MCAT Biochemistry Flashcards

This time, I'm just going to manually do everything. I'll only include flashcards from things I did not know before.

hnRNA

pre-mRNA (unprocessed form of eukaryotic mRNA)

snRNA

Small nuclear RNA, RNA that aids in splicing during post-transcriptional modifications inside of the nucleus

Adenine

Guanine

Cytosine

Thymine

Which of the nitrogenous bases are purines and pyrimidines?

Purines: A and G

Pyrimidines: C and T

Memorize “Pure As Gold” and “Purines have two rings.”

Helicase, topoisomerase, DNA Pol, Primase, and Ligase

Helicase - unzips DNA

Topoisomerase - Relives torsional strain

DNA Pol - adds dNTPs in 5’ to 3’ direction (specifically DNA Pol III)

Primase - Adds RNA primers to signal DNA Pol where to start

Ligase - Seals nicks

DNA Repair Mechanisms

Mismatch Repair (DNA Pol can detect wrong nucleotides after replication has completed)

Endonucleases (cut DNA to refill the correct base)

Methylation (in prokaryotes, methylation indicates what is the parent strand)

What are the post-transcriptional modifications in eukaryotes for mRNA? What about prokaryotes?

5’ m7G (methylguanosine cap)

Splicing (remove introns, join exons together)

Poly A tail

Prokaryotes do not do any post-transcriptional modifications

Ribosomes are made of two subunits, a large and a small. One set is 60S and 40S to give you an 80S ribosome, while the other is 50S and 30S to give you a 70S ribosome (math just doesn’t math here). Which one corresponds to prokaryotes and eukaryotes?

Prokaryotes - 70S

Eukaryotes - 80S (eukaryotes even in the tens place; 4, 6, 8)

Start and stop codons

Start - 5’ AUG 3’ (Met)

Stop - UAA, UGA, UAG

In post-translational modifications, what is lipidation, ubiquitination, glycosylation, and phosphorylation?

Lipidation - addition of a lipid to the protein

Ubiquitination - Addition of ubiquitin, a regulatory protein that often marks proteins for degradation/recyling

Glycosylation - addition of a sugar to the protein

Phosphorylation - addition of a phosphate to the protein

Proteolysis activation

When you cut the protein in order to activate it

Chaperones

Proteins that aid in the proper 3D folding of a protein by helping facilitate the noncovalent interactions in secondary through quaternary structures

In translation, the addition of each amino acid requires the input of _____ ATP across the various steps of translation.

4

Polycistronic vs monocistronic

Polycistronic - prokaryotes are capable of making multiple proteins from a single strand of mRNA at one given time

Monocistronic - eukaryotes are only capable of making one protein from a single strand of mRNA at a given time

Alternative splicing (in transcription)

We can customize a protein by only splicing together certain exons (so while the gene leads to only one protein, we can make it a little different by splicing together different exons). We call these isoforms

Euchromatin vs heterochromatin

Euchromatin are more loosely wound around histones, making them more easily accessible to transcriptional proteins and enzymes. Heterochromatin are more tightly wound around histones, so they are less accessible.

I remember this by “Eu” = “Easy for proteins”

P53

Tumor suppressor gene that sends the cell into arrest if there is damage to DNA at the growth checkpoints (if this is mutated, the cell cycle isn’t stopped if there is damage, leading to tumor growth)

Proto-oncogenes vs oncogenes

Proto-oncogenes are normal versions of genes that promote regular growth patterns, while oncogenes are cancerous versions of proto-oncogenes that promote uncontrolled and enhanced cell growth

Inducible vs Repressible Operons

Inducible Operons are those that are normally off with a repressor bound to the operator site, preventing transcription. A repressible operon is normally on, but can be shut off by the binding of a repressor

Aliphatic Amino Acids

Hydrocarbon R groups that aren’t aromatic (G, A, V, L, I, M, and P)

Doesn’t include F and W (those are aromatic)

Essential Amino Acids

The amino acids we can’t synthesize on our own (F, V, T, W, I, M, H, K, L)

Pi-Stacking Amino Acids

Have pi bonds in aromatic rings (F, Y, and W)

Commonly Phosphorylated Amino Acids

S, Y, and T (anything with OH)

Ketogenic vs Glucogenic amino acids

Ketogenic are amino acids that can be broken down into Acetyl CoA to be sent to the Krebs Cycle (L, and K)

Glucogenic are amino acids that, upon being catabolized, are turned into intermediates in glucogenesis (D and R)

Cysteine vs Cystine

Cysteine is the amino acid, while cystine is the oxidized form (contains S-S bond)

pI (isoelectric point)

the pH at which the zwitterion is reached (the overall charge of the amino acid is neutral)

Alpha helices are most commonly ____-handed. H-bonds are between every _____ amino acid, and a turn of an alpha helix is completed roughly every _____ residues.

right; 4th; 3.6

Parallel vs Antiparallel Beta Sheets (name kind of gives it away, but how can you recognize it from a structure)

In antiparallel beta sheets, the NH and C=O are right in line with each other, while in parallel beta sheets, they are staggered

Tertiary structures can have different types of turns that are classified based on how far away the hydrogen bonding amino acids are (i vs i + N). Match the following with it’s name (greek letter)

i → i + 2

i → i + 3

i → i + 4

i → i + 5

gamma

beta

alpha

pi

(Get Back And Practice)

How would you disrupt each level of protein structure?

1 - use enzymes or hydrolysis reactions

2 - denaturation (pH, increasing T, salinity, using SDS or sodium dodecyl sulfate, or using urea)

3 - Denaturing agent or condition (if you want to disrupt disulfide bonds, you need reducing conditions)

4 - Denaturing agent or condition (same as 3)

Localization sequences vs signal sequences (in proteins)

Localization sequences are a certain strain of amino acids within any part of the peptide sequence that destines the protein for movement towards a certain organelle or region of the cell

Signal sequences are similar to localization sequences, but specifically are regions of a peptide sequence typically near the N terminus that will imbed themsleves into the plasma membrane

Cofactor

Nonprotein components that are added to proteins for proper functioning of the protein (like iron to hemes). They need these cofactors or else they can’t function

Apoprotein vs holoprotein (use the term prosthetic group in your response)

Apoprotein is the inactive form, and when a prosthetic group is added, it becomes active, which is the holoprotein

Ordered vs Random ordered vs Ping-Pong Mechanism

Ordered - the substrates will bind to the enzyme in a specific, fixed order, with the substrates bound to the enzyme at the same time

Random - The order in which the substrates bind to the enzyme doesn’t matter

Ping-pong - A specific substrate will bind first in order to slightly modify the enzyme, then being released. The now modified enzymes can then bind the second substrate to create the product (substrates bind at different times)

Michaelis Menten Equation

v = (v_max [S]) / (K_M + [S])

Enzyme Kinetics Assumptions

[E] is constant (steady-state assumption)

[S] >> [E]

The reaction is irreversible

When studying the rate at a given [S], we only measure the initial rate

Efficiency of catalyst

k_cat / K_M

Turnover number (enzyme kinetics)

k_cat = v_max / [E]

Positive cooperativity. What curve does it yield?

The binding of one active site makes the binding of other active sites easier. It yields a sigmoidal curve (S-shaped)

Hill’s Coefficient

The number used to measure cooperativity (> 1 is positively cooperative, < 1 is negatively cooperative, = 1 is non-cooperative)

Describe how K_M and v_max change in competitive, uncompetitive, and non competitive inhibitors.

increase; no change

decrease; decrease

no change; decrease

Zymogens

Enzymes that are formed and secreted in their active form, later activated by a cleavage reaction from a protease or environmental conditions

What the structures from left to right?

Glucose; fructose; galactose

What makes up maltose?

Two glucose monomers linked via an alpha-1,4 glycosidic linkage

What makes up sucrose?

One glucose and one fructose monomer linked in an alpha-1,2 linkage

What makes up lactose?

One glucose and one galactose monomer linked in a beta-1,4 glycosidic linkage

What makes up trehalose?

Two glucose monomers linked via an alpha-1,1-alpha linkage

What makes up glycogen?

Contains tons of D-glucose monomers linked in alpha-1,4 linkages, as well as alpha-1,6 linkages for branching points

In the anomeric carbon, alpha means the OH group is pointing _____, while in beta, it’s pointing _____.

down; up

What makes up starch?

Less often branching (alpha-1,6) bonds than glycogen, but it’s overall very similar to glycogen

What makes up cellulose?

Glucose monomers with beta-1,4 linkages

In the Fischer projection, substituents to the left will be pointing _____, while substituents to the right will be pointing _____ when converted to the ring form.

up; down

Ring flip

Flip the chair, and all substituents shift clockwise, but change from axial to equatorial and vice versa

Mutarotation (in sugars)

The conversion of one anomer to the other (alpha to beta or beta to alpha)

D and L enantiomers. D is the same thing as an _____ configuration, just specifically applying to the penultimate carbon. L, on the other hand, is the same thing as an _____ configuration.

R; S

Mammals have _____ carbohydrates and _____ amino acids.

D; L

Do unsaturated fatty acids or saturated fatty acids have a higher boiling point?

Saturated (unsaturated fatty acids like oil are liquid at room temperature, while butter, a saturated fatty acid, is a solid at room temperature)

Amphipathic vs Amphoteric

Amphipathic - having both polar and nonpolar portions of a molecule (fatty acids are mostly nonpolar, but the carboxyl group is polar)

Amphoteric - a substance that can act as an acid or base

Triglyceride Synthesis

React glycerol with a carboxylic acid (fatty acid). The OH on glycerol attacks the carboxyl group to give you the ester

Adipocytes

Cells specifically designed for fat storage

Chylomicrons

A type of lipoprotein (fat-carrying protein) that aids in the transport of fats, cholesterols, or fat soluble vitamins (KADE) through the blood stream

Wax

A super long fatty acid esterified to long alcohols, super hydrophobic (you form this by a normal esterification reaction where a carboxylic acid and an alcohol are added together to form an ester)

Terpene

Precursors to steroids, made form isoprene units

Isoprene

Steroid

Hydrophobic molecules important in hormones or other signaling pathways, based on the structure of cholesterol

Cholesterol

Vitamin

Organic compounds used as cofactors or other important reactants in many biological processes, can be lipid soluble (hydrophobic) or water soluble (hydrophilic)

What are the fat soluble vitamins? Indicate how many rings or other notable structures in them.

K - important blood clotting factor, 2 rings with quinone

A - carotene, helps with vision in the eyes, 1 ring

D - becomes calcitriol, regulates calcium and phosphorus (vitamin D deficiency causes Rickets), 3 rings

E - Tocopherol, important aspect of antioxidants (prevent reactive oxidative species from causing damage), 2 rings, non quinone

Remember Fat KADE

List what each of the B vitamins are the precursor to

B1 - TPP

B2 - FAD (FADH2)

B3 - NAD (NADH)

B5 - CoA (acetyl CoA)

B6 - PLP

Hmm in order, TFNCP

The Fox knows (N) C/P on the MCAT??? LOL

Agarose Gel Electrophoresis

Uses a gel made of agarose instead of polyacrylamide to study the size of DNA molecules

Polyacrylamide Gel Electrophoresis (PAGE)

Uses polyacrylamide (PA) in the gel to study proteins

Polyacrylamide = polypeptide (protein)

Isoelectric Focusing (IE)

Type of gel electrophoresis that will separate proteins on the basis of their charge (pI)

Acidic amino acids will have a pI below 6, while basic amino acids will have a pI above 6

Native PAGE. Indicate what proteins are on top and what are on bottom

When nothing is added to the proteins before being added to the gel

The heaviest proteins stay near the top, and the lightest proteins migrate the furthest toward the bottom (in general, heavy = top, light = bottom)

Nonreducing SDS PAGE vs Reducing SDS PAGE

Nonreducing SDS PAGE is a specific type of PAGE where SDS (sodium dodecyl sulfate) is added to the proteins before they are run, causing them to have a uniformly negative charge, so they are only separated by the size or shape. It also disrupts non-covalent interactions that may be holding together the quaternary structure of proteins together.

Reducing SDS PAGE is the same thing, but you add a reducing agent that reduces and breaks covalent disulfide bonds (remember, cysteine has an SH group that when reduced, is bonded to another cysteine sulfur atom)

Western Blotting

A blotting technique that uses reducing SDS PAGE more-so used to identify whether or not a specific protein of interest (of a known weight) is present in a solution of proteins

It shows you relative changes in concentration, but can’t tell you the exact concentration of a protein

Ion-Exchange Chromatography, Anion-Exchange Chromatography, and Cation-Exchange Chromatography

Used to separate proteins based on their charge, either anionic or cationic, by passing a solution of proteins over beads coated either with negative or positive charges.

In anion-exchange chromatography, the beads are positive, so you retain the anions more. This means positive proteins elute first, and negative proteins elute last

In cation-exchange chromatography, the beads are negative, so you retain the cations more. So negative proteins elute first, and positive proteins elute last

Affinity Chromatography

Separates a protein of interest by coating the beads with ligands that the specific protein can bind to. Then to remove the isolated proteins, you put the solution in a very high concentration of free ligands, which displaces the protein

Immunoprecipitation (primary vs secondary antibodies)

Used to detect and separate a protein of interest from a solution of proteins by adding a y that is specific to the protein of interest to a bead. Once the bead and antibody are bound to the protein, it can be removed from the solution (it’s basically affinity chromatography, but we use antibodies instead of any ligand)

Primary antibodies directly bind to the protein, while secondary antibodies are first bound to a fluorescent tag (for visualization), then bind to the primary antibody

Radioimmunoassay

Used to monitor the concentration and amount of a certain protein in a solution by binding to the proteins of interest to antibodies and iodine so their relative light emission can be measured

Flow cytometry

Fluorescent tags are added to specific proteins on cells which are then passed under light so that the cell size or number of cells can be measured

Bradford Quantification

A quantitative lab technique that measures the concentration of protein by binding Coomassie blue (a dye) to proteins and measuring the relative absorbance of the solution (A = \epsilon bc)

Edman Degradation

Used to determine the amino acid sequence of small proteins by removing amino acids one at a time from the N terminus

Salting Out/Dialysis (no not what you give to patients who have kidney failure)

This is used to purify proteins

Salting out is when a high concentration of salt is added to a solution of proteins which causes salt to compete with the protein to interact with water, causing the proteins to precipitate/fall out of the solution to be collected

Dialysis is when molecules of different sizes separate from each other using a semipermeable membrane that allows ions to leave the solution and enter the surrounding water, leaving behinds the proteins alone

In the Ramachandran plot, where do you see right-handed alpha helices, left-handed alpha helices, and beta sheets?

Right-handed alpha helices are in the bottom left corner

Left-handed alpha helices (again, not natural) are in the top right corner

Beta sheets will appear in the top left corner

Describe the steps of PCR.

You heat the sample to denature the DNA

You cool and add primers to allow them to bind to target sequences

You hadd Taq polymerase with dNTPs to extend/synthesize new strands

Repeat the process as many times as you like (number of copies is x 2^N, where x is the number of copies at the start of PCR, and N is the number of times you do this process)

qPCR vs RT-PCR

qPCR measures the amount of concentration of a gene of interest. It does this by using a fluorescent dye that will increase as the number of strands increases and can be measured

RT-PCR identifies if a specific mRNA is present and determine when the genes are being expressed (you add reverse transcriptase to convert mRNA into cDNA)

Fluorescence in-situ hybridization (FISH)

Identifies whether a specific DNA or RNA sequence is present (if it is, it binds to the probe, which will be complementary to the gene of interest)

Hybridization is when two complementary strands bind to each other

In Vitro Mutagenesis

Identifies the functioning of a gene (random mutations are introduced into a gene to see how the functioning of the gene changes)

Restriction Fragment Length Polymorphism (RFLP)

Identify mutations or polymorphisms (you add restriction enzymes to cut gene sequences at palindromic sequences, and if the lengths are different than expected, mutations are present

Tollen’s Test vs Benedict’s Test

Both detect the presence of reducing sugars, which will have a free hydroxyl (hemiacetal or hemiketal) in ring form on the anomeric carbon

In Tollen’s Test, if a reducing sugar is present, Ag+ is reduced to Ag (S) forming a silver mirror

In Benedict’s Test, if a reducing sugar is present, Cu2+ is reduced to a red precipitate form of copper (goes from blue to red)

Gram Stain

Identify the type of bacteria present by staining it with a purple dye, washing it, and then dying it again with a pink dye

If it’s gram negative, the purple dye will be washed away, and therefore they appear pink due to the last stain

If it’s gram positive, the purple dye is not washed away, so it appeaks purple

Reporters

Any measurable signal (color, fluorescence, radioactivity, etc.)

Supernatant

The liquid that remains above a pellet/bead after centrifugation

In Vitro vs In Vivo

In Vitro - anything done outside of a liquid organism, commonly in a petri dish or test tube (it’s artificial)

In Vivo - anything done inside of a living organism (natural)

Mediating vs Moderating variable

Mediating - a variable that helps explain the relationship between the independent and dependent variables

Moderating - A variable that changes the strength or direction of the relationship between the independent and dependent variables

Vehicular Control vs Negative Control vs Placebo Control vs Positive Control

Negative Control groups don’t get anything

Vehicular Control groups receive an inert treatment (like if you are testing a vaccine, the vehicular control group would receive a shot that contains saline)

Placebo Control groups receive a placebo (fake treatment) to control for psychological effects

Positive control groups receive an effective treatment with an already understood response

Potentiation

The factor or degree with which a variable has changed, determining how significantly the variable was changed (like if it increases from 0.1 M to 0.5 M, the potentiation factor is 5)