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BioChem > Ch. 5 > Flashcards

Ch. 5 Flashcards

1
Q

Fibrous Protein

A

Simple, linear structure
Insoluble in water

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2
Q

Ex. of Fibrous Protein

A

Collagen, Keratin

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3
Q

Globular Protein

A

Spherical structure
nonpolar inside and polar outside
soluble in water

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4
Q

Ex. of Globular Protein

A

Enzymes

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5
Q

Membrane Protein

A

Embedded in cell membrane
polar inside and nonpolar outside
not soluble in water

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6
Q

Crude Isolation/Purification Techniques

A

Centrifugation, Salting out, and Dialysis

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7
Q

Centrifugation

A

Separates based on density

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8
Q

Salting out

A

Increase salt concentration until proteins precipitate out

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9
Q

Dialysis

A

Separate Proteins from small molecules/ions by diffusion across semipermeable membrane

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10
Q

Chromatography Techniques

A

Ion Exchange, Size Exclusion, Hydrophobic Interaction, Affinity Chrom., and HPLC

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11
Q

Ion Exchange

A

Separates based on charge
charged matrix
like charges move faster through matrix

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12
Q

Size Exclusion

A

Matrix made of porous beads
Larger proteins move faster bc small proteins get trapped in the beads

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13
Q

Hydrophobic Interaction

A

Matrix of covalently linked hydrophobic groups
Hydrophobic sticks, hydrophilic pass through quickly

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14
Q

Affinity Chromatography

A

Proteins bind certain functional groups or ligand
Matrix has ligand or functional group attached
Binding interaction traps proteins

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15
Q

HPLC (High-performance liquid chromatography)

A

Limited to small scale due to tightly packed matrix and high pressure
Works well with other techniques

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16
Q

Electrophoresis Techniques

A

SDS-PAGE, Isoelectric Focusing, and 2D Electrophoresis

17
Q

SDS-PAGE (Sodium dodecylsulfate)

A

Disrupts tertiary structure and gives everything a (-) charge
Proteins separated based on MW (Smaller=Faster)
Makes protein soluble

18
Q

Isoelectric Focusing

A

Based on relative amts. of acidic and basic AA
Matrix is a pH gradient from low to high, protein stops at pI

19
Q

Isoelectric Point

A

pH at which protein is neutral
Low pI = more acidic groups
High pI = more basic groups

20
Q

2D Electrophoresis

A

Mixture separated by pI then SDS-PAGE

21
Q

How to break a protein into individual AA’s

A

6M HCl and 110C

22
Q

Structure Determination Steps

A
  1. Separate and purify polypeptide chains
  2. Cleave S-S bonds
  3. Determine N-terminal and C-terminal AA
  4. Cleave polypeptide chain into shorter fragments
  5. Repeat step 4. with diff cleavage method
  6. Reconstruct AA sequence through overlaps
23
Q
  1. Separate and purify polypeptide chains
A

Disrupt noncovalent forces by
changing pH, high salt conc., treat with urea or guanidinium chloride (breaks up noncovalent interactions)

24
Q
  1. Cleave S-S bonds
A

Oxidation-performic acid
Reduction- 2-mercaptoethanol/dithiothreitol
Cap thiols to prevent disulfide bond from refroming

25
Q
  1. Determine N-terminal and C-termial
A

N-terminal - Edmans reagent
C-terminal - carboxypeptidase Y

26
Q
  1. Cleave Polypeptide Chain
A

Enzymatic and Chemical Cleavage

27
Q

Enzymatic Cleavage Methods

A

Trypsin, Chymotrypsin, Staphylcoccal

28
Q

Trypsin

A

Cuts peptide bond on C-terminal side of Lysine (Lys) and Arginine (Agn)

29
Q

Chymotrypsin

A

Cuts peptide bond on C-terminal side of Phenylalanine (Phe), Tyrosine (Tyr), and Tryptophan (Trp)

30
Q

Staphylcoccal

A

Cuts peptide bond on C-terminal side of Aspartic Acid (Asp) and Glutamic Acid (Glu)

31
Q

Chemical Cleavage Methods

A

Cyanagen bromide (CNBr)
Cuts peptide bond on C-terminal side of Methionine

32
Q

Hydrophobic Proteins are most commonly found where?

A

Globular Proteins

33
Q

Sequence Similarity implies evolutionary relatedness (Name?)

A

Homologous Proteins

34
Q

Conjugated Protein

A

Protein containing a non-protein part

35
Q

NH2 Protecting Groups

A

FMOC and BOC

36
Q

Reagent used to make OH a better leaving group in protein synthesis

A

DIPCDI

37
Q

Purification and Protection in protein synthesis

A

Attach C-terminal to insoluble resin
(Solid phase peptide synthesis)
Purification by filter

38
Q

Direction of synthesis in nature and chemically

A

Nature: Starts at N-Terminal
Chemically: Starts at C-Terminal

39
Q

Examples of Ligand Bound Proteins

A

Transport proteins, enzymes, regulatory proteins, and scaffold proteins

BioChem (5 decks)

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