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Biochemistry > Exam 3 Biochem > Flashcards

Exam 3 Biochem Flashcards

1
Q

Main Agents of Protein Biological Function

A

Catalysis
Transport
Structure
Motion

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2
Q

Amino acids have properties that are well suited to carry out a variety of biological functions:

A

capacity to polymerize
useful acid-base properties
varied physical properties
varied chemical functionality

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3
Q

Amino Acids: Classification

A

nonpolar, aliphatic (7)
aromatic (3)
polar, uncharged (5)
positively charged (3)
negatively charged (2)

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4
Q

nonpolar, aliphatic (7)

A

glycine
alanine
proline
valine
leucine
isoleucine
methionine

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5
Q

aromatic (3)

A

phenylalanine
tyrosine
tryptophan

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6
Q

polar, uncharged (5)

A

serine
threonine
cysteine
asparagine
glutamine

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7
Q

positively charged (3)

A

lysine
arginine
histidine

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8
Q

negatively charged (2)

A

aspartate
glutamate

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9
Q

Ionization of Amino Acids

A

contain at least two ionizable protons, each with its own pKa.

The carboxylic acid has an acidic pKa and will be protonated at an acidic (low) pH:

amino group has a basic pKa and will be protonated until basic pH (high) is achieved

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10
Q

carboxylic acid has an acidic pKa

A

COOH = COO− + H+

slightly more acidic than an carboxylic acids

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11
Q

The amino group has a basic pKa

A

NH4+ = NH3 + H+

Slightly less basic than in amines

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12
Q

Ionization of Amino Acids

low pH

A

the amino acid exists in a positively charged form (cation).

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13
Q

Ionization of Amino Acids

high pH

A

the amino acid exists in a negatively charged form (anion).

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14
Q

zwitterion

A

Between the pKa for each group, the amino acid exists in a zwitterion form, in which a single molecule has both a positive and negative charge.

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15
Q

Isoelectric Point (equivalence point, pI)

A

PI = (pK1 + pK2) / 2

In Zwitterions
the net charge is zero.
AA is least soluble in water.
AA does not migrate in electric field.

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16
Q

Amino Acids Can Act as Buffers

A

Amino acids with uncharged side chains, such as glycine, have two pKa values

As buffers prevent change in pH close to the pKa, glycine can act as a buffer in two pH ranges.

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17
Q

Ionizable Side Chains Also Have pKa and Act as Buffers

A

Ionizable side chains influence the pI of the amino acid.
Ionizable side chains can be also titrated.
Titration curves are now more complex, as each pKa has a buffering zone of 2 pH units.

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18
Q

How to Calculate the pI When the Side Chain Is Ionizable

A

Identify species that carries a net zero charge.

Identify the pKa value that defines the acid strength of this zwitterion: (pKR).

Identify the pKa value that defines the base strength of this zwitterion: (pK2).

Take the average of these two pKa values.

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19
Q

Amino Acids Polymerize to Form Peptides

A

Peptides are small condensation products of amino acids.
They are “small” compared with proteins (Mw < 10 kDa).

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20
Q

Naming Peptides: Start at the N-terminal

A

Numbering (and naming) starts from the amino terminus (N-terminal).

Using full amino acid names

Using the three-letter code abbreviation

For longer peptides (like proteins) the one- letter code

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21
Q

Peptides: A Variety of Functions

A

Hormones and pheromones

Neuropeptides

Antibiotics

Protection, e.g., toxins

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22
Q

Proteins are comprised of:

A

Polypeptides (covalently linked a-amino acids) + possibly:

  1. cofactors
  2. coenzymes
  3. prosthetic groups
  4. other posttranslational mods
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23
Q

cofactors

A

functional non-amino acid component
metal ions or organic molecules

24
Q

coenzymes

A

organic cofactors

25
Q

prosthetic groups

A

covalently attached cofactors

26
Q

A Mixture of Proteins Can Be Separated

A

charge
size
affinity for a ligand
solubility
hydrophobicity
thermal stability

Chromatography is commonly used for preparative separation in which the protein is often able to remain fully folded.

27
Q

Column Chromatography

A

allows separation of a mixture of proteins over a solid phase (porous matrix) using a liquid phase to mobilize the proteins.

Proteins with a lower affinity for the solid phase will wash off first; proteins with higher affinity will retain on the column longer and wash off later.

28
Q

Separation by Charge: Ion Exchange

A

proteins move through columns at rates determined by their net charge at the pH being used.

With cation exchangers, proteins with more negative net charge move faster

29
Q

Separation by Size: Size Exclusion

A

Larger molecules pass more freely and appearing in the earlier fractions first using crosslinked polymer

30
Q

Separation by Binding: Affinity

A

Protein mixture added to column contained polymer bound ligand for specific protein of interest.

Unwanted proteins are washed through the column and then protein of interested eluted by ligand solution

31
Q

Electrophoresis for Protein Analysis

A

The electric field pulls proteins according to their charge.
The gel matrix hinders mobility of proteins according to their size and shape.

The gel is commonly polyacrylamide, so separation of proteins via electrophoresis is often called polyacrylamide gel electrophoresis, or PAGE

32
Q

SDS PAGE Separates Proteins by Molecular Weight

A

SDS – sodium dodecyl sulfate – a detergent

SDS micelles bind to proteins and facilitate unfolding.

SDS gives all proteins a uniformly negative charge.

The native shape of proteins does not matter.

The rate of movement will only depend on size: small proteins will move faster.

33
Q

Isoelectric Focusing Can Be Used to Determine the pI of a Protein

A

Protein sample may be applied to one end of a gel strip with an immobilized pH gradient.

After staining, proteins are shown to be distributed along pH gradient according to their PI values

34
Q

Aromatic Amino Acids Absorb Light in a Concentration-Dependent Manner

A

Proteins typically have UV absorbance maxima around 275–280 nm.

Tryptophan and tyrosine are the strongest chromophores.

For proteins and peptides with known extinction coefficients (or sequences), concentration can be determined by UV-visible spectrophotometry using the Lambert-Beer law: A = ECL

35
Q

Protein Sequencing

A

Edman degradation (classical method):
–successive rounds of N-terminal modification, cleavage, and identification
–can be used to identify protein with known sequence

Mass spectrometry (modern method):
–MALDI MS and ESI MS can precisely identify the mass of a peptide, and thus the amino acid sequence
–can be used to determine posttranslational modifications

36
Q

Protein Sequences as Clues to Evolutionary Relationships

A

Differences indicate evolutionary divergences.

Analysis of multiple protein families can indicate evolutionary relationships between organisms, ultimately the history of life on Earth.

37
Q

native fold

A

a large number of favorable interactions within the protein

adopt a specific three-dimensional conformation with biological function

38
Q

Hydrophobic effect

A

The release of water molecules from the structured solvation layer around the molecule as protein folds increases the net entropy

39
Q

Hydrogen bonds

A

Interaction of N−H and C=O of the peptide bond leads to local regular structures such as a-helices and b-sheets

40
Q

London dispersion

A

Medium-range weak attraction between all atoms contributes significantly to the stability in the interior of the protein

41
Q

Electrostatic interactions

A

long-range strong interactions between permanently charged groups

Salt bridges, especially those buried in the hydrophobic environment, strongly stabilize the protein.

42
Q

Primary Structure

A

Peptide bond is a resonance hybrid of two canonical structures:

to be less reactive compared with esters, for example
to be quite rigid and nearly planar
to exhibit a large dipole moment in the favored trans configuration

43
Q

Secondary Structures

A

local spatial arrangement of the polypeptide backbone

44
Q

a-helix

A

stabilized by hydrogen bonds between nearby residues of an n and n + 4 amino acids

45
Q

B-sheet

A

stabilized by hydrogen bonds between adjacent segments that may not be nearby

46
Q

random coil

A

Irregular arrangement of the polypeptide chain

47
Q

Small hydrophobic residues such as Ala and Leu

A

strong helix formers

48
Q

Pro

A

a helix breaker because the rotation around the N-Ca (φ-angle) bond is impossible

49
Q

Gly

A

a helix breaker because the tiny R group supports other conformations

50
Q

Helix Dipole in Peptide Bond

A

C−O (carbonyl) negative
N−H (amide) positive

helix has a large macroscopic dipole moment

51
Q

B-sheets

A

planarity of the peptide bond and tetrahedral geometry of the a-carbon create a pleated sheet-like structure.

Sheet-like arrangement of the backbone is held together by hydrogen bonds between the backbone amides in different strands.

52
Q

B-strands

A

Multiple B-sheets

Sheets are held together by the hydrogen bonding of amide and carbonyl groups of the peptide bond from opposite strands

Parallel and anti-parallel

53
Q

B-turns

A

occur frequently whenever strands in B-sheets change the direction

180 degree turn is accomplished over four AA

stabilized by a hydrogen bond from a carbonyl oxygen to amide proton three residues down the sequence.

Proline in position 2 or glycine in position 3 are common in B-turns.

54
Q

Proline Isomers

A

Most peptide bonds not involving proline are in the trans configuration (>99.95%).

For peptide bonds involving proline, about 6% are in the cis configuration. Most of this 6% involve B-turns.

Catalyzed by proline isomerases

55
Q

Circular Dichroism (CD) Analysis

A

signals from peptide bonds depend on the chain conformation and light or right light

Biochemistry (9 decks)

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