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BIOL 200 > KH3 > Flashcards

KH3 Flashcards

1
Q

What is a protein’s primary structure?

A

The specific sequence of amino acids in a protein

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2
Q

What is the structure of linear polymers

A

Folded into definite 3D structures depending on the sequence of amino acids

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3
Q

What is the function of a protein determined by

A

Overall shape and the distribution throughout that overall shape of the amino acid side chains with their distinctive chemical properties

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4
Q

What are the two major classes of amino acid side chains

A

Hydrophilic (polar electronic charge distribution and interact well with the polar solvent water)

Hydrophobic (non-polar charge distribution and therefore do not interact well with the polar solvent water)

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5
Q

What is the hydrophobic effect

A

water molecules surrounding hydrophobic molecules dispersed in water adopt a constrained, cage-like organization (low entropy)

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6
Q

What happens if hydrophobic molecules coalesce in the hydrophobic effect

A

The total number of low entropy, constrained water molecules is reduced, and this net increase in entropy ultimately drives the formation of separate hydrophobic and aqueous phases (higher entropy when there are less water molecules after aggregation)

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7
Q

What does DNA indirectly determine in terms of proteins

A

DNA determines amino acid sequence of the protein but ultimately dictates the 3D structure and ultimately function of the protein

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8
Q

What does secondary structure refer to

A

The local conformations of the peptide chain backbone

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9
Q

What are the two major peptide chain backbone conformations

A

Alpha helix and beta sheet

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10
Q

What are the two major peptide chain backbone conformations based on

A

H-bonding between peptide bond carbonyl O atoms on one amino acid residue, and amino group hydrogens on a different amino acid residue

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11
Q

How does the bonding work in alpha helix structures

A

Amino acid n H-bonds with amino acid n+4

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12
Q

What is the periodicity of alpha helix structures

A

Titled axis of U-bonds drives periodicity of 3.6 residues per turn

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13
Q

What is the gross structure of alpha helices

A

Straight rod

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14
Q

What are surface properties of alpha helix structures dependent on

A

Side chains

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15
Q

What are surface properties of alpha helices that can be determined

A

Propensity for alpha helix to form
Interactions of the alpha helix with other parts of the protein (stability)

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16
Q

How does bonding work in beta sheets and what does it create

A

H-bonds link two adjacent beta strands, can create large surfaces

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17
Q

What property of beta sheets determines the interactions of the beta sheet with other parts of the protein and also the propensity for the beta sheet to form

A

Amino acid side chains protruding above and below the plane of the beta sheet

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18
Q

What kind of relationships can the strands of beta sheets have

A

Strands may be parallel or antiparallel (and could be from different polypeptides)

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19
Q

What are secondary structures described as and how many secondary structure elements do polypeptides have

A

Local and multiple

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20
Q

What is tertiary structure

A

Overall conformation of the polypeptide (spatial organization of the multiple secondary structure elements)

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21
Q

What is the function of amino acid side chains in tertiary structures

A

Mediate interactions between different parts of the protein and between the protein and its ligand GDP

22
Q

What are most of the structure-driving interactions among the amino acids in a protein

A

Non-covalent bonds

23
Q

What is an important covalent bond interaction that can be important

A

Side chain of the amino acid cysteine contains a sulfhydryl group that can form covalent S-S (disulfide) bonds with other cysteine side chains

24
Q

What are examples of non-covalent bonds in proteins

A
  1. H-bonds among peptide backbone carbonyl and amino groups that support alpha helix and beta sheet secondary structure
  2. H-bonds between amino acid side chains with polar side chains
  3. Ionic bonds between positively charged (basic) and negatively charged (acidic) side chains
  4. Van der Waals interactions among hydrophobic side chains
25
Q

What can disulfide bonds be and what kind of structures do the contribute to

A

Intrachain (tertiary structure)

Interchain (quaternary structure)

26
Q

What side of the polypeptide are new amino acids added to

A

C-terminus

27
Q

What kinds of representations are there of tertiary structures and which ones are generally used and not used and why

A
  1. Backbone trace (used, no distinct shape just tubes)
  2. ball and stick model (not used, shows every atom)
  3. Ribbon diagram (used, shows tubes and helix and sheet)
  4. Water accessible surface (not used, different colours)
  5. Hybrid model (used, ribbon diagram with white outer coating)
28
Q

What are motifs of protein structures

A

Combinations of secondary structures forming distinct local 3D structure

29
Q

What are the types of motifs of protein structure

A
  1. Coiled-coil motif
  2. EFhand/helix-loop-helix motif
  3. Zinc-finger motif
30
Q

What are the qualities of the coiled-coil motif

A

made up of two polypeptides, have a heptachlor repeat (every fourth molecule is a hydrophobic amino acid and every molecule in between in hydrophyllic amino acid) involved in protein:protein interactions

31
Q

What are the qualities of the EFhand/helix loop-helix motif

A

Right angle, allows the binding of Ca2+

32
Q

What are the qualities of the Zinc-finger motif

A

Common in transcription factors (binds to DNA/RNA)

33
Q

What are the qualities of motifs

A

Recognizable structure, often characteristic amino acid sequence features, generally small, local, do not contain sufficient amount of structure maintaining bonds to hold the motif in its characteristic 3D shaper if cut away from the rest of the protein

34
Q

Why are motifs not structurally independent entities

A

The rest of the protein contributes to the stability of the local motif, if cut away motif would fall apart

35
Q

What are domains

A

3D structures with proteins that are larger than motifs and contain a sufficient number of bonds to hold the domain in its characteristic shape if it is cut away from the rest of the protein

36
Q

Why are domains structurally independent entities

A

The rest of the protein contributes little to the stability of a domain (although covalently joined to the rest of the protein)

37
Q

What are the four major structural classes of proteins

A

Fibrous proteins, integral membrane proteins, globular proteins, intrinsically disordered proteins

38
Q

What are characteristics of intrinsically disordered proteins

A

Proteins that exist as random coils under physiological conditions, may adopt a specific secondary/tertiary structure upon binding to a well-structured partner protein

39
Q

What is the structural definition of tertiary structure domains

A

40 aa-long region, compactly folded, can be made of various motifs

40
Q

What is the structure of tertiary structure domains

A

Two different domains: globular domain (distal) and fibrous domain (proximal with a long protruding protein interacting with a smaller one)

Heterodimer: two different polypeptides (HA1 and HA2)

41
Q

What is the modular nature of protein domains

A

Similar domains can be found in diverse proteins, and also as multiple similar copies within any given protein

42
Q

What are the characteristics of a quaternary structure (multimeric proteins)

A

Trimmer of identical subunits each composed of an HA1 and HA2 chain held together by non-covalent bonds, subunits also held together by non-covalent bonds

43
Q

Can multimeric proteins contain any number of identical t or different polypeptides

A

Yes

44
Q

What are supramolecular complexes

A

Large molecular machines made up of multiple distinct proteins each of which may itself contain multiple subunits

45
Q

Are supramolecular complexes stable

A

No, they fall apart when job is done

46
Q

What is a characteristic of the evolution of proteins

A

Evolution was not to maintain the structure of proteins but the functions, 3D structure almost more important than amino acid sequences

47
Q

What is the hydrophobic effect

A

Tendency of hydrophobic molecules to find each other and to bond to each other in water

48
Q

What do side chain interaction affect

A

Overall stability of protein

49
Q

How does a beta sheet arrange amino acid side chains

A

Up and down

50
Q

What does the water accessible surface model show us

A

Distribution of positive and negative charges

51
Q

What can a disulfide bond between two cysteine side chains in a protein do

A

Cause change in structure and it can help hold together tertiary and quaternary structures

52
Q

Why do all hydrophobic molecules line up on pitch (3.6) of an alpha helix thus putting them all in the middle in a heptad

A

Every second hydrophobic amino acid means that 7/2 is 3.5

BIOL 200 (13 decks)

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