Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biocheem > Lecture 13 > Flashcards

Lecture 13 Flashcards

1
Q

What is the Secondary Structures of Proteins?

A

The local folding of the polypeptide backbone

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What does the Secondary Structure of polypeptides allow for?

A

Hydrogen bonding of the group in the polypeptide backbone (N-H and C=O)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

When do Regular Secondary structures occur?

A

When every amino acid in a segment of the polypeptide adopts the same geometry

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What are the two regular patterns of secondary structure?

A

Alpha-helix

Beta-sheets

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What are the two important consideration when looking at the structures that polypeptide chains might adopt?

A
  • Minimize steric conflicts

* Maximize hydrogen bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Does secondary structure break bonds or form bonds?

A

No, it is just rotating bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What do both the alpha-helix and the beta-sheets satisfy?

A

The hydrogen bonding potential and the steric restraints

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What are the H-bonds like in Alpha-helices?

A

The carbonyl oxygen of each residue forms an H-bond with the backbone - NH group four residues downstream

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is an Alpha helix?

A

A portion of a polypeptide that forms a right handed helical structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Which amino acid residues do not form hydrogen bonds in the alpha helix structure?

A

Those at the ends of the backbone

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is the helix axis?

A

The axis that all the hydrogen bonds in a alpha helix is parallel to

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is the proximity of side chains to each other in the alpha helix?

A

The side chains are close to each other in alpha helices

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is the core of an alpha helix entirely made up of?

A

The backbone

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is the arrangement of the amino acid side chains in the alpha helix?

A

They are projecting away from the helix core

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

How does the orientation of the side chains of amino acids change when going from the primary structure to the alpha helix secondary structure?

A

The amino acid side chains that are 3-4 chains apart from each other in the primary structure become a lot closer in the secondary structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What are the different ways the projecting side chains in alpha helices can interact favorably?

A
  • Positive and negative charges
  • H bond donors and acceptors
  • Hydrophobic groups near each other
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What are the different ways the projecting side chains in alpha helices can interact unfavorably?

A
  • Multiple negative or positive charges as part of their amino acid side chains
  • Too many bulky side chains
18
Q

What can unfavorable interactions between projecting side chains in alpha helices do?

A

They destabilize the structure

19
Q

What is the function of the major groove in B-form DNA?

A

It is the appropriate size to interact and bind to proteins (specifically an alpha helices)

20
Q

What is the similarity between the alpha helix and the major groove of B-form DNA?

A

They are the same diameter

21
Q

What is proline not common in the middle of a double helix?

A

Because the nitrogen is bonded to three carbons and is missing an H to form hydrogen bond interactions and proline is big

22
Q

What is the consequence of a proline being in the middle of an alpha helix?

A

It will cause a kink in the bonds

23
Q

Where is Prolin usually found in an alpha helix?

A

At the end terminal of an alpha helix so it doesn’t have to participate in H-bonds

24
Q

What are Beta-Sheets

A

Multiple beta strands arranged side by side and strands are joined by loops or other structures

25
Q

What are the two types of Beta-sheets?

A

Parallel and antiparallel sheets

26
Q

What occurs in parallel beta sheets?

A

All the strands go from N to C or from C to N

27
Q

What occurs in anti parallel beta sheets?

A

The strands alternate going from N to C and C to N

28
Q

What kind of hydrogen bonding interactions are seen in Parallel Beta sheets?

A

Alternating angled hydrogen bonds making wedged shapes

29
Q

What are the H bond interactions between antiparallel beta sheets?

A

The hydrogen bonding pattern occurs in parallel couplets

30
Q

What is the arrangement of the amino acids in beta-sheets?

A

The individual amino acid side chains alternate above and below the plane of the beta-sheet

31
Q

Which amino acid side chains are found next to each other in beta sheets?

A

Every second amino acid is found next to the other amino acids that are either two before or two after it. Every second side chain is interacting

32
Q

What forces stabilize alpha-helices and beta-sheets?

A

H-bonds between backbone CO and NH groups in the same helices

33
Q

Where do H-bonds within beta sheets come from?

A

Interactions between the individual strands

34
Q

What are the regular secondary structures?

A

Alpha helices and beta sheets

35
Q

What is meant by regular secondary structures?

A

The peptide backbone has the same configuration/conformation for every amino acid within the secondary structure

36
Q

What are distinct elements of regular secondary structures linked together by?

A

Polypeptide loops of various sizes

37
Q

What bond does a rotation required for alpha helices and beta sheets occur at?

A

All the bonds but the peptide bond (C-N)

38
Q

Why is the statement both alpha helices and beta sheets form from only consecutive amino acid residues in a polypeptide false?

A

Because beta sheets have to come from different portions of the primary structure

39
Q

What is Tertiary structure concerned with?

A

All the atoms in the structure, backbone, sidechain and in some cases the prosthetic groups

40
Q

What are the two types of tertiary structure?

A
  • Fibrous (elongated)

* Globular (compact)

41
Q

What are the characteristics of Fibrous proteins?

A
  • Insoluble in aqueous solutions
  • Form long protein filaments
  • Usually structural or connective properties
42
Q

What are the characteristics of Globular proteins?

A
  • Soluble in aqueous solution

* Fold into compact structures with nonpolar cores and polar surfaces

Biocheem (38 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions