Biochemistry Proteins and Analysis

Question 1

What is facilitated diffusion?

Answer 1

Facilitated diffusion is the passive transport of molecules down its concentration gradient. Facilitated diffusion is used to transport molecules that normally don’t easily pass through the membrane. Examples are large, polar molecules that don’t like the lipophilic environment of the membrane.

Question 2

What characterizes g protein coupled receptors?

Answer 2

All g protein coupled receptors have 7 alpha transmembrane helices.

Question 3

Describe the process of activating cAMP via epinephrine.

Answer 3

1. Epinephrine binds to the GPCR causing a conformational change.
2. Normally an gamma, beta, alpha, and GDP unit are attached to the GPCR the ligand causes this.
3. GdP is converted to GTP and, along with the alpha unit depart from the beta and gamma group.
4. GTP and Alpha activate Adenylyl cyclase which converts ATP to cAMP to start the messenger system.
5. GTP is converted to GDP and the alpha unit returns to the GPCR.

Question 4

What is isoelectric focusing?

Answer 4

Isoelectric focusing is a method for separating proteins based on its PI value. Proteins are added to a pH gradient with an electric charge. The + proteins will move towards the - and the - proteins will move towards the +. Eventually, these proteins will reach their PI value and stop moving (PH= PI) . The PI value is unique to each protein so you are then able to identify the protein.

Question 5

What is PAGE electrophoresis?

Answer 5

Separating proteins based on mass and charge.

Question 6

What is SDS PAGE electrophoresis?

Answer 6

Separating proteins based on mass alone.

Question 7

What is the Mnemonic for isoelectric focusing charges?

Answer 7

Anode side has the Acidic gel and has a positive charge.

Question 8

What is the basic concept for chromatography?

Answer 8

The more similar the molecule is to its surroundings, the more likely it will want to be around the same surroundings and will move slower through the chromatography.

Question 9

How does column chromatography work?

Answer 9

Add an unknown compound to the flask filled with silica gel. Then pour a solution into the flask. If the unknown compound has components similar to the solution then it will travel faster down the flask to the bottom.

Question 10

How does Ion Exchange chromatography work?

Answer 10

The flask is filled with similarly charged molecules. An unknown will be poured into the flask. Opposites attract and will be stuck to the flask, but the same charged molecules will move quickly through the flask.

Question 11

What is the environment for a cation exchange column?

Answer 11

Cation exchange catches cations, therefore the column will be filled with anions.

Question 12

What is the environment for an anion exchange column?

Answer 12

Anion exchange catches anions, therefore the column will be filled with cations.

Question 13

How does size exclusion chromatography work?

Answer 13

Proteins will be sent down a column filled with beads of a certain size. Proteins that fit the size of the bead will be slowed down, but the larger proteins will continue to fall due to gravity and filter out faster.

Question 14

How does affinity exclusion chromatography work?

Answer 14

Bind a specific molecule to the bead so the protein will bind to the beads and take longer to come out of the column.

Question 15

In extraction, which layer is on the bottom?

Answer 15

The more dense liquid will be in the bottom layer, usually the aqueous phase.

Question 16

Describe the process of distillation

Answer 16

Distillation is the process of seperating liquids based on their boiling point. This process is done slowly.

Question 17

Describe Paper TLC.

Answer 17

Paper is made of polar material. Non polar molecules move up the plate while polar molecules are at the bottom.

Question 18

Describe Gel Electrophoresis

Answer 18

Seperating molecules based on size and charge. Negatively charged DNA travels towards the positive side. Larger molecules move slower.

Question 19

Describe the sides of gel electrophoresis

Answer 19

Positive is the Anode
Negative is the Cathode.
Negatively charged DNA travels to the Anode.

Question 20

Describe the NMR Spectrum

Answer 20

Left: downfield, unshielded, low magnetic strength
Right: upfield, shielded, high magnetic strength

Each signal represents unique hydrogen atoms on a molecule.
Peak splitting is n+1 neighboring hydrogens.

Question 21

MCAT IR Spectrum keys

Answer 21

carboyl is 1700 cm -1
oh is 3500 cm -1
aldehyde is 2700 cm -1

Question 22

UV KEY

Answer 22

30 to 40 nm increase for conjugated bases

5 nm increase for every alkyl group

Question 23

What is tm?

Answer 23

temperature required to denature dna.

CG strands require higher temperature because it has 3 hydrogen bonds instead of just two.

Question 24

Denature vs hybridization

Answer 24

Denature is splitting dna from 2 to 1.

Hybridization is putting complementary dna back together.

Question 25

Recombinant DNA

Answer 25

Using restriction enzymes to put palindromic sequences in the dna. The dna is bound together to form artificial dna.

Question 26

Describe PCR

Answer 26

1. Increase temperature to denature DNA Strands.
2. Cool and attach primer to DNA strands
3. Attach DNA Polymerase to elongate DNA.

20^n based on the number of cycles.

Question 27

Describe the Sanger Method

Answer 27

1. Denature the DNA with base or acid.
2. ssDNA mixed with polymerase, primer, Bases, & ddnTP.
3. Allow to replicate with all ddnTP.
4. Run on gel electrophoresis.

Smallest fragments are the farthest away so you can sequence them going from the smallest to the largest based on size. 5’ is the small side.

Question 28

What is the function of RNAi?

Answer 28

Interference RNA which blocks the completion of transcription and translation. Can be used to find the effect out a gene.