MCAT Biochemistry - Amino Acids, Peptides, and Proteins

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64 Terms

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Amino acids

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

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amino functional group

-NH2

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carboxyl functional group

-COOH

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side chain/R group

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

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α-amino acids

one central (often chiral) carbon

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γ-aminobutyric acid (GABA)

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

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ornithine

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

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proteinogenic amino acids

20 α-amino acids encoded by the human genetic code

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α-carbon

chiral/stereogenic center with four differnet groups attached

EXCEPT glycine

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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

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nonpolar, nonaromatic side chains

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

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aromatic side chains

tryptophan, phenylalanine, tyrosine

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polar side chains

serine, threonine, asparagine, glutamine, cysteine

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thiol functional group

-SH

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negatively charged/acidic side chains

aspartic acid/aspartate, glutamic acid/glutamate

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positively charged/basic side chains

lysine, arginine, histidine

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imidazole

aromatic ring with two nitrogen atoms

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hydrophobic amino acids

long alkyl side chains

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hydrophillic amino acids

charged side chains

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amphiphatic amino acids

all other than alkyl chains or charged

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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

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pKa 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

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Amino acids under Acidic conditions

pH ~ 1

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

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Amino acids under intermediate conditions

pH ~ 1 - 7.4

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

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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”

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Amino acids under intermediate conditions

pH ~ 10.5

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

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Titration curve of amino acids

combination of two/three monoprotic acid titration curves

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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

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peptides

the polymer made of amino acids

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residue

amino acid subunits

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dipeptide

peptide made of two amino acid residues

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tripeptide

peptide made of three amino acid residues

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oligopeptide

small peptides, up to 20 residues

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ploypeptide

longer peptides, >20

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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

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condensation/dehydration reaction

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

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amino/N-terminus

the free amino end

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carboxy/C-terminus

the free carboxyl end

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hydrolysis

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

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hydrolytic enzymes

trypsin, chymotrypsin

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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

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secondary (2°) structure

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

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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

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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

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sequencing

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

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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

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keratin

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

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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

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Fibroin

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

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fibrous proteins

structures that resemble sheets or long strands

ex. collagen

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globular proteins

spherical

ex. myoglobin

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collagen

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

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myoglobin

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

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disulfide bond

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

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molten globules

intermediate states of protein formation

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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

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solvation layer

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

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subunit

smaller globular peptides, part of a quaternary structure

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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

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conjugated proteins

derive part of their function from prosthetic groups

ex. lipoproteins, glycoproteins, nucleoproteins

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prosthetic group

molecules covalently attached molecules

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heme

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

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urea

denatures protein by breaking disulfide bridges

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SDS (sodium dodecyl sulfate, sodium lauryl sulfate)

solubilise proteins, disrupting non-covalent bonds