LEC2: Amino Acids and Proteins Flashcards
explain the naming of carbons in amino acid side chains
named using Greek letters
alpha-carbon is carbon bound to amino and carboxyl groups of amino acid
beta-carbon is next, etc
lysine here
which conformation of optical isomer of proteins are mostly seen in humans?
L-conformation, not D
D mostly found in bacteria
how are amino acids classified?
by their R groups (aka side chains)
name the nonpolar/hydrophobic amino acids
Glycine
Alanine
Valine
Leucine
Isoleucine
Phenylalanine
Troptophan
Methionine
Proline
Cysteine (can be nonpolar or polar)
(9 or 10)
name the uncharged polar amino acids
which are alcohols? which are amides?
Alcohols: Serine, Threonine, Tyrosine
Amides: Asparagine, Glutamine
Cysteine (can be nonpolar or uncharged polar)
Which amino acids can be phosphorylated? How?
serine, threonine, tyrosine
contain a hydroxyl group, can be replaced by a phosphoryl group
phosphorylation of an amino acid in a protein > alters protein’s activity or transmits a signal
do non-polar amino acids react w/ water?
no
do polar side chain amino acids react w/ water? how?
yes
side chain can form H-bond w/ water or other groups
where are polar side chain amino acids often found?
the surface of proteins
what happens in a H-bond?
2 electronegative atoms share an e-
what is unique about cysteine?
can be described as either hydrophobic or polar
has an SH group
in environment of an oxidant, cysteine interacts w/ other cysteines, forms **disulfide bridge, **a covalent interaction
glycine
G
Gly
non-polar
Alanine
Ala
A
non-polar
Valine
Val
V
non-polar
Leucine
Leu
L
non-polar
Isoleucine
Ile
I
non-polar
Phenylalanine
Phe
F
non-polar
Tryptophan
Trp
W
non-polar
Methionine
Met
M
non-polar
Proline
Pro
P
non-polar
side chain is covalently attached to amine group, forming a rigid, not aromatic, ring > limits conformaitons proline can adopt in nature
Serine
Ser
S
polar, alcohol
Tyrosine
Tyr
Y
polar, alcohol
Threonine
Thr
T
polar, alcohol
Asparagine
Asn
N
polar, amide
Glutamine
Gln
Q
polar, amide
which amino acids can be glycosylated?
what does this mean?
what is it an example of?
what is the purpose?
**addition of chains of sugar or oligosaccharide to side chain of amino acid **
serine, threonine, asparagine
is a post-translational modification
can mark proteins to go to the membrane & be involved w/ signaling pathways
2 types of glycosylation? where does each occur?
_1) N-linked glycosylation _
sugar attaches to amide group
only Asparagine (Asp)
_2) O-linked glycosylation _
sugar attaches to **O of OH **
Serine or Threonine
what is fatty acylation?
a post-translational modification of Cysteine
hydrocarbon chain, ie farnesyl group is added to sulhydryl group of cysteine
what catylyzes phosphorylation?
enzyme kinases
name the acidic amino acids
aspartic acid
glutamic acid
have negative charges at physiologic pH
Aspartic acid
Asp
D
Glutamic acid
Glu
E
has 3 ionizable groups, so there are 4 forms of the amino acid
overall charge of glutamic acid, and protonation state, at:
- acidic environment?
- physiologic pH?
- basic environment?
acidic: all groups are protonated; +1 overall charge
physiologic pH: -1
basic environment: -2
name the basic amino acids
Histitide, Lysine, Arginine
Histidine
His
H
basic
Lysine
Lys
K
basic
Arginine
Arg
R
basic
what is unique about His and its pKa?
its side chain pKa = 6.0
therefore very close to physiologic pH
therefore can be both charged and uncharged, depending on conditions
if charged, can be an **active site for enzymes **
explain this
titration curve of histidine
shows side chain pKa = 6.0
what is this, what does it show?
titration curve of glutamic acid
has 3 groups that can be ionized
what are peptide bonds? how are they formed?
bonds that join amino acids
rxn that connects amino and carboxyl groups of amino acids, releases H2O
polar structures, participate in hydrogen bonding
what is a peptide? a protein?
peptide: < 50 amino acid chain
protein: > 50 amino acid chain
how are small peptides named?
for their constituent amino acids
start at amino terminus, add “yl” to name of each amino acid except for the one at the carboxyl terminus
name this molecule
glutaminyl-arginyl-methionine
what steric constraints are there on proteins re: primary structure?
1) peptide bond is **planar **bond, so limits interactions a protein can have
2) side chains provide a steric constraint - not all atoms can go anywhere
how is protein weight measured? unit?
what is avg size of a protein?
sum of the weights of all atoms in the protein molecule
molecular weight = in kDa, kiloDalton
avg size of a protein = 50 kDa
what is the primary structure of a protein?
its amino acid sequence - the linear order of amino acids in the chain
what is the secondary structure of a protein?
motifs?
how are they formed?
local three-dimensional conformation
alpha-helix and beta-sheet
formed from hydrogen bonds btwn hydrgoen of amino group and oxygen of carbonyl group in a peptide bond
how does an alpha helix form?
by hydrogen bonds btwn atoms in peptide bonds of a single linear chain of amino acids
what specifically bonds to form an alpha-helix?
hydrogen bond btwn:
oxygen in carbonyl gorup of amino acid R1 (C=O) and
hydrogen in amino group of amino acid (N-H) R5
therefore a 3.6 (~4) amino acid turn
which amino acid won’t appear in an alpha helix?
why?
proline
its side chain is covalently attached to the amine group, which limits the conformations it can adopt - it’s kinky
how are B-sheets formed?
hydrogen bonds formed btwn atoms in peptide bonds of same or different linear chains
can be antiparallel, where protein folds upon itself, or parallel, where N-terminus of each strand is oriented same direction
strands are connected by loops
what is protein tertiary structure?
protein’s overall 3D conformation - determined yb its amino acid sequence
peptide bond backbone and amino acid side chains both contribute to tertiary structure
what kinds of non-covalent interactions can proteins have? their effect?
form proteins’ tertiary structure
1) ionic bonds
2) hydrogen bonds
3) van der waals interactions
what are ionic bonds? where do they occur in proteins?
cohesion btwn 2 atoms of opposite (+ and -) charges
electrostatic attraction
occurs btwn a charged and a polar amino acid, i.e. glutamate and lysine
what is hydrogen bonding? where does it occur in proteins?
when electropositive hydrogen atom is partially shared by 2 electronegative atoms
occurs btwn side chains of 2 amino acids but also back bone of all amino acids in peptide chain
what are hydrophobic interactions? where do they occur, what is their effect?
weakest type of non-covalent interaction
found at close range btwn nonpolar atoms
drive protein folding
what drives protien folding?
the “hydrophobic effect”
nonpolar side chains cluster together in middle of structure; polar side chains on outside, where form H-bonds w/ H2O
what kind of bond forms btwn 2 cysteines?
what causes their formation?
where do they occur?
S-S of cysteines form **covalent **disulfide bond, **aka a cystine residue
formed by the oxidation of 2 cysteines
can be inter- or intra-molecular
common in antibodies
what is this visualization called?
what can you see?
ribbon or cartoon
shows backbone atoms, highlights secondary structure elements
arrows indicate parallel/antiparallel sheets
what is this visualization called?
what can you see?
lines or sticks
see amino acid side chains
can analyze particular residues of the protein
what is this visualization called?
what can you see?
surface
see approximated, functionally important regions that interact w/ the solvent
use to design small molecule potential drugs against proteins
are all proteins the same size/shape?
no, they come in many sizes/shapes
what is this? properties?
four-helix bundle
hydrophobic core stabilized by ionic interactions
what is this? properties?
Tim Barrel
8 alpha helicies + 8 parallel beta strands
most common fold in nature
gut of protein includes some irregular structural elements which bind to specific molecules (ligands, ions)
what is this? structure? where is it found?
immunoglobulin
7-9 beta strands
found in antibodies & signaling molecules
what is a domain
a region of a protein w/ a particular fxn
usually physically distinct from other parts of the protein
pt of the polypeptide that folds independently into a compact, stable structure
antibody structure?
function of each part?
immunoglobulin
2 identical heavy chains, 2 identical light chains
each subunit contains variable & constant domains
variable domains: bind antigen (what ab targets)
constant domains: interact w/ other immune system components
what gives an antibody specificity?
antigen binding site
what is this?
explain components
explain how structure > function
src protein kinase
has 3 domains:
kinase domain: responsible for catalytic activity
SH3, SH2 domains: important for regulation of interaction w/ other proteins
loops in btwn domains allows protein to be modular, which helps w/ interactions and turning on/off
what is quarternary structure of a protein?
non-covalent joining of more than 1 polypeptide
stabilized by noncovalent interctions, as explained (ionic, H-bonds, van der waals)
describe the structure of hemoglobin
quarternary structure made of 4 polypeptides:
2 identical alpha-globin chains; 2 identical beta-globin chains
each subunit contains a heme group, which binds to oxygen
what is this? fxn?
respiratory complex I
transports electrons in mitochondria
what are fibrous proteins?
coiled coil proteins - 2 helices, connected by long hydrophobic interaction
provide structural framework for many elongated proteins, form fibers
highly stable, highly flexible
what type of protein is keratin
fibrous
what are intrinsically disordered proteins (IDPs)?
do not adopt stable structure under physiological conditions
have low hydrophobicity, high net charge - so don’t just fold on their own
in some conditions, can fold
which amino acids can participate in hydrogen bond formation?
which amino acid side chains are likely to be found w/in a region of a protein that spans a lipid membrane?
what types of modifications are found on proteins that are excreted from cells?
why are regions of an a-helix and B-sheet found in most proteins, including those that have very different amino acid compositions?
what determines overall 3D conformation of a protein?
what interacitons stabilize the tertiary structure of proteins and multi-subunit complexes?
