Biochem Exam 2- Proteins

Front 1

Functions of proteins and examples (7)

Back 1

enzymatic catalysis (hexokinase)
mechanical support (collagen)
transport and storage (hemoglobin)
movement (actin)
transmission or nerve impulse (opsin)
regulation (insulin)
protection (immunoglobulins)

Front 2

protein suffixes and the exception

Back 2

"-in" indicates protein with non enzymatic role, "-ase" = enzyme
exception is trypsin (enzyme)

Front 3

protein composition (type of amino acid)

Back 3

alpha-L-amino acid: alpha- amino group and side chain attached to alpha carbon

Front 4

definition of "chiral" and how many amino acids are chiral?

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chiral- (has 4 different groups attached/lacks internal plane of symmetry)
19 out of 20 amino acids are chiral around alpha carbon (all but glycine, which has 2 Hs)

Front 5

D vs L designation for amino acids

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indicates relationship to D or L glyceraldehyde (not direction that given amino acid rotates polarized light); hydrogens are in same position as L/D glyceraldehyde

L= amino group on left
D (dextro) = amino on right

Front 6

diagrams of 3d structure for molecules

Back 6

fisher projection

Front 7

L vs. D glyceraldehyde

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L- OH group on left (rotates light to left)
D- OH group on right (rotates light to the right)

Front 8

Why do AAs not rotate light in the specified direction?

Back 8

because AAs have side chains, which have their own chiral centers and throws things off balance

Front 9

at physiological pH, AAs are generally...

Back 9

zwitterions (neutral charge)

Front 10

Are pKa of free amino acids are the same as pKa when incorporated into proteins? Why or why not?

Back 10

No they are not the same necessarily. This is because interactions with nearby AA side chains can affect ability of a side chain to donate or accept H+

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Are pKa of free amino acids are the same as pKa when incorporated into proteins? Why or why not?

Back 11

No they are not the same necessarily. This is because interactions with nearby AA side chains can affect ability of a side chain to donate or accept H+

Front 12

characteristics of polypeptide bond formation

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not spontaneous; require energy to form (ATP)
release an H2O
is an amide bond (O from alpha COO- or OH from COOH + H2 or H from alpha NH3+ forms a water)

Front 13

characteristics of peptide bond (2)

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1) rigid and planar; only some rotation around non-double bonds
2) partial double bond character (electron from NH group gets pulled towards electronegative O)

Front 14

phi and psi angles

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phi- N-C(alpha)
psi- C(alpha)-C(O)

Front 15

naming and structural convention of peptides

Back 15

amino (N terminus) always on left, C terminus always on right
(name it from left to right as well)

Front 16

Types of AA modification (4)

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Phosphorylation
Glycosylation
Hydroxylation
Carboxylation

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Phosphorylation

Back 17

1) done on side chains with free hydroxyl groups (replaces OH group)
2) P comes from ATP usually

Front 18

Glycosylation (3)

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1) carbohydrate groups may be attached to protein via N or O linkage
2) for O-linked, AA must have a free OH group (ser, thr, tyr)
3) produce glycans

Front 19

N-linked glycosylation

Back 19

attach to nitrogens of asparagine (eukaryotes)
polysaccharides are preformed, and then added to protein

Front 20

Hydroxylation (and examples of enzymes that catalyse it)

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1) conversion of CH group into a C-OH group
2) examples include lysyl hydroxylase and prolyl hydroxylase

Front 21

Cofactors required for hydroxylation

Back 21

O2, ascorbic acid, a-ketoglutarate, iron

Front 22

O-linked glycosylation

Back 22

polysaccharides built on via sequential addition of monosaccharide units
AA must have free OH group (ser, tyr, thr)

Front 23

hydroxlysine

Back 23

hydroxyl derivative made from lysine after lysine is incorporated into protein; can be glycosylated (O-link)

Front 24

Vitamin C and hydroxylation

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vit C required to reduce lysyl hydroxylase should it become inappropriately oxidized

Front 25

What is the hydroxylation formula for proteins? What is oxidized and reduced in the protein hydroxylation rxn?

Back 25

lysyl + a-ketoglutarate + O2 + lysyl hydroxylase--> hydroxylysyl + succinate + CO2

prolyl/lysyl residue + a-ketoglutarate are oxidized, O2 is reduced

Front 26

Carboxylation of protein

Back 26

done to a few proteins only, notably proteins involved in blood clotting (glutamyl residues)
COO- added to C of CH2 group of glutamyl (example)

Front 27

What is recycled in carboxylation rxn and how?

Back 27

Vitamin K Epoxide (recycled by adding hydrogens to it to get it back to dihydroquinone)

Front 28

What is the source of carboxyl group in carboxylation of proteins?

Back 28

CO2

Front 29

What (in general terms) helps orchestrate 3D protein folding?

Back 29

interactions between amino acid side chains, or between side chains and solvent

Front 30

Types of protein side chain/side chain, side chain/solvent interactions, in order of strong-->weak (4)

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1) Disulfide bonds
2) Ionic interactions
3) Hydrogen bonds
4) Hydrophobic interactions

Front 31

Disulfide bond: energy required to disrupt

Back 31

100 kcal/mol

Front 32

Ionic interactions: energy required to disrupt

Back 32

10 kcal/mol

Front 33

Hydrogen bonds: energy required to disrupt

Back 33

5 kcal/mol

Front 34

Hydrophobic interactions: energy required to disrupt

Back 34

3 kcal/mol

Front 35

Disulfide bridges
What are they and how can they be broken?

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covalent bonds formed by oxidations of cysteinyl residues (removal of H from 2 cys residues which are accepted by an oxidizing agent)
Broken by reduction of disulfide bone (reducing agent)

Front 36

Cystine

Back 36

diamino acid formed by oxidation of 2 cysteines to produce a disulfide bond between them
(NOT dipeptide- no peptide bond)

Front 37

Ionic interactions: frequency and when do they form?

Back 37

play modest role in stabilizing native conformation of a proteins, especially when residues are not solvated (not shielded by H2O)

Front 38

Why do solvated (in H2O) proteins not form as many ionic interactions?

Back 38

water polarity interferes with charges on functional groups

Front 39

Hydrogen bonds

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form between electronegative atom (usually O, N, S) and a hydrogen atom covalently bonded to another electronegative atom (gives H a partial + charge)

Front 40

Hydrophobic interactions: why they form

Back 40

occur between nonpolar R groups
not due to any inherent attraction of one nonpolar molecular to another, but rather the mixture of nonpolar/water is most stable when nonpolar molecules associate together (fewer H-bonds disrupted-->lower energy required to maintain-->systems proceed to most stable state)

Front 41

Why is there instability of nonpolar substance in water?

Back 41

hydrophobic molecules disrupt H-bonds between water molecules (free energy needs to be added to system to disrupt H-bonds = less stable)

Front 42

Do hydrophilic molecules disrupt H-bonds in H2O?

Back 42

Yes, but destabilization caused by the disruption is offset by the formation of new hydrogen bonds between hydrophilic molecules + H2O.

Front 43

What would happen if a protein with hydrophobic residues was dissolved in oil instead of water?

Back 43

It would flip inside out

Front 44

Example of proteins that exist in an oily solution under physiological conditions

Back 44

membrane proteins

Front 45

Primary structure of protein and what they are maintained by

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linear sequence of AA
maintained by peptide/covalent bonds

Front 46

Secondary structure of protein and what it's maintained by

Back 46

regions of proteins folding into a particular stereotypic pattern (a-helix, b-sheet)
maintained primarily by H-bonds

Front 47

Tertiary structure of protein

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overall 3D folding of protein
maintained by H-bonds, hydrophobic, and ionic interactions
(disulfide bridges only in some proteins)

Front 48

Quaternary structure of protein

Back 48

spatial arrangement of multiple polypeptide subunits (if any)

Front 49

Transcription

Back 49

DNA-->RNA

Front 50

Translation

Back 50

RNA-->AA

Front 51

Most common types of secondary structure

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a-helix
b-sheet

Front 52

alpha helix stabilization and direction of helix

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stabilized by H-bonding between amino acids located 4 residues apart from each other
R-handed helix

Front 53

Ruben diagram

Back 53

3D simplified diagram of secondary structure

Front 54

factors that destabilize alpha helices(or cause them not to be formed)

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large numbers of charged R groups
Bulky R groups (sterics)
Prolyl residues- no H on nitrogen when it bonds, because of it's unique ring form; can't form H-bonds

Front 55

parallel beta sheet

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C and N terminus of 2 independent or same polypeptide chains are on the same side.
H bonds- between adjacent regions of chain (oblique)

Front 56

anti-parallel beta sheet

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C and N terminus on opposite sides
H bonds are parallel with each other (not oblique)

Front 57

tertiary structure is determined by...

Back 57

primary structure because it dictates the location of groups available to participate in hydrophobic interactions, H-bonds, cystine bridges, and ionic interactions

Front 58

Gross classification of tertiary structure (2) and descriptions/examples of each

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1) Fibrous- rod like shape (keratin, silk/fibroin, collagen)
2) Globular- spherical shape (hemoglobin, immunoglobulin, alcohol dehydrogenase)

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secondary structure of keretin

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a-helix

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secondary structure of fibroin (silk)

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b-sheet

Front 61

secondary structure of collagen

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neither alpha-helix nor beta-sheet (alpha-chain)

Front 62

secondary structure of hemoglobin

Back 62

mostly alpha-helix

Front 63

secondary structure of Ig

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mostly beta-sheet

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secondary structure of alcohol dehydrogenase

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both alpha-helix and beta-sheet

Front 65

quaternary structure is determined by

Back 65

sub-unit interactions, which may be hydrophobic, ionic, covalent (disulfide), or hydrogen bonds

Front 66

oligomeric protein

Back 66

multiple monomers (subunits)

Front 67

homodimer

Back 67

dimer with identical subunits

Front 68

loss of structure =

Back 68

loss of function

Front 69

why does putting protein in different pH, salt conc. or temperature from it's natural environment result in loss of activity?

Back 69

loses it's structure because changes in those factors can disrupt the weak interactions that maintain native conformation

Front 70

denaturation

Back 70

breaking of weak bonds that maintain native conformation of protein

Front 71

denaturation does not involve the following (3)

Back 71

1) breaking of peptide bonds
2) loss of primary structure
3) reversibility

Front 72

why is denaturation irreversible? (2)

Back 72

1) protein usually folds up before C-terminus is complete (during synthesis)
2) often folded by chaperones (help fold proteins)
You cannot reproduce these conditions