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Biochem 2 > Lecture 1 > Flashcards

Lecture 1 Flashcards

1
Q

what are the general functions of proteins?

A

Enzymes, plasma membrane proteins, signaling, structural proteins, motor proteins, anitbodies, hormones

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2
Q

who coined the term protein?

A

Jons J Berzelius

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3
Q

which amino acids have sulfur groups?

A

cysteine and methionine

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4
Q

which amino acids have -OH groups?

A

tyrosine, serine, threonine

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5
Q

how are peptide bonds formed?

A

a-carboxyl group joined to a-amino group
includes a loss of water molecule

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6
Q

what kind of bond is a peptide bond?

A

planar bond

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7
Q

how many bonds do amino acids contribute to protein backbone?

A

3

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8
Q

steric (spatial) effect

A

effect in which the shape of a molecule influences its reactions

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9
Q

why are peptide bonds rigid?

A

carbonyl carbon atom and nitrogen atom has partial double-bond character

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10
Q

which end of a polypeptide chain is the beginning?
(amino end or carboxyl end)

A

amino end (N terminal)

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11
Q

polypeptide backbone

A

repeating atoms along the core of the polypeptide chain

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12
Q

what bonds constrain protein folding? what type of bonds are they?

A

weak non covalent bonds
hydrogen bonds, ionic bonds, van der waals

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13
Q

hydrophobic interactions

A

minimize disruption of hydrogen bonding between water molecules

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14
Q

where are non-polar side chains of amino acids? (in terms of hydrophobic interactions)

A

cluster in the interior of proteins

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15
Q

where are polar side chains of amino acids? (in terms of hydrophobic interactions)

A

outside of the proteins
hydrogen bonded to other polar amino acids or to polypeptide backbone

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16
Q

disulfide bonds

A

covalent links between the sulfur atoms in the side chains of cysteins

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17
Q

what is the function of disulfide bonds?

A

stabilize protein structure (folding or mediate attachment of protein subunits)

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18
Q

intrachain disulfide bonds

A

joining two parts of the same polypeptide

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19
Q

interchain disulfide bonds

A

joining two different polypeptide chains

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20
Q

where do disulfide bonds form?

A

ER

21
Q

why can’t disulfide bonds be formed in the cytosol?

A

high concentration of reducing agents in the cytosol

22
Q

what are the four levels of protein structure?

A

primary, secondary, tertiary and quaternary

23
Q

primary protein structure

A

order/sequence of covalently linked amino acids

24
Q

tertiary protein structure

A

3D organization of polypeptide chain
- steric relationship of amino acids that are far apart in linear sequence

24
Q

secondary protein structure

A

folding of polypeptide chains (maintained by repetitive hydrogen bonding)
- steric (spatial) relationship of amino acids that are close to one another in the linear sequence
-a-helix and b-pleated sheets

24
Q

quaternary protein structure

A

complete 3D structure of multi-subunit protein complexes (the way protein chains are packed together)

24
Q

who sequenced the first protein? what kind of protein?

A

Frederick Sanger; bovine insulin

25
Q

how are a-helix and b-pleated sheets bonded?

A

hydrogen bonding of amino and carbonyl groups in polypeptide backbone
no bonding between side chains of amino acids

25
Q

what determines the conformation of a protein?

A

amino acid sequence

25
Q

how many possible primary protein sequences can exist?

A

20^n

25
Q

how many protein sequences are known?

A

500,000

25
Q

where does the H-bond occur in a-helix?

A

every fourth peptide (3.6 amino acids)

25
Q

coiled- coil

A

a-helices when they wrap around each other (triple helix)

25
Q

how do colied-coils form?

A

two or three a-helices have their nonpolar side chains on one side -> wraps around each other with side chains facing inward

25
Q

what proteins contain a-helices?

A

cell membrane proteins (transport proteins and receptor)

-nonpolar side chains
-rich in areas that cross lipid bilayer

26
Q

what factors destabilize a-helices?

A
  • electrostatic repulsion between similarly charged R groups
  • steric hinderance due to bulky substitutions on the B- carbons of R group
26
Q

what amino acid is incompatible with the a-helix?

A

proline

26
Q

what protein was b-pleated sheets first identified in?

A

fibroin (silk)

26
Q

why is a amino acid incompatible with the a-helix?

A

proline b/c it causes bends in the polypeptide backbone
- proline amino group cannot participate in H bonding
- rotation around the bond between nitrogen of proline is restricted

27
Q

similarities of B-sheet and a-helix

A

both involve H bonding between carbonyl and amino groups of peptide bonds

28
Q

differences of B-sheet and a-helix

A
  • H bonds form between different parts of single chain (intrachain vs interchain)
  • bonds are perpendicular on b-sheet vs parallel in a-helix
29
Q

parallel pleated sheet

A

h bonded peptide chains run in same direction

30
Q

antiparallel pleated sheet

A

H bonded peptide chain run in opposite directions

31
Q

reverse turns

A

regions of secondary structure where the chains change direction or fold back

32
Q

supersecondary structure

A

secondary structures that combine (BaB, aa, B-meander unit, greek key)

33
Q

motifs

A

repeated combinations of supersecondary structure within a protein (usually short repetitive units)

34
Q

domain (module)

A
  • specific region of protein that can fold independently of the rest of the protein into a discrete stable structure that has its own function
  • modular units that construct larger proteins
  • smaller proteins = single domain
  • larger proteins = several dozen domains connected by unstructured polypeptide chains
35
Q

domain shuffling (multidomain proteins)

A

DNA sequences encoding each domain accidentally joined, creating new gene

36
Q

how many domains does fibronectin have?

A

four of fibronectin type 3 domains

Biochem 2 (5 decks)

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