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)