da meow bio/biochem

what kind of cells have cell walls?

ALL prokaryotic cells

SOME eukaryotic cells

what cells have peptidoglycan?

Bacteria, specifically prokaryotic cells, comes w cell wall

neurotransmitter pathway pre-post ganglion for sympathetic and parasympathetic neurons

SYMPATHETIC: ACh, norepinephrine

• short, long

PARASYMPATHETIC: ACh, ACh

• long, short

total gametes produced in a single cycle of spermatogenesis and oogenesis

spermatogenesis:

• 4 haploid sperm cells

oogenesis:

• 1 haploid ovum, 2-3 polar bodies

what is transformation

Transformation is the process by which a cell takes up foreign DNA from its environment, resulting in genetic change. This mechanism is commonly observed in bacteria.

what is transduction

Transduction is the process by which a virus transfers genetic material from one bacterium to another, facilitating genetic variation and adaptation. This mechanism often involves bacteriophages, which infect bacterial cells.

what is conjugation

Conjugation is the process by which two bacteria connect and transfer genetic material through a direct physical connection, often via a sex pilus. This process promotes genetic diversity and can involve plasmids.

• can include f factor (fertility plasmid)

disulphide bond are present in which protein structure(s)?

tertiary and quaternary

dehydration synthesis

formation of peptide bond by removing water

western blotting

separate proteins based on size and charge

vmax=

vmax = kcat[e]

size exclusion chromatography separates molecules by

• LARGE molecules = cannot go through pores = EASILY pass through column

• SMALL molecules = get stuck in pores = SLOWLY pass through column

pH range of an amino acid using henderson hasselbach equation

pH = pKa + log [deprotonated]/[protonated]

• ONLY in ionizable amino acids: HER DYCK

reducing sugars: monosaccharides vs disaccharides

MONO = always

DI = ONLY if 1 of the anomeric carbons is not involved in a glycosidic bond

tollens test (silver mirror)

positive = aldehydes present

make COOH

function of PFK-2 in relation to glycolysis n gluconeogenesis. (mention PFK-1 and Fructose-1,6-bisphosphatase)

• converts: F6P —> F-2,6-bisphosphate

  • this ACTIVATES glycolysis = allosterically regulate PFK1

  • INACTIVATE gluconeogenesis = stop F-1,6-bisphosphatase (RLS)

explain ketogenesis

• 2 a-CoA —> via thiolase —> acetoacetyl-CoA

• via HMG-CoA synthase —> HMG-CoA (adding another a-CoA)

• via HMG-CoA lyase —> acetoacetate

  • can do one of two things: decarboxylate to ACETONE

  • reduce to β-hydroxybutyrate

transamination pathway

amino acid + alpha ketoglutarate —> alpha keto acid + glutamate

• give amino group from amino acid to alphaketoglutarate, give a carbonyl to amino

• e.g. alanine n pyruvate, aspartate n OAA

what conditions will cause the LONGEST reannealing time for DNA

• long strands

• LOW pH = h-bond ACCEPTORS protonated, HIGH pH = h-bond DONORS deprotonated

• ionic strength: LOW [salt] = LOW stability

ATCG hydrogen donors and acceptors

AT or AU = 1 donor n 1 acceptor each

CG = GUANINE 2 donors (give) 1 acceptor, cytosine 2 acceptors 1 donor

difference between structure of ribose vs deoxyribose pentose sugars

RIBOSE = OH at 2’ carbon

DEOXYRIBOSE = H atom at 2’ carbon

what direction does dna polymerase move

moves 3’ to 5’

makes strands 5’ to 3’

what does it mean if exonuclease activity is only 3’ to 5’ on growing strand

means nucleotide bases on 3’ are repaired, not 5’ end

endonuclease vs. exonuclease

ENDO = cut into middle of backbone, break phosphodiester bonds. dimers, mismatch repair

EXO = only remove LAST nucleotide, e.g. DNA polymerase correcting as it goes

telomeres n ____ are made of _____

centromeres

made of heterochromatin (tightly condensed complex of DNA wrapped tightly around histones)

native, reducing, n non-reducing SDS page

REDUCING: using DDT, it reduces disulfide bonds and breaks quaternary structure

NONREDUCING: disulfide bonds intact, breaks quaternary structure, use polyacramide gel

NATIVE: disulfide bonds intact, quaternary structure intact, separates proteins by mass, charge and polarity

histones are rich in these 2 amino acids

arginine R

lysine K

• makes histone POSITIVE so it can attract NEGATIVELY charged DNA

• methylation = HETEROCHROMATIN, brings closer together

• acetylation = EUCHROMATIN, unwinds histone

during repolarization, Na+…

Na+ INACTIVATION gates = closed, prevents reentry into membrane

K+ channel = open, ions leave cell membrane

peptide hormones

FLAT PEG, receptors ON cell membrane, soluble in water but cannot cross phospholipid bilayer

posterior pituitary neurohormones

• NOT typical glandular cells, derived from NEURAL tissue at ectoderm

• made in hypothalamus, stored into neurosecretory neuron axons going into PP, released by exocytosis into blood

neutrophils

• usually in blood circulation

• phagocytosis of bacterial cells, INNATE immune system

basophils

• histamine

• help mast cells, anti allergen

eosinophil

• release toxins that kill bacteria/parasites, lead to tissue damage

ectoderm, mesoderm, endoderm results

ECTODERM: nervous system, hair, skin, nails, anus, mouth

MESODERM: bones, muscles, circulatory system, urinary/reproductive

ENDODERM: digestive n respiratory systems, epithelium lining

stop codons

UAG

UGA

UAA

RBC vs. WBC leukocytes location of production

RBC = renal cortex kidney

WBC = bone marrow

____ anchor MUSCLE to BONE

tendons

hyaline cartilage 4 fun facts

• avascular n receives nutrients via surrounding fluids

• endochondral ossificiation aka helps make bone (deposition), linear bone growth at epiphyseal plate in childhood

• no nerves, lacks innervation

• faciliatates joint movement

in bones: epipysis vs diaphysis, spongy vs compact bone

EPI: at the ends of long bones, surrounded by articular cartilage

DIAPH: hollow shaft aka medullary cavity filled w yellow bone marrow

SPONGY: has trabeculae, porous, red bone marrow

COMPACT: aka cortical, harder outer layer, beneath periosteum

despite beta sheets or alpha helix, secondary structures always have ____ bonds

HYDROGEN BONDS between amide n carbonyl

western blot steps

1. protein electrophoresis

2. protein transfer

3. addition of blocking protein

4. addition of primary antibodies, then secondary

5. fluorescence

what is antibody blocking in western blot?

to prevent excess signal, you add blocking protein to the protein-binding membrane (to which you have transfered your desired proteins to) so the antibodies won’t do NONSPECIFIC protein binding

chaperone proteins

help fold proteins correctly

• DECREASE protein aggregation

• INCREASE solubility (e.g. hydrophobic in, hydrophillic out)

proteins with NEGATIVE charge at physiological pH have a ____ isoelectic point pI

LOW. since their net charge of 0 occurs are low pH so pI is low. more H+.

histone n gene expression

ACETYLATION = INCREASE

methylation = DECREASE (meth = bad for you)

3 reactions occurring at complex 2 of ETC

1. succinate oxidized to fumarate, reducing FAD+ to FADH2

2. FADH2 oxidized to FAD+ as electrons shuttled through iron-sulfur center

3. ubiquinone takes electrons from ^ centers = reduced to ubiquionol

stacking interactions between WHICH 3 amino acids can stabilize secondary protein structures?

AROMATIC (Y FW?)

phenylalyine, tyrosine, tryptophan

amino acid that is favourable for beta turns

glycine

amino acid conductive to tight turns in beta sheets

proline

renin n blood pressure

in response to LOW bp = does vasoconstriction to INCREASE bp by inc. sodium n water absorption

good nucleophilic amino acid groups

hydroxyl

thiol

amine

Kd formula

= Kunbinding/Kbinding = Koff/Kon

measurements to determine protein thermal stability

activity assays, circular dichroism, heat capacity measurements

Kcat is impacted by [E]

FALSE

• but equation: Kcat = Vmax/[E]

• cat efficiency = Kcat/Km = Vmax*Km/[E]

adding more [S] or [E] impacts reaction velocity

enzyme, cuz more active sites

natural selection vs. gene flow

NS:

• INC. survival, IMPROVED probability

• BENEFICIAL alleles selected

GF:

• inbound MIGRATION (e.g. AA goes to colony of aa and mates) = small populations BENEFIT = INC. genetic diversity

hardy-weinburg assumptions (5):

1. NO new mutations

2. NO natural selection

3. NO gene flow

4. RANDOM mating

5. LARGE population size

—> allele frequences usually do not change

adaptive radiation and impact

• diversifies characteristics in a single species = diversifies population = improves fitness

kinase vs. phosphatase vs. phosphoryLASE

KINASE: p from ATP to substrate

• TRANSFERASE

phosphaTASE: use h2o, break into free p (remove p)

• HYDROLASE

phosphoryLASE: inorganic p to substrate

• TRANSFERASE

Kcat and Vmax and lineweaver-burke plot relationship

• at [E]tot constant, Kcat proportional to Vmax, even tho Kcat=Vmax/[E]

• INC. slope = DEC. catalytic efficiency = Kcat/Km

• but this also means… INC. slope = Km/Vmax

phosphodiester bond

5’ phosphate n 3’ hydroxyl

nuclear localization sequence

how proteins can enter nucleus

ubiquitination

marks proteins for degradation by a proteasome

rt-pcr can be used to_____

look at changes in protein expression at transcriptional levels

fatty acid activation n transport

autosomal dominant vs. autosomal recessive

DOMINANT:

• only ONE copy of affected gene is required for condition to be expressed

RECESSIVE:

• BOTH copies of affected gene are required for condition to be expressed

restriction enzyme sequences

PALINDROMIC sequence

osmotic vs. hydrostatic pressure

OSMOTIC:

• think MOLAR… water moves INTO HIGH solute concentration

• iB… interstitial to blood

HYDROSTATIC:

• think STATIC aka PHYSICS aka PRESSURE

• water moves from HIGH pressure to LOW pressure

helicase, ligase, topoisomerase, DNA primase, DNA polymerase

HELICASE: open DNA at replication fork, break hydrogen-bonds

LIGASE: seal okazaki fragments, create phosphodiester bond (P-O)

TOPOISOMERASE: prevent supercoiling

PRIMASE: makes RNA primase which is complementary to DNA strand, makes the start point for DNA polymerase

POLYMERASE: 3- goes from 5’-3’ extending primers to make new DNA, 1- repalces the rna primer spot

steroid vs peptide hormones

STEROID: cholesterol built, NOT soluble, NEED transport protein (think… people on steroids NEED assistance)

PEPTIDE: hydrophillic, NO transport protein, bind to receptors

during phosphorylation of tyrosine, what atoms attack what?

• KINASE removes phosphate from ATP to phosphorylate the tyrosine

• hydroxyl group from tyrosine… Hydrogen is taken OUT so tyrosine can become nucleophilic n ATTACH the phosphorus of the phosphate

• why? well the Oxygen atoms on phosphate have the negative dipole so phosphorus is electrophillic

• so… HYDROGEN of hydroxyl = EXCHANGED for PHOSPHATE on ATP

if an enzyme is continuous and upregulated, what happens to the half life of its product?

UPREGULATED = making more very quickly = LOWER half life = FAST regeneration rate

affinity of hemoglobin for oxygen n PO2 during exercise

INCREASE EXERCISE = DEcrease PO2 in muscle = DEcrease affinity for O2 = turn to anaeorbic after a certain period of time

native vs gel filtration… charge or no?

NATIVE = looks at electrophoretic mobility, length, conformation, n charge

GEL = NO charge. ONLY size

how does adding a negative molecule to a protein change its isoelectic point pI?

If you add negative weight (e.g., phosphoglycerol), you have to lower the pH (add more H⁺) to get the see-saw balanced again → pI DECREASES.

so… NEGATIVE add = counter w H+ = DECREASE pI

desmosomes vs gap junctions vs tight junctions

DESMOSOMES:

• provide strength to anchor, TENSION, MECHANICAL stress

• e.g. skin, muscle

GAP JUNCTIONS:

• communication, ions n small molecules pass

• e.g. heart/cardiac, smooth muscle

TIGHT JUNCTIONS:

• prevent water n solutes to go through

• e.g. blood brain barrier, skin, GI tract

large n small prokaryotic vs. eukaryotic subunits

PROKARYOTE: 50-30

• think…the PROs ATE (8= 5+3)

eukaryote: 60-40

what is pI isoelectric point

ratio of cationic n anionic functional groups = 1