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BMSC 200 > Module 4 > Flashcards

Module 4 Flashcards

(65 cards)

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1
Q

Peptide Bonds

A

Covalent linkages between amino acids

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2
Q

How do peptide bonds form

A

By condensation reactions involving the loss of a water molecule

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3
Q

Main chain repeating pattern

A

NCCNCC
Main chain is the constant portion and the side chains are variable

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4
Q

Partial double bond characteristics

A

Rotation around the C - N peptide bond is restricted due to its partial double bond characteristic
As a result of the partial double bond characteristic the six atoms of the peptide group are rigid and planar

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5
Q

Configuration of Peptide Bonds

A

Partial double bond of the peptide bond creates cis trans isomers
Oxygen of the carbonyl group and the hydrogen of the anode nitrogen are suavely trans to each other

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6
Q

Steric Exclusion

A

Trans configuration is favoured as the Cis configuration is more likely to cause steric interference between side chain groups

It means that 2 groups can’t occupy the same space at the same time

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7
Q

Primary Structure

A

Linear sequence of amino acids

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8
Q

Secondary Structure

A

Localized Interactions within a polypeptide

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9
Q

Tertiary Structure

A

Final folding pattern of a single polypeptide

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10
Q

Quaternary Structure

A

Folding pattern when multiple polypeptides are involved

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11
Q

How is the Primary Structure presented

A

From N (Amino Terminus) to C (Carboxyl) terminus

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12
Q

Specifics of Primary Structure

A

Information specifying correct folding in contained within the primary structure
Not possible to predict the 3d Structure based on primary structure

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13
Q

Secondary Structure

A

Represents localized patterns of folding in a polypeptide
Maintained by hydrogen bonds between main chain amide and carbonyl groups

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14
Q

Two Key rules for Secondary Structures

A

Optimize the hydrogen bonding potential of main chain carbonyl and amide groups
Represent a favoured conformation of the polypeptide chain

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15
Q

Main chain Hydrogen Bonding groups

A

Each peptide bond has a hydrogen bond donor and acceptor group
Equal number of hydrogen bond donors and acceptors within the polypeptide main chain

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16
Q

Conformation of Polypeptide Chain

A

Each alpha carbon is held within the main chain through single bonds, about which there is complete freedom of rotation

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17
Q

Phi

A

Ca - N

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18
Q

Psi

A

Ca - c

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19
Q

Ramachandran Plots

A

Illustrate the possible combinations of phi and psi

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20
Q

Alpha Helix

A

Right Handed helix with 3.6 residues/ turn
Stabilized by hydrogen bonds which run parallel to the axis of the helix
Carbonyl groups join towards the C terminus and amide groups to the N terminus

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21
Q

How many residues does the hydrogen bonding happen at

A

Each carbonyl of residue n hydrogen bonds with amide group of Residue n+4

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22
Q

A helix uncommonalities

A

Proline because of its rigidity
Glycine because of its flexibility
Amino Acids with side chain branches (Val, Thr, Ile) are less common due to steric interactions
Amino Acid groups near the main chain (Ser, Asp, Asn) are also less common

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23
Q

The helix dipole

A

Every peptide bond has a small electrical dipole
Dipole is stabilized by residues at each termini whose charge opposite the helix dipole

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24
Q

N terminus

A

has Partial positive dipole

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25
C terminus
Has a partial Negative dipole charge
26
At N terminus
Negatively charged residues (Asp, Glu)
27
At C terminus
Positively charged residues (Lys, Arg, His)
28
Amphipathic Helices
Residues operated by 3 or 4 positions in the primary sequence will be on the same side pf the helix Residues separated by 2 residues will be on the opposite sides of the helix Positioning of hydrophobic and hydrophilic residues within the primary structure generates an amphipathic helix with polar and non polar residues
29
Beta Sheets
B sheets involve multiple B Strands arranged side by side B Sheets are made up of B Strands B sheets often involve 4 or 5 strands
30
Conformation of Beta Sheets
Full extended polypeptide chains
31
Hydrogen Bonding pattern in Beta Sheets
Stabilized by hydrogen bonds between C = O and -NH on adjacent strands
32
Beta sheets can be
Parallel and Anti Parallel
33
Parallel Beta Sheet
Run in the same direction
34
Anti Parallel beta sheets
Run in opposite directions
35
What is more stable
Anti parallel because better geometry of hydrogen bonding
36
Mixed Beta Sheets
Contain both Parallel and Aniparallel Beta Strands
37
Amphipathic Beta Sheets
Side chains tend to alternate above and below the polypeptide chain Alternating polar and non polar residues within he primary structure of a beta sheet will result in an amphipathic beta sheet
38
Basic Facts about Tertiary Structure
Tertiary Structure represents the final folding patterns of a single polypeptide The biological active folding pattern is the native conformation Amino Acid sequence determines tertiary structure Teritiary structure decribes the long range aspects of sequence interactions within a polypeptide. Residues separated by great distance in primary structure may be in close proximity in the teritiary structure Different proteins have different tertiary structure which relates to their unique functions The tertiary structure of different proteins vary in their content of alpha helices and beta sheets
39
What stabilizes the protein structure
Weak Interactions
40
The protein conformation with the lowest free energy
Is the most stable and is usually the one with the maximum number of weak interactions
41
Denaturation
Disruption of native conformation with loss of biological activity Energy required for denaturation is often small, perhaps only a few hydrogen bonds Protein folding and denaturation is a cooperative process
42
Quaternary Structure
Multiple subunits in which each subunit is a separate polypeptide May Involve multiple subunits of the same polypeptide or different polypeptides Subunits usually associate through non covalent interactions Quaternary structure usually reserved for proteins of more complex biological function
43
5 important facts of protein
Function of protein depends on its structure 3d structure of a protein is determined by its amino acid sequence Non covalent forces are the most important forces stabilizing protein structure
44
Keratin
Is the principle component of hair, wool, horns and nails At primary structure keratin contains a pseudo 7 repeat
45
Which positions of Keratin have Hydrophobic residues
Positions a and d
46
What does Keratin form as secondary structure
Alpha Helix Residues from positions "a" and "d" end up on the same faced of the helix resulting in a hydrophobic strip along the length of the helix
47
How do Keratin interact
Two Amphipathic helices of keratin interact to bury their hydrophobic faces together. This creates a coiled - coil
48
Coiled - Coil
Formed when 2 or more helices entwine to form a stable structure
49
Coil coil in keratin
Involves two right handed helices wrapping around each other in a left handed fashion
50
Where does Keratin get its strength
From covalent linkages of individual units into higher order structures.
51
How was individual units linked
Disulfide bonds
52
Collagen
Major protein of Vertebrates
53
Primary Structure of Collagen
At Primary collagen contains repeats of Gly - X - Y where X is always proline
54
Secondary Structure of Keratin
Collagen forms a left handed helix of three residues per turn (As opposed to the 3.6 residues/turn of an alpha helix).
55
Coiled Coil in collagen
Three Left handed helices of collagen wrap around each other in a right handed fashion
56
Where are the Prolines
The bulky side chains of proline are on the outside of the coiled coil
57
Where are the Glycines
Small side chains of glycine residues new in tightly packed core of the coiled - coil
58
Post Translational Modification of Collagen
Strength of collagen arise from covalent linkages between the individual units into higher order structures. Rather than disulphides these linkages occur from residues that undergo post translational modification (Hydroxyproline, hydroxylysine)
59
Which enzymes perform these modifications
Vitamin C
60
Lack of Vitamin C
Scurvy
61
Silk
Produced y insects and spiders for formation own webs and cocoons At primary structure silk has a 6 residue repeat of Glycine and Serine
62
Secondary Structure of Silk
Silk os composed primarily from beta sheets
63
What gives silk its strength
Fully extended polypeptides
64
Association of strands by hydrogen bonding
Flexible
65
Association of Van Der Walls and Hydrophobic Interactions
Flexible

BMSC 200 (10 decks)

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