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BMSC 200 > Module 4 > Flashcards

Module 4 Flashcards

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
Q

C terminus

A

Has a partial Negative dipole charge

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26
Q

At N terminus

A

Negatively charged residues (Asp, Glu)

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27
Q

At C terminus

A

Positively charged residues (Lys, Arg, His)

28
Q

Amphipathic Helices

A

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
Q

Beta Sheets

A

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
Q

Conformation of Beta Sheets

A

Full extended polypeptide chains

31
Q

Hydrogen Bonding pattern in Beta Sheets

A

Stabilized by hydrogen bonds between C = O and -NH on adjacent strands

32
Q

Beta sheets can be

A

Parallel and Anti Parallel

33
Q

Parallel Beta Sheet

A

Run in the same direction

34
Q

Anti Parallel beta sheets

A

Run in opposite directions

35
Q

What is more stable

A

Anti parallel because better geometry of hydrogen bonding

36
Q

Mixed Beta Sheets

A

Contain both Parallel and Aniparallel Beta Strands

37
Q

Amphipathic Beta Sheets

A

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
Q

Basic Facts about Tertiary Structure

A

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
Q

What stabilizes the protein structure

A

Weak Interactions

40
Q

The protein conformation with the lowest free energy

A

Is the most stable and is usually the one with the maximum number of weak interactions

41
Q

Denaturation

A

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
Q

Quaternary Structure

A

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
Q

5 important facts of protein

A

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
Q

Keratin

A

Is the principle component of hair, wool, horns and nails
At primary structure keratin contains a pseudo 7 repeat

45
Q

Which positions of Keratin have Hydrophobic residues

A

Positions a and d

46
Q

What does Keratin form as secondary structure

A

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
Q

How do Keratin interact

A

Two Amphipathic helices of keratin interact to bury their hydrophobic faces together. This creates a coiled - coil

48
Q

Coiled - Coil

A

Formed when 2 or more helices entwine to form a stable structure

49
Q

Coil coil in keratin

A

Involves two right handed helices wrapping around each other in a left handed fashion

50
Q

Where does Keratin get its strength

A

From covalent linkages of individual units into higher order structures.

51
Q

How was individual units linked

A

Disulfide bonds

52
Q

Collagen

A

Major protein of Vertebrates

53
Q

Primary Structure of Collagen

A

At Primary collagen contains repeats of Gly - X - Y where X is always proline

54
Q

Secondary Structure of Keratin

A

Collagen forms a left handed helix of three residues per turn (As opposed to the 3.6 residues/turn of an alpha helix).

55
Q

Coiled Coil in collagen

A

Three Left handed helices of collagen wrap around each other in a right handed fashion

56
Q

Where are the Prolines

A

The bulky side chains of proline are on the outside of the coiled coil

57
Q

Where are the Glycines

A

Small side chains of glycine residues new in tightly packed core of the coiled - coil

58
Q

Post Translational Modification of Collagen

A

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
Q

Which enzymes perform these modifications

A

Vitamin C

60
Q

Lack of Vitamin C

A

Scurvy

61
Q

Silk

A

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
Q

Secondary Structure of Silk

A

Silk os composed primarily from beta sheets

63
Q

What gives silk its strength

A

Fully extended polypeptides

64
Q

Association of strands by hydrogen bonding

A

Flexible

65
Q

Association of Van Der Walls and Hydrophobic Interactions

A

Flexible

BMSC 200 (10 decks)

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