Week One Objectives Flashcards

Question

Describe relationship between DNA coding strand, DNA template strand, and mRNA

Answer 1

coding strand is compelmentary to template strand, mRNA is complementary to template strand but T's turn into U's

Answer 2

1.RNA polymerase holoenzyme forms (core pol plus sigma) 2.RNA pol and Sigma Factor bind to promoter, causing DNA strands to unwind and separate 3.Sigma Factor is release at approx. 10 nucleotides 4.Elongation continues until RNA pol finds termination signal a. Hairpin loop b. Binding of protein Rho c. Note- termination signals are encoded in DNA and many function by forming RNA structure that destabilizes pols grip on RNA

Answer 3

1. transcription factors bind promoter and help RNA pol bind 2. Other factors and RNA pol assemble at promoter 3.TFIIH opens helix, looses transcription factors 4. Elongation factors associate 5. topoisomerases relieve tension in supercoiling 6. Addition of 5' cap 7. Addition of 3' poly A tail 8. Introns are spliced out, exons put together 9. mRNA is bound to proteins that stabilize and transport through nuclear pores in cytosol

Answer 4

45S is cleaved to produce 18S, 28S, 5.8S

Answer 5

If there is a mutation that would change the amino acid pair with that codon, it will change the folding of the resulting protein

Answer 6

• 64 three nucleotide codons in mRNA encode for 20 amino acids, plus translation start and stop signals; most amino acids have multiple codons; codons are read 5′ to 3′ with the 5′ terminal nucleotide at the left

Answer 7

• tRNAs have clover leaf type structure with two critical spots 1. Anticodon- 3 consecutive nucleotides that pairs with the complementary codon on the mRNA 2. Short single stranded region on 3’ end which recognizes and binds to specific amino acids that correspond to the codon • tRNAs are responsible for pairing the correct amino acid with the correct codon of the mRNA sequence

Answer 8

• Tolerate mismatch at third position- tRNAs are constructed so that they require accurate base pairing only at the first two positions of the codon

Answer 9

• Initiation- eIFs put initiator tRNA into small ribo subunit, small subunit binds mRNA at 5’ end, goes until finds AUG, eIFs dissociate and allow large ribo subunit to bind • Elongation- New tRNA is put in A site, growing chain in P site, “empty” tRNA is E site, high energy bond broken between tRNA and AA, and energy put towards making new peptide bond (elongation factors drive rxn forward) • Termination- Signaled by stop codons (UAA, UAG, UGA), tRNA doesn’t recognize those and signals ribosome to stop translating

Answer 10

• Similar process • prokaryotic translation can occur during transcription (eukaryotic can’t) • Ribosome sizes are different • Prokaryotic ribosomes don’t need a 5’ cap to begin translation

Answer 11

2,3 BPG decreases hemoglobins affinity for oxygen by altering its structure, shifting curve to right

Answer 12

noenzymatic, irreversible glycosylation related to amount of hemoglobin related to amount of glucose in blood (can cause aggregation)

Answer 13

Sickle cell allele has valine at position 6 in beta chain Anemia- HbSS Carrier- HbSA Disease- HbS[not S or A] \*more aggregation occurs in deoxygenated state

Answer 14

-sickled hemoglobin results in a lot of hemolysis -liver needs to work harder produces excess bilirubin -liver is not able to excrete bilirubin

Answer 15

if pH \< pKa is acidic form (protonated) if pH \> pka is basic form (deprotonated)

Answer 16

Chaperones help to fold proteins correctly. New cancer drugs target chaperones Cancer cells have many misfolded proteins and have increased levels of chaperones By inhibiting chaperones, the cell well have to many misfolded proteins and need to commit suicide

Answer 17

increase in beta sheets leads to self-association and the formation of amyloid fibers

Answer 18

Tails of histones are modified by acetylation (by adding acetyl group the overall positive charge on lysing is removing making it more difficult to neutralize the negative charge on DNA. HATS- histone acetyltransferases- makes euchromatin -open to transcription HDAC-histone deacetyltransferases-makes heterochromatin- closed to transcription \*HDACs are upregualted in cancer cells to silence tumor suppressor gene, HDAC inhibitor are used as anticancer drugs

Answer 19

Vitamins- act as cofactors for enzymes Cofactors- binds to active site of enzyme, can be bound for lifetime of the enzymes or can bin transiently like other substrate or product Apoenzymes- enyme without its cofactor Holoenzymes- enzyme + cofactor (able to convert substrate to product)

Answer 20

Thymine dimers- heat excited pryimidines and adjacent bases form covalent dimers (nucleotide excision repair) Deamination- removal of NH3 (coverts cytosine to uracil) (base excision repair) Depurination- looses guanine or adenine (base excision repair)

Answer 21

ionizing radiation, oxidizing agents, replication errors, certain metabolic cellular products

Answer 22

Non-homologus end joining- (most common), creates overhangs, fills in, ligates together (loss of sequence)- occurs in G1 phase, utilizing Ku protein for end recognition of double stranded breaks Homolgous end joining- untilizes undamaged homolgous chromosome and general recombination mechanisms - no loss of sequence, more work for cell, RAD 51 protein mediates

Answer 23

1. Recognizes mis matched base 2. MutS binds specifically to a mismatched base 3. Mut L looks for nick (newly made strand) upstream and triggers degradation of the nicked strand all the way back through the mis match 4. DNA pol goes back to repair

Answer 24

single base repair, recognizes wrong base 1. glycosylase takes out base 2. Ap endonuclease and phosphodiesterase removes sugar and phosphate 3. DNA pol adds new nucleotides, ligase seals nick

Answer 25

- recognizes T dimers - excision nuclease takes out problem area - DNA pol adds new nucleotides, ligase seals nick

Answer 26

Pro-carcinogen produced by cigarette smoke Needs oxidation to be carcinogenic Binds covalently with guanine residues in DNA (bulky adducts, interrupts G-C base pairing and distorts double helix) Results in G to A transisition mutation (purine to purine) \*p53 tumor suppressor gene is mutant in most cancers (espcially lung cancers)

Answer 27

Glucose enters the cell by facilitated diffusion through GLUT transporters GLUT 1 & 3: most cells/ hight affinity (Kd= 1 mM) GLUT 2: liver and pancrease/ low affinity (Kd= 15-20) GLUT 4: insulin induced/ medium affinity (Kd= 5) SGLT: intestinal/ kidney (secondary active transport with Na+ gradient) Note: if blood [glucose] is \> Kd constant, cells will be utilizing those transporters

Answer 28

For M.M.: If line shifts to the left- it is an activator If line shifts to the right- it is an inhibitor If line goes from sigmoidal to hyperbolic it is allosteric activator/inhibitor For L.B.: (y-intercept is inverse Vmax, x-intercept is inverse Km) Inhibitor (slope increases) Competitive inhibition: Y intercept stays the same Non competitive inhibition: X intercept stays thesame Closer line is to 0 the bigger it gets

Answer 29

First regulatory step in glycolysis Hexokinase: found in most cells, low Km Glucokinase: found in liver, high Km Regulated by products/reactants- makes glucose 6-phophate which also inhibits it

Answer 30

Activators: AMP, and Fructose 2-6, bisphophate Inhibitors: ATP, and citrate Note\*\* fructose 2,6 bisphophate is made from fructose 6-phosphate when there is access (PFK1's reactant)

Answer 31

1. hexokinase/glucokinase 2. phosphofructorkinase 3. Pyruvate kinase

Answer 32

No trp= operon on -\> makes trp lots of trp -\> binds to repressor -\> makes repressor active and bind to DNA -\> no trp

Answer 33

Lactose present: Lactose present inceases allactose, allactose binds to repressor and removes from operator Glucose present: Glucose decreases [cAMP], cAMP no longer binds CAP(gene activator), CAP dissociates from DNA turning off operon \*In order for operon to be ON, needs to be lactose and no glucose

Answer 34

heritable, reversible changes in genome (NO CHANGE IN SEQUENCE)

Answer 35

two XX chromosomes one is randomly silenced, my single RNA (XIST) all progeny will have the same X chromosome silenced (direct inheritance of the pattern of chromosome condensation)

Answer 36

differential expression of a gene allele depending on parental origin imprinting is created in parental germ cells- if paternally imprinted- both alleles in male germ line are methylated

Answer 37

Reactions: decarboxylase Precursor: Thaimine From foods: meat, legumes Deficiency: Beri Beri (headache malaise, peripheral neurpathy, heart failure)

Answer 38

Reaction: acetyl transferase No vitamin precusor Wide spread in diet, no know deficiencies

Answer 39

Reactions: acetyl group acceptor (acyltransferase) Wide spread in diet no known deficiencies

Answer 40

Rxn :Electron acceptor (oxidizes lipoate) Precursor: Riboflavin Found in: mushrooms, organ meats, legumes Deficiency: cheilosis, glossitits, keratitis

Answer 41

Rxn: electron acceptor (oxidized FADH2) Precursor: Niacin Found in: fortified grains, meats Deficiency: Pellagra 3D's dermatits, diarrhea, dementia

Answer 42

Rxns: carboxylase Rxns wide spread in diet can be free or protein bound regeneratable Deficiency- raw eggs, Aviden binds to biotin

Answer 43

Reactions: Hydroxylase Vitamin C, no precursor/ not modified by body Deficiency- Scury slow wound healing, irritability, apathy, anemia

Answer 44

Rxns: transaminases Precursor: B6 vitamins Found in: fortified cerals, meat, bananas, rice Deficiency: peripheral neuropathy, siezures/ anemia in infants Test: If siezures resolve with pyridoxal but no pryidoxine then it is a pyridoxine oxidase deficiency If either one works then it was an antiquitin deficiency

Answer 45

Alanine Proline Valine Leucine Isolucine Tyrptophaon Phenyalanine Tyrosine (hydrophobic stacking with rings)

Answer 46

Asparagine glutamine serine threonine tryosine cysteine

Answer 47

Aspartate Glutamate Arginine Lysine Histidine