Biomed final Dr. R Van Der Hoeven

What is RNA editing

(post transcriptional regulation) nucleotides can be deleted or added

In Prokaryotes the start of transcription is denoted by

+1 site

How is mRNA modified?

- 5' cap - poly A 3 ' end - spliceosome removes introns

Intermediates in fatty acid synthesis are linked to what carrier? B-oxydation (degradation)?

- Acyl carrier protein - Coenzyme A

Calcium and AMP also affect glycogen metabolism in the muscles. How so?

- Calcium: binds calmodulin and activates phosphorylase b - AMP: allosterically binds to phosphorylase b

Prok DNA replication requires what 2 things

- Free 3'-OH - dNTPs

What are the enzymes used during glycogen degradation (3)

- Glycogen phosphorylase - Transferase - Alpha 1,6 glucosidase (deb ranching enzyme)

Which AA contribute to positive charge

- Histidine - Lysine - Arginine

What type of bonding holds tertiary structure together? (4)

- Ionic - H bonds - disulfide bonds - hydrophobic bonds

What are the 4 principles of metabolic pathways

- Irreversible - Each has a first committed step - All are regulated - Occur in specific cellular locations

How does a uncompetitive inhibitor influence Km and Vmax

- Km and Vmax decrease (needs less substrate to reach Vmax) (

How does competitive inhibitors influence Km and Vmax

- Km increases - Vmax stays the same (adding more substrate will overcome the inhibitor)

How does a non-competitive (allosteric) inhibitor influence Km and Vmax

- Km remains the same - Vmax decreases

what are the 4 complexes of the electron transport chain

- NADH dehydrogenase • complex - Succinate dehydrogenase - Cytochrome b-c complex) - Cytochrome oxidase

The reductant in fatty acid synthesis is __________, whereas the oxidants in fatty acid degradation are _____ and ______

- NADPH - NAD+ and FAD

What are the 3 rate limiting enzymes of glycolysis?

- Phosphofructokinase (PFK-1) - Pyruvate kinase - Hexokinase

What are the 2 mobile carries

- Q ubiquinone (for FADH2) Cytochrome C

What is Km (2)

- Substrate concentration at 1/2 Vmax - measure of enzyme affinity to the substrate

What are Cis-elements (2)

- TATA and CAAT boxes in eukaryote transcription - Where enhancers bind

Rate of heat transfer in conduction is dependent upon (3)

- Temperature difference - Thermal conductivity of the object - Small fraction of heat lost via conduction to surrounding air (very close to body)

What are the 3 forms of DNA

- Z DNA - B DNA (most prominent) - A DNA

Phosphorylating glycogen phosphorylase b will do what to it? Phosphorylating glycogen synthase 1 will do what to it?

- activate it - inactivate it

B-oxidation is stimulated by? Inhibited?

- adipose tissue lipase - carnitine any transferase

What are 4 chemical buffer systems in the human body

- bicarbonate - hemoglobin - phosphate - proteins

What do strong acids do when they are added to solution Weak acids?

- completely dissociate - partially dissociate (acid is converted into conjugate base)

What are the two mechanisms of cooperativity

- concerted - Sequential

What does branching enzyme do?

- creates branches on glycogen - break alpha 1,4 forms alpha 1,6

Where does fatty acid synthesis occur? B-oxydation (degradation)?

- cytosol - mitochondrial matrix

What does Protein phosphatase (PP1) do (2)

- deactivates phosphorylase kinase - activates synthase

In the liver low glucose stimulates what? Inhibits what?

- glycogen breakdown - inhibits glycolysis

What are the two enzymes involved in glycogen synthesis

- glycogen synthase - Branching enzyme

What are the enzymes involved in Prokaryote DNA replication (5)

- helicase - Single stranded binding proteins - DNA gyrase (topoisomerase) - DNA polymerase 1, 2, 3 - DNA ligase

What are the structural (irreversible) methods of enzyme activity regulation (3)

- lipid modification - y-carboxylation - glycosylation

Catabolic reactions are favored when energy charge is ______ While anabolic reactions are favored when it is ______

- low (exergonic rxn) - high (endergonic rxn)

What does glycogen do in the muscles vs the liver

- muscles: used to regenerate ATP during exercise - liver: used to supply glucose for brain

Bacteria have how many RNA polymerases? Eukaryotes?

- one RNA pol - 3 RNA pols: Type 1 (rRNA), Type II (mRNA and microRNA), Type III (tRNA)

What do single-stranded binding proteins do? (2)

- prevent strands from reassociating - prevents the single strands from being cleaved by endonucleases

What are the 4 mechanisms of heat flow

- radiation - conduction (direct contact) - Convection - Evaporation

What are microRNAs

- small RNA molecules synthesized by RNA pol II - inhibit or stall translation

In prokaryotes polymerase binds at the __ and __ sites

-10 and -35

pH= log(1/H+)= __________

-log(H+)

If all AMP, energy charge =

0

When [P]/[S] = 1.0, deltaG =

0 (equilibrium)

If all ATP energy charge =

1.0

ATPase requires an influx of how many protons to make one ATP

3

Pol I, II, and III have ________ exonuclease activity

3'-5' (pol 1 also have 5'-3' activity)

DNA is always synthesized in what direction?

5' to 3'

With cooperative binding hemoglobin releases __% of O2 Without it releases __%

66% 38%

What is normal blood pH

7.4

When [P]/[S] > 1, deltaG is

<0 (rxn favors products)

When [P]/[S] < 1, deltaG is

>0 (rxn favors reactants)

What is substrate level phosphorylation?

ADP to ATP independent of the electron transport chain

Formation of malonyl CoA is catalyzed by

Acetyl CoA carboxylase (rate limiting step)

Which AA contribute a negative charge

Aspartate glutamate (cysteine and tyrosine but at higher pH)

What does acidosis cause?

CNS depression

What does Phosphofructokinase (PFK-1) do

Converts fructose 6-phosphate to fructose 1,6-bisphosphate

What is the central dogma of molecular biology?

DNA -> RNA -> Protein

Prokaryote DNA replication, What does Pol II do

DNA Repair

What is the major DNA polymerase in Prokaryote DNA replication?

DNA pol III (synthesis continuously)

How are ketone bodies produced

From acetyl CoA when fat breakdown predominates (in Liver)

What determines the spontaneity of a rxn

Gibbs free energy between the products and reactants

Beta sheets are strands and chains held together by

H-bonding

What is Pyruvate kinase inhibited by? Stimulated?

Inhibited by: ATP, alanine Stimulated: F-1,6-BP

What is Phosphofructokinase (PFK-1) inhibited by? What is it stimulated by

Inhibited: ATP, Citrate, H+ Stim: F-2,6-BP and AMP

What does polycistronic mean?

More than one gene per one mRNA (prokaryotes)

What are the 2 electron carries of oxidative phosphorylation

NADH FADH2

Is there proof reading in prokaryote transcription

No

What is the final electron acceptor of oxidative phosphorylation?

O2

In prokaryotes replication begins at

Ori C site

In DNA replication of Eukaryotes the basic mechanism is the same as

Prokaryotes

Activators and repressors of transcription bind upstream and downstream to the start of transcription in (Prokaryotic or Eukaryotic) Promoters

Prokaryotic

When pH>pKa = (protonated/deprotonated)

Protonated

What does telomerase have

RNA containing reverse transcriptase

What is Rho dependent termination

Rho protein brings to RNA and pulls RNA from the template strand to stop transcription in prokaryotes

Eukaryote DNA replication is restricted to what phase?

S phase of cell cycle

What are ketone bodies?

They are a fuel source from fats produced in the liver.

What are the stop codons

UAA, UAG, UGA

What two substrates are used to make glycogen

UDP-glucose and glycogen

What is oxidative phosphorylation

Using the electron transport chain to make ATP

Glucose 6-phosphate functions to maintain

a constant level of glucose in the blood

Enhancers interact with transcription complex via

activators (increase transcription)

What is glycosylation?

adding a carbohydrate to a protein

What is lipid modification

adding lipids to N or C termini residues of proteins

What is secondary structure determined by?

amino acid sequence - forms securing localized structures (a-helix and beta-sheet)

In beta sheets, when strands run in opposite directions it is called

anti-parellel

DNA replication is semi-conservative and occurs where

at the replication fork

Alpha helixes have H bonding where

between peptide backbone

In prokaryotes, DNA replication replicates __directionary

bidirectionally

In fatty acid metabolism, formation of malonyl CoA requires

biotin as a cofactor

Epinephrine promotes glycogen

breakdown (and inhibition of glycogen synthesis)

What occurs in y-carboxylation

carboxylation of glutamate side groups (prothrombin to thrombin

Fatty acid entry into mitochondrial matrix requires

carnitine acyl transferase

Convection is responsible for

carrying heat away from the body

In fatty acid metabolism, Acetyl CoA carboxylase is activated by

citrate

What does Gyrase do

cleaves and rejoins DNA to relieve super coiling

What is pH

concentration of H+ ions in a solution

What does pyruvate kinase do?

converts PEP to pyruvate

What does hexokinase do?

converts glucose into glucose-6-phosphate

Where does glycolysis occur?

cytoplasm

When pH<pKa = (protonated/deprotonated)

deprotonated

In antiparallel the atoms involved in H-bonding are

directly opposite of each other

when delta G>0 the rxn is

endogonic

Where do uncompetitive inhibitors bind?

enzyme-substrate complex (irreversible)

What are allosteric enzymes

enzymes consisting of 2 or more subunits that exhibit cooperativity

deltaG <0 the rxn is

exergonic

What is a native protein

final stable 3D structure

What is the concerted model

first binding changes binding at all sites

What is tertiary structure?

folding of secondary structures into 3D structure that is dynamic and flexible

What does glycogen synthase do?

forms alpha-1,4 glycosidic bonds to add glucose to main glycogen chain

What is phosphoglucomutase

generates glucose 6-P for other pathways

Glucose 6 phosphate is not readily transported out of the cell, it needs to be converted to what first

glucose

What makes up sucrose

glucose + fructose

What makes up lactose

glucose + galactose

What makes up maltose

glucose + glucose

What is the end product of glycogen degradation?

glucose 1-phosphate

Inactivation of PKA and activation of PP1 will promote ____________ synthesis after insulin binding

glycogen

Glucose acts as a allosteric modifier of

glycogen phosphorylase

What are Rho independent hairpin loops

hairpin loop in RNA that terminated transcription in prokaryotes

The O2 binding curve for myoglobin is what shape?

hyperbola

What is the temperature regulating center of the brain

hypothalamus

When acetyl CoA levels are high, pyruvate dehydrogenase is

inactivated

In prokaryotes, DNA replication requires what?

initiator protein DNAA

Where is ATP synthase located

inner mitochondrial membrane

At high concentration, the rate is maximal. What does this mean

it is independent of the substrate concentration

What does DNA ligase do?

joins Okazaki fragments together

What does Pol delta do?

leading strand synthesis

What is primary structure?

linear sequence of amino acids in a polypeptide chain (covalent bonds)

Eukaryote DNA replication, is bidirectional and has starts at

many origins (origin recognition complex ORC)

Glucose-6-phosphatase is present in the liver but not in the

muscles (muscles and brain will convert glucose 6 phosphate to pyruvate to create ATP) (The liver will convert G-6-P back to glucose so it can be transported back to the blood to be used by other tissues)

Active site forms what kind of bonds with substrates

non-covalent

What does alkalosis cause?

over excitability of CNS and PNS

If [A-]/[HA]<1 what does this mean

pKa is greater than pH (more weak acid)

If [A-]/[HA]>1 what does this mean

pKa is less than pH (more conjugator base than weak acid)

In beta sheets, when strands run in the same direction it is called

parallel

What is the structure of a nucleotide

pentose sugar, phosphate, nitrogenous base

What are the 3 regulatory (reversible) mechanisms of enzyme activity control

phosphorylation, acetylation, ribosylation

What does Pol alpha do?

primase activity and lagging strand synthesis

Which AA is absent in a-helix

proline

In prokaryotes initiation occurs at

promoter sites

What does alternative splicing result in

protein variants

What are trans elements

proteins that bind to cis-elements

At low substrate concentrations [s] < Km means what

rate is directly proportional to the substrate concentration

What is acetylation

regulation of gene expression by adding an acetyl group to the lysine of a histone

What does glycogen phosphorylase do?

release glucose 1-phosphate (used phosphate to lysis alpha 1,4 linkage)

What do phosphatases do?

remove phosphate group

Prokaryote DNA replication, Pol I does what

removes RA primer and fills gap

The O2 binding curve for hemoglobin is what shape?

sigmoidal

In parallel the atoms involved in H-bonding are

skewed, one aa is H-bonded to two aa in the opposite strand

splicing is preformed by

small nuclear RNAs

What is the sequential model

stepwise alteration of sites

What does a small Km =

strong affinity

Insulin promotes what in glycogen

synthesis of glycogen (activates protein phosphatase 1 (PP1) )

Each amino acid is carried by a

tRNA

What does transferase do?

takes 3 glucose residues leaving only a single glucose linked via alpha 1,6 linkage

Eukaryote DNA replication, Ends of DNA have what

telomeres which interact with telomerase

The active site of the ATP synthase is facing

the matrix

What are chaperones (heat shock proteins)

they assist in protein folding process (overcoming kinetic barriers)

Where does a noncompetitive inhibitor bind to on an enzyme?

to another site other than the substrate binding site

In prokaryotes, transcription creates what that progresses along the DNA template

transcription bubble

What is ribosylation?

transfers the ADP-ribose group onto arginine, glutamate, or aspartate residues - inhibits protein synthesis (baterial toxins are ADP-ribosyltransferases)

What does DNA helicase (DnaB) do

unwinds parent strands

What does a large pKa mean?

weak acid

When pH=pKa, this means?

weak acid will be half dissociated

What does a large Km =

weak affinity

How does initiation being in eukaryotic transcription

when transcription factors bind to cis elements and complex with RNA polymerase II