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biochem > ch 6 > Flashcards

ch 6 Flashcards

1
Q

what are the five forces responsible for maintaining protein shape? from strongest to weakest

A
  1. ionic, 2. dipole-ion, 3.hydrogen bonding, 4. dipole dipole, 5. london dispersion forces
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2
Q

hydrogen bonding can hold what peptide structures together?

A

secondary structures to quaternary structures

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3
Q

what peptide structures are biologically active?

A

tertiary and quaternary structures

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4
Q

what is a quaternary structure?

A

Protein quaternary structure refers to the structure of proteins which are themselves composed of two or more smaller protein chains.

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5
Q

what is a tertiary structure?

A

The tertiary structure will have a single polypeptide chain “backbone” with one or more protein secondary structures, the protein domains. Amino acid side chains may interact and bond in a number of ways.

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6
Q

what is a secondary structure structure?

A

local folded structures that form within a polypeptide due to interactions between atoms of the backbone. Will have alpha helices and beta pleated sheets in localized areas.

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7
Q

what is a primary structure structure?

A

a single polypeptide chain of amino acids.

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8
Q

In a Ramachandran plot, what does each dot represent?

A

a single amino acid that has a certain angle configureation.

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9
Q

In a Ramachandran plot, where do you usually find beta sheets?

A

on the upper left side of the plot, usually between 50-180 degrees on the y axis and -45 and (-180) on the axis.

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10
Q

In a Ramachandran plot, where do you usually find RIGHT HANDED alpha helices?

A

on the lower left side of the plot, usually between 30-(-50) on the y axis and -45 to -180 on the x .

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11
Q

what is designated on the right side of the Ramachandran plot?

A

LEFT HANDED alpha helices

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12
Q

what kind of angles are most favorable for amino acids?

A

staggered.

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13
Q

alpha and beta sheets can be what three things?

A

all nonpolar, all polar, and amphiplilic

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14
Q

what do amphiphilic alpha helices look like?

A

NP P P P NP NP NP P P P P NP NP P P (doesnt have to be one after the other)

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15
Q

what do amphiphilic beta sheets look like?

A

NP P NP P NP P NP P NP P NP P (they have to be sequential)

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16
Q

What does hydrogen bonding look like in alpha helices?

A

the N terminus and the C terminus are bonded together with the hydrogen from the N terminus bonding to the oxygen in the carbonyl on the c terminus.

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17
Q

how do you count the hydrogen bonding in a alpha helix?

A

The N terminus is N and at every peptide bond, you count as one after. N is not counted (N+4 if you have peptide bonds)

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18
Q

what does the directionality of the molecules do to the alpha helix?

A

one end is negative (top) and the other is positive (bottom)

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19
Q

what kind of beta sheets are most common in the body?

A

antiparallel

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20
Q

what are antiparallel beta sheets very strong?

A

they have linear hydrogen bonds

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21
Q

what does an antiparallel beta sheet look like?

A

one chain of the polypeptide starts at the N terminus while the other across it starts at the C terminus. this causes the oxygen of the carbonyl to bond to the hydrogen of the N terminus making these linear hydrogen bonds.

22
Q

why are parallel beta sheets weaker than antiparallel beta sheet?

A

they have diagonal hydrogen bonding.

23
Q

what does a parallel beta sheet look like?

A

both polypeptide chains start on the same N terminus.

24
Q

what do R groups in an antiparallel beta sheet want?

A

they want the R groups they’re near to be either Polar Polar or Nonpolar Nonpolar because they’re facing each other.

25
Q

what amino acids are alpha helices most likely to have

A

MALEK

26
Q

What type of secondary structure would this fragment be most likely to adopt? ADLKVS

A

amphiphilic beta sheet

27
Q

what are turns in amino acids?

A

allows the chain to reverse direction

28
Q

what are the two AA’s that turns usually have?

A

proline (causes kinks) and glycine (small)

29
Q

what is a type 1 turn? a type 2?

A

type 1 turn turns left and type 2 turns right

30
Q

how many residues are needed for turns in amino acids?

A

4

31
Q

what is the factor that would influence the formation of a beta sheet or an alpha helix?

A

the sequence of AA’s

32
Q

what does the surface of a water soluble protein made of? the interior?

A

surface: polar: hydrophilic, interior: non polar: hydrophobic

33
Q

what are the characteristics of fibrous proteins?

A

structural, long and narrow, insoluble, less sensitive to changes, repetitive sequences

34
Q

what are the characteristics of globular proteins?

A

rounded, functional, soluble, irregular sequence, more sensitive to changes

35
Q

what is a supersecondary structure?

A

2 or more secondary structures

36
Q

what are the three types of supersecondary structure?

A
  1. coiled coil 2. stack of beta sheets 3.triple helices (3 collagen helices)
37
Q

what is the supersecondary structure of collagen?

A

triple helix, every third AA is GLYCINE, HYDROPHOBIC AF

38
Q

what is the supersecondary structure of silk fibroin?

A

stacked beta sheets, starts with Gly and paired with either ser or ala, HYDROPHOBIC

39
Q

what is the supersecondary structure of alpha keratin?

A

coiled coil, it has seven residues repeats with A+D

40
Q

what are the two special amino acids that collagen has?

A

hydroxyproline and hydroxylysine

41
Q

hydroxyproline

A

helps the proline stay in shape to create the triple helix

42
Q

hydroxylysine

A

helps with proteins to connect sugars in the body and helps with the cross links that holds the helices together.

43
Q

why is hair elastic? why is silk not?

A

hair is made of alpha keratins made of alpha helices that can be uncoiled and straighten out while the silk is made of beta sheets that are already straightened out.

44
Q

why is vitamin c important for hydroxyproline and hydroxylysine?

A

vitamin c oxidizes proline and lysine to create Hyp and Hyl and results in no cross link

45
Q

what are the factors that determines how a protein will fold?

A
  1. AA sequence 2.environment (ph, space, salt concentration)
46
Q

what did scientist Anfinsen do?

A

he used a reducing agent called urea to break disulfide bonds. once he removed the urea, the protein went back to its OG shape. he found that the sequence of AA made this possible.

47
Q

what is denaturation?

A

anything that disrupts the vanderwaals forces. from 4-1 structures, NOT FROM PRIMARY STRUCTURES TO INDIVIDUAL AMINO ACIDS

48
Q

what are five examples of denaturation

A
  1. ph change 2. reducing agent like urea 3. bad metals like lead and mercury 4. heat 5. acid and bases
49
Q

what does disulfide isomerases do in protein folding

A

it shuffles disulfide bonds

50
Q

why are prions SO COOL?

A

they are infectious proteins that will cause healthy proteins to misfold BAD PEER PRESSURE

51
Q

what does peptidyl isomerases do in protein folding?

A

turns cis molecules to trans

52
Q

what is a molecular chaperone

A

assists the folding of the protein and prevents misfolding and aggregation of proteins

biochem (9 decks)

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