Lecture 2: Proteins Flashcards by Ryley Tegler

How many amino acids are there?

side chain types: polar, nonpolar, and charged side chains

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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

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enzymes:

change reaction rate, not equilibrium

activity is very regulated

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makeup of amino accids

tetraherdral bonds
amino grouo
carboxyl group
hydrogen 
R group (differs for all)

center is a chiral alpha carbon

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which sterioisomer config do the amino aicds have?

L sterioisomer (mirror image of D isomer)
L is most common in bio

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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

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charged amino acids

found mainly on the surface of proteins

aspartate
glutamate
lysine
arginine
histadine

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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

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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

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aromatic amino acids

absorb UV light in range of 250-280 nm

phenylalanine
tyrosine
tryptophan

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aspartate

Asp
carboxylate group
neg charge at physio pH
like glutamate

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glutamate

Glu
carboxylate group
neg charge at physio pH
like aspartate

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lysine

Lys
charged nitrogen group

like arginine

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arginine

Arg
charged nitrogen group

like lysine

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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

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serine

Ser
hydroxyl group
like Threonine
uncharged at physio pH
Can H-bond with hydrogen or each other

residues often target of kinases

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threonine

Thr
hydroxyl group
like serine 
uncharged at physio pH
Can H-bond with hydrogen or each other

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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

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asparagine

Asn
amine group
like glutamate
uncharged at physio pH
Can H-bond with hydrogen or each other

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glutamine

Gln
like aspargine 
amine group 
uncharged at physio pH
Can H-bond with hydrogen or each other

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hydrogen bonding

weak bond/interaction

sharing a hydrogen atom

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more info about serine and threonine

have OH group; can be phosphorylated by kinases (enzyme type)
residues often target of kinases

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kinases

often take phosphate group from ATP and add to serine or threonine to make phosphorlated amino acid

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phosphotases

remove phosphate groups

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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

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

1. enzymes usually bind substrates with high affinity and specificity 2. substrate binding to the active site involves structural changes in the enzyme 3. 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

1. allosterically: bind small reg. molecs (allosteric regulators) 2. 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

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

Lecture 2: Proteins Flashcards

(65 cards)