Chapter 15 Quiz

Question 1

JAK-STAT pathway

Answer 1

cytosines and growth factors bind to JAKs/Janus Kinases (transmembrane receptors)

When cytosine binds to its receptor, JAKs transfer a phosphate group to other proteins. The phosphate group causes a conformational change in STATs. When STAT proteins bind to a receptor, JAKs add another phosphate group to the STAT proteins, causing them to dissociate from the receptor and bind to each other. STAT dimers translocate to the nucleus and activate target genes.

Question 2

Antigens

Answer 2

Antigens: foreign proteins

Question 3

Antibodies

Answer 3

proteins used to detect antigens in immune system

recognizes certain region of antigen known as “epitope”

Monoclonal or Polyclonal

• monoclonal: identical, recognizes same epitope
• polyclonal: mixture of several antibodies, recognizes different epitopes of the same antigen

Question 4

Aptamers

Answer 4

alternative to antibodies

They are nucleic acid or peptide-based molecules that bind to a specific target molecule

Question 5

Purifying proteins and two common methods?

Answer 5

Purifying proteins: allows generating antibodies, determining protein’s sequence and determine a protein’s binding partners

Two common methods:

• Chromatography
• Immunoprecipitation (IP)

Question 6

Chromatography

Answer 6

Allows mixture of proteins in a solution to be separated on a column

Question 7

Gel-filtration Chromatography

Answer 7

proteins are separated based on their size

Question 8

Ion-exchange Chromatography

Answer 8

proteins are separated based on their charge

Question 9

Affinity Chromatography

Answer 9

uses small molecules, fixed to the matrix, to bind to proteins that may have high affinity

Question 10

Immunopreceipitation (IP)

Answer 10

uses antibodies to purify protein of interest out of solution

Question 11

Western Blot (WB/Immunoblot)

Answer 11

Most common used method to measure expression of a protein in a tissue of cell sample

Question 12

SDS-PAGE

Answer 12

Sodium dodecylsulfate - polyacylamide gel electrophoresis

It’s a negatively charged detergent that binds to hydrophobic regions of the protein, allowing it to become soluble

Question 13

How do smaller and larger proteins travel?

Answer 13

Larger proteins travel slowly

Smaller proteins travel quickly

Question 14

Cell fractionation

Answer 14

Used to see where in cells the protein is localized

Question 15

Enzyme-linked immunoabsorbent assay (ELISA)

Answer 15

used to measure expression of a protein

Alternative to a WB

Question 16

Radioimmunoassay (RIA)

Answer 16

measures very low concentrations of proteins

Question 17

Immunohistochemistry (IHC)

Answer 17

used to determine the spatial expression pattern of a protein

Question 18

Immunoelectron microscopy (IEM)

Answer 18

Used to visualize protein expression within subcellular structures
- can show protein is localized in a particular subcellular compartment

Question 19

Reporter Protein

Answer 19

attached to proteins of interest and allows determining expression/location of a protein in living cells

Question 20

Co-immunoprecipitation

Answer 20

determines if a protein physically interacts with another protein

Question 21

Protein Affinity Chromatography

Answer 21

used to isolate and identify proteins that physically interact with each other

Question 22

Mass Spectrometry

Answer 22

determines the identities of potential binding partners

• identify and sequence proteins by breaking them apart and determining the mass to charge ratio of their fragment

Question 23

Mass spectrometry

Answer 23

determines identity of binding partners

Question 24

Yeast two-hybrid assay

Answer 24

investigates protein-protein interactions

In normal cell: GAL4 binds to UAS

Gal4: transcription factor
UAS: promoter region (upstream activating sequence)

Question 25

Posttranslational modification (PTM)

Answer 25

modification that happens to one or more aminoacids on a protein after it’s translated by a ribosome

Question 26

Kinase Assay

Answer 26

determine whether one protein is capable of phosphorylating another protein

Question 27

Methyltransferase or Acetyltransferase Assays

Answer 27

determines if protein is capable of adding a methyl or cetyl group to a target protein

Question 28

Electrophoretic Mobility Shift Assay

Answer 28

used to determine if a protein is directly able to interact with a short specific sequence of DNA

Question 29

Chromatin Immunoprecipitation (chIP)

Answer 29

shows if protein interacts with specific region of DNA

Question 30

chIP on chip assay

Answer 30

Determines if all DNA sequences are bound to protein

DNA sequences from chIP expt are run on a DNA microarray

Question 31

Luciferase Assay

Answer 31

determines if protein can activate or repress expression of target gene

establishes functional connection between protein and amount of gene product made

Question 32

Luciferase

Answer 32

enzyme used for bioluminase

If protein upregulates transcription of target gene: cells express luciferase
If protein downregulates transcription: expresses less luciferase than normal

Question 33

Next generation sequencing (NGS)

Answer 33

makes sequencing large stretches of DNA cheaper and faster

Question 34

Hybridization

Answer 34

phenomenon whereby two complementary nucleic acid strands bind to each other

Question 35

Southern Blot

Answer 35

identifies if known DNA sequence is present in a sample by using a specific prob to identify the sequence

Question 36

Northern Blot

Answer 36

identifies presence of RNA