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MSI Unit I > 1-39 Protein Sequence, Structure, and Function Relationships > Flashcards

1-39 Protein Sequence, Structure, and Function Relationships Flashcards

1
Q

alpha carbon (Ca)

A

carbon bound to the carboxyl group, amino group, R group, and hydrogen

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2
Q

the phi bond?

A

N-Ca bond

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3
Q

the psi bond?

A

Ca-C bond

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4
Q

why are the phi and psi angles restricted?

A

some angles would lead to steric interference in the protein - allows us to deduce the types of secondary structures that are possible for a given aa squence.

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5
Q

What does the ramachandran map show us?

A

easy way to visualize the distribution of the dihedral angles of a protein structure

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6
Q

What are four non-covalent forces that operate on proteins and all other biomolecules in aqueous solution

A

Electrostatic forces
hydrogen bonding
van der waals forces
hydrophobic effect

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7
Q

electrostatic forces

A

attractive/repulsive interactions between charged species. Calculated via coulombs law

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8
Q

hydrogen bonding

A

interactions between highly EN atoms (S, O, N) and hydrogen atoms bound to (S, O, N).

hydrogen takes a slightly + character, and is noncovalently attracted to the non-bound EN atom.

(the atom bound to it steals some e- density)

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9
Q

linearity of hydrogen bonds?

A

The more linear the hydrogen bond is with respect to the covalent bonds of the hydrogen and the electronegative atom, the stronger the interaction will be.

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10
Q

van der waals forces

A

atoms close together, charge distribution of electron cloud becomes uneven, creating transient dipoles.

when an atom takes a temporary dipole state, can influence neighbor to do the same.

weak and temporary

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11
Q

hydrophobic effect

A

certain molecules (uncharged, non polar) tend to interact more with themselves than with water in aqueous environment.

water also will more favorably interact with itself

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12
Q

electrostatics and protein secondary structures

A

proteins fold to maximize favorable charge-charge and charge-water interactions

determines which aa are on inside or outside of protein structure. charged tend to be on exterior

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13
Q

hydrogen bonding and protein secondary structure

most common occurance?

A

hydrogen bonds always satisfied in proteins.

every hydrogen bond donor is paired with a receiver

most commonly occurs from interactions between peptide bonds - this is why alpha helices and beta sheets are so common

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14
Q

why are beta sheets and alpha helices so common?

A

hydrogen bonding frequently occurs between peptide bonds

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15
Q

van der walls and protein secondary structure

A

proteins fold to MAXIMIZE van der waals energy.

do this by packing atoms close together - as a result, proteins are incredibly dense organic molecules

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16
Q

why are proteins so dense?

A

they fold to maximize their van der waals energy in a way that packs their atoms closely together

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17
Q

hydrophobic effect and secondary structure

A

hydrophobic residues will remain away fom the exterior of the protein structure, will want to stay buried

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18
Q

what is a dipole?

A

two charges separated by a distance. No formal charge needed to be dipolar, area withdrawing electrons from another portion

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19
Q

hydrogen bonding is a special case of…

A

electrostatic interactions, 2 EN atoms compete for same H+

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20
Q

what makes a strong hydrogen bond?

A

peptide-charged carboxylate = strong
peptide-peptide = weak
peptide -noncharged carboxylate = weakest

linear = strong
bent=weak

21
Q

the most important bond/force in terms of protein structure

A

hydrophobic effect

22
Q

rise vs exended rise, turn of alpha helix

A

rise 1.5, extended fully is 4.5

1 turn = 3.6 residues

23
Q

why a 3.6 residue repeat?

A

favorable backbone dihedral angles
near optimal h bond geometry
good van der waals contacts between backbone atoms

24
Q

what is a giveaway that section of aa is an alpha helix?

A

lots of alanines, no prolines

25
Q

pKa of a protein?

A

pH at which 50% of the molecules are ionized and deionized

26
Q

peptide bond forms between the

A

carboxyl of one amino acid and the NH of another

27
Q 
c alpha?
c beta?
c gamma?
c delta? 
c epsilon?
A

c-alpha, the central alpha that the R group hangs off of

c beta - first carbon of r group
c gamma - second carbon of r goup
c delta - …..

28
Q

two words that describe the peptide bone

how many rotatable bonds per residue?

A

planar and trans (side groups alternate)

2

29
Q

what does planarity do?

A

reduces bond rotations

not planar - 3 rotations per bond residue
planar - 2

30
Q

ramachandran map

A

maps allows phi and psy angles

dark gray - allowed
dashed area - tolerated

31
Q

individuality of proteins is provided by

A

side chains

hydrophobic (non polar)
hydrophilic (polar) (charged or polar but uncharged)

unique (pro, gly, cys)

32
Q

aliphatic AA

what are they?

A

aliphatic are most hydrophobic

ala, val, leu, ile, pro

33
Q

aromatic and sulfur containing are…

A

less hydrophobic

Phe, Tyr, Trp, Met

34
Q

pKa is the

pHpKa

A

pH at whcih half of the ionizing groups are pronated

pHpKa = lower H+ concentration, H+ drawn off

35
Q

pKa of terminal amine and carboxylic acid?

A

terminal amine, pKa of 8

carboxylic acid pKa = 4

36
Q

unique side chains

A

Gly - lack of side chain makes it flexible

Pro - cis peptide bond favors kinks, turns, no h-bond donor

cys - thiol group can oxidize s-s, way crosslinks are introduced

37
Q

what determines the individual functions of proteins

A
  1. polymer length
  2. amino acid composition

These factors specify the unique 3D structure that dictates function

38
Q

proteome

A

content of proteins within the cell at any given time

39
Q

TF

the proteome is more complex than the genome

A

T. Genome stays constant, proteome changes.

40
Q

proteins are less relavent than genes in respect to disease

A

F - the defective gene is not what makes you sick, it is the abherent function of the corresponding protein that makes you sick

41
Q

the alpha helix bonds are between..

A

between the peptide NH of residue i and the peptide CO of residue i+4,

42
Q

helix forming residue

A

Ala - lack of sidechain

43
Q

strong helix breakers

A

proline - lacks NH to hydrogen bond

glycine- is too flexible

44
Q

medium helix breakers

A

Val, Thr, Trp, Phe - lose too much rotation freedom (entropy) when in a helix

45
Q

entropy -

A

rotational freedom

46
Q

helix indifferent aa’s

A

long-straght chains (Arg, Lys, glu)

lose less rotational freedom

47
Q

planarity _____ bond rotations

A

reduces

48
Q

phi, psy angles are limited by…

A

steric clashes

MSI Unit I (52 decks)

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