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Advanced Cell Biology > Exam 2 Ch.4: Protein Structure and Function > Flashcards

Exam 2 Ch.4: Protein Structure and Function Flashcards

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1
Q

Enzymes

A

catalyze covalent bond breakage or formation

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2
Q

Structural Proteins

A

provide mechanical support to cells and tissues

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3
Q

Transport Proteins

A

carry small molecules or ions and transport them throughout the body

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4
Q

Motor Proteins

A

generate movement in cells and tissues

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5
Q

Storage Proteins

A

store amino acids or ions

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6
Q

Signal Proteins

A

carry extracellular signals from cell to cell

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7
Q

Receptor Proteins

A

detect signals and transmit them to the cells response machinery

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8
Q

Transcription Regulators

A

bind to DNA to switch genes on or off

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9
Q

Special-Purpose Proteins

A

highly variable

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10
Q

Disulfide bond

A

can form between two cysteine side chains

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11
Q

Primary Level of Protein Structure

A

Chain of amino acids

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12
Q

What dictates the overall 3D shape of a protein?

A

side chains

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13
Q

What stabilizes protein conformation?

A
  • the sum of weak forces
    -van der Waals, electrostatic attractions, hydrogen bonds,
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14
Q

Backbone to backbone bond

A

hydrogen bond

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15
Q

What governs specific folding of proteins?

A
  • making the most energetically favorable bonds
  • meaning proteins folds into the lowest free energy conformation
  • folding is a spontaneous process and will release heat
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16
Q

Example of Spontaneous Protein Folding and Refolding

A
  1. Protein is exposed to high concentration of urea
  2. causes denatured protein
  3. remove urea
  4. protein refolds
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17
Q

Chaperone Proteins

A
  • assist with protein folding
  • spontaneous folding can be time-consuming so chaperones speed up protein folding rates
  • come bind to partly fold chains
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18
Q

Benefit and Drawback of Isolation Chambers

A
  • can help prevent aggregation of multiple proteins
  • can isolate a single protein
  • takes more energy
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19
Q

How do isolation chambers work?

A
  1. one polypeptide chain is sequestered by the chaperone
  2. chamber cap closes chaperone
  3. isolated polypeptide chain folds correctly
  4. correctly folded protein is released when cap dissociates
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20
Q

What stage is a protein done in the chaperone protein?

A

depends because proteins show incredible structural diversity

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21
Q

What are some basic functions of proteins?

A

transport, structure, signaling, catalyzing reactions

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22
Q

For a polypeptide chain:
What is the structure of its backbone?
Which end is the 1st amino acid? The last?

A
  • they have an N-C-C backbone
  • 1st amino acid is the N-terminus
  • last amino acid is the C-terminus
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23
Q

What are the forces that govern a strict and specific folding pattern of a single protein?

A
  • proteins folding into the lowest free energy conformation to make the most energetically favorable bonds
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24
Q

What bonds are responsible for protein folding? Where can these bonds occur?

A
  • weak forces such as electrostatic attractions, hydrogen bonds, and van der Waals are responsible for protein folding
  • they can occur backbone to backbone, backbone to side chain, side chain to side chain
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25
Q

Secondary Protein Structure

A

Alpha helix and beta sheet

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26
Q

What stabilizes alpha helices?

A
  • stabilized by hydrogen bonding along the backbone
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27
Q

Structure of Alpha helices?

A
  • amino and carboxyl groups of every 4th amino acid engage in hydrogen bonding
  • r groups pointed outwards
  • can be right or left handed
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28
Q

bonds from backbone to backbone

A

hydrogen bond between atoms of two peptide bonds

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29
Q

backbone to side chain

A

hydrogen bond between atoms of a peptide bond and an amino acid side chain

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30
Q

side chain to side chain

A

hydrogen bond between atoms of two amino acid side chains

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31
Q

Tertiary Protein Structure

A
  • 3D arrangement of secondary structures
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32
Q

Why is it good that the R groups in alpha helices point outward?

A
  • Because alpha helices are commonly found in membranes
  • Hydrophobic R-groups point outward away from the core of the helix and towards hydrophobic membrane
  • backbone is typically hydrophilic
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33
Q

What forms coiled- coils and why are they beneficial?

A

-2-7 alpha helices can form coiled- coils
- helices wrap around each other to minimizes exposure of hydrophobic amino acids side chains to aqueous environment

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34
Q

What holds together beta sheets?

A
  • held together by hydrogen bonds between the strands (backbone of strand)
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35
Q

Direction of beta sheets and r groups?

A

R-groups poke out on alternating sides (pleated) (top-bottom-top-bottom…)
-can be parallel or antiparallel

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36
Q

Consequence of misfolding proteins?

A
  • can lead to aberrant protein structures which build up and lead to cell death
  • causes diseases like Alzheimers, Parkinson’s, Huntingtons
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37
Q

Example of misfolding causing disease?

A

In Alzheimers and Parkinsons disease, insoluble amyloid fibers are made from misfiled alpha-synuclein, which builds up to a toxic concentration and kills neurons

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38
Q

What are prions?

A

an infectious form of misfodled proteins
- Ex: mad-cow disease, chronic wasting disease, Creutzfeldt-Jakob disease

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39
Q

How do prions work?

A

can induce normal proteins of the same type to misfiled in to the same misfolded form

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40
Q

What would the differences in R-groups be between an alpha-helix in a cytoplasmic protein versus an alpha-helix in a transmembrane protein?

A

cytoplasmic protein: alpha helices in a coiled coil to minimize exposure of hydrophobic amino acid side chains to aqueous environment
transmembrane protein: hydrophobic r-groups point outward away from the core of the helix, backbone is usually hydrophilic

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41
Q

What forces form a coiled-coil?

A

2-7 Alpha helices that wrap around each other to minimize exposure of hydrophobic amino acids side chains to aqueous environment

42
Q

What makes a Beta-sheet pleated? Parallel or anti-parallel?

A

pleated - r-groups poke out of alternating sides
Parallel vs antiparallel: n-terminus/ c-terminus going the same way vs not

43
Q

Tertiary Structure

A

3D arrangement of secondary structure
Main types: fibrous and globular
- Globular: enzymes, etc
- Fibrous: structural/ strength

44
Q

What is a protein domain?

A

any segment of a polypeptide chain that can fold independently into a compact stable structure
- associated with specific functions (DNA binding domain, catalytic activity, etc.

45
Q

Effect of mutation in a domain?

A

mutation in a specific domain can affect the function of that domain

46
Q

Protein Families

A

Families have proteins with similar structures, but over time have gained slight differences that give them slightly different functions

47
Q

Quaternary Structure

A
  • multiple subunits (optional)
48
Q

Subunit

A

individual folded polypeptide chain
- dimer/trimer/tetratrimer
- Heterodimer vx homodimer

49
Q

Homodimer

A

two proteins with the same amino acid sequence that bind together to form a function

50
Q

Heterotetramer

A
  • four individual subunit with differing amino acid sequences that work together to perform a function
51
Q

What are the types of structures that subunits form?

A
  • helices, rings
52
Q

Actin fibers

A

helical structures made up of many individual actin proteins

53
Q

Microtubules

A

long hollow tubes of the protein tubulin

54
Q

Protein Cross-Linking
- what it does
- where it’s common
- example

A
  • proteins can be stabilized by covalent cross linking
  • very common in extracellular matrix proteins
  • a type of cross linking is the formation of disulfide bond between cysteine amino acids
55
Q

Elastin

A

an ECM protein that’s stabilized by covalent cross links

56
Q

How do proteins work?

A

their properties/functions depend on physical interactions with other molecules

57
Q

Ligands

A

a substance that forms a complex with (binds to) a specific protein

58
Q

How do ligands form a complex?

A

-forms a complex thanks to the sum of its non-covalent interactions
- these interactions define is specificity, “Hand in glove” or “Lock in Key”

59
Q

Structure of IgG antibodies?

A

are made up of 2 heavy chains, and 2 light chains

60
Q

Antigen

A
  • something that causes an immune response
    (each antibody can recognize one specific antigen)
61
Q

Antigen binding sites

A

-where antigens bind to an antibody
- antigens are bound at the antigen-binding sites at two ends of an IgG antibody

62
Q

Antibody specificity

A

each antibody binds with a distinct antigen

63
Q

Structure of an antibody?

A
  • 2 heavy chain, 2 light chain
  • constant domains: sequences constant from antibody to antibody
  • variable domains: vary between antibodies; antigen binding domains vary between antibodies
  • structure determines function
64
Q

How do antibodies defend us against infection?

A
  • antibodies cross-link antigens into aggregates (clump together)
  • antibody-antigen aggregates are ingested by phagocytic cells
65
Q

Uses of Antibodies in research?

A

1) molecule purification
2) protein visualization

66
Q

Molecule Purification

A
  • using antibodies to purify molecules
  • immunoprecipitation
  • immunoaffinity column chromatography
67
Q

Protein visualization

A

once antibodies are bound to protein of interest with fluorescent tag, we can shine specific light and see the protein

68
Q

Steps of molecule purification? Know both types

A
69
Q

What are 3 ways that enzymes can catalyze a reactions?

A

(a) enzyme binds to two substrate molecules and orients them precisely to encourage a reaction to occur between them
(b) binding of substrate to enzyme rearranges electrons in the substrate, creating partial negative and positive charges that favor a reaction
(c) enzyme strains the bound substrate molecule, forcing it towards a transition state that favors a reaction

70
Q

Vmax

A

maximum rate of a reaction

71
Q

KM

A

the concentration of a substrate where an enzyme works at half its maximum speed
- small KM: strong binding (strong affinity)
- large KM: weak binding

72
Q

Enzyme reaction rate

A

determined by substrate concentration and affinity
- measured by Vmax and KM

73
Q

Therapeutics

A
  • drugs mostly target enzymes
    ex: Rifampin and Gleevac (Imatinib)
74
Q

Coenzymes

A

small molecules that aid the function of enzymes
- ex: heme groups bound to hemoglobin (heme groups reversibly bind to oxygen gas through its iron atom) (without heme, hemoglobin can bind oxygen)

75
Q

Why is it important to regulate protein activity?

A
  • prevents waste
  • some reactions are only beneficial at certain times and in certain cellular locations
76
Q

Proteasome Parts

A
  • regulatory cap (blocks core to stop proteasome from destroying stuff)
  • catalytic core
  • regulatory cap
77
Q

1st Strategy to regulate protein activity

A
  • balance proteins production (transcription/translation) and degradation
78
Q

2nd Strategy to regulate protein activity

A

Control the location of the protein

79
Q

3rd Strategy to regulate protein activity

A

Feedback inhibition

80
Q

4th Strategy to regulate protein activity

A

Phosphorylation of the protein

81
Q

Process of Feedback Inhibition

A
  • the end product of a downstream reaction binds and inhibits an enzyme earlier in the pathway of the downstream reaction
  • binds to a regulatory site on the enzyme
  • this is a form of negative regulation (positive regulation also exist)
82
Q

How does Feedback Inhibition work?

A
  • works through an allosteric site
  • enzymes have at least 2 sites: active site, allosteric site
  • binding of inhibitor to allosteric site induces conformational change
    • lowers affinity of active site for substrate
83
Q

What are the advantages of feedback inhibition?

A
  • Ex. synthesis of amino acids form aspartate
  • very specific
  • nearly instantaneous
  • can be reversed as soon as concentrations of product decrease
84
Q

Phosphorylation

A
  • serine, threonine, and tyrosine amino acids side chains can become phosphorylated
  • Phosphorylation can activate or inactivate a protein
  • causes conformational change
85
Q

Kinases vs Phosphatases

A
  • phosphorylation is reversible
  • Kinsases: phosphorylation
  • Phosphatases: removes phosphate
  • phosphate is usually transferred from ATP
86
Q

How do protein modifications impact protein function?

A

Things impacted: activity, stability, binding partners and cellular location
- many proteins have multiple/many sites of covalent modification

87
Q

Phosphorylation

A

on/off switch; also creates docking site for binding partners

88
Q

homogenization

A

gently mechanical procedures where the plasma membrane of cells can be ruptured so that the cell contents are released
Types:
- break apart cells with high-frequency sound
- use a mild detergent to make holes in plasma membrane
- force cells through small hole using pressure
- shear cells between a close-fitting rotating plunger and the thick walls of a glass vessel

89
Q

homogenate or extract

A

thick soup, contains large and small molecules form the cysts, such as enzymes, ribosomes, and metabolites, as well as all of the membrane-enclosed organelle

90
Q

Differential Centrifugation

A
  • repeated centrifugation at progressively higher speeds with fractionate cell homogenates into their components
  • centrifugation separates cell competes on the basis of size and density. the larger and denser components experience the greatest centrifugal forces and move most rapidly. they sediment to form a pellet at the bottom of the tube, while smaller, less dense components remaining suspension above, a portion called the supernatant
91
Q

Gel electrophoresis

A

when an electric field is applied to a solution containing protein molecules, the proteins will migrate in a direction and at a speed that reflects their size and net charge.

92
Q

SDS polyacrylamide-gel electrophoresis (SDS-PAGE)

A

individual polypeptide chains forma complex with negatively charged molecules of sodium dodecyl sulfate (SDS) and therefore migrate as

93
Q

Gel Electrophoresis - Western Blotting

A
  • proteins from gel electrophoresis are transferred onto a membrane
  • Antibodies are used to detect a specific protein of interest
94
Q

Immunoprecipitation

A
  • mixture of antibodies
  • add specific anti-A antibodies
  • collect aggregate of A molecules and anti-A antibodies by centrifugation
95
Q

Immunoaffinity Column Chromatography

A
  • bead coated with anti-A antibodies
  • column packed with these beads
  • mixture of molecules flows through column
  • flow through is discarded
  • elute antigen A from beads
  • collect pure antigen a
96
Q

Acetylation

A

on lysine amino acid
- impacts protein: DNA interaction of histones

97
Q

Ubiquitination

A

targets proteins for degradation

98
Q

How can antibodies be used in research?

A
  • Molecule Purification
    ->Immunoprecipitation
    ->Immunoaffinity column chromatography
  • Protein Visualization
99
Q

What is Molecule Purification and what types are there?

A
  • uses antibodies to purify molecules
    - Immunoprecipitation
    - Protein Visualization
100
Q

What is Immunoprecipitation

A

1) mixture of molecules,
2) add specific anti-A antibodies
3) collect aggregate of A molecules
and anti-A molecules by centrifugation

101
Q

What is immunoaffinity column chromatography?

A

1) mixture of molecule
2) goes into column packed with beads coated with anti-A antibodies
3) discard flow through
4) elute antigen A from beads
5) collect pure antigen A

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