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Cell Bio > L 7. Protein Structure & Function II > Flashcards

L 7. Protein Structure & Function II Flashcards

1
Q

explain protein families

A
  • within each family, amino acid sequences and the 3D shape closely resemble each other
  • proteins within families may have different roles bc they have different enzymatic activity
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2
Q

define ligand

A

any substance that is bound to a protein

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3
Q

how to enzymes regulate metabolic pathways

A

one enzyme can catalyze a molecule and another enzyme will catalyze the same molecule and so on

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4
Q

how do enzymes catalyze reactions

A
  • it lowers the activation energy
  • so it requires less energy for a reactant to turn into a product
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5
Q

how do ligands bond to proteins

A
  • they have to physically interact
  • the ligand binds through noncovalent bonds
  • the enzyme will fold and create a pocket for substrate to bind
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6
Q

ligand-protein binding - what happens at the pocket of the enzyme

A
  • amino acids within particular areas in the protein will cause noncovalent bonds to interact with the ligand
  • this will cause a conformational change in the protein resulting in the protein completing its task
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7
Q

structure of a protein - binding sites

A

bind and orient substrate/ligand

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8
Q

structure of a protein - catalytic site

A

reduces chemical activation energy

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9
Q

what are the ways a protein and ligand can bind

A
  • Orientation/proximity
  • Rearrangement of e-
  • Strain
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10
Q

protein-ligand binding - orientation/proximity

A
  • enzyme binds to two substrate molecules
  • orientates them precisely to encourage a reaction
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11
Q

protein-ligand binding - rearrangement of e-

A
  • binding of substrate to enzyme rearranges electrons in the substrate
  • creates partial negative charge and positive charges that favor a reaction
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12
Q

protein-ligand binding - strain

A
  • enzyme strains the bound substrate molecule
  • forcing it towards a transition state to favor a reaction
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13
Q

explain enzyme substrate interaction

A
  1. substrate + enzyme are separate
  2. enzyme-substrate binds
  3. enzyme-product (substrate becomes product)
  4. enzyme + product separate
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14
Q

explain feedback inhibition (negative regulation)

A
  • Prescence of end product stops the pathway
  • Prevents further reactions down that pathway
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15
Q

negative feedback - What would happen if there were no feedback regulation?

A

the cell would keep making enzymes it does not need and wastes energy

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16
Q

negative feedback - how exactly does the end product stop the pathway

A
  • End product binds on regulatory sites
  • enzyme undergoes conformational change to stop pathway
17
Q

how does protein phosphorylation change the function of the protein

A
  • phosphorylation causes a conformational change
  • turns it on/off depending on protein
18
Q

protein phosphorylation - explain how it works

A
  • Kinase – adds a phosphate
  • Phosphatase – removes a phosphate
19
Q

explain other types of covalent protein modifications

A

different post-translational modifications can alter proteins

20
Q

explain motor protein myosin

A
  • myosin is an ATPase
  • can walk along actin filaments during muscle contraction by hydrolyzing ATP
21
Q

explain protein complexes

A
  • they are made of individual proteins that collaborate to perform a specific task
  • the function is coordinated by the hydrolysis of ATP
22
Q

explain how you can gather proteins to study them

A
  1. Take out of source tissue, if it is abundant
  2. Producing them artificially, If not abundant but you know the gene that expresses the protein
23
Q

explain homogenization

A
  • breaking cells and tissues
  • can do it in 4 ways:
    1. break cells with high-frequency sound (ultrasound)
    2. use a mild detergent to make holes in the plasma membrane
    3. force cells through a small hole using high pressure
    4. sheer cells between a close-fitting rotating plunger and the thick walls of a glass vessel
24
Q

how do you isolate protein complexes

A
  • Immobilize protein and fish out proteins that you know interacts with it
  • Can then break the interaction on proteins and break off a singular specific protein
25
Q

what is column chromatography

A
  • Separate proteins based on a specific criteria
  • three kinds of criteria:
    1. ion exchange
    2. gel-filtration
    3. affinity
26
Q

column chromatography - ion exchange

A
  • Fish things out based on charge
  • Beads are a positive charge
  • negative charge molecules will bind to beads
  • the negative molecules will slowly change pH and collect fractions
  • the negative charge molecules takes longer to take out the column
  • positive molecules come out first
27
Q

column chromatography - gel filtration

A
  • a porous substrate takes in proteins
  • Smaller molecules get stuck in pores and come out after bigger molecules
  • Big molecules move around pores and comes out first
28
Q

column chromatography - affinity

A
  • Use a bead that has an affinity for a protein to capture the protein
  • needed protein binds and you wash off other proteins, allowing only that specific protein to come out
29
Q

what are antibodies

A
  • they are proteins that tightly bind to their targets (antigens)
  • they have specificity
  • they are used to separate and identify specific proteins
30
Q

explain B cell clonal expansion

A
  • a B cell makes an antibody and it stimulates the cell to divide
  • this results in a clone of cells
  • some then develop into plasma cells that secret the same antibody
  • other develop into memory cells that have the antibody but do not secrete it
31
Q

what are the two ways antibodies can be produced

A
  1. polyclonal
  2. monoclonal
32
Q

production of antibodies - polyclonal

A

Multiple cells are activated that recognizes different parts of a protein

33
Q

production of antibodies - monoclonal

A

One B cell and it only binds to one protein

34
Q

how can you use antibodies to purify molecules

A

Don’t have to activate protein, antigen can activate protein and you can study the protein

35
Q

Sodium-Dodecyl Sulphate Polyacrylamide gel electrophoresis (SDS-PAGE)

A
  • Denature protein and boil so they are mineralized
  • Coat them with something that gives it a negative charge
  • All proteins go towards positive side of the gel
  • Protein that are lower molecular weight go through faster than ones that are bigger
36
Q

Western blot

A
  • Add a membrane to a gel and apply current in different direction
  • the current pulls protein out of gel and onto membrane
  • proteins then come in contact with different antibodies and it amplifies the signal
  • the signal indicates how much protein is there and how long the protein sticks around

Cell Bio (21 decks)

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