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Biochem 385 Unit 1 > Lecture 2: Proteins > Flashcards

Lecture 2: Proteins Flashcards

1
Q

How many amino acids are there?

A

20

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

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2
Q

4 levels of structure:

A

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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3
Q

enzymes:

A

change reaction rate, not equilibrium

activity is very regulated

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4
Q

makeup of amino accids

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

center is a chiral alpha carbon

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5
Q

which sterioisomer config do the amino aicds have?

A 
L sterioisomer (mirror image of D isomer)
L is most common in bio
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6
Q

4 subfamilies of amino acids (based on interaction w/ aqueaous environment of cell)

A

charged amino acids
hydrophillic amino acids
hydrophobic amino acids
aromatic amino acids

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7
Q

charged amino acids

A

found mainly on the surface of proteins

aspartate
glutamate
lysine
arginine
histadine
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8
Q

hydrophillic amino acids

A

(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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9
Q

hydrophobic amino acids

A

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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10
Q

aromatic amino acids

A

absorb UV light in range of 250-280 nm

phenylalanine
tyrosine
tryptophan

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11
Q

aspartate

A

Asp
carboxylate group
neg charge at physio pH
like glutamate

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12
Q

glutamate

A

Glu
carboxylate group
neg charge at physio pH
like aspartate

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13
Q

lysine

A

Lys
charged nitrogen group

like arginine

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14
Q

arginine

A

Arg
charged nitrogen group

like lysine

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15
Q

histidine

A 
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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16
Q

serine

A 
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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17
Q

threonine

A 
Thr
hydroxyl group
like serine 
uncharged at physio pH
Can H-bond with hydrogen or each other
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18
Q

cysteine

A

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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19
Q

asparagine

A 
Asn
amine group
like glutamate
uncharged at physio pH
Can H-bond with hydrogen or each other
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20
Q

glutamine

A 
Gln
like aspargine 
amine group 
uncharged at physio pH
Can H-bond with hydrogen or each other
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21
Q

hydrogen bonding

A

weak bond/interaction

sharing a hydrogen atom

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22
Q

more info about serine and threonine

A

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

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23
Q

kinases

A

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

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24
Q

phosphotases

A

remove phosphate groups

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25
Q

why phosphyrolate

A

adding a phosphate group changes size of protein and adds neg. charge.
this can turn enzymes on or off

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26
Q

Glycine

A

Gly
very small
side chain is simply H

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27
Q

Proline

A

Pro
contains covalent bond, so not flexible. Good for tight turns
harder for it to H bond

28
Q

Valine

A

Val

29
Q

Leucine

A

Leu

30
Q

Isoleucine

A

Ile

31
Q

Methionine

A

Met

contains sulfer

32
Q

Alanine

A

Ala

33
Q

phenylalanine

A

Phe

34
Q

tyrosine

A

Tyr

can be phospholated

35
Q

tryptophan

A

Trp

primarily responsible for UV absorbance of proteins

36
Q

most proteins…

A

are colorless. This is why aromatic proteins are useful, their ability to absorb UV light lets us see where proteins are

37
Q

Peptide bonds

A

hold aas togther

condesation reaction between carboxulic acid and amine groups of 2 aas (relase of H2O) forms them

38
Q

condesation reaction to form peptide bonds catalyzed by…

A

RNA component of ribosomes (enzyme)

39
Q

KNOW WHICH AMINO ACIDS ARE CHARGED

A

KNOW WHICH AMINO ACIDS ARE CHARGED

40
Q

proteases

A

break peptide bonds

41
Q

amino acid chains start and end with

A

start with amino terminus

end with carboxyl terminus

42
Q

practice finding peptide bonds!

A

PRACTICE FINDING PEPTIDE BONDS

43
Q

alpha helix structures stabilized by…

A

hydrogen bonding between H atom on amide nitrogen and carbonyl oxygen in amino acid residue that is FOUR residues away

44
Q

backbone and side chain orientation in alpha helices

A

backbone goes up the inside of the helix

side chains are found on the outside

45
Q

residues:

A

any amino acid incorporated into peptide chain

pretty much nay amino acid

46
Q

most alpha helicies in proteins are

A

right handed

47
Q

amphipathic alpha helicies

A

one part of molec is hydrophobic, other part hydrophillic

48
Q

amphipathic arrangement allows for…

A

hydrophobic core of proteins

hydrophiiloc surface that interacts with aqueous environment

49
Q

Beta sheets held together by..

A

hydrogen bonding between backbone NH and Co groups on separate strands

50
Q

hydrogen bonds in alpha helicies and beta strands are

A

DISTINCT from each other

DIFFERENT

51
Q

if there is more than one beta strand…

A

then it is a beta sheet!

52
Q

Fatty acid binding proteins

A

transports fatty acids through cytosol

mostly a large anti-parallel beta sheet thts twisted to form a hydrophobic binding pocket for the FA

53
Q

ways that proteins and enzyme active sites work to interact with certain molecules

A

charge
shape
size
chemical complmentarity

54
Q

true or false: proteins are very static

A

FALSE
proteins wiggle a lot and change their shapes by breaking and reforming weak interactions.

they can undergo large or small changes

55
Q

enzyme active site

A

where the chemistry takes place

56
Q

true or false: enzymes are used up in reactions

A

FALSE: enzymes are returned to starting states and start all over again

57
Q

why enzymes work on their substrates

A

they have the right shapes and correct charges to attract substrates (negative with postive for ex)

58
Q

3 important aspects of enzyme structure and function

A
  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
59
Q

enzyme cofactors/coenzymes

A

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

60
Q

regulation of enzyme activity: ways to control catalytic efficieny

A
  1. allosterically: bind small reg. molecs (allosteric regulators)
  2. covalent modification: phosphorylation of Ser, Thr, or Tyr residues
61
Q

allosteric regulators

A

molecules that bind somewhere other than the active site, but help regulate activity

62
Q

STUDY SLIDE 23

A

STUDY SLIDE 23

63
Q

phosphorylation:

A

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

64
Q

glycogen phosphorylase

A

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

65
Q

AMP

A

allosteric regulator

Biochem 385 Unit 1 (13 decks)

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