BIO Flashcards
ubiquination
targets protein for degradation by proteasome
structure of purine vs pyrimidine
Purine: two rings ( G has carbonyl, adenine has amine) Pyrimidine: one ring. Uracil/T has two carbonyl, cytosine has amine)
What methodology to use to examine post-translational modifications to proteins (i.e. histone acetylation)
Western Blot
Prion
abnormally folded protein that induces a normally folded version of the protein to also adopt the abnormal structure, which is often deleterious
where in male reproductive system do gametes become motile
Epididymis. Sperm is produced in the seminiferous tubules of the testes, completes maturation and becomes motile in the epididymis
Why don’t microfilament lengths NOT change when sarcomere shortens in a muscle contraction?
the - end of the microfilaments are capped by Z lines, and the + ends are capped by another protein. actin monomers cannot be added or subtracted
Conjugation (bacteria)
the plasmid genes of one bacterium direct the building of a cytoplasmic bridge (sexpilus) between that organism and a bacteria lacking it
bacterial form of mating (sex reproduction)
what structure do bacteria use to carry out ox phos
PM
what stage would a nondividing cell most likely be in
Go or G1. cell remains metabolically active, but is not replicating DNA
effect of opiates on eyes
pinpoint pupils. constrict. PSNS stimulation cause iris to contract
when do mitotic divisions of oogonia occur in women
before birth
adaptive radiation
divergence of one species into multiple species over time, which can occur when subgroups of the original species are separated or isolated in different environments so that these subgroups evolve independently of one another
Hardy Weinberg
p^2 + 2pq + q^2 = 1 where p^2= freq dominant allele q^2= freq recessive 2pg= freq hetero
ectoderm
NS, epidermis
mesoderm
blood cells, connective tissue (muscles, bones), several organs (heart, gonads, kidney)
endoderm
lining of digestive tract, associated organs (i.e. liver)
which a.a. can be phosphorylated
serine and threonine (OH)
average molecular weight of a.a.
110 Da
Hill coefficient
measure of cooperativity. Hill coefficient >1 means enzyme demonstrates positive cooperativity n<1= negative cooperativity n=1: no cooperativity
catalytic efficient
kcat/km Kcat= turnover number (substrates –> product/ sec) Km= affinity
noncompetitive inhibitor
bind E and ES with same affinity decrease Vmax (not Km)
competitive inhibitor
bind in place of S, increase Km
uncompetitive
bind allosteric site after S has bound. decreases Km and Vmax (ratio might be same)
mixed inhibitor
bind allosteric site either before or after S has bound, but has higher affinity for one state over the other. if binds more readily to enzyme, Km is higher if binds more readily to ES, Km is lower DECREASE Vmax
lineweaver burke plot
slope: Km/Vmax Y intercept: 1/Vmax X intercept: 1/Km
Michaelis Menten eq
Vo= Vmax[S]/ (Km + [S] )
kcat
Vmax/[E]t how many S and E can turn into P per second at max speed
how are different protein isoforms created?
synthesized from same gene through alternative splicing, during which sections of introns and exons are spliced. different combos of exons can create different protein isoforms
effect of reducing agent on protein
cleaves disulfide bonds
convergent evolution
distantly related organisms independtly evolve similar traits (i.e. dolphins and sharks)
what does fasting and starvation lead to
fasting: glycogen breakdown, gluconeogenesis continued fasting: sustained FA oxidation, thereby production ketone bodies
restriction enzymes
recognize specific DNA sequences, cut in predictable manner. most recognize palindroic sequences: both strands of DNA will have same sequence when read 5-3
what type of restriction enzyme could recognize this sequence CCCCGGGC
4 bp or 6 bp
imprinted gene
expressed in parent-specific manner
order in which filtrate passes through nephron
BC, PT, Loop of Henle, DT, CD
cytochrome P450 mechanism
monooxygenases, where an oxygen atom is inserted into a substrate (the drug of interest), thereby resulting in the oxidation of the substrate.
fatty acid oxidation location
MITOCHONDRIA. carnitine shuttle, transports fatty acids into the mitochondria for oxidization
henry’s law
The Henry’s Law constant kH relates the solubility of a gas S to the pressure of that gas Pg above the solution and is written as S = kH•Pg
vaccine suitability
there are two aspects to consider: immunogenicity and toxicity can’t choose part of pathogen that is toxic
eukaryote vs prokaryote ribosome size
Eukaryotes=even 40s, 60s, and 80s 60s=large Prokaryotes= 30s, 50s, 70s large subunit=50s
order of aminoacyl transferase tRNA translation
A site –> P site –> E site
quantitative vs RT PCR
quantitative: measure DNA RT: mRNA RT-PCR = Reverse Transcriptase PCR. Amplifies RNA by making cDNA and then amplifying it. Lets you know if the RNA you are looking for is in sample. qPCR = Quantitative PCR. Fluorescent probes are added to genetic material to count how much you have. 1 Fluorescent Event = 1 Additional Transcript amplified. A computer reads fluorescence and lets you know how how much genetic material you have quantitatively.
native page
Native PAGE is used to separate molecules based on their electrophoretic mobility, relying on length, conformation, and charge.
gel filtration chromatogrpahy
Gel filtration chromatography separates protein only on the basis of their size.
tight junction
intercellular junctions that prevent the movement of solutes within the space between adjacent cells. In blood capillaries, neighboring endothelial cells form tight junctions with one another to restrict the diffusion of harmful substances and large molecules into the interstitial fluid surrounding the brain BBB
non-disjunction
sister chromatids fail to separate during cell division
SER
redominant site of lipid synthesis specifically of phospholipids and cholesterol
stop and start codons
initiation: AUG termination: UAA, UGA, UAG ur an ass, ur giant ass, ur a giant
4 complexes of ETC
- NADH-CoQ oxidoreductase: Uses Fe-S cluster to transfer e- NADH –> NAD+ & H+ (4 protons pumped into IMM space)
- Succinate-CoQ oxidoreductase. Uses Fe-S cluster to transfer e- Succinate –> Fumarate + 2H+. NO PROTONS PUMPED
- CoQH2-Cytochrome C oxidoreductase: uses Fe-S cluster to transfer e- from CoQH2 to heme, forming cytochrome C (FOUR PROTONS PUMPED)
- Cytochrome C Oxidase: Uses cytochromes and Cu to transfer e in form of H- from cytochrome C to O2 forming water (TWO PROTONS PUMPED
glycogen synthase
creates α-1,4 glycosidic links between glucose molecules. It is activated by insulin in the liver and muscles
branching enzyme
moves a block of oligoglucose from one chain and connects it as a branch using an α-1,6 glycosidic link.
summary E yield from carb metabolism
- Glycolysis: 2 ATP, 2 NADH
- pyruvate dehydrogenase: 2 NADH
- TCA: 6 NADH, 2 FADH2, 2 GTP
each NADH=2.5 (2.5*10)= 25 ATP
each FADH2= 1.5 (1.5*2)= 3
GTP=ATP= 2
ATP: 2
total yield: 30-32
glycogen phosphorylase
removes single glucose 1-phosphate molecules by breaking α-1,4 glycosidic links. In the liver, it is activated by glucagon to prevent low blood sugar. In exercising skeletal muscle, it is activated by epinephrine and AMP to provide glucose for the muscle itself
debranching enzyme
moves a block of oligoglucose from one branch and connects it to the chain using an α-1,4 glycosidic link
gluconeogenesis
where does tit occur?
three irreversible steps
occrs in cyto and Mi, predominantly in liver
mostly the reverse of glycolysis using same enzymes
The three irreversible steps of glycolysis must be bypassed by different enzymes:
- Pyruvate carboxylase and PEP carboxykinase bypass pyruvate kinase
- Fructose-1,6-bisphosphatase bypasses phosphofructokinase-1
- Glucose-6-phosphatase bypasses hexokinase/ glucokinase
pentose phosphate pathway
- diverts Glucose-6-phosphate from glycolysis
- key enzyme (RL): glucose-6-phosphate dehydrogenase
- forms NADPH (reducing agent in FA synthesis) & ribose-5-phosphate (nucleotide synthesis)
- stimulated by NADP+, inhibited by NADPH
postprandial metabolic state
well-fed (absorptive)
insulin secretion high, anabolic catabolism prevails
postabsorptive state
fasting
insulin secretion low, glucagon and catecholamine secretion icnreases
how are lipids transported
chylomicrons, VLDL, IDL, LDL, HDL
HMG-CoA reductase
key enzyme in cholesterol synthesis
palmitic acid
only FA that humans can synthesize, produced in cytoplasm from acetyl CoA transported out of Mi
FA oxidation
occurs in mitochondria following tranposrt by cartinine shuttle
via beta oxidation
end up with x/2 acetly coA molecules, where x is number of C in chain
ketogenesis
protein digestion
primarily in small intestine. carbon skeletons of a.a. used for energy, either through gluconeogenesis or ketone bodie formatino
amino groups fed into urea cycle for excretion
tissue-specific metabolism:
liver
adipose
resting muscle
active muscle
heart
brain
- Liver: maintains blood glucose through glycogenolysis and gluconeogenesis. Processes lipids, cholesterol, bile, urea, and toxins.
- Adipose: stores and releases lipids
- Resting muscle: conserves carbohydrates as glycogen and uses free fatty acids for fuel
- Active muscle: may use anaerobic metabolism, oxidative phosphorylation, direct phosphorylation (creatine phosphate), or fatty acid oxidation
- Cardiac muscle: uses fatty acid oxidation
- Brain: uses glucose except in prolonged starvation, when it can use ketolysis
SER vs RER
RER: ribosomes stud outside. site synthesis proteins destined for secretion or inertion into a membrane
SER: lipid synthesis, detoxification
peroxisome
organelle containing hydrogen peroxide, site of β-oxidation of very long chain FA
gram + vs - bacteria
gram +: large quantities PG in cell wall
gram-: smaller quantites PG with LPS
cell cycle
G1: cell increases its organelles and cytoplasm
S: DNA replication
G2: same as G1
M: cell division
(G1+G2+S= interphase. Go=permanently stuck in interphase)
MITOSIS
PMAT
Prophase:nucleolus dissapears, spindles/kinetochores appear, nuclear envelope converts into vesicles
Metaphase: chromosomes line up at metaphase plate, pulled to opposite pole
Anaphse: spindle fibres shorten, centromeres pull apart
telophase: nuclear membrane forms around chromosomes
MEIOSIS
production haploid from diploid
in males, meiosis occurs in testis, haploid spermatazoa are end result
in F, meiosis begins in ovaries, completed after fertilization. arrested in prophase 1 for decades, reeneter meiosis at puberty. ovulation after meiosis 1 yields secondary oocyte and polar body, 2nd meiosis only occurs if fertilized.
(spermatagonia and oogonia undergo meiosis)
Prophase 1: chromosomes condense, nuc envelope breakdown. homologous chromosomes pair in synapsis to form tetrad. DNA is cut, genes are crossed over (recombination)
Metaphase 1: align at plate
Anaphase 1: homologous chromosomes separate, sisters remain together
telophase 1: cell divides into 2 (still haploid), each cell has single set of chromosomes. NO FURTHER DNA REPLICATION BEFORE MEIOSIS 2
meiosis 2: basically same as mitosis, but no replication
4 stages of early development
Cleavage: mitotic divisions
Implantation: embryo implants during blastula stage
Gastrulation: ecto, endo, mesoderm form
Neurulation: germ layers develop into NS
CIG, NOW!
3 germ layers
Ecto (attracto): brains, and looks (NS, epidermis), lens of eye, inner ear
Meso (middle): bones, blood, muscles, circulatory
Endo (anus is the end): digestive, respiratory, liver, pancreas
layers of skin
Epidermis: keratinocytes, melanocytes, langerhans, Merkel
- Stratum corneum
- Stratum lucidum
- stratum granulosum
- stratum spinosum
- stratum basale
(come lets get sub burnt)
Dermis
- papillary dermis
- reticular dermis
(pretty red)
- nerves, capillary
SubQ
- vein, artery
Aldosterone and ADH
Aldosterone: stimulates Na+ reabsorption, K+ and H+ secretion (interstitial –> filtrate), increasing water reabsorption, BV & BP
ADH: increase CD permeability to water, increase water reabsorption
Anterior Pituitary hormones
FLAT PEG
FSH: stimulate follicle maturation, spermatogenesis
LH: stimulate ovulation, T synthesis
ACTH: stimulate adrenal cortex to make/release GCs
TSH:stimulate Thyroid to produce TH
PRL: milk production
Endorphins: inhibit pain perception in brain
GH:stimulate bone/muscle grow, lipolysis
Posterior pituitary hormones
OT, ADH/vasopressin
Thyroid hormones
TH: stimulate metabolic activity
calcitonin: decreases (TONES down) blood Ca level
“calciTONin, TONES down CA”
PTH
increases blood Ca
glucocorticoids & mineralcorticoids
GC: increase blood glu levels, decrease protein synthesis, antiinflammatory
MC: increase H2O reabosprtion kidney
Adrenal medulla hormones
EP, NE. increse HR and blood glu
pancrease hormones
insulin: decrease blood glu, increase glycogen store
glucagon: increase blood glu, stimulate conversion glycogen –> glu
somatostatin: suppress secretion of glucagon and insulni
hormone from heart
atrial natriuretic peptide
osmoregulation, vasodilation
thymus hormone
thymosin
stimulate TC developement
4 stages menstrual cycle
- Follicular: FSH causes growth of a follicle
- Ovulation: LH causes follicle to release egg
- Luteal: corpus luteum forms
- Menstruation: endometrial lining sheds
sarcomere
Z: end of sarcomere (z is end of alphabet)
I: only thin filaments (I is thin letter)
H: region with only thick (H is thick)
M line: middle
A: both thick and thin
circulatory pathway through heart
Superior and inferior vena cava → right atrium → right ventricle → pulmonary arteries → lungs→ pulmonary veins → left atrium → left ventricle → aorta → body
3 portal systems
hepatic, kidney, brain (hypophyseal)
fetal circulation
- Foramen ovale: connects right and left atria
- Ductus arteriosus: connects pulmonary artery to aorta. Along with foramen ovale, shunts blood away from lungs
- Ductus venosus: connects umbilical vein to inferior vena cava, connecting umbilical circulation to central circulation
componenets of blood
Plasma: aqueous mix of nutrients, wastes, hormones, blood proteins, gases, and salts Erythrocytes (red blood cells): carry oxygen
factors that lead to a right shift of Oxy-HGB curve
(right shift = decreased affinity)
- ↑ Temperature
- Bohr Effect ↓ pH, ↑ PCO2
- O2 release to tissues enhanced when H+ allosterically binds to Hb. ↑ PCO2 leads to ↑ [H+]:
platelet function
clotting
platelets release thromboplastin. converts inactive prothrombin into thrombin. thrombin converts fibrinogen into firbin, surrounds blood cells to form clot
law of segregation
what happens if both parents are Rr
homologous alleles (chromosomes) separate so that each gamete has one copy of each gene
if both parents are Rr, the alleles separate to give a genotypic ratio of 1:2:1, and a phenotype ratio of 3:1
law of independent assortment
alleles of unlinked genes assort independently in meiosis
for two trais: AaBb parents will produce AB, Ab, aB, ab gametes
the phenotypic ratio is 9:3:3:1
codominance vs incomplete
co: both alleles expressed. both traits show up. (i.e. get red and blue flowers)
incomplete: mix of alleles in genotype seen in phenotype (i.e. red and blue parent flowers: get purple)
patterns of inheritance: autosomal recessive, dominant & X-linked
- Autosomal recessive: skips generations
- Autosomal dominant: appears in every generation
- X-linked (sex-linked): no male-to-male transmission, and more males are affected
Hardy-Weinberg equation and assumption
Assume:
- no mutations
- large population
- random mating
- no migration
- equal reproductive success
p + q = 1 p2 + 2pq + q2 = 1
p = frequency of dominant allele
q = frequency of recessive allele
p2 = frequency of dominant homozygotes
2pq = frequency of heterozygotes
q2 = frequency of recessive homozygotes
lytic vs lysogenic viruses
