid (W)

Lipids (oleaginous) are chiefly fatty acid esters, and are the basic building blocks of biological membranes. Another biological role is energy storage (e.g., triglycerides). Most lipids consist of a polar or hydrophilic head (typically glycerol) and one to three nonpolar or hydrophobic fatty acid tails, and therefore they are amphiphilic. Fatty acids consist of unbranched chains of carbon atoms that are connected by single bonds alone (saturated fatty acids) or by both single and double bonds (unsaturated fatty acids). The chains are usually 14-24 carbon groups long, but it is always an even number.

For lipids present in biological membranes, the hydrophilic head is from one of three classes:

Other lipids include prostaglandins and leukotrienes which are both 20-carbon fatty acyl units synthesized from arachidonic acid. They are also known as fatty acids

 





Structures of some common lipids. At the top are cholesterol and oleic acid. The middle structure is a triglyceride composed of oleoyl, stearoyl, and palmitoyl chains attached to a glycerol backbone. At the bottom is the common phospholipid phosphatidylcholine.


Structure of the saccharolipid Kdo2-lipid A. Glucosamine residues in blue, Kdo residues in red, acyl chains in black and phosphate groups in green.


Self-organization of phospholipids: a spherical liposome, a micelle, and a lipid bilayer.


Structure of a triacylglycerol lipid.

📂Lipid

Lipid (W)

In biology and biochemistry, a lipid is a macrobiomolecule that is soluble in nonpolar solvents. Non-polar solvents are typically hydrocarbons used to dissolve other naturally occurring hydrocarbon lipid molecules that do not (or do not easily) dissolve in water, including fatty acids, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E, and K), monoglycerides, diglycerides, triglycerides, and phospholipids.


The functions of lipids include storing energy, signaling, and acting as structural components of cell membranes. Lipids have applications in the cosmetic and food industries as well as in nanotechnology.

Scientists sometimes define lipids as hydrophobic or amphiphilic small molecules; the amphiphilic nature of some lipids allows them to form structures such as vesicles, multilamellar/unilamellar liposomes, or membranes in an aqueous environment. Biological lipids originate entirely or in part from two distinct types of biochemical subunits or "building-blocks": ketoacyl and isoprene groups. Using this approach, lipids may be divided into eight categories: fatty acids, glycerolipids, glycerophospholipids, sphingolipids, saccharolipids, and polyketides (derived from condensation of ketoacyl subunits); and sterol lipids and prenol lipids (derived from condensation of isoprene subunits).

Although the term "lipid" is sometimes used as a synonym for fats, fats are a subgroup of lipids called triglycerides. Lipids also encompass molecules such as fatty acids and their derivatives (including tri-, di-, monoglycerides, and phospholipids), as well as other sterol-containing metabolites such as cholesterol. Although humans and other mammals use various biosynthetic pathways both to break down and to synthesize lipids, some essential lipids can't be made this way and must be obtained from the diet.

 



📹 Lipids & Fatty Acids (VİDEO)

📹 Lipids & Fatty Acids (LINK)

This video is taught at the high school level. I use this PowerPoint with my biology class at Beverly Hills High School. This video does not discuss dehydration synthesis and hydrolysis of lipids.

 



📹 Lipids / Bozeman Science (VİDEO)

📹 Lipids / Bozeman Science (LINK)

In this video Paul Andersen describes the lipids (of the fats). He explains how they are an important source of energy but are also required to cell membranes. He explains how the hydrocarbon tails in triglycerides contain energy available for life. He also explains how phospholipids construct, and cholesterol molecules main the cell membrane.

 




m
macromolecule
A macromolecule is a very large molecule, such as protein, commonly composed of the polymerization of smaller subunits called monomers. They are typically composed of thousands of atoms or more. The most common macromolecules in biochemistry are biopolymers (nucleic acids, proteins, and carbohydrates) and large non-polymeric molecules (such as lipids and macrocycles), synthetic fibers as well as experimental materials such as carbon nanotubes.



Chemical structure of a polypeptide macromolecule.
 
Miller–Urey experiment

The Miller–Urey experiment (or Miller experiment) was a chemical experiment that simulated the conditions thought at the time (1952) to be present on the early Earth and tested the chemical origin of life under those conditions. The experiment at the time supported Alexander Oparin's and J. B. S. Haldane's hypothesis that putative conditions on the primitive Earth favoured chemical reactions that synthesized more complex organic compounds from simpler inorganic precursors. Considered to be the classic experiment investigating abiogenesis, it was conducted in 1952 by Stanley Miller, with assistance from Harold Urey, at the University of Chicago and later the University of California, San Diego and published the following year. (W)

📂Miller–Urey experiment

Miller-Urey experiment (W)

The Miller–Urey experiment (or Miller experiment) was a chemical experiment that simulated the conditions thought at the time (1952) to be present on the early Earth and tested the chemical origin of life under those conditions. The experiment at the time supported Alexander Oparin's and J. B. S. Haldane's hypothesis that putative conditions on the primitive Earth favoured chemical reactions that synthesized more complex organic compounds from simpler inorganic precursors. Considered to be the classic experiment investigating abiogenesis, it was conducted in 1952 by Stanley Miller, with assistance from Harold Urey, at the University of Chicago and later the University of California, San Diego and published the following year.

After Miller's death in 2007, scientists examining sealed vials preserved from the original experiments were able to show that there were actually well over 20 different amino acids produced in Miller's original experiments. That is considerably more than what Miller originally reported, and more than the 20 that naturally occur in life. More recent evidence suggests that Earth's original atmosphere might have had a composition different from the gas used in the Miller experiment, but prebiotic experiments continue to produce racemic mixtures of simple-to-complex compounds under varying conditions.

Experiment
The experiment used water (H2O), methane (CH4), ammonia (NH3), and hydrogen (H2). The chemicals were all sealed inside a sterile 5-liter glass flask connected to a 500 ml flask half-full of water. The water in the smaller flask was heated to induce evaporation, and the water vapour was allowed to enter the larger flask. Continuous electrical sparks were fired between the electrodes to simulate lightning in the water vapour and gaseous mixture, and then the simulated atmosphere was cooled again so that the water condensed and trickled into a U-shaped trap at the bottom of the apparatus.

After a day, the solution collected at the trap had turned pink in colour, and after a week of continuous operation the solution was deep red and turbid. The boiling flask was then removed, and mercuric chloride was added to prevent microbial contamination. The reaction was stopped by adding barium hydroxide and sulfuric acid, and evaporated to remove impurities. Using paper chromatography, Miller identified five amino acids present in the solution: glycine, α-alanine and β-alanine were positively identified, while aspartic acid and α-aminobutyric acid (AABA) were less certain, due to the spots being faint.

In a 1996 interview, Stanley Miller recollected his lifelong experiments following his original work and stated: "Just turning on the spark in a basic pre-biotic experiment will yield 11 out of 20 amino acids."

The original experiment remained in 2017 under the care of Miller and Urey's former student Jeffrey Bada, a professor at the UCSD, Scripps Institution of Oceanography. As of 2013, the apparatus used to conduct the experiment was on display at the Denver Museum of Nature and Science.

Chemistry of experiment

One-step reactions among the mixture components can produce hydrogen cyanide (HCN), formaldehyde (CH2O), and other active intermediate compounds (acetylene, cyanoacetylene, etc.):

CO2 → CO + [O] (atomic oxygen)
CH4 + 2[O] → CH2O + H2O
CO + NH3 → HCN + H2O
CH4 + NH3 → HCN + 3H2 (BMA process)


The formaldehyde, ammonia, and HCN then react by Strecker synthesis to form amino acids and other biomolecules:

CH2O + HCN + NH3 → NH2-CH2-CN + H2O
NH2-CH2-CN + 2H2O → NH3 + NH2-CH2-COOH (glycine)


Furthermore, water and formaldehyde can react, via Butlerov's reaction to produce various sugars like ribose.

The experiments showed that simple organic compounds of building blocks of proteins and other macromolecules can be formed from gases with the addition of energy.

 





The experiment.

 
molecular biology

Molecular biology is the branch of biology that concerns the molecular basis of biological activity in and between cells, including molecular synthesis, modification, mechanisms and interactions. The central dogma of molecular biology describes the process in which DNA is transcribed into RNA then translated into protein.


William Astbury
described molecular biology in 1961 in Nature, as:


“ ...not so much a technique as an approach, an approach from the viewpoint of the so-called basic sciences with the leading idea of searching below the large-scale manifestations of classical biology for the corresponding molecular plan. It is concerned particularly with the forms of biological molecules and [...] is predominantly three-dimensional and structural – which does not mean, however, that it is merely a refinement of morphology. It must at the same time inquire into genesis and function.”


Some clinical research and medical therapies arising from molecular biology are covered under gene therapy whereas the use of molecular biology or molecular cell biology in medicine is now referred to as molecular medicine. Molecular biology also plays important role in understanding formations, actions, and regulations of various parts of cells which can be used to efficiently target new drugs, diagnose disease, and understand the physiology of the cell. (W)

 
monomer
A monomer (mono-, "one" + -mer, "part") is a molecule that can be reacted together with other monomer molecules to form a larger polymer chain or three-dimensional network in a process called polymerization. (W)



This nylon is formed by condensation polymerization of two monomers, yielding water.
 
monosaccharide
Monosaccharides (from Greek monos: single, sacchar: sugar), also called simple sugar, are the simplest form of sugar and the most basic units of carbohydrates. They cannot be further hydrolyzed to simpler chemical compounds. The general formula is CnH 2nOn. They are usually colorless, water-soluble, and crystalline solids. Some monosaccharides have a sweet taste.

Examples of monosaccharides include glucose (dextrose), fructose (levulose), and galactose. Monosaccharides are the building blocks of disaccharides (such as sucrose and lactose) and polysaccharides (such as cellulose and starch). Each carbon atom that supports a hydroxyl group is chiral, except those at the end of the chain. This gives rise to a number of isomeric forms, all with the same chemical formula. For instance, galactose and glucose are both aldohexoses, but have different physical structures and chemical properties.

The monosaccharide glucose plays a pivotal role in metabolism, where the chemical energy is extracted through glycolysis and the citric acid cycle to provide energy to living organisms. Some other monosaccharides can be converted in the living organism to glucose. (W)



d- and l-glucose.

📥 Monosaccharide (W)

 





n
nucleic acid

Nucleic acids are the biopolymers, or large biomolecules, essential to all known forms of life. The term nucleic acid is the overall name for DNA and RNA. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. If the sugar is a compound ribose, the polymer is RNA (ribonucleic acid); if the sugar is derived from ribose as deoxyribose, the polymer is DNA (deoxyribonucleic acid). (W)



Nucleic acids RNA (left) and DNA (right).

📹 Nucleic Acids / Beverly (VİDEO)

📹 Nucleic Acids /Beverly (LINK)

 



nucleotide

Nucleotides are molecules consisting of a nucleoside and a phosphate group. They are the basic building blocks of DNA and RNA. (W)



This nucleotide contains the five-carbon sugar deoxyribose (at center), a nitrogenous base called adenine (upper right), and one phosphate group (left). The deoxyribose sugar joined only to the nitrogenous base forms a Deoxyribonucleoside called deoxyadenosine, whereas the whole structure along with the phosphate group is a nucleotide, a constituent of DNA with the name deoxyadenosine monophosphate.

📂 Nucleotide

Nucleotide (W)

Nucleotides are molecules consisting of a nucleoside and a phosphate group. They are the basic building blocks of DNA and RNA.

They are organic molecules that serve as the monomer units for forming the nucleic acid polymers deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth. Nucleotides are the building blocks of nucleic acids; they are composed of three sub unit molecules: a nitrogenous base (also known as nucleobase), a five-carbon sugar (ribose or deoxyribose), and a phosphate group consisting of one to three phosphates. The four nitrogenous bases present in DNA are guanine, adenine, cytosine and thymine; in RNA uracil is used in place of thymine.

Nucleotides also play a central role in metabolism at a fundamental, cellular level. They carry packets of chemical energy — in the form of the nucleoside triphosphates Adenosine triphosphate (ATP), Guanosine triphosphate (GTP), Cytidine triphosphate (CTP) and Uridine triphosphate (UTP) — throughout the cell to the many cellular functions that demand energy, which include: synthesizing amino acids, proteins and cell membranes and parts, moving the cell and moving cell parts (both internally and intercellularly), dividing the cell, etc.In addition, nucleotides participate in cell signaling (cyclic guanosine monophosphate or cGMP and cyclic adenosine monophosphate or cAMP), and are incorporated into important cofactors of enzymatic reactions (e.g. coenzyme A, FAD, FMN, NAD, and NADP+).

In experimental biochemistry, nucleotides can be radiolabeled with radionuclides to yield radionucleotides.

 




o
 
organic acid

An organic acid is an organic compound with acidic properties. The most common organic acids are the carboxylic acids, whose acidity is associated with their carboxyl group –COOH. Sulfonic acids, containing the group –SO2OH, are relatively stronger acids. Alcohols, with –OH, can act as acids but they are usually very weak. The relative stability of the conjugate base of the acid determines its acidity. Other groups can also confer acidity, usually weakly: the thiol group –SH, the enol group, and the phenol group. In biological systems, organic compounds containing these groups are generally referred to as organic acids.


A few common examples include:

(W)



A tetrapeptide (example Val-Gly-Ser-Ala) with green marked amino end (L-Valine) and blue marked carboxyl end (L-Alanine).


 
organic base

An organic base is an organic compound which acts as a base. Organic bases are usually, but not always, proton acceptors. They usually contain nitrogen atoms, which can easily be protonated, for example amines have a lone pair of electrons on the nitrogen atom and can thus act as proton acceptors (bases).. Organic bases combine with monosaccharides to form nucleotides. Amines and nitrogen-containing heterocyclic compounds are organic bases. Examples include:

 
organic chemistry

Organic chemistry is a branch of chemistry that studies the structure, properties and reactions of organic compounds, which contain carbon in covalent bonding. Study of structure determines their chemical composition and formula. Study of properties includes physical and chemical properties, and evaluation of chemical reactivity to understand their behavior. The study of organic reactions includes the chemical synthesis of natural products, drugs, and polymers, and study of individual organic molecules in the laboratory and via theoretical (in silico) study. (W)

Line-angle representation / Ball-and-stick representation / Space-filling representation
Three representations of an organic compound, 5α-Dihydroprogesterone (5α-DHP), a steroid hormone. For molecules showing color, the carbon atoms are in black, hydrogens in gray, and oxygens in red. In the line angle representation, carbon atoms are implied at every terminus of a line and vertex of multiple lines, and hydrogen atoms are implied to fill the remaining needed valences (up to 4).
 
organic compound (organic molecule)

In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen bonds. Due to carbon's ability to catenate (form chains with other carbon atoms), millions of organic compounds are known. The study of the properties, reactions, and syntheses of organic compounds comprises the discipline known as organic chemistry. For historical reasons, a few classes of carbon-containing compounds (e.g., carbonate anion salts and cyanide salts), along with a handful of other exceptions (e.g., carbon dioxide), are not classified as organic compounds and are considered inorganic. Other than those just named, little consensus exists among chemists on precisely which carbon-containing compounds are excluded, making any rigorous definition of an organic compound elusive.


Although organic compounds make up only a small percentage of the Earth's crust, they are of central importance because all known life is based on organic compounds. Living things incorporate inorganic carbon compounds into organic compounds through a network of processes (the carbon cycle) that begins with the conversion of carbon dioxide and a hydrogen source like water into simple sugars and other organic molecules by autotrophic organisms using light (photosynthesis) or other sources of energy. Most synthetically produced organic compounds are ultimately derived from petrochemicals consisting mainly of hydrocarbons, which are themselves formed from the high pressure and temperature degradation of organic matter underground over geological timescales. This ultimate derivation notwithstanding, organic compounds are no longer defined as compounds originating in living things, as they were historically.


In chemical nomenclature, an organyl group, frequently represented by the letter R, refers to any monovalent substituent whose open valence is on a carbon atom. (W)



The L-isoleucine molecule, C6H13NO2, showing features typical of organic compounds. Carbon atoms are in black, hydrogens gray, oxygens red, and nitrogen blue.

 

📹 Organic Molecules (VİDEO)

📹 Organic Molecules (LINK)

This video discusses Carbon as the building block of organic molecules.

 





p
peptide

Peptides (from Greek language πεπτός, peptós "digested"; derived from πέσσειν, péssein "to digest") are short chains of between two and fifty amino acids, linked by peptide bonds. Chains of less than ten or fifteen amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides.

A polypeptide is a longer, continuous, and unbranched peptide chain of up to fifty amino acids. Hence, peptides fall under the broad chemical classes of biological oligomers and polymers, alongside nucleic acids, oligosaccharides, polysaccharides, and others.


When a polypeptide contains more than fifty amino acids it is known as a protein. Proteins consist of one or more polypeptides arranged in a biologically functional way, often bound to ligands such as coenzymes and cofactors, or to another protein or other macromolecule such as DNA or RNA, or to complex macromolecular assemblies.


Amino acids that have been incorporated into peptides are termed residues. A water molecule is released during formation of each amide bond. All peptides except cyclic peptides have an N-terminal (amine group) and C-terminal (carboxyl group) residue at the end of the peptide (as shown for the tetrapeptide in the image). (W)



A tetrapeptide (example Val-Gly-Ser-Ala) with green marked amino end (L-Valine) and blue marked carboxyl end (L-Alanine).
 
peptide bond
A peptide bond is an amide type of covalent chemical bond linking two consecutive alpha-amino acids from C1 (carbon number one) of one alpha-amino acid and N2 (nitrogen number two) of another along a peptide or protein chain.



Peptide bond.

📂Peptide bond

Peptide bond (W)

A peptide bond is an amide type of covalent chemical bond linking two consecutive alpha-amino acids from C1 (carbon number one) of one alpha-amino acid and N2 (nitrogen number two) of another along a peptide or protein chain.

It can also be called an eupeptide bond to separate it from an isopeptide bond, a different type of amide bond between two amino acids.

Synthesis

When two amino acids form a dipeptide through a peptide bond it is a type of condensation reaction. In this kind of condensation, two amino acids approach each other, with the non-side chain (C1) carboxylic acid moiety of one coming near the non-side chain (N2) amino moiety of the other. One loses a hydrogen and oxygen from its carboxyl group (COOH) and the other loses a hydrogen from its amino group (NH2). This reaction produces a molecule of water (H2O) and two amino acids joined by a peptide bond (-CO-NH-). The two joined amino acids are called a dipeptide.

The amide bond is synthesized when the carboxyl group of one amino acid molecule reacts with the amino group of the other amino acid molecule, causing the release of a molecule of water (H2O), hence the process is a dehydration synthesis reaction.



Peptide bond formation via dehydration reaction.

The formation of the peptide bond consumes energy, which, in organisms, is derived from ATP. Peptides and proteins are chains of amino acids held together by peptide bonds (and sometimes by a few isopeptide bonds). Organisms use enzymes to produce nonribosomal peptides, and ribosomes to produce proteins via reactions that differ in details from dehydration synthesis.

Some peptides, like alpha-amanitin, are called ribosomal peptides as they are made by ribosomes, but many are nonribosomal peptides as they are synthesized by specialized enzymes rather than ribosomes. For example, the tripeptide glutathione is synthesized in two steps from free amino acids, by two enzymes: glutamate–cysteine ligase (forms an isopeptide bond, which is not a peptide bond) and glutathione synthetase (forms a peptide bond).



The dehydration condensation of two amino acids to form a peptide bond (red) with expulsion of water (blue).

Degradation

A peptide bond can be broken by hydrolysis (the addition of water). In the presence of water they will break down and release 8–16 kilojoule/mol (2–4 kcal/mol) of Gibbs energy. This process is extremely slow, with the half life at 25 °C of between 350 and 600 years per bond.

In living organisms, the process is normally catalyzed by enzymes known as peptidases or proteases, although there are reports of peptide bond hydrolysis caused by conformational strain as the peptide/protein folds into the native structure. This non-enzymatic process is thus not accelerated by transition state stabilization, but rather by ground state destabilization.

 




 
polymer

A polymer (Greek poly-, "many" + -mer, "part") is a large molecule, or macromolecule, composed of many repeated subunits. (W)




DNA er biopolymerer.

 

📂Polymer

Polymer (W)

A polymer (Greek poly-, "many" + -mer, "part") is a large molecule, or macromolecule, composed of many repeated subunits. Due to their broad range of properties, both synthetic and natural polymers play essential and ubiquitous roles in everyday life. Polymers range from familiar synthetic plastics such as polystyrene to natural biopolymers such as DNA and proteins that are fundamental to biological structure and function. Polymers, both natural and synthetic, are created via polymerization of many small molecules, known as monomers. Their consequently large molecular mass, relative to small molecule compounds, produces unique physical properties including toughness, viscoelasticity, and a tendency to form glasses and semicrystalline structures rather than crystals. The terms polymer and resin are often synonymous with plastic.

The term "polymer" derives from the Greek word πολύς (polus, meaning “many, much”) and μέρος (meros, meaning “part”), and refers to a molecule whose structure is composed of multiple repeating units, from which originates a characteristic of high relative molecular mass and attendant properties. The units composing polymers derive, actually or conceptually, from molecules of low relative molecular mass. The term was coined in 1833 by Jöns Jacob Berzelius, though with a definition distinct from the modern IUPAC definition. The modern concept of polymers as covalently bonded macromolecular structures was proposed in 1920 by Hermann Staudinger, who spent the next decade finding experimental evidence for this hypothesis.


Polymers are studied in the fields of biophysics and macromolecular science, and polymer science (which includes polymer chemistry and polymer physics). Historically, products arising from the linkage of repeating units by covalent chemical bonds have been the primary focus of polymer science; emerging important areas of the science now focus on non-covalent links. Polyisoprene of latex rubber is an example of a biological polymer, and the polystyrene of styrofoam is an example of a synthetic polymer. In biological contexts, essentially all biological macromolecules—i.e., proteins (polyamides), nucleic acids (polynucleotides), and polysaccharides—are purely polymeric, or are composed in large part of polymeric components—e.g., isoprenylated or lipid-modified glycoproteins, where small lipidic molecules and oligosaccharide modifications occur on the polyamide backbone of the protein.

The simplest theoretical models for polymers are ideal chains.

 



 
protein

Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells, and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity. (W)




A representation of the 3D structure of the protein myoglobin showing turquoise α-helices. This protein was the first to have its structure solved by X-ray crystallography. Toward the right-center among the coils, a prosthetic group called a heme group (shown in gray) with a bound oxygen molecule (red).
 


Chemical structure of the peptide bond (bottom) and the three-dimensional structure of a peptide bond between an alanine and an adjacent amino acid (top/inset). The bond itself is made of the CHON elements.
 


A ribosome produces a protein using mRNA as template.

📹📹📹 Protein (VİDEO)

📹 Proteins / Bozeman Science (VİDEO)

📹 Proteins / Bozeman Science (LINK)

Paul Andersen explains the structure and importance of proteins. He describes how proteins are created from amino acids connected by dehydration synthesis. He shows the importance of chemical properties in the R-groups of individual amino acids in the polypeptide. He explains the four levels of protein folding and gives you an opportunity to fold proteins of your own using the game Foldit:

 



📹 What is a Protein? (VİDEO)

📹 What is a Protein? (LINK)

Proteins play countless roles throughout the biological world, from catalyzing chemical reactions to building the structures of all living things. Despite this wide range of functions, all proteins are made out of the same twenty one amino acids, but combined in different ways. The way these twenty amino acids are arranged dictates the folding of the protein into its unique final shape. Since protein function is based on the ability to recognize and bind to specific molecules, having the correct shape is critical for proteins to do their jobs correctly.

 



📹 From DNA to Protein — 3D (VİDEO)

📹 From DNA to Protein — 3D (LINK)

This 3D animation shows how proteins are made in the cell from the information in the DNA code.

 



 





r
redox (reduction-oxidation)

Redox (reduction–oxidation) is a type of chemical reaction in which the oxidation states of atoms are changed. Redox reactions are characterized by the actual or formal transfer of electrons between chemical species, most often with one species (the reducing agent) undergoing oxidation (losing electrons) while another species (the oxidizing agent) undergoes reduction (gains electrons). The chemical species from which the electron is removed is said to have been oxidized, while the chemical species to which the electron is added is said to have been reduced. In other words:

  • Oxidation is the loss of electrons or an increase in the oxidation state of an atom, an ion, or of certain atoms in a molecule.
  • Reduction is the gain of electrons or a decrease in the oxidation state of an atom, an ion, or of certain atoms in a molecule. (W)




Sodium and fluorine atoms undergoing a redox reaction to form sodium fluoride. Sodium loses its outer electron to give it a stable electron configuration, and this electron enters the fluorine atom exothermically. The oppositely charged ions – typically a great many of them – are then attracted to each other to form a solid.
 
reduction → redox
 
residue

In biochemistry and molecular biology, a residue refers to a specific monomer within the polymeric chain of a polysaccharide, protein or nucleic acid. One might say, "This protein consists of 118 amino acid residues" or "The histidine residue is considered to be basic because it contains an imidazole ring." Note that a residue is different from a moiety.


The concept that suggested this term is presumably the nature of the condensation reaction by which such classes of monomeric building blocks, such as amino acids or monosaccharides, are strung together to form a polymeric chain, such as a polysaccharide or a peptide; some atoms, typically in the form of a water molecule, are discarded from each building block, leaving only a "residue" of the building block, that ends up in the finished product. A residue might be one amino acid in a polypeptide or one monosaccharide in a starch molecule. (W)

 
ribonucleotide

In biochemistry, a ribonucleotide is a nucleotide containing ribose as its pentose component. It is considered a molecular precursor of nucleic acids. Nucleotides are the basic building blocks of DNA and RNA. The monomer itself from ribonucleotides forms the basic building blocks for RNA. However, the reduction of ribonucleotide, by enzyme ribonucleotide reductase (RNR), forms deoxyribonucleotide, which is the essential building block for DNA. There are several differences between DNA deoxyribonucleotides and RNA ribonucleotides. Successive nucleotides are linked together via phosphodiester bonds by 3'-5'.


Ribonucleotides are also utilized in other cellular functions. These special monomers are utilized in both cell regulation and cell signaling as seen in adenosine-monophosphate (AMP). Furthermore, ribonucleotides can be converted to adenosine triphosphate (ATP), the energy currency in organisms. Ribonucleotides can be converted to cyclic adenosine monophosphate (cyclic AMP) to regulate hormones in organisms as well. In living organisms, the most common bases for ribonucleotides are adenine (A), guanine (G), cytosine (C), or uracil (U). The nitrogenous bases are classified into two parent compounds, purine and pyrimidine. (W)



General Ribonucleotide Structure: phosphate group, Ribose, Nucleobase.
 
ribose

Ribose is a simple sugar and carbohydrate with molecular formula C5H10O5 and the linear-form composition H−(C=O)−(CHOH)4−H. The naturally-occurring form, d-ribose, is a component of the ribonucleotides from which RNA is built, and so this compound is necessary for coding, decoding, regulation and expression of genes. It has a structural analog, deoxyribose, which is a similarly essential component of DNA. l-Ribose is an unnatural sugar that was first prepared by Emil Fischer and Oscar Piloty in 1891. It was not until 1909 that Phoebus Levene and Walter Jacobs recognised that d-ribose was a natural product, the enantiomer of Fischer and Piloty's product, and an essential component of nucleic acids. Fischer chose the name "ribose" as it is a partial rearrangement of the name of another sugar, arabinose, of which ribose is an epimer at the 2' carbon; both names also relate to gum arabic, from which arabinose was first isolated and from which they prepared l-ribose. (W)

β-d-ribofuranose α-d-ribopyranose d-ribose l-ribose
Left: Haworth projections of one of each of the furanose and pyranose forms of d-ribose
Right: Fischer projection of the open chain forms of d- and l-ribose

 


s
saccharide (→ carbohydrate ⇑)

The term [scccaride] is most common in biochemistry, where it is a synonym of saccharide, a group that includes sugars, starch, and cellulose. The saccharides are divided into four chemical groups: monosaccharides, disaccharides, oligosaccharides, and polysaccharides. Monosaccharides and disaccharides, the smallest (lower molecular weight) carbohydrates, are commonly referred to as sugars. The word saccharide comes from the Greek word σάκχαρον (sákkharon), meaning "sugar". While the scientific nomenclature of carbohydrates is complex, the names of the monosaccharides and disaccharides very often end in the suffix -ose, as in the monosaccharides fructose (fruit sugar) and glucose (starch sugar) and the disaccharides sucrose (cane or beet sugar) and lactose (milk sugar). (W)


Saccharides

Saccharides (W)

Monosaccharides are the simplest form of carbohydrates with only one simple sugar. They essentially contain an aldehyde or ketone group in their structure. The presence of an aldehyde group in a monosaccharide is indicated by the prefix aldo-. Similarly, a ketone group is denoted by the prefix keto-. Examples of monosaccharides are the hexoses, glucose, fructose, Trioses, Tetroses, Heptoses, galactose, pentoses, ribose, and deoxyribose. Consumed fructose and glucose have different rates of gastric emptying, are differentially absorbed and have different metabolic fates, providing multiple opportunities for 2 different saccharides to differentially affect food intake. Most saccharides eventually provide fuel for cellular respiration.

Disaccharides are formed when two monosaccharides, or two single simple sugars, form a bond with removal of water. They can be hydrolyzed to yield their saccharin building blocks by boiling with dilute acid or reacting them with appropriate enzymes. Examples of disaccharides include sucrose, maltose, and lactose.

Polysaccharides are polymerized monosaccharides, or complex carbohydrates. They have multiple simple sugars. Examples are starch, cellulose, and glycogen. They are generally large and often have a complex branched connectivity. Because of their size, polysaccharides are not water-soluble, but their many hydroxy groups become hydrated individually when exposed to water, and some polysaccharides form thick colloidal dispersions when heated in water. Shorter polysaccharides, with 3 - 10 monomers, are called oligosaccharides. A fluorescent indicator-displacement molecular imprinting sensor was developed for discriminating saccharides. It successfully discriminated three brands of orange juice beverage. The change in fluorescence intensity of the sensing films resulting is directly related to the saccharide concentration.

 



 
structural formula

The structural formula of a chemical compound is a graphic representation of the molecular structure (determined by structural chemistry methods), showing how the atoms are possibly arranged in the real three-dimensional space. The chemical bonding within the molecule is also shown, either explicitly or implicitly. Unlike chemical formulas, which have a limited number of symbols and are capable of only limited descriptive power, structural formulas provide a more complete geometric representation of the molecular structure. For example, many chemical compounds exist in different isomeric forms, which have different enantiomeric structures but the same chemical formula. (W)



Representation of molecules by molecular formula.
 
 

v
valence
In chemistry, the valence or valency of an element is a measure of its combining power with other atoms when it forms chemical compounds or molecules. (W)

📂Valence

Valence (W)

In chemistry, the valence or valency of an element is a measure of its combining power with other atoms when it forms chemical compounds or molecules.

Description

The combining power, or affinity of an atom of a given element is determined by the number of hydrogen atoms that it combines with. In methane, carbon has a valence of 4; in ammonia, nitrogen has a valence of 3; in water, oxygen has a valence of 2; and in hydrogen chloride, chlorine has a valence of 1. Chlorine, as it has a valence of one, can be substituted for hydrogen. Phosphorus has a valence of 5 in phosphorus pentachloride, PCl5. Valence diagrams of a compound represent the connectivity of the elements, with lines drawn between two elements, sometimes called bonds, representing a saturated valency for each element. The two tables below show some examples of different compounds, their valence diagrams, and the valences for each element of the compound.


Compound H2
Hydrogen
CH4
Methane
C3H8
Propane
C2H2
Acetylene
Diagram
Valencies
  • Hydrogen: 1
  • Carbon: 4
  • Hydrogen: 1
  • Carbon: 4
  • Hydrogen: 1
  • Carbon: 4
  • Hydrogen: 1
Compound NH3
Ammonia
NaCN
Sodium cyanide
H2S
Hydrogen sulfide
H2SO4
Sulfuric acid
Cl2O7Dichlorine heptoxide
Diagram Ammoniak.png Sodium cyanide-2D.svg Hydrogen sulfide.svg Sulfuric acid chemical structure.png Dichlorine heptoxide.svg
Valencies
  • Nitrogen: 3
  • Hydrogen: 1
  • Sodium: 1
  • Carbon: 4
  • Nitrogen: 3
  • Sulfur: 2
  • Hydrogen: 1
  • Sulfur: 6
  • Oxygen: 2
  • Hydrogen 1
  • Chlorine, 7
  • Oxygen, 2

Electrons and valence

The Rutherford model of the nuclear atom (1911) showed that the exterior of an atom is occupied by electrons, which suggests that electrons are responsible for the interaction of atoms and the formation of chemical bonds. In 1916, Gilbert N. Lewis explained valence and chemical bonding in terms of a tendency of (main-group) atoms to achieve a stable octet of 8 valence-shell electrons. According to Lewis, covalent bonding leads to octets by the sharing of electrons, and ionic bonding leads to octets by the transfer of electrons from one atom to the other. The term covalence is attributed to Irving Langmuir, who stated in 1919 that "the number of pairs of electrons which any given atom shares with the adjacent atoms is called the covalence of that atom". The prefix co- means "together", so that a co-valent bond means that the atoms share a valence. Subsequent to that, it is now more common to speak of covalent bonds rather than valence, which has fallen out of use in higher-level work from the advances in the theory of chemical bonding, but it is still widely used in elementary studies, where it provides a heuristic introduction to the subject.

In the 1930s, Linus Pauling proposed that there are also polar covalent bonds, which are intermediate between covalent and ionic, and that the degree of ionic character depends on the difference of electronegativity of the two bonded atoms.

Pauling also considered hypervalent molecules, in which main-group elements have apparent valences greater than the maximal of 4 allowed by the octet rule. For example, in the sulfur hexafluoride molecule (SF6), Pauling considered that the sulfur forms 6 true two-electron bonds using sp3d2 hybrid atomic orbitals, which combine one s, three p and two d orbitals. However more recently, quantum-mechanical calculations on this and similar molecules have shown that the role of d orbitals in the bonding is minimal, and that the SF6 molecule should be described as having 6 polar covalent (partly ionic) bonds made from only four orbitals on sulfur (one s and three p) in accordance with the octet rule, together with six orbitals on the fluorines. Similar calculations on transition-metal molecules show that the role of p orbitals is minor, so that one s and five d orbitals on the metal are sufficient to describe the bonding.

 



 
vitamin

A vitamin is an organic molecule (or related set of molecules) that is an essential micronutrient which an organism needs in small quantities for the proper functioning of its metabolism. Essential nutrients cannot be synthesized in the organism, either at all or not in sufficient quantities, and therefore must be obtained through the diet. Vitamin C can be synthesized by some species but not by others; it is not a vitamin in the first instance but is in the second. The term vitamin does not include the three other groups of essential nutrients: minerals, essential fatty acids, and essential amino acids. Most vitamins are not single molecules, but groups of related molecules called vitamers. For example, vitamin E consists of four tocopherols and four tocotrienols. Though some sources list fourteen by including choline, major health organizations list thirteen: vitamin A (as all-trans-retinol, all-trans-retinyl-esters, as well as all-trans-beta-carotene and other provitamin A carotenoids), vitamin B1 (thiamine), vitamin B2 (riboflavin), vitamin B3 (niacin), vitamin B5 (pantothenic acid), vitamin B6 (pyridoxine), vitamin B7 (biotin), vitamin B9 (folic acid or folate), vitamin B12 (cobalamins), vitamin C (ascorbic acid), vitamin D (calciferols), vitamin E (tocopherols and tocotrienols), and vitamin K (quinones).


Vitamins have diverse biochemical functions. Vitamin A acts as a regulator of cell and tissue growth and differentiation. Vitamin D provides a hormone-like function, regulating mineral metabolism for bones and other organs. The B complex vitamins function as enzyme cofactors (coenzymes) or the precursors for them. Vitamins C and E function as antioxidants. Both deficient and excess intake of a vitamin can potentially cause clinically significant illness, although excess intake of water-soluble vitamins is less likely to do so.


Before 1935, the only source of vitamins was from food. If intake of vitamins was lacking, the result was vitamin deficiency and consequent deficiency diseases. Then, commercially produced tablets of yeast-extract vitamin B complex and semi-synthetic vitamin C became available. This was followed in the 1950s by the mass production and marketing of vitamin supplements, including multivitamins, to prevent vitamin deficiencies in the general population. Governments mandated addition of vitamins to staple foods such as flour or milk, referred to as food fortification, to prevent deficiencies. Recommendations for folic acid supplementation during pregnancy reduced risk of infant neural tube defects.


The term vitamin is derived from the word vitamine, which was coined in 1912 by Polish biochemist Casimir Funk, who isolated a complex of micronutrients essential to life, all of which he presumed to be amines. When this presumption was later determined not to be true, the "e" was dropped from the name. All vitamins were discovered (identified) between 1913 and 1948. (W)


w
water

Water is an inorganic, transparent, tasteless, odorless, and nearly colorless chemical substance, which is the main constituent of Earth's hydrosphere and the fluids of most living organisms. It is vital for all known forms of life, even though it provides no calories or organic nutrients. Its chemical formula is H2O, meaning that each of its molecules contains one oxygen and two hydrogen atoms, connected by covalent bonds. Water is the name of the liquid state of H2O at standard ambient temperature and pressure. It forms precipitation in the form of rain and aerosols in the form of fog. Clouds are formed from suspended droplets of water and ice, its solid state. When finely divided, crystalline ice may precipitate in the form of snow. The gaseous state of water is steam or water vapor. Water moves continually through the water cycle of evaporation, transpiration (evapotranspiration), condensation, precipitation, and runoff, usually reaching the sea. (W)



Model of hydrogen bonds (1) between molecules of water.
San Andrés island, Colombia.
🔎

📂Water

Water (W)

Water is an inorganic, transparent, tasteless, odorless, and nearly colorless chemical substance, which is the main constituent of Earth's hydrosphere and the fluids of most living organisms. It is vital for all known forms of life, even though it provides no calories or organic nutrients. Its chemical formula is H2O, meaning that each of its molecules contains one oxygen and two hydrogen atoms, connected by covalent bonds. Water is the name of the liquid state of H2O at standard ambient temperature and pressure. It forms precipitation in the form of rain and aerosols in the form of fog. Clouds are formed from suspended droplets of water and ice, its solid state. When finely divided, crystalline ice may precipitate in the form of snow. The gaseous state of water is steam or water vapor. Water moves continually through the water cycle of evaporation, transpiration(evapotranspiration), condensation, precipitation, and runoff, usually reaching the sea.

Water covers 71% of the Earth's surface, mostly in seas and oceans. Small portions of water occur as groundwater (1.7%), in the glaciers and the ice caps of Antarctica and Greenland (1.7%), and in the air as vapor, clouds (formed of ice and liquid water suspended in air), and precipitation (0.001%).

Chemical and physical properties
Water (H2O) is a polar inorganic compound that is at room temperature a tasteless and odorless liquid, nearly colorless with a hint of blue. This simplest hydrogen chalcogenide is by far the most studied chemical compound and is described as the "universal solvent" for its ability to dissolve many substances. This allows it to be the "solvent of life": indeed, water as found in nature almost always includes various dissolved substances, and special steps are required to obtain chemically pure water. Water is the only common substance to exist as a solid, liquid, and gas in normal terrestrial conditions.

Density

Water differs from most liquids in that it becomes less dense as it freezes. In 1 atm pressure, it reaches its maximum density of 1,000 kg/m3 (62.43 lb/cu ft) at 3.98 °C (39.16 °F). The density of ice is 917 kg/m3 (57.25 lb/cu ft), an expansion of 9%. This expansion can exert enormous pressure, bursting pipes and cracking rocks (see Frost weathering).

In a lake or ocean, water at 4°C sinks to the bottom and ice forms on the surface, floating on the liquid water. This ice insulates the water below, preventing it from freezing solid. Without this protection, most aquatic organisms would perish during the winter.

Triple and critical points

On a pressure/temperature phase diagram (see figure), there are curves separating solid from vapor, vapor from liquid, and liquid from solid. These meet at a single point called the triple point, where all three phases can coexist. The triple point is at a temperature of 273.16 K (0.01 °C) and a pressure of 611.657 pascals (0.00604 atm); it is the lowest pressure at which liquid water can exist. Until 2019, the triple point was used to define the Kelvin temperature scale.

The water/vapor phase curve terminates at 647.096 K (373.946 °C; 705.103 °F) and 22.064 megapascals (3,200.1 psi; 217.75 atm). This is known as the critical point. At higher temperatures and pressures the liquid and vapor phases form a continuous phase called a supercritical fluid. It can be gradually compressed or expanded between gas-like and liquid-like densities, its properties (which are quite different from those of ambient water) are sensitive to density. For example, for suitable pressures and temperatures it can mix freely with nonpolar compounds, including most organic compounds. This makes it useful in a variety of applications including high-temperature electrochemistry and as an ecologically benign solvent or catalyst in chemical reactions involving organic compounds. In Earth's mantle, it acts as a solvent during mineral formation, dissolution and deposition.




Phase diagram of water simplified.


Polar molecule

In a water molecule, the hydrogen atoms form a 104.5° angle with the oxygen atom. The hydrogen atoms are close to two corners of a tetrahedron centered on the oxygen. At the other two corners are lone pairs of valence electrons that do not participate in the bonding. In a perfect tetrahedron, the atoms would form a 109.5° angle, but the repulsion between the lone pairs is greater than the repulsion between the hydrogen atoms.



Tetrahedral structure of water.

 

Other substances have a tetrahedral molecular structure, for example, methane (CH4) and hydrogen sulfide (H2S). However, oxygen is more electronegative (holds on to its electrons more tightly) than most other elements, so the oxygen atom retains a negative charge while the hydrogen atoms are positively charged. Along with the bent structure, this gives the molecule an electrical dipole moment and it is classified as a polar molecule.

Water is a good polar solvent, that dissolves many salts and hydrophilic organic molecules such as sugars and simple alcohols such as ethanol. Water also dissolves many gases, such as oxygen and carbon dioxide — the latter giving the fizz of carbonated beverages, sparkling wines and beers. In addition, many substances in living organisms, such as proteins, DNA and polysaccharides, are dissolved in water. The interactions between water and the subunits of these biomacromolecules shape protein folding, DNA base pairing, and other phenomena crucial to life (hydrophobic effect).

Many organic substances (such as fats and oils and alkanes) are hydrophobic, that is, insoluble in water. Many inorganic substances are insoluble too, including most metal oxides, sulfides, and silicates.


Hydrogen bonding



Model of hydrogen bonds (1) between molecules of water.

Because of its polarity, a molecule of water in the liquid or solid state can form up to four hydrogen bonds with neighboring molecules. Hydrogen bonds are about ten times as strong as the Van der Waals force that attracts molecules to each other in most liquids. This is the reason why the melting and boiling points of water are much higher than those of other analogous compounds like hydrogen sulfide. They also explain its exceptionally high specific heat capacity (about 4.2 J/g/K), heat of fusion (about 333 J/g), heat of vaporization (2257 J/g), and thermal conductivity (between 0.561 and 0.679 W/m/K). These properties make water more effective at moderating Earth's climate, by storing heat and transporting it between the oceans and the atmosphere. The hydrogen bonds of water are around 23 kJ/mol (compared to a covalent O-H bond at 492 kJ/mol). Of this, it is estimated that 90% is attributable to electrostatics, while the remaining 10% is partially covalent.

These bonds are the cause of water's high surface tension and capillary forces. The capillary action refers to the tendency of water to move up a narrow tube against the force of gravity. This property is relied upon by all vascular plants, such as trees.

 



📹 Properties of Water — Hydrogen Bonding in Water (VİDEO)

📹 Properties of Water — Hydrogen Bonding in Water (LINK)

Why is water essential for Life to exist on Earth? We are about 60% water - and there are some organisms that are as much as 90% water! What is so important about water? How does it support life?

In this video, we discuss the special properties of water that make it the “Solvent of Life.” Chief among these properties is the extensive Hydrogen Bonding between water molecules that make water an extremely cohesive liquid (the molecules stick together). Due to the extensive hydrogen bonding, water has some emergent properties that impact life on Earth in many ways. These include:
Cohesion
Adhesion
High surface tension
High specific heat
High heat of vaporization
Ice Floats (Ice is less dense as a solid than liquid water)

For each of these properties, we discuss how they impact living creatures on Earth.

 



 




 


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