Chapter 1- Amino Acids, Peptides, and Proteins Flashcards
proteinogenic amino acids
20 amino acids that are encoded by the human genetic code
only amino acid that is not optically active
glycine, its also achiral
only amino acid with an R configuration
cysteine
amino acids that are nonpolar and have nonaromatic side chains
GAPVLIM
glycine (only an H)
ALKYL SIDE CHAIN W/ 1-4 CARBONS alanine valine leucine isoleucine
methionine (sulfur and methyl group)
proline (cyclic)
amino acids that are uncharged and have aromatic side chains
FYW
tryptophan (largest), phenylalanine (relatively nonpolar), tyrosine (relatively polar)
amino acids that are polar and NOT aromatic
STCNQ
OH groups in side chains (highly polar/ participate in H bonding)
serine
threonine
AMIDE SIDE CHAINS (dont gain/lose protons with pH change and do not become charged)
asparagine
glutamine
cystine [thiol (SH)]
amino acids that are negatively charged (acidic)
DE
INSTEAD OF AMIDES THESE HAVE CARBOXYLATE (COO-) aspartic acid (aspartate) glutamic acid (glutamate)
amino acids that are positively charged (basic)
KRH
ALL HAVE POSITIVELY CHARGED NITROGENS
lysine (terminal primary amino group)
arginine (3 nitrogen atoms)
histidine (aromatic ring with 2 nitrogens, called imidazole)
what happens to ionizable groups in acidic and basic conditions?
acidic- gain protons (protonated at low pH)
basic- lose protons (deprotonated at high pH)
pKa
pH at which half molecules of the species are deprotonated
what happens to majority species if pH is less than pKa
protonation
what happens to majority species if pH is more than pKa
deprotonation
pKa for carboxyl and amino group
c- 2
a- 9-10
Ionization under acidic, intermediate, and basic conditions
A- positively charged
I- zwitterionic (carboxylic acid deprotonates)
B- negatively charged
Alkaline
Basic
is a carboxyl group or amino group more acidic
carboxyl is more acidic so it will deprotonate first
how to pH and pKa relate in buffer regions
pKa and pH have similar values
isoelectric point (pI)
pH at which every molecule in a solution is electrically neutral
typical pI for amino acids with nonionizable side chains
around 6
pH trend for amino acids with acidic or basic side chains
acidic- low isoelectric point (pI below 6)
basic- high isoelectric point (pI above 6)
oligopeptide vs. polypeptide
o- relatively small peptides (up to 20)
p- longer chains (over 20)
what functional group forms when a peptide bond forms
COO- and NH3+ form the functional group -C(O)NH-
what type of reaction is a peptide bond formation
condensation (dehydration) b/c it involves the removal of a water molecule
how do enzymes catalyze hydrolysis
adding a hydrogen atom to the amid nitrogen and an OH group to the carbonyl carbon
primary structure
linear arrangement of amino acids coded in an organisms DNA. stabilized by the formation of covalent peptide bonds between adjacent amino acids. encodes all the info needed for folding at all higher structural levels.
secondary structure
primarily a result of hydrogen bonding b/w nearby amino acids. (2 most common structures are a-helices and B-pleated sheets)
a-helices
rodlike structure, coils around (important in keratin structure- fibrous structural protein found in skin, hair, and fingernails)
B-pleated sheet
either parallel or anitiparallel. peptide chains lie alongside on another forming rows or strands held together by intramolecular h-bonds b/w carbonyl oxygen of one chain and amide hydrogen of an adjacent chain (fibroin- primary protein of silk fibers is composed of B-sheets)
what does proline to in a peptide chains secondary structure?
put a kink in the chain (usually found in turns of B-sheet and at the start of an a-helix chain)
tertiary structure
primarily due to moving hydrophobic amino acid side chains to interior of protein. important structure- disulfide bonds.
example of fibrous protein
collagen, resemble sheets or long strands
example of globular protein
myoglobin, tend to be spherical
disulfide bonds
form when 2 cysteine molecules become oxidized to form cystine (requires loss of 2 protons and 2 electrons). create loops in protein chain. determine how wavy or curly hair is (more bonds = curlier)
molten globules
intermediate state in between when hydrophobic interactions and hydrogen bonds cause protein to collapse into its proper 3D structure. (very rapid process)
denaturation
protein loses its tertiary structure
quaternary structure
interactions b/w separate subunits of a multisubunit protein. for proteins with more than 1 polypeptide chain. (ex: hemoglobin w/ 4 distinct subunits)
4 potential roles of quaternary structures?
- more stable
- reduce amount of DNA needed to encode protein complex
- bring catalytic sites close together so 1 reaction can quickly shuttle to the next one
- allosteric effects (cooperativity)- one subunit can undergo conformational/structural changes to enhance or reduce activity of other subunits
prosthetic groups
major role in determining function of proteins (ex: prosthetic group in hemoglobin is called heme- contains iron which binds to/carries oxygen)
why are proteins denatured by heat/solutes?
heat- increased KE of molecules thus disrupting hydrophobic interactions
solutes- directly interfering with forces that hold proteins together
