Flashcards in Biochemistry Proteins and Analysis Deck (28):
What is facilitated diffusion?
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.
What characterizes g protein coupled receptors?
All g protein coupled receptors have 7 alpha transmembrane helices.
Describe the process of activating cAMP via epinephrine.
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.
4. GTP is converted to GDP and the alpha unit returns to the GPCR.
What is isoelectric focusing?
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.
What is PAGE electrophoresis?
Separating proteins based on mass and charge.
What is SDS PAGE electrophoresis?
Separating proteins based on mass alone.
What is the Mnemonic for isoelectric focusing charges?
Anode side has the Acidic gel and has a positive charge.
What is the basic concept for chromatography?
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.
How does column chromatography work?
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.
How does Ion Exchange chromatography work?
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.
What is the environment for a cation exchange column?
Cation exchange catches cations, therefore the column will be filled with anions.
What is the environment for an anion exchange column?
Anion exchange catches anions, therefore the column will be filled with cations.
How does size exclusion chromatography work?
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.
How does affinity exclusion chromatography work?
Bind a specific molecule to the bead so the protein will bind to the beads and take longer to come out of the column.
In extraction, which layer is on the bottom?
The more dense liquid will be in the bottom layer, usually the aqueous phase.
Describe the process of distillation
Distillation is the process of seperating liquids based on their boiling point. This process is done slowly.
Describe Paper TLC.
Paper is made of polar material. Non polar molecules move up the plate while polar molecules are at the bottom.
Describe Gel Electrophoresis
Seperating molecules based on size and charge. Negatively charged DNA travels towards the positive side. Larger molecules move slower.
Describe the sides of gel electrophoresis
Positive is the Anode
Negative is the Cathode.
Negatively charged DNA travels to the Anode.
Describe the NMR Spectrum
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.
MCAT IR Spectrum keys
carboyl is 1700 cm -1
oh is 3500 cm -1
aldehyde is 2700 cm -1
30 to 40 nm increase for conjugated bases
5 nm increase for every alkyl group
What is tm?
temperature required to denature dna.
CG strands require higher temperature because it has 3 hydrogen bonds instead of just two.
Denature vs hybridization
Denature is splitting dna from 2 to 1.
Hybridization is putting complementary dna back together.
Using restriction enzymes to put palindromic sequences in the dna. The dna is bound together to form artificial dna.
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.
Describe the Sanger Method
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.