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biochemistry 2065 > Lecture 9: The Structure of Proteins > Flashcards

Lecture 9: The Structure of Proteins Flashcards

1
Q

the sequence of amino acids is specified by the __ sequence encoding the protein

A

gene

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2
Q

amino acid polymers of less than 50 amino acids are called __

A

peptide

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3
Q

a peptide bond is formed between which two groups in a peptide chain?

A

carboxyl group of the first and the amino group of the second

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4
Q

the H and R groups are opposite the ___ in a peptide bond to avoid steric clash

A

o in the carbonyl

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5
Q

the equilibrium of making a peptide bond favours the ___ side

A

left (hydrolysis)

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6
Q

why does the peptide equilibrium favour the hydrolysis rather than synthesis?

A

because the synthesis requires free energy

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7
Q

the alpha carbon can always be identified because it has the ___ attached to it

A

R group

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8
Q

each amino acid in a peptide chain is called a __

A

residue

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9
Q

every peptide chain begins with a ___ residue and ends in a __ residue

A

amino, carboxyl

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10
Q

the amino acid at the beginning of the chain is called the __

A

amino / N terminus

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11
Q

the amino acid at the end of the chain is called the __-

A

carboxly / C terminus

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12
Q

the geometry of an aa about a peptide bond is __

A

planar

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13
Q

what makes the peptide bond rigid? (not free to rotate)

A

resonance from the carboxyl makes the bond not purely single and therefore unable to freely rotate

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14
Q

the psi and phi bonds flank the ___ of each amino acid

A

alpha carbon

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15
Q

what bonds are free to rotate in amino acids?

A

the phi and psi bonds

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16
Q

the phi bond forms between the alpha carbon and the

A

amino group

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17
Q

the psi bond forms between the alpha carbon and the

A

carbonyl group

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18
Q

what does a Ramachandron plot show?

A

the permissible phi and psi bond angles allowed in a polypeptide backbone

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19
Q

the range of permissible angle combinations reflect the ___ and ___structure of proteins

A

secondary and tertiary

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20
Q

the polypeptide structure will have inherent __ and ___ within the constraints dictated by the permissible angles

A

flexibility and mobility

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21
Q

the secondary structure of proteins is stabilized by __ bonds between N and carboxyl groups in linear squence

A

H bonds

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22
Q

due to combination of bond angles and H bonding effects, certain aa segments ____ form secondary structures

A

spontaneously

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23
Q

what are the 3 types of secondary structures?

A

aplha helix , beta sheets, turns and loops

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24
Q

proteins can be made exclusively of alpha helix/beta sheets, or a mix of both (T/F)

A

true

25
Q

turns and loops function to __

A

connect helices or sheets together

26
Q

alpha helixes are segments of amino acids that form ___ handed helical structure (rotates ___ (cw.ccw)

A

right; clockwise

27
Q

what is the average length of an alpha helix?

A

10 amino acids

28
Q

there are about ___ amino acids per complete turn along the the alpha helix

A

3.6

29
Q

in the alpha helix, every ___ amino acid interacts via hydrogen bonding

A

4

30
Q

side chains extend in what direction with respect to the helix?

A

outwards

31
Q

what makes some amino acids unsuited for helix formation?

A

geometry or size of side chains

32
Q

about ___ % of all soluble proteins are composed of alpha helices

A

25

33
Q

the B sheets are made by multiple __ of amino acids in a ___ sequence rather than coiled in a helix

A

adjacent segments; fully extended

34
Q

adjacent segments in a B sheet interact by __ interactions

A

hydrogen bonding

35
Q

adjacent B strands can be in anti-parallel or parallel (T/F)

A

true

36
Q

in antiparallel B sheets, each amino acid is bonded to __ on the other strand

A

one amino acid

37
Q

in parallel B sheets, each amino acid is bonded to __ on the other strand

A

2 different amino acids

38
Q

in parallel B sheets, the two strands run in the ___ direction

A

same

39
Q

in antiparallel b sheets, the two strands run in the ___ direction

A

opposite

40
Q

B strands associate to become __

A

B sheets

41
Q

B sheets are stabilized by intracellular ___ bonds

A

H

42
Q

arrows representing B sheets point in the direction of the ___ terminal end

A

carboxyl

43
Q

Beta sheets can be flat, but most adopt a ___ shape

A

twisted

44
Q

what two amino acids participate in forming turns?

A

proline and glycine

45
Q

there is open space in the interior of a protein (T/F)

A

no; little to none

46
Q

name 5 things that stabilize tertiary structure

A
  1. charge interactions
  2. H bonding
  3. van der waal between side chains
  4. hydrophobic effect
  5. disulphide bonds b tween cysteine side chains
47
Q

myoglobin is an example of a __ protein

A

globular

48
Q

myoglobin is an extremely compact molecule made of __ polypeptide chain(s) of ___ (#) amino acids

A

1; 153

49
Q

about 70% of the myoglobin structure is made of __

A

alpha helices

50
Q

tertiary structures of many proteins can be divided into __ and ___ units

A

structural and functional

51
Q

some proteins fold into multiple tertiary structures called __

A

domains

52
Q

each domain may posses a unique ___ that may be quite functional even id separated from the protein

A

enzymatic function

53
Q

discrete sub-structures in a protein with special structural/functional significance are called __

A

motifs

54
Q

what motif is typically found in proteins that bind double-stranded DNA?

A

helix–turn–helix

55
Q

each polypeptide chain in a protein complex is called a __

A

subunit

56
Q

quaternary structure refers to the arrangement of ___ and the nature of their interactions

A

subunits

57
Q

what is homotypic association?

A

proteins assemble within each other

58
Q

what is heterotypic association?

A

different proteins assemble into multi-subunit complexes

59
Q

example of a heterotypic protein

A

DNA polymerase

biochemistry 2065 (19 decks)

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