Brainscape's Knowledge GenomeTM

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


See full index

Biochemistry > Lecture 3: Protein secondary structure, How does the polypeptide chain fold up? > Flashcards

Lecture 3: Protein secondary structure, How does the polypeptide chain fold up? Flashcards

secondary structure of proteins alpha helix and beta sheet fibrous proteins globular proteins

1
Q

What does it mean by primary structure?

  • the sequence of covalently joined amino acids in a polypeptide chain
  • linear sequence
A
  • the order in which amino acids are covalently linked together
  • the ‘one dimensional’ first step in specifying the 3dimensional structure of protein
  • determines other levels of structure
  • sequence is critical to proper protein function
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What does it mean by secondary structure?

  • characterized by the repetitive organization of the peptide backbone
  • most common are alpha helix and beta helix
  • fibrous protein, globular protein
  • the nature of the bonds in the peptide backbone plays an important role here
A
  • the arrangement in space of the atoms in the peptide BACKBONE
  • have repetitive interactions resulting from HYDROGEN BONDING between the amide N-H and carbonyl groups C=O of the peptide backbone
  • the conformations of the side chains of the amino acids are NOT part of the secondary structure
  • in many proteins the folding parts of the chain can occur independently, these portions of independently folded proteins are known as DOMAINS or SUPER SECONDARY STRUCTURES
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What does it mean by tertiary structure?

  • refers to the complete 3-dimensional structure of the protein
A
  • includes the 3-dimensional arrangement of ALL THE ATOMS IN THE PROTEIN
  • including those in the side chains
  • and any prosthetic groups ( groups of atoms other than amino acids)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What does it mean by subunit?

A

multiple polypeptide chains

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

What does it mean by Quaternary structure?

  • describes a protein that has multiple polypeptide chains
A
  • the arrangement of subunits with respect to one another
  • interaction between subunits is mediated by NON COVALENT INTERACTIONS
    eg.
    hydrogen bonds
    electrostatic interactions
    hydrophobic interactions
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What are the 2 common folding patterns of secondary structures?

A

alpha helix

beta pleated sheet

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

Describe the characteristics of an alpha helix structure

A
  • the polypeptide chain coils into a RIGHT HANDED HELICAL STRUCTURE
  • this structure contains 3.6 amino acids per turn,
  • this means that amino acids 4 residues apart in a linear structure are close in this secondary structure
  • hydrogen bonds occur along the helix between C=O and N-H group from AMINO ACIDS SEPARATED BY 4 RESIDUES IN THE LINEAR SEQUENCE
    eg. the C=O group of residue 1 forms H-bond with NH group of residue 5
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is the distance traveled of each alpha helix per turn ?

A

0.54 nm (0.15nm * 3.6)

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

true or false the alpha helix is a fairly rigid rod?

A

true

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

true or false the amino acid side chains (R-groups) project out from the rod?

A

true

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

It it possible that some amino acids with bulky side chains may not fit in the a-helix structure?

A

true

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

What is the beta pleated sheet?

A
  • forms BETWEEN strands of polypeptides which run PARALLEL ( in the same direction) or in opposite directions, ANTI PARALLEL
  • stabilized by H-bonds between the strands
  • side chains point up and down below the sheet
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What are fibrous protein compose of of?

A

composed entirely of ONE type of secondary structure

  • almost completely secondary structure
  • highly regular, repetitive structure
  • used for mechanical strength and structural properties
  • examples: keratin (wool), fibroin (silk), collagen (skin, nails)
  • often repetitive sequences
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Give examples of fibrous proteins

A

a- keratin

hair sequences

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

Describe a-keratin

A
  • fibrous or filamentous protein
  • major component of hair and finger nails
  • belongs to a broad group of proteins known as INTERMEDIATE FILAMENT PROTEINS
  • these play an important role in the nucleus and cytoplasm of cells
  • these proteins are exclusively a-helix
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Describe hair sequences

A
  • 300 amino acids
  • form a-helices and ASSOCIATE IN PAIRS and becomes a coiled coil structure
  • every 4th amino acid tends to be that one FACE of the helix that is STICKY , and thus will BIND to SIMILAR FACE of the a-keratin chain
  • the chain also contains a large number of Cys (Cysteine) residues which provide Di-Sulphide cross links
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What is a dimer?

A

a molecule or molecular complex which consisting of two identical molecules linked together

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

State in order the structure of keratin type intermediate filaments

A

monomer
dimer
protofilament
protofibril

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Describe what occurs to form a protofibril in keratin type intermediate filaments?

A
  1. ) 2 MONOMERS pair via a parallel coiled coil form
  2. ) this will form the 50 nm long DIMER
  3. ) these then associate to form first a 4 strand PROTOFILAMENT
  4. ) and then an 8 strand PROTOFIBRIL
  5. ) the regular spacing of 25 nm along the fibers is accounted for by the overlap
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Define monomer

A

a molecule that can be bonded to other identical molecules to form a polymer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What is B-keratin? Where is it found?

A
  • found mainly in birds and reptiles

- in feathers and scales exclusively composed of beta sheets

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Describe the characteristics of silk fibres

  • variable spacing and interdigitation
  • layered B- sheet structure
A
  • contain protein FIBROIN which is also made of beta sheets
  • almost every other residue is Gl with Ala and Ser lying between them
  • this arrangement alows INTERDIGITATION of the Ala or Ser side chains and Gly
  • these polypeptides are quite stretched; thus easily broken (flexible however)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Definition of interdigitation

A

An interlinking in which resembles the fingers of two hands being interlocked

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What are examples of human diseases which are the result of misfolding of proteins

A
  • huntington’s disease
  • cystic fibrosis
  • amyotrophic lateral sclerosis
  • type 2 diabetes
  • transmissible spongiform encephalopathies (prion disease = mad cow)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What appears to cause these diseases?

A
  • caused by the formation of fibrous structures amyloid fibrils
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What are amyloid fibrils?

A
  • these occur when sections of polypeptide from separate molecules form B-sheets that cause many molecules to clump together in large aggregates
27
Q

How are these B-sheets stabilized?

A

stabilized by hydrogen bonding, and stack together by packing of side chains in between the sheets

28
Q

When do these amyloids usually occur?

  • results in molecule aggregating into large B- sheet assemblies which accumulate in deposits in the body
A

when proteins that should be globular are incorrectly folded

- therefore these are called misfolding diseases

29
Q

What causes these misfolding diseases?

A
  • mutation in a gene; causing the protein to be susceptible to unfolding from its normal structure
  • exposing sections of polypeptide chains that can form amyloid like B-sheets
30
Q

Describe the characteristics of collagen

A
  • forms the matrix of bone
  • major portion of tendons
  • important component of skin
  • structure (Gly- X- Y)
  • X = is often Pro
  • Y = either Pro or hydroxyproline
  • helix : left handed
  • 3 residues per turn
    3 chains around each other –> triple helix (H-bonds) ; (tropocollagen)
31
Q

What is the significance of the hydroxylation of Proline

A
  • makes the collagen structure more stable

-

32
Q

What is hydroxyproline?

A
  • formed from proline
  • by specific hydroxylating enzyme ( proline hydroxylase) after the amino acids are linked together
  • THE TRIPLE HELIX IS ARRANGED SP THAT EVERY 3RD RESIDUE ON EACH CHAIN IS INSIDE THE HELIX; only Gly is small enough to fit in the small space available
33
Q

What does the enzyme proline hydroxylase require?

A

vitamin C

34
Q

What is hydroxyproline an example of?

A
  • post translational modification
35
Q

What does post translational modification mean?

A

the chemical alteration of a protein after its incorporation into a protein

36
Q

What is a fibrous protein?

A
  • composed entirely of one type of secondary structure
  • insoluble
  • elongated molecules; in which the secondary structure forms the dominant structure
  • often form regular repeating structures
37
Q

What is a globular protein?

A
  • spherical (“globe-like”) proteins
  • soluble
  • form compact spheroidal molecules in water.
  • All have tertiary structure and some have quaternary; in addition to secondary structure
38
Q

true or false; the side chains of an alpha helix pokes outwards?

A

true

39
Q

true or false; helices are often straight?

A

true

40
Q

Does Proline disrupt the helices?

A

yes

41
Q

why is the a-helix so prevalent?

A

its helical conformation allows linear arrangement of the atoms in the hydrogen bonds

  • this gives bonds maximum strength
  • thus a very stable helical conformation
42
Q

What is the pitch (linear distance between corresponding points on successive turns) of alpha helix?

A

54 nm

43
Q

What factors disrupt the alpha helix?

A

amino acid Proline (Pro); creates a bend in the backbone because of its cyclic structure,

It cannot fit into the a-helix because:
1.) rotation around the bond between the nitrogen and the a-carbon are restricted

  1. ) prolines’ alpha amino group cannot participate in intrachain hydrogen bonding.
    other:
  2. ) side chains: electrostatic repulsion due to several groups of the SAME SIGN eg. (+) Arg and Lys

4.) steric repulsion/ crowsding: if a- carbon is bonded to 2 atoms other than hydrogen

44
Q

How is B-sheet different from the a- helix?

A
  • peptide backbone in the B-sheet is almost completely extended
  • hydrogen bonds can be formed between different parts of the single chain
    that is:
  • doubled back on itself (intrachain)
  • between different chains ( interchain)
45
Q

What gives rise to the repeated zigzag structure?

A

hydrogen bonding between peptide chains

- hydrogen bonds are perpendicular to the direction of the protein chain; NOT PARALLEL TO AS IN A-HELIX

46
Q

What is a motif?
indicates:
- folding pattern not biological activity

A

is a repetitive super secondary structure/ domain

47
Q

true or false collagen is the most abundant protein in vertebrates?

A

true

48
Q

true or false, collagen is NOT a component of bone and connective tissue?

A

false, it is both

49
Q

in water is collagen soluble?

A

no, its a fibrous protein, hence it is INsoluble

50
Q

Describe the collagen fibre (like a stiff rod)

A
  • consists of 3 polypeptide chains
  • wrapped around each other in a ropelike twist or triple helix ( tropocollagen; super coiled, tensile strength)
  • each of the 3 chains REPEATING residues of Gly- X-Y
51
Q

true or false, each collagen chain themselves helices that differ from the a-helix?

A

true

52
Q

What are the 3 strands in a collagen molecule held together by?

A

hydrogen bonds

- involving hydroxyproline and hydroxyproline residues

53
Q

true or false, collagen is both intermolecularly & intramolecularly linked by covalent bonds

A

true

- covalent bonds formed by reactions of histidine and lysine residues

54
Q

What happens in collagen; when proline is not hydroxylated to hydroxyproline?

A
  • less stable than usual collagen
  • scurvy, bleeding gums, skin discoloration
  • enzyme which hydroxylates proline requires vitamin C to remain active
55
Q

Shape of fibrous protein?

A
  • long and narrow rod
56
Q

formation of globular protein?

- a protein whose overall shape is more or less spherical

A
  • the backbone folds back on itself to produce more or less spherical shape
  • water soluble
  • have compact structure
57
Q

What is spidroin?

A

spider silk

58
Q

describe spider silk (spidroin)

A
  • unique combination of tensile strength and extensibility
  • strong and stretchy
  • stronger than steel ( 1/2 that of kevlar)
    but tougher than both
59
Q

Define toughness

A

is the ability to absorb energy and plastically deform without fracturing

60
Q

What is spidroin composed of?

A
  • mixture of beta sheet, semi crystalline regions and amorphous regions
61
Q

define amorphous

A

without a clear, defined shape

62
Q

What is the spiders’ secret?

A

lots of SHORT 4 stranded beta sheets with sets of ~ 4 H-bonds between strands
eg. 1 HB weak, 2 HB better, 3HB better, 4HB very strong
5+ HB weak!!

63
Q

What is the repetitive sequence of collagen?

A

(Gly- X-Y)n

64
Q

true or false, there is no C=O and H-N hydrogen bonds to link the tropocollagen

A

true …

Biochemistry (5 decks)

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