Lecture 1.2: Amino Acids & Protein Primary Structure

What is a Protein?

A biological macromolecule made of amino acids linked together in a chain. Proteins are the most abundant macromolecules in cells and perform many biological functions.

What is a Macromolecule?

A large biological molecule. The four major macromolecule groups are proteins, nucleic acids, carbohydrates, and lipids.

What is the most abundant macromolecule in cells

Proteins are the most abundant macromolecules in cells. Living tissue is mostly water by weight, but proteins make up a large portion of cellular macromolecules.

What is an Amino acid?

The monomer or basic building block of proteins. There are 20 common amino acids found in nature, and each has a unique chemical composition.

What is a Protein polymer?

A protein is a polymer chain made from amino acid monomers. The amino acids are connected by peptide bonds to form a polypeptide.

What is a Polypeptide?

A chain of amino acids linked by peptide bonds. A protein can contain one polypeptide chain or multiple polypeptide subunits.

What is a Peptide bond?

The covalent bond that connects amino acids in a protein. It forms between the carboxyl group of one amino acid and the amino group of another amino acid.

What is a Protein function?

Proteins perform many functions, including redox regulation, metabolism, oxygen transport, signal transduction, protein folding, RNA synthesis, nitrogen metabolism, and muscle contraction.

What is a Protein size variation?

Proteins vary widely in amino acid length and molecular mass. Some are small, such as human thioredoxin, while others are extremely large, such as human titin.

What is a Protein subunit?

One polypeptide chain within a larger protein complex. Some proteins have one subunit, while others contain multiple subunits.

What is a Globular protein?

A compact folded protein with a roughly spherical shape. Hydrophobic amino acids are often buried in the interior, while polar or charged amino acids are often found on the surface.

What is a Hydration layer?

The layer of water molecules surrounding a folded protein. Hydrophilic amino acids on the surface interact with this water layer.

What is the Hydrophobic interior?

The inside of a folded protein where nonpolar amino acids are often buried away from water.

What is the general amino acid structure

Most amino acids contain a central alpha carbon, an amino group, a carboxylate group, a hydrogen atom, and an R group side chain.

What is an R group or side chain?

The variable part of an amino acid. It determines whether the amino acid is hydrophobic, polar, charged, aromatic, small, bulky, reactive, or flexible.

What is an amino group?

The nitrogen-containing group of an amino acid. At physiological pH, it is usually protonated as -NH3+.

What is a Carboxylate group?

The acidic carboxyl group of an amino acid. At physiological pH, it is usually deprotonated as -COO-.

What is a Zwitterion?

A molecule with both a positive charge and a negative charge but no overall net charge. Free amino acids at physiological pH commonly exist as zwitterions with -NH3+ and -COO-.

L-amino acid

The amino acid enantiomer generally used in proteins.

D-amino acid

The mirror-image form of an L-amino acid. D-amino acids are not the usual form incorporated into proteins.

Exception to amino acid chirality

Glycine is the main exception because its R group is hydrogen, so its alpha carbon does not have four different groups and is not chiral.

Glycine abbreviation

Glycine is abbreviated Gly or G.

Alanine abbreviation

Alanine is abbreviated Ala or A.

Valine abbreviation

Valine is abbreviated Val or V.

Leucine abbreviation

Leucine is abbreviated Leu or L.

Isoleucine abbreviation

Isoleucine is abbreviated Ile or I.

Methionine abbreviation

Methionine is abbreviated Met or M.

Proline abbreviation

Proline is abbreviated Pro or P.

Phenylalanine abbreviation

Phenylalanine is abbreviated Phe or F.

Tryptophan abbreviation

Tryptophan is abbreviated Trp or W.

Tyrosine abbreviation

Tyrosine is abbreviated Tyr or Y.

Serine abbreviation

Serine is abbreviated Ser or S.

Threonine abbreviation

Threonine is abbreviated Thr or T.

Cysteine abbreviation

Cysteine is abbreviated Cys or C.

Aspartic acid abbreviation

Aspartic acid or aspartate is abbreviated Asp or D.

Glutamic acid abbreviation

Glutamic acid or glutamate is abbreviated Glu or E.

Asparagine abbreviation

Asparagine is abbreviated Asn or N.

Glutamine abbreviation

Glutamine is abbreviated Gln or Q.

Histidine abbreviation

Histidine is abbreviated His or H.

Lysine abbreviation

Lysine is abbreviated Lys or K.

Arginine abbreviation

Arginine is abbreviated Arg or R.

What are the 5 Amino Acid Categories?

five major categories:
- nonpolar/hydrophobic
- positively charged
- negatively charged
- uncharged polar
- aromatic.

Nonpolar or hydrophobic amino acids

Amino acids with side chains that do not interact well with water. They are commonly found buried in the interior of folded proteins.

Positively charged amino acids

Amino acids with side chains that often carry a positive charge at physiological pH. The major examples are lysine, arginine, and sometimes histidine.

Negatively charged amino acids

Amino acids with acidic side chains that are usually negatively charged at physiological pH. The examples are aspartate and glutamate.

Uncharged polar amino acids

Amino acids with polar side chains that can form hydrogen bonds but usually do not carry a full charge at physiological pH.

Aromatic amino acids

Amino acids with ring-containing side chains. The aromatic amino acids discussed are phenylalanine, tyrosine, and tryptophan.

Nonpolar R group

A side chain that is mostly hydrocarbon-like and hydrophobic. These side chains tend to avoid water.

Hydrophobic effect

The tendency of nonpolar groups to cluster away from water. This helps drive protein folding by burying hydrophobic side chains in the protein interior.

Glycine special property

Glycine is very small and flexible. Because its side chain is hydrogen, it is achiral and gives the protein backbone more conformational freedom.

Alanine side chain

Alanine has a methyl group, -CH3, as its side chain, making it small and nonpolar.

Proline special property

Proline's side chain loops back to the amino nitrogen, forming a ring. This restricts the conformations proline can adopt.

Proline and hydrogen bonding

In a polypeptide, proline's backbone nitrogen lacks a normal hydrogen for hydrogen bonding, which can disrupt regular secondary structures.

Leucine vs isoleucine

Leucine and isoleucine have the same molecular mass but different side-chain branching patterns. Both are hydrophobic.

Methionine special role

Methionine is often the first amino acid in newly made polypeptides.

What is the difference in Methionine’s and Cysteine’s sulfur group?

Methionine contains sulfur in a thioether group. Unlike cysteine sulfur, methionine sulfur is not highly reactive.

Acid

A proton donor. An acid donates H+ and becomes its conjugate base.

Base

A proton acceptor. A base accepts H+ and becomes its conjugate acid.

Conjugate base

The form produced when an acid loses a proton. For HA ⇄ H+ + A-, A- is the conjugate base.

Conjugate acid

The form produced when a base gains a proton. For B + H+ ⇄ HB+, HB+ is the conjugate acid.

Acid ionization

The process where an acid releases a proton. General form: HA ⇄ H+ + A-.

Carboxylic acid ionization

A carboxylic acid can lose a proton: R-COOH ⇄ R-COO- + H+. After losing H+, it becomes negatively charged.

Why is water Amphoteric?

Water can act as either an acid or a base. It can lose H+ to form OH- or accept H+ to form H3O+.

Water as a weak base

Water can accept a proton: H2O + H+ ⇄ H3O+.

What happens to acids in water?

When an acid loses H+ in aqueous solution, it often becomes negatively charged, such as R-COOH becoming R-COO-.

What happens to bases in water?

When a base gains H+ in aqueous solution, it often becomes positively charged, such as R-NH2 becoming R-NH3+.

What is the acid dissociation constant, Ka?

The equilibrium constant for acid ionization. For HA ⇄ H+ + A-, Ka = [H+][A-]/[HA].

Strong acid

An acid with a high Ka because it dissociates strongly and releases protons readily.

Weak acid

An acid with a low Ka because it does not dissociate as much and holds onto protons more strongly.

pH

A measure of total hydrogen ion concentration in solution. Formula: pH = -log[H+].

Neutral pH

A solution is neutral at pH 7 because pure water has [H+] = 1 x 10^-7 M.

Acidic solution

A solution with pH below 7. It has a higher H+ concentration than neutral water.

Basic solution

A solution with pH above 7. It has a lower H+ concentration than neutral water.

pKa

A log-scale measure of acid strength. Formula: pKa = -log(Ka).

Low pKa meaning

A low pKa means the group gives up H+ easily and is a stronger acid.

High pKa meaning

A high pKa means the group holds onto H+ more strongly and is a weaker acid.

Henderson-Hasselbalch equation for acids

For HA ⇄ H+ + A-, the equation is pH = pKa + log([A-]/[HA]). It helps calculate the ratio of acid to conjugate base.

Henderson-Hasselbalch equation for bases

For HB+ ⇄ H+ + B, the equation is pH = pKa + log([B]/[HB+]). It helps determine the ratio of neutral base to protonated conjugate acid.

When pH equals pKa

The protonated and deprotonated forms are equal. For acids, [A-] = [HA]. For bases, [B] = [HB+].

When pH is greater than pKa

The deprotonated form dominates. For acids, [A-] > [HA]. For bases, [B] > [HB+].

When pH is less than pKa

The protonated form dominates. For acids, [A-] < [HA]. For bases, [B] < [HB+].

Physiological pH amino acid form

At physiological pH, most free amino acids have a deprotonated carboxyl group and a protonated amino group, making them zwitterions.

When are both carboxyl and amino groups protonated?

At very low pH. Both the carboxyl group and amino group are protonated, giving -COOH and -NH3+.

When are both carboxyl and amino groups protonated?

At very high pH. Both groups are deprotonated, giving -COO- and -NH2.

Lysine side chain

Lysine has a long hydrocarbon chain ending in an amino group that is usually protonated at physiological pH.

Arginine side chain

Arginine contains a guanidinium group that is strongly basic and remains positively charged under most biological conditions.

Histidine side chain

Histidine contains an imidazole ring that can be either positively charged or neutral depending on the environment.

What does Histidine look like at physiological pH

Because histidine's side-chain pKa is close to physiological pH, it can switch between protonated and neutral forms, making it useful for proton transfer in enzymes.

Aspartate side chain

Aspartate has a short carboxylate-containing side chain. At physiological pH, the side-chain carboxyl group is usually deprotonated as -COO-.

Glutamate side chain

Glutamate has a longer carboxylate-containing side chain than aspartate. At physiological pH, it is usually negatively charged.

Aspartate vs glutamate

Both are acidic and negatively charged at physiological pH. Glutamate has one extra methylene group compared with aspartate, making its side chain longer.

Aromatic R group

A side chain containing an aromatic ring with conjugated electrons. Aromatic amino acids include phenylalanine, tyrosine, and tryptophan.

Phenylalanine UV absorption

Phenylalanine only weakly absorbs ultraviolet light compared with tyrosine and tryptophan.

Tyrosine amphipathic character

Tyrosine has hydrophobic character from its aromatic ring and hydrophilic character from its hydroxyl group.

Tyrosine UV absorption

Tyrosine absorbs ultraviolet light at about 280 nm.

Tryptophan side chain

Tryptophan contains an indole ring. The ring nitrogen can form weak hydrogen bonds, making tryptophan amphipathic.

Tryptophan UV absorption

Tryptophan strongly absorbs ultraviolet light at 280 nm, which is important for measuring protein concentration.

Aromatic amino acids and UV light

Tyrosine and tryptophan absorb strongly at 280 nm, while phenylalanine absorbs weakly. This property helps with protein detection.

Transient modification

A temporary chemical change made to a protein. Transient modifications can regulate protein activity, location, interactions, or signaling.

Phosphorylation

The addition of a phosphate group to an amino acid side chain. It is an important transient modification in protein regulation.