MCAT Bio/Biochem Flashcards

Aldose

Only one C next to the carbonyl (aldehyde)

Ketose

C on either side of the carbonyl (ketone)

DNA passes what components from parent to daughter?

Nucleosides - Pentose sugar, nitrogenous base (ATCG), phosphate back bone

→ passes phosphorus and nitrogen

Truncated meaning

Early translation termination causes a production of a shortened protein

Mutation that would lead to a truncated protein

Anything that would cause a stop codon to appear

Ex. Insertion of A after second nucleotide in TGG → TGA which corresponds to UGA (stop codon)

Stop codons

UAA - U Are Annoying

UAG - U Are Gone

UGA - U Go Away

*mRNA T becomes U

Someone has a 50% of carrying an autosomal dominant mutation, and if they carry it, a 50% chance of transmitting it → probability of child inheriting it?

½ * ½ = ¼ = 25%

What side chains would interact best with Ca2+?

Negative → D and E (aspartate, glutamate)

What major homeostatic functions do the kidneys perform?

• Excrete nitrogenous wastes like urea, creatine

• Regulate blood pH by controlling H+ and HCO3-

• Regulate water and electrolytes

• Regulate blood pressure via renin

• Produce EPO (erythropoietin) → stimulates erythrocyte/RBC production

Kcat

Enzyme catalytic turnover number, reactions catalyzed per second per active site.

*A change in the conformational stability of an enzyme does not necessarily affect function

Sarcomeres

Contain thin filaments (actin) and thick filaments (myosin)

→ muscle contraction depends on the interaction between those 2

→Resting: overlap between actin and myosin, gap between the ends of the actin filaments and the M line. Allows for the maximum binding of myosin heads to actin on contraction.

What interactions in protein folding stabilize secondary, tertiary or quaternary structures?

Hydrogen bonds, van der Waals, ionic bonds

Secondary - Hydrogen bonds: between backbone carbonyl oxygen and backbone amide hydrogen

Tertiary - Van der Waals forces and ionic bonds: alpha helices and beta sheets, salt bridges

Quaternary - also Van der Waals and ionic bonds

Why NOT peptide bonds?

→ those stabilize the primary structure, they are the covalent linkages between amino acids

Why can’t proline be found in binding domains, and why is it found in loops/linker regions?

It’s structurally rigid and introduces a kink in the chain that is useful for sharp turns but disrupts alpha-helices.

Why can Cysteine have 3 pKa’s?

The side chain is ionizable, the thiol (SH) side chain can become deprotonated and negatively charged

If a peptide contains n different amino acids, how many different possible sequences can be made?

N! (N factorial)

Because you are rearranging the same amino acids not independently choosing an amino acid for each position.

What does a lower p value indicate?

P < 0.05 = lower probability of random chance, therefore higher probability that the observed difference is real (statistically significant if p<0.05)

Decrease in pH (more acidic)

Results in the protonation of ionizable residues (H+)

Increase in the pH (basic)

Results in the deprotonation of positively charged side chains

Ionic strength

Measure of ions in solution

Na+, Cl- disrupt ionic interactions by competing for ionic bonds

→ doesn’t alter the protonation state of amino acid side chains

What two amino acids are known for disrupting alpha helices?

Glycine and Proline

Neither of these are likely to be found within an alpha helix

What amino acids are likely to be found in alpha helices?

Both polar and nonpolar aa’s

Non polar = hidden in protein-protein interfaces

Polar = exposed to an aqueous environment

Tertiary structure is stabilized by…

Noncovalent interactions between side chains, bringing aa’s that are far apart in the primary structure closer together

→ covalent is wrong because they are in peptide bonds which are the basis for primary protein structure

Ternary complexes

Groups of three molecules bound together

→ many form in a particular order or random order, depending on the specific molecules involved

→ CANT bind simulaneously, the molecules would collide at the same time, extremely unlikely and rare

Why is NATIVE page used for electrophoresis experiments?

Native gel preserves the 3D folded forms of the proteins, which allow for interactions between proteins and other molecules to occur within the gel.

Why is SDS used in electrophoresis experiments?

SDS is a detergent that causes the protein to denature (unfold) and coats it with a negative charge.

→ equal charge-to-mass ratios

What does native form of proteins mean?

Many proteins consisting of polypeptide chains: dimers, trimers, tetramers

→ SDS gel separates multimer subunits by size

Binding cooperativity

Occurs when the binding of one ligand increases (or decreases) the affinity of that protein for another ligand at a separate binding site

→ example was that affinity of PABP for mRNA poly-A tails increases 10 fold when the protein elF4G was added (at a different site, not the poly-A tail)

What do histones interact with?

The backbone of DNA (phosphate backbone).

*If lysine binds to this, it neutralizes the negative charge which causes the DNA histone interaction to weaken which leads to the up-regulation of gene expression (decreases the binding interaction)

Proline’s secondary amino group

It’s side chain loops back and bonds with the amino nitrogen, which makes it attached to two carbons (-NH-) so it makes it a secondary amine.

Size-Exclusion Chromatography

• Smaller molecules = enter pores more often, progress is slowed

• Larger molecules = cannot enter pores, pass through very quickly

Endoplasmic Reticulum vs Cytosol chemical environments:

Endoplasmic Reticulum (ER): Oxidizing, forms disulfide bonds

-proteins destined for secretion or membranes, oxidizing environment helps them form stabilizing disulfide bonds (loose electrons/hydrogens to connect)

Cytosol: Reducing, disulfide bonds break/stay reduced

-cytosol separates, keeps cytesine residues as separate -SH groups

*remember OIL RIG for this question

Reducing vs Non-Reducing disulfide bonds

Reducing: reducing agents break S-S bonds, subunits separate

Non-Reducing: disulfide bonds stay intact, disulfide linked subunits remain connected

*Disulfide bonds form the best in oxidizing environments!

Native Gel vs SDS PAGE

SDS PAGE = separates only based on molecular weight, does this by coating proteins with SDS giving them a uniform negative charge AND denatures them by disrupting noncovalent interactions (unfolded into their primary structure).

Native PAGE = separates based on charge and mass without denaturing proteins.

What do kinases to?

Enzymes that catalyze the transfer of phosphate groups from nucleotide triphosphates like ATP, GTP to diphosphates like ADP, GTP.

Atoms that are good nucleophiles

Sulfur (S), Nitrogen (N), Oxygen (O, anything with a negative charge (can donate lone pairs/electrons).

GTP hydrolysis increases, what happens to the GTP dependent signaling like Ras → cell growth

If there is more GTP hydrolysis, then there will be LESS active GTP, therefore less signaling. This leads to decreased cell growth/division.

*activator of hydrolysis, inhibitor of cell growth and division

Why is Glycine achiral?

It has 2 hydrogens on the alpha carbon

Cysteine is the only ___ configuration amino acid

Only R configuration

All residues except Glycine and Cysteine are…

S configuration and L configuration

How to know if something is in the L vs D position

L = amino group on the LEFT

At the same pH, how can I tell which molecule is MORE protonated if they have different pKa values?

Higher pKa (more distance from pH)= MORE protonated

Lower pKa (less distance from pH)= LESS protonated

PKA tells you how easy something is to protonate, it tells you where the pH group is exactly 50% protonated and 50% deprotonated

*Higher pKa means the group holds onto H+ more strongly

Why is pH important for nucleophilic attacks?

PH will determine whether a nucleophile is protonated or deprotonated

In nature, what conformation of amino acids are all biomolecules designed to work with?

L-amino acids (L conformation)

-Proteases recognize this, so if it was D then the peptide would remained uncleaved and have a longer physiological half life than their counterparts

How to calculate % yield from enzyme purfication table:

1. Specific Activity

Total activity / total protein mass

2. Yield (%)

Activity after purification/initial activity x 100

Primary Structures

Defined by covalent bonds between the carbonyl carbon of an amino acid and backbone nitrogen.

Which way does a current run?

Anode to Cathode

Hydrophilic amino acids

Weak hydrophobic affect because they are exposed on the protein surface and like to interact with water

Isoelectric Point

PH at which the net charge of the protein is neutral. If the ambient pH is lower than the protein’s pi, then the protein gains protons and becomes positively charged. Move closer to the pI, don’t exceed it.

How does phosphorylation vs dephosphorylation change the charge of a protein?

Phosphorylation = adding a phosphate, makes it more NEGATIVE

Dephosphorylation = phosphate is removed, makes it less negative & more POSITIVE

*Phosphate = negative, add a phosphate is adding a negative charge

Branched, alkyl chain amino acids:

Leucine, Isoleucine, Valine

Importance of Glutamine in Beta-Sheets

Aligned glutamine side chains in adjacent strands can form hydrogen bonds with each other because they can act as both donors and acceptors/

What amino acids participate in stacking interactions that stabilize secondary structures?

Aromatic side chains like: phenylalanine, tyrosine, tryptophan

What does protein folding do? What happens if it is reversed?

Protein folding is driven by the hydrophobic effect → hides as many hydrophobic residues in the interior of the protein as possible

If it changes: misfolding/aggregation causes the hydrophobic residues to be exposed to the aqueous environment, resulting in a significant decrease in the solubility of the protein

Beta turns in beta sheets connect…

ANTIPARALLEL (not adjacent) strands, because those strands reverse direction

How are beta sheets stabilized?

Hydrogen bonds between backbone carbonyl C=O groups and backbone NH groups of adjacent strands

Alpha helix are stabilized by…

Hydrogen bonding in backbone between C=O and NH groups, but diff from beta sheets because it follows i → i+4 while beta sheets just do it between neighboring strands

What do molecular chaperone proteins do?

Facilitate the proper folding of other proteins, prevent or reverse aggregation, increasing the solubility of the protein

Double-Stranded DNA Breaks must be repaired by…

It breaks the backbone, so it must rejoin the binding between the deoxyribose sugar and a phosphate (those make up the backbone).

What type of DNA is not readily able to be transcribed?

In a portion of the chromosome that is tightly wound around histones *not easily accessible

How to find the template strand of something:

Flip the 5’ and the 3’, line up the new strand and match it to the previous one, but replace T with U (RNA)

What happens in the nucleolus (Nucleoli)?

Ribosome Production

-rRNA is made

-ribosomal subunits are assembled

Why do histone complexes have positively charged amino acids?

Since DNA is negatively charged, histone proteins must have a net positive charge to facilitate DNA binding.

→ rich in ARGININE and LYSINE

*The nucleosome core has a positive net charge

What happens during SDS page?

-Reducing agents break disulfide bonds

-SDS detergent masks the intrinsic protein charge - made negative

-molecules are run through a highly cross linked polyacrylamide gel

Protonated form favors

HIGH PKA → less willing to give that proton up

Kd = equilibrium dissociation constant

OFF/ON or Unbinding/Binding

Ex. If finding the strongest overall binding affinity…

• you want a small kd for unbinding, shows that theres a strong affinity

• You want a large kd for binding, shows strong affinity

Thiol Group

(-SH) = cysteine

Transmembrane Domain Amino Acids

Hydrophobic groups (nonpolar)

Salt bridges

Dont have to do with sulfur

They are non covalent electrostatic interactions between a + and - charge

Proteases and Polypeptide bonds

Proteases catalyze the hydrolysis of peptide bonds

→ double bond character gives the bonds restricted rotation

What must be true for myoglobin to bind oxygen?

-Intact tertiary structure - forms 3D pocket/correct folding to form the heme pocket and hold heme correctly so that O2 can bind

-Must exist as a holoprotein (protein + heme group → can bind to oxygen) holo = whole, complete, functional

Structure of hemoglobin

Has an Fe2+ center (Iron)

If Gibbs free energy is positive then…

Kd must be between 0 and 1 because ln(Kd) between 0 and 1 is negative (opposite).

What does a SOUTHERN blot detect?

DNA

What does a NORTHERN blot detect?

RNA → including mRNA and tRNA

What does a WESTERN blot detect?

Protein

Whats a good way to remember all of the different blots?

SNOW DROP

S (south) → D (dna)

N (north) → R (rna)

W (west) → P (protein)

*East = Extras → protein modifications ex. Glycosylation

DNA transposons

Fragments of DNA that can move between different areas of the genome

Retrotransposons

Move via an RNA intermediate that is transcribed from DNA, translated into specialized enzymes, converted back into DNA and reinserted into a new genomic location (travels within dna)

Retroviruses

ENVELOPED viruses that have RNA genomes, upon entering a host cell the envelope and capsid disassemble, releasing viral RNA and proteins

Chemotaxis

Bacteria respond to chemical stimuli in the extracellular environment by moving away from or toward increasing concentrations of signal molecules, allowing them to adjust the direction of their movement toward target cells

Parts of a flagellum and what they do:

Filament (tail) - propels bacterium

Hook (middle of body) - transmits forms

Basal body (body) - works as a molecular motor that generates motion (torque)

Viral Life Cycle of a Bacteriophage - LYTIC

1) Attachment to cell wall

2) Viral genome entry - inject into cytoplasm of bacterial host

3) Host genome degration - enzymes degrade the OG genome and provide the building blocks for replication of the viral genome

4) Synthesis - ribosomes begin to synthesize the components needed for new viral progeny

5) Release - new assembled progeny are released as the bacterium disintegrates (lysis) due to the action of lysozymes on the host cell wall

Prophase

First part of the M phase, Chromosomes condense

Interphase

Consists of G1 → S → G2

Viruses vs Prokaryotes

Both lack membrane-bound organelles

TO TELL THEM APART:

-Virsues: may posses DNA or RNA genomes, and lack the transcriptional and translational (RIBOSOMES) found in prokaryotes and eukaryotes

What cell-cell junction would help skin cells withstand mechanical stress by directly anchoring the IF of adjacent cells?

DESMOSOMES → provides tensile strength to epithelial cell sheets by anchoring the cytoskeleton

→ not gap junctions or tight junctions, those mediate communication and solutes respectively

Conjugation

Transfer of genetic information from one bacterial cell to another via direct contact (F-FACTOR plasmid, found outside the bacterium’s genome, can integrate into bacterial chromosome)

Transformation

Cellular uptake of foreign DNA from the environment, not other bacteria

Transduction

DNA transfer from one bacterial cell to another via BACTEROPHAGE

Transfection

EUKARYOTIC CELLS → process of which genetic material is introduced

Prokaryotic organisms are classified by…

Shape / MORPHOLOGY

-Bacilli = rod shaped

-Cocci = spherical

-Spirlli = spiral

Gene duplication

Distinct genes within an organism that have high sequence identity, most likely evolutionarily related or having a common origin, arise by gene duplication

→ alternative splicing would be from the same segment of DNA but would produce a similar result

Open Reading frame

Contains a start and stop codon within the same reading frame

Insertion of 3 nucleotide repeats

Won’t shift the reading frame, it would maintain it and would incorporate the same amino acid. It would form an abnormally long protein.

Hybridization

Annealing of two complementary nucleic acid strands, mRNA is a single nucleic acid that is present only in the cytosol of cells that express the corresponding gene

→ helps to determine whether a certain cell expresses a certain gene using another mRNA that is known to be specific to the cell type of interest