MCAT Review!!

Amino acid

Have four groups attached to a central alpha carbon. Amino, carboxylic acid, hydrogen atom, and R group.

Interference

The phenomenon when light is passed through a screen with two slits, a pattern of bright and dark bands is projected onto a wall behind the screen

Specific gravity

At 1 atm and 4 degrees Celsius, water has a density of exactly 1 g/cm3. Therefore the equation is:SG = p (density) / (1 g/cm^3)

Parabolic trajectory

the time each rocket spends in the air is equal to twice the time it takes to fall from the maximum height it reaches

Ectoderm

Gives rise to the epidermis, nervous system, and eyes

Mesoderm

Gives rise to muscoloskeletal tissue

Glycolosis

This takes place in the cytoplasm, and is designed to break down glucose into two pyruvate molecules, which yields a net amount of 2 ATP and 2 NADH.

Citric Acid/Krebs cycle

This cycle harvests energy by oxidizing acetyl-CoA into carbon dioxide. It also generates four high-energy electron carriers, the first of which is the NADH produced by the conversion of isocitrate to ⍺‑ketoglutarate. It requires oxygen!

Can I keep selling seashells for money, officer?

Mnemonic for the order of the substrates of the Krebs cycle. Citrate, isocitrate, ketoglutarate, succinyl CoA, succinate, fumurate, malate, oxaloacetate

Anaerobic metabolism

This involves glycolysis, which catabolizes glucose into two molecules of pyruvate, and lactic acid fermentation, which reduces pyruvate to lactate and oxidizes NADH to NAD+

Isocitrate

Compound that acts as the substrate during the first reduction of an electron carrier in the citric acid cycle.

Mirror neurons

neurons which fire both when an individual performs a particular behavior and also observes someone else doing that behavior. These neurons are believed to be important in observational learning

Isoleucine

Branched alkyl amino acid with two chiral centers

Secondary appraisal

the process of evaluating if the stress caused by a certain event is something that the organism performing the appraisal can cope with. It includes evaluation of harm (damage caused by the event), threat (the potential for future damage), and challenge (the potential to overcome and possibly benefit from the event)

-1, 0, 1

Hydrogen’s oxidation states when bonded to metal, itself, and a vast majority of molecules respectively

Newton’s Third Law

Force (N) = mass (kg) x gravity (10 m/s2)

If Object A exerts a force on Object B, then Object B must exert a force of equal magnitude and opposite direction back on Object A

Calcium

This ion serves a role in clotting blood, muscle contraction, bone structure and strength

Parathyroid hormone

This serves as an antagonist to calcitonin by raising blood calcium levels

Restriction Enzymes

These enzymes catalyze the reaction of phosphodiester bonds in DNA

R group

Determines chemistry and function of its amino acid

Alpha carbon stereochemistry

L for all chiral eukaryotic amino acids; D for prokaryotic amino acids

Cysteine

Only amino acid without an S configuration

Glycine

Only amino acid with a hydrogen atom as its R group

Nonpolar, monatomic side chains

valine, alanine, glycine, leucine, isoleucine, methionine, proline

Aromatic side chains

tyrosine, phenylalanine, tryptophan

Polar side chains

Cysteine, glutamine, asparagine, threonine, serine

Negatively charged (acidic) side chains

Aspartate, glutamate

Positively charged (basic) side chains

Histidine, arginine, lysine

Amphoteric

Amino acids can accept or donate protons

pKa

The pH at which half of the species are deprotonated

Protonated

The amino acid is this at low (acidic) pH

Zwitterion

At pH near the pI of the amino acid, it is this

Deprotonated

An amino acid is this at high (alkaline) pH

Isoelectric point (pI)

An average of two pKa values in an amino acid without a charged side chain

Flat titration curve

at the pKa values of the amino acid

Vertical titration curve

At the pI of the amino acid

pI 6

pI of amino acids without charged side chains

pI below 6

pI of acidic amino acids

pI above 6

pI of basic amino acids

condensation or dehydration reaction

Reaction that releases one molecule of water and forms a peptide bond

Nucleophilic amino group

Attacks the electrophilic carbonyl group of another amino acid

Amide bonds

Rigid because of resonance

Hydrolysis reaction

reaction that breaks a peptide bond

Primary structure

The linear sequence of amino acids in a peptide and is stabilized by peptide bonds

Secondary structure

The local structure of neighboring amino acids, and is stabilized by hydrogen bonding between amino groups and nonadjacent carboxyl groups

Alpha helices

Clockwise coils around a central axis

Beta pleated sheets

Rippled strands that can be parallel or antiparallel

Proline

Can interrupt secondary structure because of its rigid cyclic structure

Tertiary structure

The three-dimensional shape of a single polypeptide chain, and is stabilized by hydrophobic interactions, acid-base interactions (salt bridges), hydrogen bonding, and disulfide bonds

Hydrophobic interactions

Push hydrophobic R groups to the interior of a protein, which increases entropy of the surrounding water molecules and creates a negative Gibbs free energy

Disulfide bonds

Occur when two cysteine molecules are oxidized and create a covalent bond to form cystine

Quaternary structure

The interaction between properties in proteins that contain multiple subunits

Conjugated proteins

Proteins with covalent attached molecules

Central dogma

DNA is transcribed to RNA which is translated to protein

Termination (stop) codons

UAA, UGA, UAG

Wobble

Third base in the codon

Silent mutations

mutation that has no effect on protein synthesis

Nonsense (truncation) mutation

Mutation that produces a premature stop codon

Missense mutation

Mutation that produces a codon that codes for a different amino acid

Frame shift mutation

Mutation that results from nucleotide addition or deletion and changes the reading frame of subsequent codons

mRNA

RNA that carries the message from DNA in the nucleus via transcription of the gene; it travels into the cytoplasm to be translated

tRNA

RNA that brings in amino acids and recognizes the codon on the mRNA using its anticodon

rRNA

RNA that makes up the ribosome and is enzymatically active

RNA Polymerase II

bonds to the TATA box within the promoter region of the gene (25 base pairs upstream from the first transcribed base)

hnRNA

RNA synthesized from the DNA template (antisense) strand

7-methylguanylate triphosphate cap

Posttranscriptional cap added to the 5’ end

Polyadenosyl (poly-A) tail

Posttranscriptional cap added to the 3’ end

snRNA and snRNP

These complete splicing in the spliceosome

Spliceosome

where introns are removed in a lariat structure and exons are ligated together

Polycistronic genes

Genes that can help prokaryotic cells increase the variability of gene products from one transcript

Alternative splicing

Where eukaryotic cells can increase variability of gene products through combining different exons in a modular fashion to acquire different gene products

Ribosomes

The factories where translation (protein synthesis) occurs

prokaryotic initiation

A stage of translation when the 30S ribosome attaches to the Shine-Dalgarni sequence and scans for a start codon; it lays down N-formylmethionine in the P site of the ribosome

Eukaryotic initiation

A stage of translation that occurs when the 40S ribosome attaches to the 5’ cap and scans for a start codon; it lays down methionine in the P site of the ribosome

Elongation

A stage of translation that involves the addition of a new aminoacyl-tRNA into the A site of the ribosome and transfer of the growing polypeptide chain from the tRNA in the P site to the tRNA in the A site. The now uncharged tRNA pauses in the E site before exciting the ribosome

Termination

A stage of translation that occurs when the codon in the A site is a stop codon

Release factor

Places a water molecule on the polypeptide chain and thus releases the protein

Jacob-Monod model

Model of repressors and activators that explains how persons work

Operons

Inducible or repressible clusters of genes transcribed as a single mRNA

Inducible systems (lac operon)

System bonded to a depressor under normal conditions; they can be turned on by an inducer pulling the depressor from the operator site

Repressible systems (trp operon)

System transcribed under normal conditions; can be turned off by a corepressor coupling with the repressor and binding of this complex to the operator site

Transcription factors

Search for promoter and enhancer regions in the DNA

Promoters

region within 25 base pairs of the transcription start site

Enhancers

Regions more than 25 base pairs from the transcription site

Histone acetylation

Modification of chromatin structure that increases enzyme accessibility of DNA

DNA methylation

Modification of chromatin structure that decreases enzyme accessibility of DNA

A site

Binds incoming aminoacyl-tRNA using codon-anticodon pairing

P site

Holds growing polypeptide until peptidyl transferase forms peptide bond and polypeptide is handed to A site

E site

transiently holds uncharged tRNA as it exits the ribosome

Fluid mosaic model

Accounts for the presence of lipids, proteins, and carbohydrates in a dynamic, semisolid plasma membrane that surrounds cells

Flippases

Specific membrane proteins that maintain the bidirectional transport of lipids between layers of

Triaglycerols and free fatty acids

These acts as phospholipid precursors and are found in low levels in the membrane

Glycerophospholipids

Replace one fatty acid with a phosphate group which is often linked to other hydrophilic groups