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Biochem > Lecture 1: Levels of Protein Structure > Flashcards

Lecture 1: Levels of Protein Structure Flashcards

1
Q

Key Types of Proteins

A
  • Enzymatic
  • Defensive
  • Storage
  • Transport
  • Hormonal
  • Receptor
  • Contractile/motor
  • Structural
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2
Q

Primary Structure is based on…

A

Amino acid sequence

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3
Q

Structure of amino acids

A
  • central tentrahedral carbon (alpha carbon)
  • linked to:
    1. amino group
    2. side chain, r group
    3. hydrogen atom
    4. carboxylic acid
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4
Q

Most common form of amino acids

A

L form

*this means that the amino group is on the left, H on the right in fischer projection

*doesnt say anything about rotation of light!

(except glycine)

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5
Q

Enantiomers vs Diastereomers

(as it relates to amino acids)

A

enantiomers = mirror images

diastereomers = not mirror images but same connective order

This matters because there are L and D forms of amino acids

  • L is more common, D is less common
  • enantiomers are not interchangeable, usually one version is used/important and another version is not
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6
Q

Classifications of amino acids

(categories)

A

what are their characteristics at pH7?

  • non-polar, aliphatic (alkyl groups)
  • aromatic (ring)
  • polar, uncharged
  • positively charged (Basic)
  • negatively charged (Acidic)
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7
Q

Nonpolar Aliphatic Amino Acid R Groups (acronym?)

A
  • Glycine
  • Alanine
  • Proline
  • Valine
  • Leucine
  • Isoleucine
  • Methionine
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8
Q

Aromatic Amino acids

A
  • Phenylalanine
  • Tyrosine
  • Tryptophan
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9
Q

Spectroscopic Properties of aromatic amino acids

A

Absorb in the 280-300 range

Can Id/measure proteins in samples

*Different ones absorb more, but that general range is wehre absorption is seen

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10
Q

Polar, uncharged amino acids

A

STCAG

  • serine
  • Threonine
  • cysteine
  • asparagine
  • glutamine
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11
Q

cysteine and reversible disulfide bond formation

A

Cysteine forms disulfide bonds because has a -Ch2-SH R group

  • C - CH2 - S - H
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12
Q

Positively charged amino acids

A

LAH

  • lysine
  • arginine
  • histidine
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13
Q

Unique Property of Histidine

A
  • Good to have at an active site to both stabilize and destabilize a substrate
  • side chain has a pKa of 6.5 –> near a physiological pH
  • exists in the protonated and deprotonated form at the same time
  • R groups are what make the protein reactive, but it is still only reactive if it is reactive at a physiological pH
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14
Q

Negatively charged amino acids

A
  • aspartate (-CH2 - COO)
  • glutamate (- CH2 - CH2 - COO)
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15
Q

Zwitterion form of amino acid

A
  • protonated amino group (NH3+)
  • deprotonated carboxyl group (COO-)

*both are protonated at low pH

*both are deprotonated at high pH

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16
Q

Zwitterion formation based on ph

A
  • 0-2: both protonated, NH3+ and COOH
  • 2-9: zwitterion, NH3+ and COO-
  • 9-14: both deprotonated, NH2 and COO-
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17
Q

Henderson Hasselbeck Equation

A

Describes the shape of the titration curve of any weak acif or amino acid

Ka = [H+] [A-] / [HA]

–> in terms of H+

–> negative of both sides

–> -log = ph or pKa

pH = pKa - log ([HA]/[A-])

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18
Q

Titration Curve of amino acid

A

Buffer regions

Equivalence point/PI

pKa

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19
Q

Key Pieces of info from Titration curve

A
  1. quant measure of the pKa of each of the two ionizing groups
  2. buffering regions
  3. relationship between net charge and pH of solution
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20
Q

PI (Isoelectronic point)

A
  • characteristic pH at which net charge is zero
  • equal amounts of + and - charged acid and zwitterions
  • can be arithmetic mean of the two pKa values
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21
Q

Peptide Bond Formation Structure? Reaction?

A

two amino acids can be covalently joined through a substituted amide linkage (peptide bond) to yield dipeptide

loss of a water molecule, dehydration an form multiple –> oligopeptides, polypeptides

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22
Q

Properties of peptide bonds:

A
  • resistant to hydrolysis and kinetically stable (high Ea and reverse Ea makes it unfavorable/difficult to go in reverse)
  • planar due to partial double bond character of C-N bond
  • contain a hydrogen bond donor (NH) and hydrogen bond acceptor (CO)
  • uncharged, allowing proteins to form tightly packed globular structures
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23
Q

Resonance of Peptide bonds

A
  • carbonyl is partially negative
  • amide is aprtially positive

trans and cis

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24
Q

In what form are peptide bonds in proteins?

A
  • trans
  • steric clashes arise from cis

(proline is exception)

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25
Q

Peptide bonds that are cis

A
  • X-pro
  • Proline: nitrogen is bonded to two tetrahedral carbon atoms so steric differences between cis and trans are less significant
  • Glycine: R group is just an H so it is very flexible
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26
Q

Single Bonds vs Peptide Bonds

Phi and Psi

A
  • in contrast with the peptide bond, the bonds between the amino group and the a-carbon are purely single
  • freedom of rotation about the bonds (torsion angles phi and psi) allows proteins to fold in many dofferent ways

–> many rotational combinations are forbidden because of steric collissions

–> Ramachandran diagram reveals there are only three regions physically accessible

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27
Q

Ramachandran Diagram of Peptide Bonds

What does it reveal?

A

Defines what is possible to build in the secondary structure

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28
Q

What is the secondary structure of a protein?

A

regular spatial arrangement

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29
Q

What is regular Spatial Arrangements?

A
  • “local spatial arrangement of the main chain atoms in a selected segment of a polypeptide chain”
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30
Q

Most common secondary structures

A
  • a- helix
  • b-strand (b sheets, pleated sheets)
  • b-turn (b-bend, reverse turn or hairpin turn)
  • o-loop (loop or omega loop)
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31
Q

Characteristics of helices

A

p = pitch (angle it is at)

n = number of repeating units per turn

(>0 right handed/clockwise, <0 left handed/counterclockwise)

d = helical rise of repeating units per turn (p/n)

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32
Q

Most common rotation of helix

A

Right handed

Left handed are rare

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33
Q

Interactions between helices (how do helices come together to make super helices?)

A
  • form superhelices
    1. helical coiled coils (alpha keratin)
  • 2 alpha helices wound left handed
    2. triple helices (collagen)
  • three left handed helices wound right handed
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34
Q

Where do superhlieces exist

A

Fibrous proteins

  • protective, connective or supportive material (hair, skin, tendon, bone)
  • motility (muscles, cilia)

Disulfide bonds determine curliness of hair

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35
Q

a-Keratin:

What is its structure?

A
  • coiled-coil proteins
  • 2 a-helixes in Right handed rotation, coiled around eachother in left handed rotation
  • two helices wind around one another to form a super helix as part of higher order structures
  • result of hydrophobic interactions with water (whenever you repel water two molecules get close to eachother)
36
Q

Heptad repeats of a-keratin

A
  • every 7th residue within each of the two helices is leucine
  • held together by van der waals interactions primarily between the leucine residues
37
Q

Collagen

Where is it?

What is its structure?

A
  • 3 special helices coiled left handed, coiled together in a right handed structure
  • main fibrous component of skin, bone, tendon, cartilage and teeth
  • coiled coil proteins but three separate polypeptides supertwisted about eachother
  • every cell is connedcted via collagen
38
Q

Glyceine in Collagen

A
  • every third residue in the amino acid sequence
  • glyceine - proline - hydroxyproline pattern recurs frequently
39
Q

Hydroxyproline

A

derivative of proline that has hydroxyl group in place of one of the hydrogen atoms on the pyrrolidine ring

40
Q

Secondary structures: Strands and sheets

A
  • b-strands are almost fully extended rather than being tightly coiled as in a-helices
  • two or more can be arranged in parallel or antiparallel b-sheets
41
Q

Parallel b-sheets

A
42
Q

Antiparallel b-sheets

A

loops between each strand

43
Q

Types of connections of b-strands in b-sheets:

A
  1. hairpin
  2. right handed crossover (clockwise, top - if looking at starting sheet)
  3. FORBIDDEN: left handed crossover (counterclockwise, bottom)
44
Q

Fatty Acid Binding in b-sheets

A
  • all adjacent b-strands run in opposite direction, b sheets are purely antiparallel
  • sheets twist and arrange in a barrel shape
45
Q

Structure of silk

A

antiparallel b-sheets

46
Q

Secondary structure: Turns and loops

A
  • proteins have globular shapes owing to the reversals in the direction of their polypeptide chains
  • connecting elements that link runs of a-helices or b-strands
  • less regularly structured
  • invariably lie on the surface of proteins and thus often partiicpate in interactions between proteins and other molecules
  • most common forms are b-turns and o-loops

*some of the most important parts a protein are the turns and loops which interact with other molecules

47
Q

Proline b-turns

A

cis structure

natural kink

48
Q

Glycine b-turns

A

small, minimizes steric hindrance

49
Q

Loops and role in interactions

A

Loops become the location of interactions, mediate them

50
Q

Secondary Structure: Propensities of amino acids to form secondary structures

A
  • how amino acid sequence of a protein specifies its tertiary structure depends on whether specific sequences form structures such as a-helices of b-strands
    1. some amino acids occur at higher frequencies in certain secondary structures
    2. some amino acids have steric constraints
    3. prediction is difficult though
51
Q

Single sequences with multiple structures

A
  • same peptide sequence can be in a-helices or b-sheets
  • alter overall protein structure
52
Q

Tertiary Structure

A

General amino acid distribution

53
Q

Features of tertiary structures of water soluble proteins:

A
  1. an interior formed of amino acids with hydrophobic side chains
  2. a surface formed largely of hydrophilic amino acids that interact with the aqueous environment
54
Q

Hydrophobic interactions

A
  • driving force for the tertiary structure formation of water soluble proteins
55
Q

Membrane proteins and tertiary structure

A
  • proteins existing in a hydrophobic environment (such as cell membrane) display the inverse distribution of hydrophobic on the outside and hydrophilic interior
  • form channels through which cations and anions pass
56
Q

Tertiary structure: Interactoins stabilizing protein shape

A
  • interactions between amino acid side chains along backbone

Based on:

  • hydrophobic forces (atraction of hydrocarbon side chains by LDF)
  • hydrogen bonds
  • ionic bonds (charged side chains +/-)
  • covalent bonds (disulfide bridges)
57
Q

Tertiary Structure: motifs, folds and domains

A

describe structural pattern in a polypeptide chain

58
Q

Motif

A

Recognizable pattern involving two or more elements of secondary structure and the connections between them

59
Q

fold

A

combinations of motifs

60
Q

domain

A

structural unit within a polypeptide chain that folds independently and is independently stable

61
Q

Common motifs

A

bab

b-hairpin turn

aa motif

62
Q

Greek Key motif

A

1,2 on inside 3 and 4 on either side

Hairpin turns in between

Longer between 3 and 4

63
Q

domain classificaitons

A
  • a-domains
  • b-domains
  • a/b-domains
64
Q

a-domains

topologies

A
  • 4 helix bundle
  • globulin fold?

Examples: globin fold in myoglobin or hemoglobin, 4-helix bundle in cytochrome b562 or HGH

  1. up, down, up, down
  2. up, up, down down (up. loop. up. turn. down. loop. down)
65
Q

b-domains

topology

A
  • containing only b-sheets

Examples: immunoglobulin fold in most immune system proteins

  1. Immunoglobulin fold
  2. up and down b-barrel
  3. jelly roll barrell
66
Q

a/b-domains

topology

A
  • both a-helices and b-sheets
    examples: a/b barrels and open b sheets
    1. a/b barrel = 8 tandem b/a units
    2. Rossman Fold/Open B sheets
67
Q

Unstructued domains

A
  1. molten globule
  2. unstructured
68
Q

Open b-sheet domains

Topology

A

Rossman fold

babab arrangement

  • able to bind mono or dinucleotides such as NAD= or NADP +
  • founds in nearly all dehydrogenases and many other enzymes
69
Q

Quaternary Structure

A

subunit interaction

70
Q

Subunit interaction

A
  • proteins consisting of more than one polypeptide chain display quaternary structure
  • each individual polypeptide chain is called a subunit
  • multiple interacting subunits: dimer, trimer, tetramer, oligomer, polymer
  • interacting subunits can be identical/homomers or different/heteromers
  • protomers: repeating structural units in multimeric proteins (single or groups of subunits)
71
Q

Hemoglobin

A

a2b2 heterotetramer

(4 subunits)

72
Q

Quaternary Structure: symmetric patterns

A
  • identical subunits of multimeric proteins are generally aranged in one or a limited set of syemtric patterns

Types:

  • rotational
  • helical
73
Q

Rotational Symmetry

A

-subunits pack around the rotatoinal axes to form closed structures

74
Q

rotatinal symmetry: cyclic

A

Nomenclature is “c”

  • twofold
  • threefold
75
Q

Rotational symmetry: dihedral

A

“D”

  • twofold
  • fourfold
76
Q

Rotational synnetry: icosahedral

A

fivefold, threefold and twofold

77
Q

Importance of icosahedral symmetry

A
  • only need three different proteins to make a ball structure
  • a few genes
  • structure can carry genome
78
Q

Helical symmetry

A
  • makes tower, house structure
  • “brick” subunits

tobacco mosaic virus

79
Q

Proteins behave like amino acids because…

A

1) the R groups are charged
2) terminal ends

80
Q

Why does histidine have 3 pKas?

A

1) R group (+ charged)
2) carboxyl group charged
3) amino group

*Histidine is part of LAH in “positively charged R group”

81
Q

What causes scurvy?

A
  • vitamin c/ascorbic acid is required for hydroxylation of proline and lysine in collagen
  • humans are missing ascorbate which is an enzyme needed in the process
  • glycine - x/Cy endo proline = y/Cy exo hydroxyproline
  • coupled enzymatic reaction in which: x does not get hydroxylated and Y does
  • w/o ascorbate, X gets hydroxylated and Y does not

–> leads to an unstable structure

  • Need the * coupled reacion, otherwise the the wrong structure results
82
Q

Phi vs Psi

A

Phi is between Carbon and Nitrogen

Psi is between Carbon and Carboxyl Carbon

83
Q

Special amino acid in Keratin

A

Leucine

Every 7th residue

84
Q

Special amino acid in collagen

A

Glyceine

Every third residue

Gly-Pro-Hydroxyproline sequence occurs frequently

85
Q

4 Special Amino Acids

A

Histidine: protonated and deprotonated form, pKa is near physiological pH

cysteine: disulfide bond formation

Proline: In b-hairpin turns, cis conformation is favored

Glycine: in b-hairpin turns, flexible to swivel into cis conformation

86
Q

Main Bonds in primary structure

A
  • peptide bonds
87
Q

Main bonds in secondary structure

A
  • hydrogen bonds

Biochem (15 decks)

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