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BioChem > Lecture 2 > Flashcards

Lecture 2 Flashcards

1
Q

Dimer

A

Made of two polypeptides

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2
Q

How many beta strands to make a beta sheet?

A

2

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3
Q

Primary structure of a protein

A

The primary sequence of amino acids

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4
Q

Homodimer

A

two dimers that are the same polypeptide (quaternary protein structure)

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5
Q

4 main agents of protein function

A

Catalysis, Transport, Structure, and Motion

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6
Q

4 properties of Amino acids that make them a good building block

A

Capacity to polymerize, useful acid-base properties, varied physical properties, and varied chemical functionality

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7
Q

Chiral carbon

A

carbon with 4 different constituents

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8
Q

Naming of amino acids starts and ends where

A

starts the N terminus (amino) and ends at the C terminus (carboxyl)

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9
Q

Nonpolar, aliphatic amino acids

A

Gly, Ala, Pro, Val, Leu, Ile, Met

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10
Q

Aromatic amino acids

A

Phe, Tyr, Trp

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11
Q

Polar, uncharged amino acids

A

Ser, Thr, Asn, Gln, Cys

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12
Q

Positively charged amino acids

A

His, Lys, Arg

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13
Q

Negatively charged amino acids

A

Asp, Glu

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14
Q

Zwitterions

A

when the net charge of an amino acid is zero. When the carboxyl group is deprotonated and the amino group is protonated.

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15
Q

Isoelectric point

A

when it is net neutral

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16
Q

Peptide formation of amino acids is through

A

condensation. Forming an amide.

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17
Q

Cofactor

A

functional non-amino acid component.

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18
Q

Coenzyme

A

organic cofactors.

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19
Q

Prosthetic groups

A

covalently attached cofactors.

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20
Q

Lipoproteins

A

Lipids as the prosthetic group. Likely will go to the membrane

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21
Q

Glycoproteins

A

Carbohydrates as the prosthetic group. Provide protection and important for cell to cell signaling

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22
Q

Phosphoproteins

A

phosphate group as the prosthetic group

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23
Q

Hemoproteins

A

Heme (iron porphyrin) as the prosthetic group.

24
Q

4 favorable interactions in protein folding

A

Hydrophobic effect, hydrogen bonding (dipole dipole interactions), Van der Waals interactions, electrostatic interactions

25
Q

Hydrophobic effect

A

release of water molecules from the structured salvation layer around the molecule as protein folds (increases the entropy)

26
Q

Hydrogen bonding

A

Interaction of N-H and C=O of the peptide bonds leads to local regular structures such as alpha helices and beta strands

27
Q

Van der Waals

A

London dispersion and steric repulsion. Medium-range weak attraction between all atoms contributes significantly to the stability in the interior of the protein

28
Q

Electrostatic interactions

A

Long-range strong interactions between permanently charged groups. Salt-bridge stabilize the protein

29
Q

Phi angle

A

angle around the alpha carbon and amide nitrogen bond

30
Q

psi angle

A

around the alpha carbon and the carbonyl carbon bond

31
Q

Alpha helix

A

stabilized by hydrogen bonds between nearby residues. Side chains point out perpendicular to the helical axis. Peptide 1 is directly above peptide 8.

32
Q

Beta sheet

A

stabilized by hydrogen bonds between adjacent segments that may not be nearby in the primary sequence. Side chain protrude from the sheet in an alternating up/down direction. Thus can be amphipathic.

33
Q

How many residues in a turn for an alpha helix

A

3.6 residues

34
Q

Good alpha helix residue makers

A

alanine and leucine

35
Q

Helix breakers

A

Proline and glycine

36
Q

Parallel and antiparallel orientation

A

Parallel - strands run in same direction.

Antiparallel - strands run in opposite directions.

37
Q

How many residues does it take to complete a beta turn?

A

4

38
Q

Proline position for a beta turn

A

2 (I have 2 pee)

39
Q

Glycine position for a beta turn

A

3

40
Q

Common secondary motifs

A

B-A-B loop, Beta barrel

41
Q

Fibrous proteins

A

typically insoluble, made from a single secondary structure

42
Q

Globular protein

A

water-soluble and lipid-soluble proteins

43
Q

Tough fibrous protein structure

A

cross-linked alpha helixes. Rigid linker (S-S). Such as keratin

44
Q

Non-stretching fibrous protein structure

A

cross-linked triple-helixes. flexible linker (Lys-HyLys). Such as collagen

45
Q

Soft, flexible fibrous protein structure

A

Non-covalently held B sheets and Van der Waals interactions. Such as silk fibroin

46
Q

Collagen structure and 3 important residues

A

left-handed helix. Gly, Pro, and hydroxyPro. Then 3 chains form a right-handed superhelical triple helix

47
Q

Ways proteins can be denatured

A

heat or cold, pH extremes, organic solvents (extract hydrophobic parts), and chaotropic agents such as urea and guanidine hydrochloride (bind up water)

48
Q

Chaperones

A

help to prevent misfolding. Can refold a partly denatured protein

49
Q

The monomers of proteins…

A

Amino Acids

50
Q

Amino Acid Nomenclature (Biochemist method)

A

Start from alpha-carbon and go down the R group

–N-terminus to C-terminus

51
Q

Which is the only amino acid without an amino group attached to the alpha carbon?

A

Proline

52
Q

Cofactor (protein)

A

Functional non-amino acid component (ex. metal ions or organic molecules)

53
Q

Coenzyme

A

Organic cofactors (ex. NAD+)

54
Q

Prosthetic Group

A

Covalently attached cofactors (ex. heme in myoglobin)

55
Q

What are the jobs of DnaJ and DnaK?

A

To help fold other proteins

56
Q

GroEL and Gro ES

A

Garbage can looking structure

  • -Denatured Proteins go inside –> come out correctly folded
  • -Has polar and nonpolar side chains

BioChem (14 decks)

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