bio/biochem meow 1

concepts, questions, unsure/learn

The association observed experimentally between the expression of miRNAs and mRNAs in AR kidney transplants indicates that miRNAs regulate the expression of genes implicated in which type(s) of immune response(s)?

• A. Adaptive immunity only

• B. Humoral immunity only

• C. Innate and cell-mediated immunity only

• D. Adaptive and innate immunity only

A: adaptive immunity

• involves B cells n T cells, memory cells (long lasting protection), SPECIFIC pathogen response

• Humoral: antibody production, B cells (plasma n memory B cells), depend on helper T cells for full activation n B cell differentiation

cells involved in cell-mediated vs. humoral immunity, target, mechanism

cell-mediated:

• cytotoxic T cells, helper T cells, memory T cells, natural killer cells

• target: intracellular pathogens n cancer cells

• mechanism: DIRECT cell killing, regulate immune responses

humoral:

• B cells (plasma n memory), helper T cells

• target: extracellular pathogens like bacteria/virus in blood n mucous

• mechanism: produce antibodies = neutralize pathogens = help remove

cells involved in innate immunity, target, mechanism

• macrophage, neutrophils, dendritic cells, natural killer cells, BEN, mast cells, monocyte

• target: broad, non-specific range of pathogens

• mechanism: immediate, non-specific, phagocytosis, inflammation

what are acetate, propionate, and butyrate examples of? glucose (mono n poly) to what in the GI tract via bacteria?

SHORT CHAIN FATTY ACIDS

disulphide bond vs phosphodiester bonds

disulphide bridge/bond

• between 2 cysteine amino acids in close proximity on a polypeptide chain form COVALENT bond

phosphodiester bond

• between 5’ phosphate and 3’ hydroxyl OH of deoxyribose sugar

Based on the passage, to which phylum does Enterobacter most likely belong?

• A. Actinobacteria

• B. Firmiculate

• C. Bacteroidete

• D. Proteobacteria

D:

• passage said: TWO ** means highly INCREASED. also states CD impacted individuals have highly INCREASED gram negative Proteobacteria… since enterobacter is INCREASED, we can conclude that it belongs in this phylum.

paracrine n autocrine vs endocrine signalling

endocrine: transported by blood vessels to impact tissues all over

autocrine: secrete messengers that act on themselves, act locally

paracrine: secrete messengers that act on cells nearby, act locally

ALL: bind to receptors on or in cells

significance of protein glycosylation

• CRUCIAL for structural conformation of protein, which determines if a ligand will activate its receptor

• function in energy storage, adhesion, and intracellular trafficking, as well as signaling through cell-to-cell interactions

• happens in endoplasmic reticulum n Golgi apparatus

can glycoproteins cross the plasma membrane on their own?

NO, usually too large n charged, polar, has a receptor on plasma surface

In an experiment in which IBU alone was administered to normal mice in order to determine whether long-term treatment with the analgesic can cause behavioral symptoms of depression, what would be the appropriate control group?

• A. Normal mice treated with an SSRI

• B. Depressed mice treated with IBU

• C. Normal mice treated with a placebo

• D. Depressed mice treated with cytokines

C:

• C: CORRECT: shows baseline. mice without IBU vs. mice w IBU (Exp)

• A: WRONG: SSRI decreased depression, so not effective to assess if IBU CAUSES it

• B: WRONG: already depressed mice, IBU is testing on non-depressed mice. to insure that observed symptoms are CAUSED by IBU, must be non-depressed mice

• D: WRONG: already depressed ^.

Which comparison best determines whether IFNγ is necessary for antidepressant-induced increases in the expression of p11?

Expression levels of p11 in:

• A. wild-type mice versus IFNγ knockout mice, both treated with p11

• B. wild-type mice versus IFNγ knockout mice, both treated with an SSRI

• C. wild-type mice treated with IFNγ versus wild-type mice treated with an SSRI

• D. wild-type mice treated with IFNγ versus wild-type mice treated with ibuprofen

B:

• independent variable: IFNy given or not

• dependent variable: p11 expression

• subject: those on antidepressants, SSRI

How does the Unit Membrane Model differ from the Fluid Mosaic Model?

• A. The location of proteins differs in the two models.

• B. The Unit Membrane Model has a monomolecular layer of protein on each surface, while the Fluid Mosaic Model has a bimolecular layer of protein on each surface.

• C. The Unit Membrane Model has one layer of phospholipids, while the Fluid Mosaic Model has two layers.

• D. The Unit Membrane Model contains dissolved protein, while the Fluid Mosaic Model is coated with a monomolecular layer of protein on each surface.

A:

• UMM: proteins form monomolecular layer OUTSIDE n INSIDE bilayer, NO penetration.

• FMM: proteins inserted inside bilayer

BASICS: transformation vs transduction vs conjugation

transFORMATION: transfer genetic material environment —> bacteria

transDUCTION: nucleic acids virus —> cells. During the assembly of new bacteriophages (virus), fragments of bacterial DNA are mistakenly packaged into phage capsids. The phages then inject this DNA into new host cells.

conjugation: EXCHANGE nucleic acids between bacteria

fatty acid chain length, saturation, membrane fluidity, and cholesterol

RIGID N LOW FLUIDITY:

• lots Van Der Waal forces, LONGER chains, saturated

• cholesterol INCREASES fluidity

PERMEABLE N HIGH FLUIDITY:

• less Van Der Waal forces, SHORTER chains, unsaturated

• cholesterol DECREASES fluidity

coding, noncoding, template, mRNA transcript: differences, TOP to BOTTOM

• coding/non-template/SENSE strand @ top. SAME nucleotide sequence as mRNA transcript, but the latter has uracil instead of thymine

• NON-coding/template/ANTI-sense strand @ bottom. mRNA codes from this. both mRNA n sense strand have the OPPOSITE sequence as this

• mRNA transcript @ in between. SAME nucleotide sequence as CODING/non-template/sense strand except w uracil.

where do transcription factors bind?

enhancer or promotor regiion

enterocyte function

• intestinal cells that produce ENZYMES that digest carbs, specifically, disaccharides like LACTOSE

A particular diploid organism is heterozygous in each of 3 unlinked genes. Considering only these 3 genes, how many different types of gametes can this organism produce?

• A. 3

• B. 4

• C. 6

• D. 8

D: 8

• 2³ = 8

• gametes are HAPLOID. organism has 2 options (heterozygous) for each gene, and limited to one allele. 3 gene spots in the haploid chromosome with possibility of 2 alleles each. so 2×2×2

• ABC, ABc, AbC, aBC, Abc, aBc, abc, abC

• if a was HOMOZYGOUS, then 2² = 4. ABC, AbC, ABc, Abc since only 1 option in homozygous

Which type of reaction has a K_eq > 1 and is kinetically fast?

Exergonic with low activation energy level

isoelectric focusing

Separates proteins based on their pIs n uses an electric field and a pH gradient which causes proteins to stop moving at a pH equal to their pI

In an enzyme-catalyzed reaction where enzyme concentration is held constant and substrate concentration is relatively low, which kinetic parameter will increase with the addition of more substrate?

(Note: Other than substrate concentration, assume no other changes to reaction conditions.)

• A. K_M

• B. k_cat

• C. V_max

• D. V₀

D:

• K_M, the rate constant of a reaction, does not change with changes in substrate concentration.

• K_cat is the reaction turnover number and does not change with changes in substrate concentration.

• V_max is the maximum velocity of a reaction and is a constant property which does not change with the addition of more substrate.

• V₀ is the initial velocity of an enzymatic reaction. At low concentrations of substrate and constant enzyme concentration, adding more substrate will increase V₀ until the maximal velocity is reached.

what is the ratio of the cationic (+) to anionic (–) functional groups in a protein at its pI? what about the net charge of the cationic (+) and anionic (–) functional groups?

RATIO at its pI isoelectric point is always ONE 1

NET charge at its pI isoelectric point is ZERO

ionophores

compounds that bind to ions and facilitate their movements across membranes

gel filtration vs. ion exchange chromatography

• gel filtration is done by SIZE of proteins

• ion exchange chromatography is done by CHARGE difference of proteins

3 amino acids w beta branches

isoleucine, valine, threonine

TIV

reduced carbonyl

alcohol group

oxidized aldehyde or ketone

carboxylic acid (extreme for ketone)

what molecule is this

adenine, purine

what molecule is this

guanine, purine

what molecule is this

cytosine, pyrimidine

what molecule is this

thymine, pyrimidine

what molecule is this

uracil, pyrimidine

what happens to the pOH and [OH-] as you go from a HIGHLY acidic environment to a less acidic one?

• HIGH acidic = LOW pH… transition to LOW acidic… HIGH pH

• this means LOW pOH, which means HIGH [OH-]

electrolytic vs galvanic cell

electrolytic: DECOMPOSITION, non-spontaneous, delta G>0, endergonic, electric current supplied

galvanic: DECOMPOSITION, SPONtaneous, delta G<0, exergonic, electric current produced (opposite of electron flow)

purpose of a boiling chip

provide nucleation sites so the liquid boils smoothly without becoming superheated or bumping

3 common metals that form green precipitate, n why

chromium, iron, nickel

transition metals, partly filled D orbitals

acid + metal carbonate —>

—> salt + water + CO2

resonance effect vs inductive effect

is a molecule more or less stable when a side group is ionized and can form hydrogen bonds with another side group?

more stable

strong acids n bases

What is the sum of the protons, neutrons, and electrons in strontium–90?

mass number 90 = pro + neutrons

atomic number 38 = pro and electrons

sum = mass number + 38 electrons = 128

A lower-than-normal blood pressure will cause what effect on the rate of plasma clearance of Substance A?

low BP = LOW glomerular filtration rate aka how fast the filtrate moves through system = MORE time for water reabsorption = DECREASE RATE of plasma clearance n urine output

3 properties of DNA in prokaryotes

1. circular DNA

2. double-stranded DNA

3. NO telomeres

fermentation in prokaryote vs eukaryote

PROKARYOTE: pyruvate —> alcohol

EUKARYOTE: pyruvate —> lactic acid

NADH to NAD+

DNA mismatch repair system 4 steps

1. detect mismatch

2. endonuclease enzyme cleaves mismatched nucleotide n ADJACENT ones

3. DNA polymerase replaces n adds correct nucleotides

4. DNA ligase forms phosphodiester bonds n seals the nicks

KEY WORDS associated w these 3:

• endocytosis

• phagocytosis

• pinocytosis

endo - inward budding

phago - extend n engulf

pino - invagination, non-receptor binding

lipid rafts facts 3

• cholesterol rich

• contain a higher concentration of the phospholipid sphingom

• Signalling hotspots that LONG transmembrane proteins (LATERAL migration) can live in

peroxisome

• have REDOX enzymes

• help keep oxidation of cell (make H2O2 hydrogen peroxide)

protein secretory pathway, explain it

1. mRNA sent to cytosol to be translated

2. ribosomes detect special signal sequence for secretory proteins n then are sent to RER to have post-translational modifications

3. protein packaged into vescicles = sent to golgi

4. golgi processes n packages proteins —> sent to fuse w membrane n become receptor proteins

kinetochore is…

• metaphase

• where the spindle fibres made from microtubules connect to

does inhibiting lysosomal trafficking impact viral protein processing?

NO because lysosomes play a part in inhibiting ENTRY of viruses but once they are inside, lysosomal function is to degrade MACROMOLECULES not proteins