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