1. Amino Acids, Peptides, and Proteins

In an α helix, the amino acids get oriented in such a manner that the carbonyl (C=O) group of the nth amino acid can form a hydrogen bond with the amido (N-H) group of the (n+4)^​th amino acid.

This results in a strong hydrogen bond that has an optimum hydrogen to oxygen (H....O) distance of 2.8 Å. These hydrogen bonds between the amino acids stabilize the α-helix structure

In β-pleated sheets, which can be parallel or antiparallel, the peptide chains lie alongside one another, forming rows or strands held together by intramolecular hydrogen bonds between carbonyl oxygen atoms on one chain and amide hydrogen atoms in an adjacent chain.

To accommodate as many hydrogen bonds as possible, the β-pleated sheets assume a pleated, or rippled, shape. The R groups of amino residues point above and below the plane of the β-pleated sheet.

amphoteric species

can either accept a proton or donate a proton; how they react depends on the pH of their environment.

The residues in peptides are joined together through peptide bonds

a specialized form of an amide bond, that forms between the -COO group of one amino acid and the NH group of another amino acid. This forms the functional group -C(O)NH-.

polar, hydrophilic, Negatively Charged (Acidic) Side Chains

aspartic acid (aspartate) and glutamic acid (glutamate)

Amino acids with acidic side groups

carry a net negative charge at physiologic pH.

proline

has secondary alpha amino group, alpha helix breaker

acid hydrolysis

heat, non-specific means of breaking a peptide bond

polar, Positively Charged (Basic) Side Chains

histidine, arginine, lysine

When you change the pH surrounding a protein you have disrupted of

ionic bonds which includes tertiary and Quaternary structures

epigenetics

the study of influences on gene expression that occur without a DNA change. DNA methylation and histone modifications

transcription

(genetics) the organic process whereby the DNA sequence in a gene is copied into mRNA

translation

(genetics) the process whereby genetic information coded in messenger RNA directs the formation of a specific protein at a ribosome in the cytoplasm

Peptide bonds are covalent bonds formed by the nucleophilic addition-elimination reaction between the carboxylic group of one amino acid and the amino group of another amino acid, releasing a molecule of water as the by product.

A peptide bond is essentially an amide bond

At physiologic pH, basic functional groups will be protonated, attaining a positive charge.

A polypeptide with a net positive charge at physiologic pH most likely has a basic R group.

KEY CONCEPT 8

Amino acids with acidic side chains have pI values well below 6; amino acids with basic side chains have pI values well above 6.

Because amide groups have delocalizable π electrons in the carbonyl and in the lone pair on the amino nitrogen, they can exhibit resonance; thus, the C-N bond in the amide has partial double bond character.

As a result, rotation of the protein backbone around its C-N amide bonds is restricted, which makes the protein more rigid. Rotation around the remaining bonds in the backbone, however, is not restricted, as those remain single (σ) bonds. When a peptide bond forms, the free amino end is known as the amino terminus or N-terminus, while the free carboxyl end is the carboxy terminus or C-terminus. By convention, peptides are drawn with the N-terminus on the left and the C-terminus end on the right; similarly, they are read from Nterminus to C-terminus.

denaturation, in which a protein loses its three-dimensional structure. Although it is sometimes reversible, denaturation is often irreversible; whether its denaturation is reversible or not, unfolded proteins cannot catalyze reactions. The two main causes of denaturation are heat and solutes.

As with all molecules, when the temperature of a protein increases, its average kinetic energy increases. When the temperature gets high enough, this extra energy can be enough to overcome the hydrophobic interactions that hold a protein together, causing the protein to unfold. This is what happens when egg whites are cooked: In the uncooked egg whites, albumin is folded, which makes it transparent; cooking them causes the albumin molecules to denature and aggregate, forming a solid, rubbery white mass that will not revert to its transparent form. On the other hand, solutes such as urea denature proteins by directly interfering with the forces that hold the protein together. They can disrupt tertiary and quaternary structures by breaking disulfide bridges, reducing cystine back to two cysteine residues. They can even overcome the hydrogen bonds and other side chain interactions that hold α-helices and β-pleated sheets intact. Similarly, detergents such as SDS (sodium dodecyl sulfate, also called sodium lauryl sulfate) can solubilize proteins, resulting in a hydrophobic core that promotes denaturation of the protein.

KEY CONCEPT 5

At highly acidic pH values, amino acids tend to be positively charged. At highly alkaline pH values, amino acids tend to be negatively charged.

Leucine has an aliphatic side chain.

At physiological pH, leucine exists as a zwitterion.

At pH 1 (below even the pH of the stomach), there are plenty of protons in solution. Because we're far below the pK of the amino group, the amino group will be fully protonated (-NH ), and thus positively charged.

Because we're also below the pK of the carboxylic acid group, it too will be fully protonated (-COOH), and thus neutral. Therefore, at very acidic pH values, amino acids tend to be positively charged,

If we increase the pH of the amino acid solution from pH 1 to pH 7.4, the normal pH of human blood, we've moved far above the pK of the carboxylic acid group. At physiological pH, you will not find amino acids with the carboxylate group protonated (-COOH) and the amino group unprotonated (-NH ). Under these conditions, the carboxyl group will be in its conjugate base form and be deprotonated, becoming -COO .

Conversely, we're still well below the pK of the basic amino group, so it will remain fully protonated and in its conjugate acid form (-NH^3+ ). Thus we have a molecule that has both a positive charge and a negative charge, but overall, the molecule is electrically neutral. We call such molecules dipolar ions, or zwitterions. The two charges neutralize one another, and zwitterions exist in water as internal salts.

replication

Copying process by which a cell duplicates its DNA

central dogma

DNA -> RNA -> Protein

KEY CONCEPT 11

Denatured proteins lose their three-dimensional structure and are thus inactive.

Peptides are composed of amino acid subunits, sometimes called residues.

Dipeptides consist of two amino acid residues; tripeptides have three. The term oligopeptide is used for relatively small peptides, up to about 20 residues; while longer chains are called polypeptides

KEY CONCEPT 2

Except for glycine, all amino acids are chiral—and except for cysteine, all of them have an (S) absolute configuration.

Proline plays a central role in the FORMATION of alpha helices and beta sheets. While proline's unique structure may also disrupt both alpha helixes and beta sheets, it's ability to make sharp turns facilitates the

FORMATION of both structures, with proline commonly being found at the beginning of alpha helices or at the turns in beta sheets.

The pK of a group is the pH at which, on average, half of the molecules of that species are deprotonated; that is, [protonated version of the ionizable group] = [deprotonated version of the ionizable group] or [HA] = [A ].

If the pH is less than the pK , a majority of the species will be protonated. If the pH is higher than the pK , a majority of the species will be deprotonated.

Because of these acid-base properties, amino acids are great candidates for titrations. We assume that the titration of each proton occurs as a distinct step, resembling that of a simple monoprotic acid. Thus, the titration curve looks like a combination of two monoprotic acid titration curves (or three curves, if the side chain is charged).

Imagine an acidic 1 M glycine solution. At low pH values, glycine exists predominantly as NH3CH2COOH; it is fully protonated, with a positive charge. As the solution is titrated with NaOH, the carboxyl group will deprotonate first because it is more acidic than the amino group. When 0.5 equivalents of base have been added to the solution, the concentrations of the fully protonated glycine and its zwitterion, +NH3CH2COO-, are equal; that is, [+NH3CH2COOH] = [+NH3CH2COO-]. At this point, the pH equals pK . Remember: when the pH is close to the pK value of a solute, a solution is acting as a buffer, and the titration curve is relatively flat, as demonstrated in the blue box in the diagram.As we add more base, the carboxylate group goes from half-deprotonated to fully deprotonated. The amino acid stops acting like a buffer, and pH starts to increase rapidly during this phase. When we've added 1.0 equivalent of base, glycine exists exclusively as the zwitterion form (remember, we started with 1.0 equivalent of glycine). This means that every molecule is now electrically neutral, and thus the pH equals the isoelectric point (pI) of glycine. This is true of all amino acids: the isoelectric point is the pH at which the molecule is electrically neutral. For neutral amino acids, it can be calculated by averaging the two pK values for the carboxylic acid and amino groups: As we continue adding base, glycine passes through a second buffering phase as the amino group deprotonates; again, the pH remains relatively constant. When 1.5 equivalents of base have been added, the concentration of the zwitterion form equals the concentration of the fully deprotonated form; that is, [ NH CH COO ] = [NH CH COO ], and the pH equals pK . Once again, the titration curve is nearly horizontal. Finally, when we've added 2.0 equivalents of base, the amino acid has become fully deprotonated, and all that remains is NH CH COO ; additional base will only increase the pH further.

KEY CONCEPT 4

Like all polyprotic acids, each ionizable proton has its own pK at which it is "half deprotonated."

Lysine, on the other hand, has two amino groups and one carboxyl group. Thus, its charge in its fully protonated state is +2, not +1. Losing the carboxyl proton, which still happens around pH 2, brings the charge down to +1.

Lysine does not become electrically neutral until it loses the proton from its main amino group, which happens around pH 9. It gets a negative charge when it loses the proton on the amino group in its side chain, which happens around pH 10.5. Thus, the isoelectric point of lysine is the average of the pK values for the amino group and side chain; the pI is around 9.75.

Milk of magnesia, which is often used as an antacid. At that pH, the carboxylate group is already deprotonated and thus remains -COO .

On the other hand, we are now well above the pK for the amino group, so it deprotonates too, becoming -NH . So, at highly basic pH, glycine is now negatively charged,

Only L-amino acids are constituents of proteins. Our body synthesizes most of its own L-amino acids and these then get incorporated into proteins.

Proteins are catalysts for most of the biochemical reactions that take place in our body. Along with DNA and RNA, proteins constitute the genetic machinery of living organisms. Proteins are in fact termed as the "building blocks of life"

reverse transcription

RNA to DNA

First, the amino acids with long alkyl side chains— alanine, isoleucine, leucine, valine, and phenylalanine—are all strongly hydrophobic and thus more likely to be found in the interior of proteins, away from water on the surface of the protein.

Second, all the amino acids with charged side chains—positively charged histidine, arginine, and lysine, plus negatively charged glutamate and aspartate—are hydrophilic, as are the amides asparagine and glutamine. The remaining amino acids lie somewhere in the middle and are neither particularly hydrophilic nor particularly hydrophobic.

hydrophilic, neutral, polar side chains

Serine, Threonine, Asparagine, Glutamate, Cysteine, tyrosine

Because of its rigid cyclic structure, proline will introduce a kink in the peptide chain when it is found in the middle of an α-helix. Proline residues are thus rarely found in α-helices, except in helices that cross the cell membrane.

Similarly, it is rarely found in the middle of pleated sheets. On the other hand, proline is often found in the turns between the chains of a β-pleated sheet, and it is often found as the residue at the start of an α-helix.

Ionizable groups tend to gain protons under acidic conditions and lose them under basic conditions.

So, in general, at low pH, ionizable groups tend to be protonated; at high pH, they tend to be deprotonated.

Mechanism of peptide bond formation

Step 1: Nucleophilic amino group of second amino acid attacks the electrophilic carbonyl group of the first amino acid Step 2: Carbonyl bond reforms, with the elimination of hydroxide ion Step 3: The hydroxide ion abstracts a proton (elimination of water), the positive charge on nitrogen is neutralized. This results in the formation of a new bond - peptide bond between the two amino acids

"Double bond" character of the peptide bond

The bond between the carbonyl carbon and nitrogen acquires a partial double bond character; and just like any double bond, rotation around this peptide bond is now restricted. Also, as with all double bonds, the atoms of the peptide bond have planar geometries. The planar geometry causes the peptide bond to be either in the cis or the trans configuration.

Quaternary structures only exist for proteins that contain more than one polypeptide chain. For these proteins, the quaternary structure is an aggregate of smaller globular peptides, or subunits, and represents the functional form of the protein.

The classic examples of quaternary structure are hemoglobin and immunoglobulins. Hemoglobin consists of four distinct subunits, each of which can bind one molecule of oxygen. Similarly, immunoglobulin G (IgG) antibodies also contain a total of four subunits each. The formation of quaternary structures can serve several roles. First, they can be more stable, by further reducing the surface area of the protein complex. Second, they can reduce the amount of DNA needed to encode the protein complex. Third, they can bring catalytic sites close together, allowing intermediates from one reaction to be directly shuttled to a second reaction. Finally, and most important, they can induce cooperativity, or allosteric effects.

The primary structure of a protein is the linear arrangement of amino acids coded in an organism's DNA. It's the sequence of amino acids, listed from the N-terminus, or amino end, to the C-terminus, or carboxyl end.

The primary structure alone encodes all the information needed for folding at all of the higher structural levels; the secondary, tertiary, and quaternary structures a protein adopts are the most energetically favorable arrangements of the primary structure in a given environment. The primary structure of a protein can be determined by a laboratory technique called sequencing. This is most easily done using the DNA that coded for that protein, although it can also be done from the protein itself.

KEY CONCEPT 9

The primary structure of a protein is the order of its amino acids. The two main secondary structures are the α-helix and β-pleated sheet, which both result from hydrogen bonding.

KEY CONCEPT 1

The side chains (R groups) of amino acids determine their chemical properties.

KEY CONCEPT 3

The surface of a protein tends to be rich in amino acids with charged side chains. Strongly hydrophobic amino acids tend to be found on the interior of proteins.

KEY CONCEPT 10

The tertiary structure of a protein is primarily the result of moving hydrophobic amino acid side chains into the interior of the protein.

A protein's secondary structure is the local structure of neighboring amino acids. Secondary structures are primarily the result of hydrogen bonding between nearby amino acids.

The two most common secondary structures are α-helices and β-pleated sheets. The key to the stability of both structures is the formation of intramolecular hydrogen bonds between different residues.

Proteins can be broadly divided into fibrous proteins, such as collagen, that have structures that resemble sheets or long strands, and globular proteins, such as myoglobin, that tend to be spherical (that is, like a globe).

These are caused by tertiary and quaternary protein structures, both of which are the result of protein folding.

The enhanced freedom of rotation with regards to these two bonds allows proteins to fold into a variety of shapes. These folded structures are referred to as secondary protein structures and are essentially of two types - alpha helix and beta pleated sheets.

These folded secondary structures are stabilized by the formation of hydrogen bonds between the amino acids.

A protein's tertiary structure is its three-dimensional shape. Tertiary structures are mostly determined by hydrophilic and hydrophobic interactions between R groups of amino acids. Hydrophobic residues prefer to be on the interior of proteins, which reduces their proximity to water. Hydrophilic N-H and C=O bonds found in the polypeptide chain get pulled in by these hydrophobic residues.

These hydrophilic bonds can then form electrostatic interactions and hydrogen bonds that further stabilize the protein from the inside. As a result of these hydrophobic interactions, most of the amino acids on the surface of proteins have hydrophilic (polar or charged) R groups; highly hydrophobic R groups, such as phenylalanine, are almost never found on the surface of a protein.

Conjugated proteins derive part of their function from covalently attached molecules called prosthetic groups. These prosthetic groups can be organic molecules, such as vitamins, or even metal ions, such as iron. Proteins with lipid, carbohydrate, and nucleic acid prosthetic groups are referred to as lipoproteins, glycoproteins, and nucleoproteins, respectively.

These prosthetic groups have major roles in determining the function of their respective proteins. For example, each of hemoglobin's subunits (as well as myoglobin) contains a prosthetic group called heme. The heme group, which contains an iron atom in its core, binds to and carries oxygen; as such, hemoglobin is inactive without the heme group. These groups can also direct the protein to be delivered to a certain location, such as the cell membrane, nucleus, lysosome, or endoplasmic reticulum.

Unlike the rigid peptide bond, the bond linking the amino group to the alpha carbon atom and the bond linking the alpha carbon atom to the carbonyl carbon are single bonds.

These two bonds are free to rotate about the amide bonds, allowing the amino acids in the polypeptide chain to take on a variety of orientations

Peptide bond formation is an example of a condensation or dehydration reaction because it results in the removal of a water molecule (HO); it can also be viewed as an acyl substitution, which can occur with all carboxylic acid derivatives.

When a peptide bond forms, the electrophilic carbonyl carbon on the first amino acid is attacked by the nucleophilic amino group on the second amino acid. After that attack, the hydroxyl group of the carboxylic acid is kicked off. The result is the formation of a peptide (amide) bond.

Because glutamic acid has two carboxyl groups and one amino group, its charge in its fully protonated state is still +1. It undergoes the first deprotonation, losing the proton from its main carboxyl group, just as glycine does. At that point, it is electrically neutral.

When it loses its second proton, just as with glycine, its overall charge will be -1. However, the second proton that is removed in this case comes from the side chain carboxyl group, not the amino group! This is a relatively acidic group, with a pK of around 4.2. The result is that the pI of glutamic acid is much lower than that of glycine, around 3.2.

Tertiary structure

When several secondary structures come together, tertiary structures are formed. In tertiary structures, in addition to hydrogen bonding, amino acid side chains of the various secondary structures start interacting with each other in a number of ways. Vanderwall forces, hydrogen bonding, disulfide bonds

Quaternary structure:

When several tertiary structures come together, a quaternary protein structure is formed. For example, hemoglobin is a functional quaternary protein formed by the coming together of 4 tertiary structures (called globin proteins). Same forces of interactions operate in a quaternary structure, as in the case of a tertiary structure.

KEY CONCEPT 6

When the pH of a solution is approximately equal to the pK of the solute, the solution acts as a buffer.

KEY CONCEPT 7

When the pH of an amino acid solution equals the isoelectric point (pI) of the amino acid, it exists as electrically neutral molecules. The pI is calculated as the average of the two nearest pKa values. For amino acids with non-ionizable side chains, the pI is usually around 6.

In living organisms, hydrolysis is catalyzed by hydrolytic enzymes such as trypsin and chymotrypsin. Both are specific, in that they only cleave at specific points in the peptide chain: trypsin cleaves at the carboxyl end of arginine and lysine, while chymotrypsin cleaves at the carboxyl end of phenylalanine, tryptophan, and tyrosine.

While you don't need to know the exact mechanism of how these enzymes catalyze hydrolysis, you do need to understand the main idea: they break apart the amide bond by adding a hydrogen atom to the amide nitrogen and an OH group to the carbonyl carbon.

α-Helices

a rodlike structure in which the peptide chain coils clockwise around a central axis. The helix is stabilized by intramolecular hydrogen bonds between a carbonyl oxygen atom and an amide hydrogen atom four residues down the chain. The side chains of the amino acids in the α-helical conformation point away from the helix core. The α-helix is an important component in the structure of keratin, a fibrous structural protein found in human skin, hair, and fingernails.

In β sheets hydrogen bonding occurs between neighboring polypeptide chains rather than within the same polypeptide as in the case of an α helix. Sheets exist in two forms:

a) antiparallel β sheet, in which neighboring hydrogen-bonded polypeptide chains run in opposite directions i.e. one polypeptide chain starts from the terminal carboxylic group and ends at the terminal amino group (left to right); while the other polypeptide chain starts from the terminal amino group and ends at the terminal carboxylic group (left to right) b) parallel β sheet, in which the hydrogen-bonded chains extend in the same direction.

Amino acids

are molecules that contain two functional groups: an amino group (-NH ) and a carboxyl group (-COOH). In addition to the amino and carboxyl groups, the α-carbon has two other groups attached to it: a hydrogen atom, and a side chain, also called an R group, which is specific to each amino acid. The side chains determine the properties of amino acids, and therefore their functions.

Electrophoretic separation

depends on the existence of a negative net charge.

RNA virus

ex. Human immunodeficiency virus

Hydrophobic Nonpolar, alkyl Side Chains

glycine, valine, alanine, leucine, isoleucine, methionine, proline

glycine

no chiral alpha carbon, very flexible hence free rotation, alpha helix breaker

ncRNA

non-coding RNA; RNA that is not translated into protein, including tRNA, rRNA, snRNA, miRNA, etc

histidine

pKa of 6.5 which is close to physiological pH. pH>pKa=deprotonated, ph<pKa=protonated, great in active site able to be used in both forms

Proteins

polypeptides that range from just a few amino acids in length up to thousands. They serve many functions in biological systems, such as enzymes, hormones, membrane pores and receptors, and elements of cell structure. Proteins are the main actors in cells; the genetic code, after all, is simply a recipe for making thousands of proteins.

A chemical denaturent destroys hydrogen bonds which corresponds to all levels except

primary

Whenever a solute dissolves in a solvent, the nearby solvent molecules form a solvation layer around that solute. From an enthalpy standpoint, even hydrocarbons are more stable in aqueous solution than in organic ones (Δ H < 0). However, when a hydrophobic side chain, such as those in phenylalanine and leucine, is placed in aqueous solution, the water molecules in the solvation layer cannot form hydrogen bonds with the side chain. This forces the nearby water molecules to rearrange themselves into specific arrangements to maximize hydrogen bonding—which means a negative change in entropy, ΔS. Remember that negative changes in entropy represent increasing order (decreasing disorder) and thus are unfavorable. This entropy change makes the overall process nonspontaneous (Δ G > 0).

putting hydrophilic residues such as serine or lysine on the exterior of the protein allows the nearby water molecules more latitude in their positioning, thus increasing their entropy (Δ S > 0), and making the overall solvation process spontaneous. Thus, by moving hydrophobic residues away from water molecules and hydrophilic residues toward water molecules, a protein achieves maximum stability.

A particularly important component of tertiary structure is the presence of disulfide bonds, the bonds that form when two cysteine molecules become oxidized to form cystine. Disulfide bonds create loops in the protein chain. In addition, disulfide bonds determine how wavy or curly human hair is: the more disulfide bonds, the curlier it is. Note that forming a disulfide bond requires the loss of two protons and two electrons (oxidation). The extracellular (oxidizing) space favors disulfide bridges. Intracellular space is reducing environment due to antioxidants.

secondary structures probably form first, and then hydrophobic interactions and hydrogen bonds cause the protein to "collapse" into its proper three-dimensional structure. Along the way, it adopts intermediate states known as molten globules. Protein folding is an extremely rapid process: from start to finish, it typically takes much less than a second. If a protein loses its tertiary structure, a process commonly called denaturation, it loses its function.

proteolysis

specific means of breaking a peptide bod, protease, trypsin cleaves C terminal Arginine and lysine

Primary

stabilized by Covalent bond (amide/ peptide bond)

Secondary

stabilized by Hydrogen bonds

Tertiary & Quaternary

stabilized by Ionic bonds, disulfide bonds, hydrophobic interactions, hydrogen bonding

Primary structure

the linear sequence of amino acids joined to each other through peptide bonds. The sequence of amino acids determines the basic structure of the protein.

hydrophobic, non-polar, aromatic

tryptophan, phenylalanine, tyrosine

When you change the temperature of a protein by heating it up

you destroy all the levels of a protein structure except primary