Lecture 2: Proteins Flashcards
How many amino acids are there?
20
side chain types: polar, nonpolar, and charged side chains
4 levels of structure:
primary: Sequence
secondary: alpha helix/beta strand
tertiary: domains and folds
quatrinary: only when there are more than one polypeptide chains. can be made up of same or differnt polypeptide chains
enzymes:
change reaction rate, not equilibrium
activity is very regulated
makeup of amino accids
tetraherdral bonds amino grouo carboxyl group hydrogen R group (differs for all)
center is a chiral alpha carbon
which sterioisomer config do the amino aicds have?
L sterioisomer (mirror image of D isomer) L is most common in bio
4 subfamilies of amino acids (based on interaction w/ aqueaous environment of cell)
charged amino acids
hydrophillic amino acids
hydrophobic amino acids
aromatic amino acids
charged amino acids
found mainly on the surface of proteins
aspartate glutamate lysine arginine histadine
hydrophillic amino acids
(polar, uncharged)
neutral under physio pH
hydrogen bond with water or with each other
typically found on surface of proteins so they can bind with water
serine threonine cystine asparagine glutamine
hydrophobic amino acids
found mostly within protein to avoid water
protein folding function
mostily just Cs and Hs
glycine alanine proline valine leucine isoleucine methionine
aromatic amino acids
absorb UV light in range of 250-280 nm
phenylalanine
tyrosine
tryptophan
aspartate
Asp
carboxylate group
neg charge at physio pH
like glutamate
glutamate
Glu
carboxylate group
neg charge at physio pH
like aspartate
lysine
Lys
charged nitrogen group
like arginine
arginine
Arg
charged nitrogen group
like lysine
histidine
His pka of 6 close to physio pH can exist in charged state (pos) or loose H and go to neutral state great at donating or accepting protons often does catalysis
serine
Ser hydroxyl group like Threonine uncharged at physio pH Can H-bond with hydrogen or each other
residues often target of kinases
threonine
Thr hydroxyl group like serine uncharged at physio pH Can H-bond with hydrogen or each other
cysteine
Cys
thyol group: form disulfide bridges. by redox reactions so that cys residues ban be linked together (covalent linkage, very strong)
this is very stabilizing to protein structure
uncharged at physio pH
Can H-bond with hydrogen or each other
asparagine
Asn amine group like glutamate uncharged at physio pH Can H-bond with hydrogen or each other
glutamine
Gln like aspargine amine group uncharged at physio pH Can H-bond with hydrogen or each other
hydrogen bonding
weak bond/interaction
sharing a hydrogen atom
more info about serine and threonine
have OH group; can be phosphorylated by kinases (enzyme type)
residues often target of kinases
kinases
often take phosphate group from ATP and add to serine or threonine to make phosphorlated amino acid
phosphotases
remove phosphate groups
why phosphyrolate
adding a phosphate group changes size of protein and adds neg. charge.
this can turn enzymes on or off
Glycine
Gly
very small
side chain is simply H
Proline
Pro
contains covalent bond, so not flexible. Good for tight turns
harder for it to H bond
Valine
Val
Leucine
Leu
Isoleucine
Ile
Methionine
Met
contains sulfer
Alanine
Ala
phenylalanine
Phe
tyrosine
Tyr
can be phospholated
tryptophan
Trp
primarily responsible for UV absorbance of proteins
most proteins…
are colorless. This is why aromatic proteins are useful, their ability to absorb UV light lets us see where proteins are
Peptide bonds
hold aas togther
condesation reaction between carboxulic acid and amine groups of 2 aas (relase of H2O) forms them
condesation reaction to form peptide bonds catalyzed by…
RNA component of ribosomes (enzyme)
KNOW WHICH AMINO ACIDS ARE CHARGED
KNOW WHICH AMINO ACIDS ARE CHARGED
proteases
break peptide bonds
amino acid chains start and end with
start with amino terminus
end with carboxyl terminus
practice finding peptide bonds!
PRACTICE FINDING PEPTIDE BONDS
alpha helix structures stabilized by…
hydrogen bonding between H atom on amide nitrogen and carbonyl oxygen in amino acid residue that is FOUR residues away
backbone and side chain orientation in alpha helices
backbone goes up the inside of the helix
side chains are found on the outside
residues:
any amino acid incorporated into peptide chain
pretty much nay amino acid
most alpha helicies in proteins are
right handed
amphipathic alpha helicies
one part of molec is hydrophobic, other part hydrophillic
amphipathic arrangement allows for…
hydrophobic core of proteins
hydrophiiloc surface that interacts with aqueous environment
Beta sheets held together by..
hydrogen bonding between backbone NH and Co groups on separate strands
hydrogen bonds in alpha helicies and beta strands are
DISTINCT from each other
DIFFERENT
if there is more than one beta strand…
then it is a beta sheet!
Fatty acid binding proteins
transports fatty acids through cytosol
mostly a large anti-parallel beta sheet thts twisted to form a hydrophobic binding pocket for the FA
ways that proteins and enzyme active sites work to interact with certain molecules
charge
shape
size
chemical complmentarity
true or false: proteins are very static
FALSE
proteins wiggle a lot and change their shapes by breaking and reforming weak interactions.
they can undergo large or small changes
enzyme active site
where the chemistry takes place
true or false: enzymes are used up in reactions
FALSE: enzymes are returned to starting states and start all over again
why enzymes work on their substrates
they have the right shapes and correct charges to attract substrates (negative with postive for ex)
3 important aspects of enzyme structure and function
- enzymes usually bind substrates with high affinity and specificity
- substrate binding to the active site involves structural changes in the enzyme
- enzyme activity is highly regulated in cells
enzyme cofactors/coenzymes
provide extra chem groups to supplement chem of amino acid side chains
often inorganic ions like Fe2+, Mg 2+, Cu2+, Zn2+
these are needed in enzymes that catalyze redox reactions
regulation of enzyme activity: ways to control catalytic efficieny
- allosterically: bind small reg. molecs (allosteric regulators)
- covalent modification: phosphorylation of Ser, Thr, or Tyr residues
allosteric regulators
molecules that bind somewhere other than the active site, but help regulate activity
STUDY SLIDE 23
STUDY SLIDE 23
phosphorylation:
addition of phsophate group makes something that was polar but neutral carry a pos charge
effects protein function by changing interactions in this area of the protein with the changed aa residue
glycogen phosphorylase
break down of glycogen
Coenzyme: pyridoxal phosphate (PLP) (bound to active site)
site of phosphorylation: is at Ser14 (done by a kinase) (Ser-> phosphoSer). changes here propogated to active site
in this case, phosphorylation turned ON enzyme activity
allosteric regulator: AMP. Conf changes here propogated to active site to change enzyme activity
AMP
allosteric regulator
