Block 1 Flashcards
Non-polar Amino Acids
MILFY GAP VW
Polar Amino Acids (non charged)
STNQC
Polar Amino Acids (charged)
HERD K
Aromatic Amino Acids
Tryptophan
Phenylalanine
Tyrosine
pKa
pH at which a group is 50% protonated and 50% unprotonated
Raising pH 1 unit from pKa.. what is ratio of unprot. to prot.
10:1
isoelectric point
pI
pH where the AA. peptide, or protein will have a net charge of zero
buffering region
where the pH of the solution is near the pKa of an ionizable group
pI equation
pk1 +pk2 / 2
nascent
newly synthesized
what AA always on N terminal
Methionine
S-H –> S-S
cysteine to cystine bond
common in extracellular proteins b/c increases stability but not intracellular
can have interchain and intrachain
Why are there limits to possible conformation states for a polypeptide?
what conformation?
strong electroneg of carbonyl O and amide N in peptide bond
forms partial double bond, delocalizes e- and creates resonance
chooses trans conformation
what is largest driving factor to protein folding?
hydrophobic forces
Explain funnel analogy
- reversible, local interactions that are both correct and incorrect happen but the correct ones cause alignment that facilitates more correct ones and increases stability.
as you get closer to the native state, less possible conformations are incorrect (funnel)
primary-quat structure
1: AA sequence
2: folding -> a helix vs b sheet
3: create domains/subunits
4: combination of subunits
alpha helix (characteristics)
R handed
3.6 residues/turn
stabilized by H bonds between carbonyl carbon of AA i and amide proton of AA i+4
h bonds parallel to helix axis, R groups project outward
a helices on surface of protein are amphipathic
B sheet (characteristics)
H bonds run between carbonyl o and amide H of non-contiguous parts of a chain
H bonds coplanar with the B sheet
R groups alternately project above and below the plane of the sheet
often form the hydrophobic core
Parallel B sheet
N–C
N–C
N–C
bonds look diagonal
Antiparallel B sheet
N–C
C–N
N–C
bonds look straight up and down
Can you have mixed B sheets?
yes
relative stability of beta sheets?
all equivalent and allow dense packing
Reverse/B/hairpin turns
found in antiparallel beta sheets if strands are part of same chain
know type 1 occurs 2x as frequently (just differ on orientation of peptide bonds between 2 and 3)
why does 2nd structure matter with hydrophobic cores?
peptides bonds are polar and 2nd structure allows for H bonding between the polar areas of AA instead of those polar areas binding H20
what is special about proline and 2ndary structure?
proline cannot form H bonds of a helix or b sheets so often found where they end
domain
smallest thermodynamically stable unit of protein
often account for a particular part of an enzyme’s active site
subunits interacting is what structure?
quaternary
metomorphic proteins
2 funnel holes
multiple options for structures that are equal in native state energy
alpha keratin what type of helix
2 R handed alpha-helices intertwined in a L handed supercoil (alpha coiled coil)
what type of bonding between coils of a-keratin?
non covalent and covalent (disulfide bonds) between coils
moderate # of disulfide bonds to allow stretch and recoil
what family does a keratin belong to?
large family of coiled-coil proteins that also include scaffolding for cells and myosin and tropomyosin
Collagen general facts
20-25% of protein in your body (most abundant protein in the body)
superfamily of molecs.
rich in proline (gives rigidity) and glycine (every 3rd position to fit into space where three strands come together)
Collagen structure
long rigid structure where 3 polypeptides are wond around each other in a rope-like triple helix
individual chains of collagen
alpha chains
left handed helices (not left handed alpha helices though)
three wound in R handed triple helix
other words for coiled coil
super coil or triple helix
collagen microfibrils
multiple triple helices
what is the Y in Gly-X-Y
hydroxyproline or hydroxylysine
formed through post-translational hydroxylation
enzymes that catalyze this require Vit C (ascorbate)
what is the X in Gly-X-Y
usually proline
symptoms of scurvy
corkscrew hair
dental problems
pathway of collagen
procollagen – ecm– collagen –peptidases cleave terminal propeptides– tropocollagen (mature collagen triple helix) –self-assemble fibrils with crosslinking– mature collagen fibers
Elastin facts
connective tissue protein w/ rubber-like properties
lungs, arterial walls, elastic ligaments
composed primarliy of small nonpolar aa
rich in proline and lysine but not hydroxylated
degradation
alpha1-antitrypsin inhibits elastase which degrades elastin
a1-antitrypsin insufficiency what how and why
if nothing inhibits elastase, then it can destroy alveolar epithelium
genetic insufficiency and environmental (cig smoke oxidizes met residue.. a1-AT cannot inactivate elastase)
what is elastase released by?
neutrophils
precursor to elastin and mech
tropoelastin (excreted into ecm) becomes elastin by glycoprotein microfibril interaction
