MCAT Biochemistry - Amino Acids, Peptides, and Proteins

Amino acids

Amino acids

molecules that contain amino and carboxyl functional groups attached to carbon; other groups are a hydrogen and an R/side group

amino functional group

-NH2

carboxyl functional group

-COOH

side chain/R group

other group attached to α-carbon; specific to each amino acid

α-amino acids

one central (often chiral) carbon

γ-aminobutyric acid (GABA)

amino group on the gamma (γ) carbon, three carbons away from the carboxyl group.

ornithine

intermediates in the urea cycle, not specified by a codon in the genetic code or incorporated into proteins

proteinogenic amino acids

20 α-amino acids encoded by the human genetic code

α-carbon

chiral/stereogenic center with four differnet groups attached

EXCEPT glycine

L-amino acids

all chiral amino acids in eukaryotes, amino gourp is left in a fischer projection; S absolute configuration in Cahn-Ingold-Prelog EXCEPT cysteine

nonpolar, nonaromatic side chains

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

aromatic side chains

tryptophan, phenylalanine, tyrosine

polar side chains

serine, threonine, asparagine, glutamine, cysteine

thiol functional group

-SH

negatively charged/acidic side chains

aspartic acid/aspartate, glutamic acid/glutamate

positively charged/basic side chains

lysine, arginine, histidine

imidazole

aromatic ring with two nitrogen atoms

hydrophobic amino acids

long alkyl side chains

hydrophillic amino acids

charged side chains

amphiphatic amino acids

all other than alkyl chains or charged

amphoteric species

compound that can function as acid or base; either accept or donate protons; typically protonated at low pH and deprotonated at high pH

pK_a of amino acid

pH at which half molecules are deprotonated; [HA] = [A^-]; first is for carboxyl group (~2) and second is for amino group (~9-10); third for ionizable side chain

Amino acids under Acidic conditions

pH ~ 1

amino group is fully protonated: -NH₃⁺; carboxyl group is fully protonated and neutral: - COOH

Amino acids under intermediate conditions

pH ~ 1 - 7.4

amino group is fully protonated: -NH₃⁺; carboxyl group is deprotonated: - COO^-

zwitterions/dipolar ions

a molecule that has both a positive charge and a negative charge, but overall, the molecule is electrically neutral; from German zwitter “hybrid”

Amino acids under intermediate conditions

pH ~ 10.5

amino group is deprotonated: -NH₂; carboxyl group is deprotonated: - COO^-

Titration curve of amino acids

combination of two/three monoprotic acid titration curves

isoelectric point (pI)

the pH at which the molecule is electrically neutral; for neutral amino acids, it can be calculated by averaging the two pKa values for the amino and carboxyl groups; average the R group and carboxyl group for acidic amino acids and the R group and amino group for basic amino acids

peptides

the polymer made of amino acids

residue

amino acid subunits

dipeptide

peptide made of two amino acid residues

tripeptide

peptide made of three amino acid residues

oligopeptide

small peptides, up to 20 residues

ploypeptide

longer peptides, >20

peptide bond

amide bond between the carboxyl group of one amino acid and the amino group of another; forms the functional group -C(O)NH^-

first - electrophilic carbonyl carbon on the first amino acid is attacked by the nucleophilic amino group on the second amino acid, second - the hydroxyl group of the carboxylic acid is kicked off

partial double bond character between C-N bond

condensation/dehydration reaction

reaction that removes a water molecule in order to bond two reactants

amino/N-terminus

the free amino end

carboxy/C-terminus

the free carboxyl end

hydrolysis

reaction that adds a water molecule in order to break part a large reactant; often catalysed by hydrolytic enzymes in living organisms

hydrolytic enzymes

trypsin, chymotrypsin

primary (1°) structure

sequence of amino acids, listed from the N-terminus, or amino end, to the C-terminus, or carboxyl end; stabilised by the formation of covalent peptide bonds btwn adjacent amino acids

secondary (2°) structure

local structure of neighboring amino acids; primarily the result of hydrogen bonding

tertiary (3°) structure

its three-dimensional shape; determined by hydrophilic and hydrophobic interactions between R groups of amino acids; hydrophobic residues prefer interior of protein

quaternary (4°) structure

an aggregate of subunits and represents the functional form of the protein; not all proteins have this; increases stability, reduces amount of DNA to encode protein complex, brings catalytic sites close together, and induces cooperativity

ex. hemoglobin, immunoglobins

sequencing

means to determine the primary structure of an unbranched biopolymer, i.e. proteins

α-helix

a rodlike structure in which the peptide chain coils clockwise around a central axis; stabilised by intramolecular hydrogen bonds between a carbonyl oxygen atom and an amide hydrogen atom four residues down the chain

proline will kink in the middle; but will often be at the start

keratin

a fibrous structural protein found in human skin, hair, and fingernails; α-helix shaped

β-Pleated Sheet

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; pleated/ripples shape to accommodate as many hydrogen bonds as possible; parallel or anti-parallel

proline often in the turns between chains

Fibroin

the primary protein component of silk fibers; composed of β-pleated sheets.

fibrous proteins

structures that resemble sheets or long strands

ex. collagen

globular proteins

spherical

ex. myoglobin

collagen

main structural protein in the extracellular matrix of a body's various connective tissues

myoglobin

iron- and oxygen-binding protein found in the cardiac and skeletal muscle tissue of vertebrates in general and in almost all mammals

disulfide bond

bonds that form when two cysteine molecules become oxidized to form cystine; create loops in protein chain; determine curliness of human hair

molten globules

intermediate states of protein formation

denaturation

loss of a protein’s tertiary structure and therefore function; often irreversible; caused by heat (overcoming hydrophobic interactions) and solutes (interfere with forces that hold protein together

solvation layer

the structured layer of solvent molecules that surround a solute particle, such as an ion or a molecule, in a solution

subunit

smaller globular peptides, part of a quaternary structure

cooperativity/allosteric effects

the regulation of an enzyme or a protein's function through the binding of a molecule at a site other than the enzyme's active site, known as the allosteric site

conjugated proteins

derive part of their function from prosthetic groups

ex. lipoproteins, glycoproteins, nucleoproteins

prosthetic group

molecules covalently attached molecules

heme

prosthetic group in hemoglobin containing an iron core that binds to and carries oxygen; hemoglobin is inactive without it

urea

denatures protein by breaking disulfide bridges

SDS (sodium dodecyl sulfate, sodium lauryl sulfate)

solubilise proteins, disrupting non-covalent bonds