Lecture 1: Levels of Protein Structure Flashcards Preview

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Flashcards in Lecture 1: Levels of Protein Structure Deck (87):
1

Key Types of Proteins

- Enzymatic

- Defensive

- Storage

- Transport

- Hormonal

- Receptor

- Contractile/motor

- Structural

2

Primary Structure is based on...

Amino acid sequence

3

Structure of amino acids

- central tentrahedral carbon (alpha carbon)

- linked to:

1. amino group

2. side chain, r group

3. hydrogen atom

4. carboxylic acid

4

Most common form of amino acids

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)

5

Enantiomers vs Diastereomers

 

 

(as it relates to amino acids)

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

6

Classifications of amino acids

(categories)

what are their characteristics at pH7?

- non-polar, aliphatic (alkyl groups)

- aromatic (ring)

- polar, uncharged

- positively charged (Basic)

- negatively charged (Acidic)

7

Nonpolar Aliphatic Amino Acid R Groups (acronym?)

- Glycine

- Alanine

- Proline

- Valine

- Leucine

- Isoleucine

- Methionine

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Aromatic Amino acids

- Phenylalanine

- Tyrosine

- Tryptophan

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Spectroscopic Properties of aromatic amino acids

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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Polar, uncharged amino acids

STCAG

 

- serine

- Threonine

- cysteine

- asparagine

- glutamine

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cysteine and reversible disulfide bond formation

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

 

   - C - CH2 - S - H

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Positively charged amino acids

LAH

- lysine

- arginine

- histidine

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Unique Property of Histidine

- 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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Negatively charged amino acids

- aspartate (-CH2 - COO)

- glutamate (- CH2 - CH2 - COO)

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Zwitterion form of amino acid

- protonated amino group (NH3+)

- deprotonated carboxyl group (COO-)

 

*both are protonated at low pH

*both are deprotonated at high pH

16

Zwitterion formation based on ph

- 0-2: both protonated, NH3+ and COOH

- 2-9: zwitterion, NH3+ and COO-

- 9-14: both deprotonated, NH2 and COO-

17

Henderson Hasselbeck Equation

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-])

18

Titration Curve of amino acid

Buffer regions

Equivalence point/PI

 

pKa

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Key Pieces of info from Titration curve

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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PI (Isoelectronic point)

- 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

21

Peptide Bond Formation Structure? Reaction?

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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Properties of peptide bonds:

- 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

23

Resonance of Peptide bonds

- carbonyl is partially negative

- amide is aprtially positive

 

trans and cis

 

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In what form are peptide bonds in proteins?

- trans

 

- steric clashes arise from cis

 

(proline is exception)

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Peptide bonds that are cis

 

- 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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Single Bonds vs Peptide Bonds

 

Phi and Psi

 

- 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

27

Ramachandran Diagram of Peptide Bonds

 

What does it reveal?

 

Defines what is possible to build in the secondary structure

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What is the secondary structure of a protein?

regular spatial arrangement

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What is regular Spatial Arrangements?

- "local spatial arrangement of the main chain atoms in a selected segment of a polypeptide chain"

 

30

Most common secondary structures

- a- helix

 

- b-strand (b sheets, pleated sheets)

- b-turn (b-bend, reverse turn or hairpin turn)

- o-loop (loop or omega loop)

31

Characteristics of helices

 

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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Most common rotation of helix

 

Right handed

 

Left handed are rare

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

- 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

34

Where do superhlieces exist

Fibrous proteins

- protective, connective or supportive material (hair, skin, tendon, bone)

- motility (muscles, cilia)

 

Disulfide bonds determine curliness of hair

35

a-Keratin:

What is its structure?

 

- 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)

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Heptad repeats of a-keratin

- every 7th residue within each of the two helices is leucine

- held together by van der waals interactions primarily between the leucine residues

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Collagen

Where is it?

What is its structure?

 

- 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

 

 

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Glyceine in Collagen

- every third residue in the amino acid sequence

- glyceine - proline - hydroxyproline pattern recurs frequently

 

 

 

 

39

Hydroxyproline

 

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

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Secondary structures: Strands and sheets

 

- 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

Parallel b-sheets

 

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Antiparallel b-sheets

 

loops between each strand

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

 

1. hairpin

2. right handed crossover (clockwise, top - if looking at starting sheet)

3. FORBIDDEN: left handed crossover (counterclockwise, bottom)

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Fatty Acid Binding in b-sheets

 

- all adjacent b-strands run in opposite direction, b sheets are purely antiparallel

- sheets twist and arrange in a barrel shape

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Structure of silk

 

antiparallel b-sheets

46

Secondary structure: Turns and loops

 

- 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

Proline b-turns

 

cis structure

natural kink

 

 

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Glycine b-turns

 

small, minimizes steric hindrance

 

 

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49

Loops and role in interactions

Loops become the location of interactions, mediate them

50

Secondary Structure: Propensities of amino acids to form secondary structures

 

- 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

Single sequences with multiple structures

 

- same peptide sequence can be in a-helices or b-sheets

- alter overall protein structure

52

Tertiary Structure

 

General amino acid distribution

53

Features of tertiary structures of water soluble proteins:

 

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

Hydrophobic interactions

 

- driving force for the tertiary structure formation of water soluble proteins

55

Membrane proteins and tertiary structure

 

- 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

Tertiary structure: Interactoins stabilizing protein shape

 

- 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)

 

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Tertiary Structure: motifs, folds and domains

 

describe structural pattern in a polypeptide chain

 

58

Motif

 

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

59

fold

combinations of motifs

60

domain

 

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

61

Common motifs

 

bab

b-hairpin turn

aa motif

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Greek Key motif

 

1,2 on inside 3 and 4 on either side

Hairpin turns in between

Longer between 3 and 4

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domain classificaitons

 

- a-domains

- b-domains

- a/b-domains

64

a-domains

 

topologies

 

- 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

b-domains

 

topology

 

- 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

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a/b-domains

 

topology

- 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

 

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Unstructued domains

 

1. molten globule

2. unstructured

68

Open b-sheet domains

 

Topology

 

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

Quaternary Structure

 

subunit interaction

70

Subunit interaction

 

- 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

Hemoglobin

 

a2b2 heterotetramer

(4 subunits)

72

Quaternary Structure: symmetric patterns

 

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

Types:

- rotational

- helical

73

Rotational Symmetry

 

-subunits pack around the rotatoinal axes to form closed structures

 

 

 

 

74

rotatinal symmetry: cyclic

Nomenclature is "c"

- twofold

- threefold

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Rotational symmetry: dihedral

 

"D"

- twofold

- fourfold

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Rotational synnetry: icosahedral

 

fivefold, threefold and twofold

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Importance of icosahedral symmetry

 

- only need three different proteins to make a ball structure

- a few genes

 

- structure can carry genome

78

Helical symmetry

 

- makes tower, house structure

- "brick" subunits

 

tobacco mosaic virus

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Proteins behave like amino acids because...

 

1) the R groups are charged

2) terminal ends

80

Why does histidine have 3 pKas?

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1) R group (+ charged)

2) carboxyl group charged

3) amino group

 

*Histidine is part of LAH in "positively charged R group"

81

What causes scurvy?

 

- 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

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Phi vs Psi

 

 

Phi is between Carbon and Nitrogen

 

Psi is between Carbon and Carboxyl Carbon

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Special amino acid in Keratin

 

Leucine

Every 7th residue

84

Special amino acid in collagen

 

Glyceine

Every third residue

Gly-Pro-Hydroxyproline sequence occurs frequently

85

4 Special Amino Acids

 

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

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Main Bonds in primary structure

 

- peptide bonds

87

Main bonds in secondary structure

- hydrogen bonds