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Kaplan MCAT Biology Ch. 15: Amino Acids, Peptides and Proteins

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Amino Acids
-an amine group and a carboxyl group to a single carbon atom (the alpha carbon)

-alpha hydrogen and R group

-alpha carbon, chiral (stereogenic) center --> optically active

-naturally occurring (20) are all L-enantiomers, amino group on the left

-S config (except for cysteine, R, priority by sulfur)
R group
attached to alpha carbon
glycine
simplest AA, not chiral
acid-base characteristic
-basic amino group (pos when protonated) and acidic carboxyl group (neg charge when depro) --> amphoteric

-depend on terms and conditions

-pH --> lots of protons -->AA as base (vice versa)

-try to achieve equilibrium

-since two diff locations, can either be pro or depro, having least two diff disso. constants Ka1 and Ka2, to pH, or Kb1 and Kb2, pOH

-neutral AA in acidic sol --> fully protonated --> amino pro easily than carboxyl (need fairly acidic)
-if even basic solution, become fully depro, easilly for carboxyl group than amino group.
amphoteric
-species acting both acids and bases (ex: h20)

-
zwitterion
both charged on amino and carboxyl at same time --> neutralize --> so at neutral pH --> internal salts
isoelectric point (pI)/isoelectric pH
-intermediate pH, which AA exists as zwitterion (uncharged)

-between pKa1 and pKa2 (pKa is pH which disasso. occurs)
titration of amino acids
-looks like a combo of two or three monoprotic acids (three is acidic or basic R group)

-when add base, carboxyl group deprotonates first, than amino group

-two moles of base to deprotonate one mole of most amino acids

-buffering capacity greatest at or near pH of two diss. constants, pKa1 and pKa2; at isoelectric point, capacity is min., vertical line

-some have acidic or basic side chains, to find pI, avg two acidic pKa;s if side chain acidic, two basic pKa's if basic

-can perform by adding acid to base, sequence is reversed.
henderson-hasselbalch equation
-relationship by relating the pH to the ratio of CA to CB

-when pKa known, ratio at particular pH can be determined

-can prepare effective buffer solutions of AAs; buffering regions of AA within one pH unit of pKa or pKb.
amino acid side chains
-side chains (R groups) give character and give proteins distinguishing features

-
types of amino acid side chains
nonpolar, polar (uncharged), acidic, basic
nonpolar amino acids
-most R groups are saturated hydrocarbons --> hydrophobic -->dec the solubility in water --> prefer bured inside proteins away from aq. cell enviwronment

-tryptophan has N atom w/ lone pair, resonated through aromatic ring --> doesn't exhibit basic properties --> nucleating residue when proteins fold

-often found at core of globular proteins or transmembrane regions of proteins in contact w/ hydrophobic portion of phospholipid membrane
polar amino acids
-uncharged polar R- groups that are hydrophilic --> inc. solubity in water --> surface of proteins
acidic amino acids
-R-group has carboxyl group, neg charge at physiological pH (7.4) so exist in salt form in body

-roles in substrate-binding site of enzymes, require proton transfer

-name ends in -acid

-have three distinct pKa's; has three groups (two COOH (overlap) and one NH3+), because of add. carboxyl group, isoelectric point shifted towards acidic pH, founding by avg. both acidic pKa's

-3 moles of base needed for deprotonation
basic amino acids
-side chain is amino group

-net pos charge at pH 7.4

-add. amino group, three disso. constant (amino's overlap)

-pI towards alkaline pH, avg two basic pKas

-three moles of acid
Predicting AA charge
using pI:

-pH < pI --> pos
-pH > pI --> neg
peptides
-amino acid subunits , sometimes called residues

-carboxyl one end, amino at other --> combine is peptide bond

-small proteins, < 50 residues
residues
amino acid units for peptides
peptide bond
two amino acids combine --> amine bond forms between them
dipeptide
two amino acids joined
tripeptide
three amino acids joined
polypeptide
many amino acids
rxns, forming peptide bonds
-condensation rxn occurs (water is lost)

-reverse, hydrolysis (cleavage by adding water), catalyzed by an acid or base

-certain enzymes digest specific peptide linkage (given in passage)
properties of peptides
-terminal amino acids
1. free alpha amino group - amino terminal, N terminal
2. free carboxyl group - carboxy-terminal, C terminal
read from N to C (left to right)

-amides have two resonance structures, w/ partial DB character between N and C --> C-N bond restrict (rigid and stable) of backbone of proteins
amino terminal, N terminal
free alpha amino group of terminal amino acid
carboxy-terminal, C terminal
free carboxyl group of terminal amino acid
proteins
-polypeptides

-range in length

-many functions
1. hormones
2. enzymes
3. membrane pores
4. receptors
5. elements of cell structures
6. main actors of bio system

-ther are four levels
primary structure of protein
-structure coded in DNA of organism

-sequence of AA, from N-term to C-term, linked by peptide bonds

-most fund. structure, seq. determines higher levels of protein structure (2,3,4 most energetically favorable)

-determined in lab through sequencing, easily done on DNA that produced protein
sequencing
1st structure determined in lab this way, easily done on DNA that produced protein
secondary structure
-local structure of neighboring AAs

-result of H bonding between AAs

-two most common types are alpha helix and beta pleated sheet
alpha helix
-rodlike structure, peptide chain coils clockwise about central axis

-helix stablized by intramolecular H bonds between carbonyl oxygen atoms and amide H atoms foru residues away from each other (n +4 H bond)

-side chains point away from helix core, interacting w/ cell environment

-typical protein w/ structure is keratin
keratin
fibrous structural protein; hair and fingernails
B pleated sheet
-may be parallel or antiparallel

-peptide chains lie alongside each other, forming rows

-chains held by intramolecular H bonds, between carbonyl O atoms on one peptide chain and amine H atom on another

-rippled, or pleated, shape

-R-groups of amino residues point above and below plane

-ex: silk fibers
tertiary structure
-3D shape

-determined by hydrophobic and hydrophilic between R groups of amino acids

-also determined by distribution of disulfide bonds (create loops)

-proline --> ring --> can't fit every location of alpha helix --> kink in chain

-two major classifications: fibrous proteins and globular proteins
cysteine
disulfide bonds results when these two moleculse become oxidized to from cystine
fibrous proteins
like collagen, as sheets or long strands
globular proteins
like myoglobin, are spherical
two major classifications of tertiary structures
fibrous and globular proteins
quarternary structure
-more than one polypeptide subunit

-refers way these subunits arrange themselves yield functional protein

-ex: hemoglobin
hemoglobin
-O2-transporting machines --> fill red bloodcells

-composed of 4 diff. globular protein subunits
Conjugated Proteins
-part of function from covalently attached molecules called prosthetic groups

-proteins w/ lipid, carb, and nucleic acid prosthetic groups: lipoproteins, glycoproteins, nucleoproteins.

-major roles in determining function of their respective proteins

-Hemoglobin's subunit (also myoglobin) have heme group
prosthetic roups
-conjugated proteins get part of function from these covalently attached molecules.

-can be organic (vitamins) or even metals ions
heme group
-prosthetic group of hemoglobin (cooperative) (and myoglobin subunits
(inactive w/o)
-composed of organic porphyrin ring w/ iron atom in center

-binds to and carrier oxygen
denaturation of proteins
-also known as melting

-protein loses 3D structure and revert to a random-coil state
random-coil
-state achieved after protein loses 3D structure

-completely functionless, damage usually permanent; gentle denaturing agent (urea) don't permanently

-methods: detergent, change in pH, temp, or even solute concentration; removing reagent might renature (regain structure and function)

-weak intermolecular forces --> protein stable and function --> disrupted

-reversible
renature
removing reagent that denatures protein brings to this state