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BIOCH 200 > 3. Protein Structure > Flashcards

3. Protein Structure Flashcards

1
Q

State why all isolated amino acids bear at least one positive and one negative charge

A
  • Amino group NH₃+ bears a (+) charge
  • carboxyl group COO- bears a (-) charge
  • this makes isolated amino acids “zwitterion”, having equal + and - charges = net neutral

only the terminal amino and carboxylate groups in a peptide retain their charge. the others are eliminated by the formation of peptide bonds

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2
Q

pKa of the carboxyl and amino ends of amino acids

A

COOH (pKa < 7)
NH₃+ (pKa > 7)

when side chain carries no charge:

  • charge at pH 1 = +1 (COOH/NH3+)
  • charge at pH 14 = -1 (COO-/NH2)
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3
Q

Which amino acid(s) are chiral, which are non chiral?

A

all amino acids except for glycine are chiral - glycine’s side chain is a hydrogen, therefore isn’t attatched to 4 separate groups

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4
Q

What is pKa? What is the relationship of pKa to strength of an acid?

A
  • a measure of protonation + deprotonation relative to pH: an acids tendancy to ionize
    (HA → H+ + A-)
  • ‘strength’ of a weak acid
  • pka ↓ with stronger acids
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5
Q

relationship between pH and pka

A

when pH < pka → [HA] > [A-]
when pH > pka → [HA] < [A-]

pka - acid dissociation

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6
Q

Why is it important to know the properties of amino acid side chains?

A

the different types of amino acids will behave differently, change the secondary/tertiary structures of the protein and serve differnt functions

  1. hydrophobic amino acids: lack relative functional groups, have mainly hydrocarbon side chains
  2. polar amino acids: reactive due to presence of functional groups. polar amino acids have side chains that contain an electronegative atom
  3. charge amino acids: possess an electric charge due to the presence of ionizable groups in their side chain
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7
Q

hydrophobic amino acids & their 3 letter cods

A
  1. Alanine (Ala)
  2. Valine (Val)
  3. Phenylalinine (Phe)
  4. Tryptophan (Trp)
  5. Leucine (Leu)
  6. Isoleucine (Ile)
  7. Methionine (Met)
  8. Proline (Pro)
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8
Q

Polar amino acids & their 3 letter codes

A
  1. Serine (Ser)
  2. Threonine (Thr)
  3. Tyrosine (Tyr)
  4. Cysteine (Cys)
  5. Asparagine (Asn)
  6. Glutamine (Gln)
  7. Histidine (His)
  8. Glycine (Gly)
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9
Q

Charged amino acids, their charge at pH 7 & 3 letter codes

A
  1. Aspartate (-), Asp
  2. Glutamate (-), Glu
  3. Lysine (+), Lys
  4. Arginine (+), Arg
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10
Q

Exceptions to abbreviations being first 3 letters of the amino acid

A
  1. Asparagine - Asn
  2. Glutamine - Gln
  3. Isoleucine - Ile
  4. Tryptophan - Trp
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11
Q

Why are peptides described as having a “sense of direction”

A

amino acids in a polypeptide are arranged in a asymmetric, specific manner

the c-terminal end of one residue is always connected to the n-terminal end of another residue → creates a peptide amide bond

  • this means that a polypeptide always begins with an N-terminus and ends with a C terminus
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12
Q

Peptide nomenclature

A
  • dipeptide: 2amino acids joined by a peptide bond
  • tripeptide: 3 amino acids joined by a peptide bond
  • tetrapeptide: 4 amino acids joined by a peptide bond
    etc…
  • peptides/oligopeptides: < 40 residues
  • polypeptide: long chain of amino acids, >40 residues
  • protein: large polypeptide (or >1 polypeptide) with a biological function
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13
Q

primary structure for a polypeptide

A

determines polypeptide function

  • sequence of amino acids
  • amino acids joined by peptide bonds: rigid & planar
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14
Q

explain why amino acids in a polypeptide are called residues

A

they are called “residues” because during the process of forming a polypeptide or protein, each amino acid contributes to the chain by losing a specific part: a water molecule is released when 2 aa’s join by dehydration synthesis or a condensation reaction.

amount of peptides = 1 more than peptide bonds

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15
Q

Explain why peptide bonds are planar and rigid

A
  • electrons in peptide bonds are somewhat delocalized (two resonance forms)
  • peptide bonds therefore exhibit a partial double bond character, with no rotation about the C-N bond
  • functional groups are potential H-bond acceptors/donors
  • The polypeptide backbone can still rotate around the N-C⍺ and C⍺-C bonds
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16
Q

Define the term “polypeptide backbone”

A
  • formed by a repeating structure of peptide bonds that link the c-terminus end of an amino acid to the n-terminus of the next
  • includes C⍺ atoms and those involved in the peptide bond
  • side chains project out from the backbone
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17
Q

Define the four major levels of protein structure

A
  1. primary: sequence of amino acid residues
  2. secondary: the spatial arrangement of the polypeptide backboke
  3. tertiary: the three-dimensional structure of an entire polypeptide, including all its side chains
  4. quaternary: the spatial arrangement of polypeptide chains in a protein with multiple subunits

primary structure determines the 3D structure
3D structure determines function

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18
Q

State how the properties of peptide bonds limit the possible conformations a polypeptide can adopt

A
  • rotation of polypeptide backbones is limited, therefore folding conformations are limited
  • primary structure aims to minimize steric hinderance within the polypeptide
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19
Q

Describe structural features of an alpha-helix

A

except for amino acid residues at either end, all backbone CO and NH groups are hydrogen bonded to one another in the helix:

  • carbonyl oxygen of each residue forms an H-bond with the backbone -NH four residues downstream: C1…N5 C2…N6 (residue’s 3-4 apart in the primary structure are close in the secondary structure)
  • right handed helical structure
  • side chains/R groups face outward
  • core of helix: comprises completely of the backbone (van der Waals contact with one another in the center)

groups that interact unfavourably (3-4 residues apart) destabilize the sturcture

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20
Q

Describe structural features of parallel and antiparallel beta sheets

A

parallel: neighbouring chains run in the same direction

  • N → C (same directionality)
  • alternating diagonal H-bonds

antiparallel: neighbouring chains run in opposite directions

  • N → C, C → N
  • parallel H-bonds

**for both: **

  • Each residue forms two hydrogen bonds with a neighboring strand - all hydrogen-bonding requirements are met, except in the first and last strands of the sheet
  • every 2nd aa will be found on the same side of the sheet
  • side chains are located above and below the plane of the sheet (pleated aspect)

again, steric hinderance is minimized and H-bonding is maximized

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21
Q

Distingush between regular and irregular secondary structure

A

regular occurs when every amino acid in a segment of the polypeptide adopts the same geometry (alpha helices and beta sheets; maximize H-bonding, minimize steric hinderance)

irregular - does not mean disorder; just means there is no repeating geometry - necessary to form the compact protein structures

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22
Q

State how secondary structures are stabilized

A
  • ⍺-helices: H-bonds between backbone CO and NH groups in the same helices (within a continous set of aa)
  • β-sheets: H-bonds between backbon CO and NH groups of neighbouring strands (aren’t formed with the consecutive strand)
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23
Q

Define tertiary and quaternary levels of protein structure

A

tertiary: arrangment of secondary structures in relation to one another (positions of amino acid sidechains, prosthetic groups)

quaternary: proteins composed of more than 1 polyppetide chain - each polypeptide chain is called a subunit

24
Q

fibrous and globular protein structures

A
  1. fibrous (elongated) - aq insoluble, form long protein filaments, structural or connective proteins (collagen)
  2. globular (compact) - fold in on themselves, more varied (mix of ⍺ helix, irregular, β sheet), aq soluble, fold into compact structures ith nonpolar cores and polar surfaces
25
Q

State how the surface and core regions of soluble globular proteins differ

A
  • hydrophobic side chains generally reside on the interior of a globular protein
  • hydrophilic side chains are most likely to be found on the surface of a globular protein - can interact with water
  • hydrophobic effect: predominant force in folding of soluble globular proteins - the shape of the globular proteins depends on the position of the hydrophobic amino acids in the primary structure
26
Q

Identify amino acids that are most likely to be found at the core of a soluble globular protein

A
27
Q

Explain why irregular secondary structure is more likely to be found at the surface of a globular protein than alpha helices and beta sheets are

A

secondary structures likewise typically reside on the interior of globular proteins and loops/irregular structures are on the exterior as their H-bonding is not fully satisfied and can interact with water

28
Q

State how the tertiary and quaternary levels of protein structure are stabilized

A

tertiary

  • weak H-bonds b/w closely positioned side chains, as well as backbone groups and side chains (fine tune)

quaternary:

  • stabilized by same forces as 3° structure (hydrophobic int, H-bonds), typically don’t include disulphide bridges
29
Q

naming quaternary structures

A

named by number and type of subunits
- dimer (2), trimer (3), tetramer (4)
- identical subunits: homo - dimer/trimer..
- non-identical subunits: hetero - dimer/trimer…

30
Q

Describe the terms ion pair (salt bridge), H-bond, and disulphide bridge (disulphide bond) and state their roles in protein tertiary structure

A

Ion Pair: electrostatic interactions between closely-positioned charged groups
- fine tune 2° and 3° structures
- positive and negatively charged groups
- (+) N terminus, Lys, Arg, (His @ high pH)
- (-) C terminus, Asp, Glu (Tyr, Cys @ low pH)

Disulphide bridge: covalent bonds b/w closely positioned cysteines
- form stabilizing cross-links for extracellular proteins (or proteins in the lumen)
- disulphide bonds maintain structure in extracellular environments
- in the cytosol, cysteines do not oxidize to cystine (it’s a reducing environment)
- reducing agents (DTT) can disrupt disulphide bridges

31
Q

Define the term “prosthetic group” and state why proteins need them

A

a non-peptide component that is permanently incorporated into a protein, these provide:
- structure (Zn2+ in zinc fingers)
- functional chemical groups (heme in hemoglobin)

32
Q

define domain and motif

A

domain: polypeptide egment that has folded into a single structural unit with a hydrophobic core - proteins may contain more than one domain
“sleeve of a sweater”

motif: a short region of polypeptide with a recognizable 3D shape
“cable pattern of sweater”

33
Q

What type of interactions cause protein folding

A

non-covalent interactions:
- hydrogen bonding
- van der waals
- ion pairs
- disulphide bridges
- hydrophobic interactions

34
Q

Define apoprotein and holoprotein

A

apoproteins: polypeptide without prosthetic group

holoproteins: polypeptide with associated prosthetic group

35
Q

How do globular proteins get denatured? (4)

A
  1. heat - H-bonds/hydrophobic int
  2. changes in pH - salt bridges/H-bonds
  3. salt - salt bridges/ion pairs
  4. detergents - hydrophobic int
36
Q

Describe and compare the structures of myoglobin and hemoglobin

A

myoglobin: monomer (no quaternary structure)

  • heme prosthetic group exists in the hydrophobic pocket between helicies E&F
  • porphyrin ring held in place by hydrophobic interactions AND coordination bond between iron2+ and proximal histidine (aa 93) HisF8
    1. ~153 amino acids
    2. 8 ⍺-helices identified by letters A-H (A is first helix, H is the last helix)
    3. irregular structures
    3. heme prosthetic group

hemoglobin: heterotetramer (has quaternary structure)

  • tetramer with two types of globin - 2 alpha, 2 beta subunits
  • has 4 heme prosthetic groups
37
Q

state the physiological functions of myoglobin and hemoglobin

A

myoglobin: facilitates oxygen diffusion through muscle tissues, local reserve of oxygen during intense exercise, stores oxygen in aquatic animals (anaerobically)

hemoglobin: in red blood cells - binds O₂ in the lungs and releases it in the tissues (aerobic)

both bind oxygen reversibly but bind it under different conditions

38
Q

describe structural feautures of heme

A
  • heme is circular and planar: porphyrin ring with a Fe²⁺ ion coordinated between four N atoms
  • two propionyl groups at the bottom of the ring (polar and charged) - rest of the molecule are non-polar aliphatic groups
  • heme is in a hydrophobic pocket between helices E and F
39
Q

what is a ligand and properties of ligands

A
  • small molecule that binds to another molecule
  • the greater the affinity of the ligand for the protein, the more of the ligand-protein complex we will have at any concentration of ligand/protein
40
Q

describe the oxygen binding site in myoglobin

A
  • the oxygen binds to the 6th coordinated position on the heme prosthetic group in myoglobin
  • binds at an angle to form interactions with the iron atom

the distal histidine (HisE7) assists with O2 binding by:
1. increasing oxygen binding affinity
2. lowering affinity for other molecules (carbon monoxide)
3. increasing specificity for oxygen

41
Q

T/F myoglobin has quaternary structure and prosthetic group is apart of this

A

False - myoglobin does not have quaternary sturcture. Prosthetic group is apart of the tertiary structure

42
Q

outline the general molecular mechanism behind cooperative binding

A

binding of the first ligand to the protein increases affinity for the other binding sites located on the protein by inducing a conformational change.

eg. hemoglobins binding sites are not independant but instead communicate with each other in order to work in a unified fashion

43
Q

Describe the general mechanism of action of an allosteric effector

A
  • allosteric effectors: binding of this compound alters the affinity of other binding sites
  • homoallostery: binding of the effector causes more binding of the same compound
  • heteroallostery: binding of the compound causes more binding of another compounds
  • activator/+ effector: increases binding affinity
  • inhibitor/- effector: decreases binding affinity

oxygen is a homoallosteric activator of hemoglobin

44
Q

Describe the molecular mechanism by which oxygen causes hemoglobin to switch states (3)

A
  1. no oxygen is bound = T state
  2. O₂ binding to an alpha subunit: iron moves into the plane of the heme, HisF8 moves along with the heme, helix F moves.
  3. SUBUNIT INTERFACE CHANGES all other subunits change to the R state - increasing the binding affinity of other binding sites
45
Q

function of oxygen binding site

A

oxygen binding sites are designed precisely to optimize binding specificity and affinity

46
Q

define specificity and affinity

A

specificity: the selectivity of a molecule towards it’s target, reflecting how precisely a molecule interacts with it’s intended partner or target molecule

affinity: how strongly a molecule interacts/binds with it’s target, how tightly they bind together

47
Q

What is the Bohr effect?

A

The decrease in oxygen binding affinity of hemoglobin in response to a decrease in pH/increase in H+ atoms

48
Q

Describe the mechanism by which H+ ions stabilize the T state of hemoglobin

A
  1. lowering pH = protonation of side chains and functional groups (His + H = His+, NH2 + H = NH3+)
  2. groups associated with BPG binding become protonated (+) - ↑ BPG binding, ↓ O2 binding
  • lowering pH leads to increased O2 delivery in muscles and lower affinity of hemoglobin for oxygen
49
Q

The effect of BPG on the oxygen binding behaviour of hemoglobin

A
  • stabilizes the T state of hemoglobin
  • acts as a (-) allosteric effector of oxygen binding
  • increase [BPG] = decreased O₂ binding
50
Q

Outline the mechanism by which BPG exerts its effect on hemoglobin

A
  1. BPG binds to the central cavity in deoxymyoblobin (T-state)
  2. BPG negative charges interact with the positively charged groups on the protein that are directed into the central cavity - 2N terminal residues, 4 His, 2 Lys
  3. BPG causes conformational changes to the oxygen binding sites

overall action of BPG is to decrease the affinity of hemoglobin to O₂

51
Q

Identify four specific roles for histidine residues in hemoglobin function

A

The proximal histidine (HisF8):
1) Binds heme into the heme-binding pocket
2) Prevents oxidation of iron atom

The distal histidine:
3) ↑ oxygen binding affinity by assisting in binding and ↓ affinity for other molecules (increasing specificity for O₂)

His in central cavity:
4) BPG binding

52
Q

Differentiate between conservative and critical amino acid substitutions

A

function of a protein is determined entirely by it’s structure → amino acid sequence is key

Conservative:
- relatively minor effects on structure/function

Critical:
- change structure and function depending on location

53
Q

How do binding curves differ for the oxygen binding behaviour of fetal and adult hemoglobins

A

fetal hemoglobin - sigmoidal shift to the left = more O₂ affinity and less O₂ delivery

Adult hemoglobin - sigmoidal shift to the right = less O₂ affinity and more O₂ delivery

54
Q

State how fetal hemoglobin differs structurally from adult hemoglobin

A
  • 2 alpha and 2 gamma subunits
  • His143 is sub for serine in fetal gamma subunit
55
Q

Explain how the structural difference between fetal and adult hemoglobin results in their different oxygen binding behaviours

A

His143 is involved in BPG binding
- no His143 = ↓ BPG binding therefore ↑ O₂ affinity

BIOCH 200 (7 decks)

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