lecture 3- proteins Flashcards

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1
Q

proteins are…

A

polypeptides made of amino acids attached to each other via peptide bonds

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2
Q

___ are the building blocks of proteins and have these 4 groups

A

amino acids
amino (NH3), carboxyl (COO-), hydrogen, R group

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3
Q

name the nonpolar, alipathic amino acids

A

glycine
alanine
proline
valine
leucine
isoleucine
methionine

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4
Q

name the 3 nonpolar, aromatic amino acids

A

tyrosine
phenylalanine
tryptophan

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5
Q

name the polar, uncharged amino acids

A

serine
threonine
cysteine
asparagine
glutamine

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6
Q

name the polar, positively charged amino acids

A

lysine
histidine
arginine

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7
Q

name the polar, negatively charged amino acids

A

aspartate
glutamate

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8
Q

R groups of the amino acids next to each other face opposite direction- ___ conformation most common

A

trans

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9
Q

list the structures getting to a protein

A

primary structure (linear sequence of aa’s) — secondary structure — tertiary (protein) — quaternary

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10
Q

describe secondary structure

A

regular repeats resulting from hydrogen bonds involving the backbone

1- alpha helix (coil, 10-15 aa long)
2- beta pleated sheet (a fold, 3-10 aa long)

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11
Q

What sequences of amino acids form alpha helices?

A
  • no consecutive bulky or long R groups
  • no consecutive like-charged R groups
  • few with polar R groups, especially: Serine, threonine, asparagine, aspartate (these destabilize the helix)
  • infrequent glycine (very flexible) or proline (not flexible)
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12
Q

describe beta sheets

A

parallel (n terminuses on same side and C terminuses on same side)
or antiparallel
- beta sheets consist of at least two beta strands

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13
Q

name three supersecondary structural elements involving alpha helices

A

1- helix-turn-helix
2- coiled-coil
3- four-helix bundle

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14
Q

describe helix-turn-helix

A

in proteins, the HTH is a major structural motif capable of binding DNA
- C terminal binds to major groove, N terminal helps to position the complex

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15
Q

name three supersecondary structural elements involving beta sheets

A

1- beta hairpin
2- antiparallel B sheet
3- B barrel

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16
Q

supersecondary structural elements can also be ___, and combine several superseoncary elements, including both alpha helices and beta sheets

A

mixed

17
Q

tertiary structure is determined by…

A

primary and secondary structures combined with interactions between R groups and the environment (most important interaction is hydrophobic exclusion***)

  • others are van der Waals, hydrogen bonding, disulfide, ionic
18
Q

proteins composed of multiple polypeptide chains = ___
name the 2

A

oligomers

homooligomers- identical subunits
heterooligomers- nonidentical subunits

19
Q

proteins may be ________…. 1/3 of all proteins in higher eukaryotes may lack fixed tertiary structure entirely or at least contain unstructured sections or regions- diversity in binding

A

intrinsically unstructured

20
Q

name one homooligomer and one heterooligomer

A

E. coli B clamp (homodimer)

hemoglobin

21
Q

due to a toxin called ___ produced by streptococcus auerus, beta barrel can form pores in the ___ and kill the cell

A

hemolysin
cell membrane

22
Q

in a nucleotide- the nitrogenous base is linked to the ___’ carbon or ribose/deoxyribose and the phosphate group is linked to the ___’ carbon

A

1’
5’

23
Q

is the transfer of information into RNA irreversible?

A

no

24
Q

the double helix of DNA under physiological conditions is in what form?

A

B form

25
Q

What is more stable, G-C or A-T, why?

A

G-C (3 hydrogen bonds, not 2)

26
Q

T or F:

all nucleic acids with complementary sequences can form duplexes

A

true

27
Q

deoxiribose differs from ribose by having

A

one less oxygen

28
Q

the DNA double helix always has a uniform diameter because ___, which have one ring always pair with ___, which have two rings

A

pyrimidines
purines

29
Q

Which molecules form the backbone of DNA?

A

deoxyribose (sugar) and phosphate

30
Q

primary structure of proteins is maintained by ___ bonds

A

peptide