Flashcard maker : Richard Lattimore



Topoisomerases regulate the supercoiling of DNA


DNA Replication read/write

reads 3′ -; 5′

oh -> phos


Writes 5′ -; 3′

Eurkaryotic DNA Synthesis

Topoisomerase unwinds DNA Supercoil


Helicase – unwinds the two strands of DNA

•SSBs(single-stranded DNA binding protein) – keep the single strands apart during unwinding and copying


•DNA polymerase δ – synthesizes the complementary strand of DNA from 5’to 3’ leading strand


•Primase – RNA primer then DNA polymerase α & PCNA and then DNA polymerase δ


•RNaseH1 removes the RNA primers

•DNA ligase seals and completes the lagging strand

Okazaki fragments

Lagging strand growth


strand lags after the fork

1kb piece

Prokaryote Translation




Ribosomesbind mRNA while mRNA is still being synthesized


 Multiple ribosomesbind to each mRNA, proteins are made rapidly


Longest peptides are on ribosomesfurthest from the start codonAUG

DNA Repair

exonuclease cuts out damage


helicase melts double helix and damage is removed


DNA Polymerase I fills gap and DNA ligase seals strand

lac Regulation

expression – low glucose, available lactose



lacY brings lactose into cell and lactose derepresses lac operon by preventing lacI inhibitor to bind to O site, low glucose means high cAMP binds to CAP to allow, RNA polymerase binds and translates, lactose converted to glucose by lacZ, 

trp operon regulation in Ecoli

Trp repressor activated by tryptophan and it repressing expressing when active


Concentration of tryptophan is:


high: doesn’t need to make it, TrpR a repressor is activated preventing tryp from being made 3-4 loop RNA polymerase reaches loop and is stoped


Starvation: TrpR and TrpL deactivated, Tryp is made at max rate 2,3 loop stall ribosome, RNA polymerase makes Trp




reductive amination/transamination


What does THF or Follic Acid do?
they are a one carbon mover
Essential vs Nonessential
Essential must be gotten through diet. Nonessential we make in sufficient quantities

glucogenic amino acid:


one whose carbon skeleton is degraded to pyruvate or oxaloacetate, both of which may then be converted to glucose or go into TCA cycle
-most flexible

ketogenic amino acid:

one whose carbon skeleton is degraded to acetyl-CoA or acetoacetyl-CoA, both of which may then be converted to ketone bodies or go into TCA cycle


ketone-energy for the brain

The Urea Cycle

1) CO2 + NH4 + 2ATP -> Carbamoyl Phosphate + ADP + H2O


2) Carbamoyl Phosphate + Ornithine -> Citrulline


3) Aspartate + Citrulline -> Argininosuccinate


4) Argininosuccinate -> Fumarate + Arginine


5) Arginine -> Urea + Ornithine

Why go through the Urea Cycle

urea denatures protein

ammonium, ammonia, urea are toxic

2 ATP to dispose of urea



Inhibited by?

1) IMP + Aspartate + GTP -> Adenylosuccinate + GDP + P

2) Adenylosuccinate -> Fumarate + AMP


IMP = Inosine

AMP = Adenosine


*Inhibited by Accumulation of products



Inhibited by?

1) IMP + NAD+ + H2O -> Xanthosine + NADH + H+

2) Xanthosine + Gln + ATP + H2O -> Glu + ADP + PP + Guanosine


*Accumulation of product limits synthesis

Pyridimine Anabolism

1) Aspartate + Carbamoyl -> N-Carbamoyl-L-aspartate

2)N-Carbamoyl-L-aspartate -> Dihydroorotate + H2O

3)Dihydroorotate + NAD+ -> Orotate + NADH

4) Orotate + PRPP -> OMP

5) OMP -> UMP + CO2




1)UTP + Glutamine + ATP -> CTP + Glutamate + ADP+P

G-Protein Amplification

Hormone binds to receptor

alpha +GTP bind to adenalate cyclase to activate it = uses ATP for cAMP

GTP turns to GDP, deactives and aplha recombines with Y and Beta


cAMP increases activity of cAMP dependant protein kinases which in turn activate enzymes in glycogen breakdown and glucaneogensis (more glucose = more energy) and slow glycogen storage by making LESS F26BP

PIP2 second messenger

Hormone binds to PIP2 in cell membrane activating PLC

PLC catalyses hydrolysis of PIPP2 to IP3 and DAG

IP3 stimulates release of CA2+

DAG activates PKC

PKC phosphorylates CA2+ channel proteins controlling the flow of CA2+







Nucleotide = Base, Sugar, Phophoric Acid

Nucleoside = Base, Sugar




The top O- of the phophate replaces with the -OH on the 3′ Carbon




Negative charge due to phosphate backbone




A-T has 2 H bonds

G-C has 3 bonds


G-C is much harder to break

Why does mRNA have a short turn over time
mRNA represents a cells change to cope with new environmental stimulus.Once stimulus is gone, dont want to be changed for it.
3 Types of RNA

mRNA = messenger RNA = template for produce proteins

tRNA = transfer RNA = binds to target mRNA for protein production

rRNA = ribosomal RNA = translation of mRNA to polypeptide


Held together by disulfide bridges

Stimulates glucose uptake, glucokinase for G6P, Phosphofructokinase and Pryruvate dehydrogenase


activates glucogons syn and fatty acid syn


Type I

Type II

•Type 1 diabetes occurs due to loss of insulin production
-Often results from damage to the cells in the pancreas that are responsible for insulin production This is remedied by insulin injections
•Type 2 diabetes is often called onset diabetes
-This occurs in older people and is most often due to lack of insulin action
-Either from improper binding to the receptor OR improper functioning of steps following insulin binding
-Treatment with insulin will NOT overcome this type of diabetes


Reading direction

DNA Synthesis

RNA Repair


DNA Synthesis 3 – 5 adds new pair to 3

RNA Repair 3 -5 adds new pair to 3

Proofreading 5 – 3 adds new pair to 5


writes new strand oppostie

Synthesizing DNA

DNA Polymerase adds on nucleotides on the 3′ end


ozaki fragments needed for lagging strand

primase starts ozaki and polymerase III completes it

exonuclease removes primer

Polymerase I fills primer gap

Ligase joins end


# of nucleotides added before dna polymerase pops off
Differences between eurkayotes and Prokaryotes

Prokaryotes: one origin of replication

Ozaki : 1-2 kb

Polymerase I and III


Eurk: Many origins of replication

Ozaki: .1 – .2kb

Telomeres to 3′ of leading strand

spontaneous deamination
CG ->Cytosine -nh3 becomes =O uracil ->TA

rho independant

rho dependant

rho indenpendent: stem loops bump off RNA polymerase

rho dependant: stem loop causes RNA polymerase to pause, rho catches up and bumps off RNA polymerase

prokaryotic mRNA

Eukaryotic mRNA

Pro: mRNA code for several proteins in an operon


Euk: Code for introns and exons but exons are functional

Prokaryotes Transcription

Enzyme: DNA-dependent RNA polymerase but requires ATP, CTP, GTP, UTP, and MG2+


RNA Polymerase reads DNA 3-5 but grows 5-3 hydrolysis of pyrophosphate for energy


1) RNA polymerase has for subunits alpha, 2 Beta, sigma

sigma binds to promoter site T & A rich, and unwinds DNA double helix

2) sigma pops off and core enzyme continues and can make all three types of RNA

Eukaryote Transcription

Polymerase I: rRNA

Poly II: mRNA

Poly III: tRNA


TFIID binds to TATA box follwed by Pol II and TF: A,B,F,H,E to begin transcription


DNA opens B,E,H comes of and Pol II moves along until termination site

Modification of RNA

Add a cap to 5′ End and poly A tail to 3′ in eurkaryotes


AG|G marks change point of exons and introns. introns are cut out exons bind together via spliceosome


Also cut for better loops in tRNA

Inducible Operon

Not normally expressed, Cataboloic, induced by substrate

lac operon


Normally expressed, Anabolic, Repressed by product


Trp operon

2 types of Protein Kinases

how do they recognize site

recognize site by adjacent proteins

inactive until needed unless cleaning

phosphorlyate proteins from .5 mins to 15 hrs


Serine/Threonine Protein Kinase

regulates metabolism

98% of protein phosphorylation

found through cell


Tyrosine Protein Kinase

regulates growth

.2%-2% of phosphate depend on cell division more when active

found throughout cell

2 types of phosphatases

Recognize Tert. structure


dephosphorylate phosphoserine/threonine

regulation of metabolism

5 types

found throughout the cell


Dephosphorylate phosphotyrosine

crtical in regulation of growth control

many many types

found throughout cell

Carbamoyl Phosphate
Transamination in general
Recognize SAM

Synthetase attaches amino acid to tRNA at the 2′ or 3′ Carbon but then is changed to the 3′

rRNA is 70s made up of a 30S section and a 50s Section

30s = 16s + 21 proteins

50s = 23S + 5s + 34 proteins

AA ->tRNA = 2ATP

translation =2ATP + 4GTP


1) 30S with IF1 and IF3 combine with tRNA+IF2+GTP forimng the 30s initiation complex on the start AUG codon a few steps down stream of the SD sequence in prok NO SD in Euk

2) IF1,2,3 leave with GDP and 50S joins 30s to make 70s initiation complex

3)Reads mRNA 5′ -> 3′



A=incoming amino acid

P attachment


4) EF-Tu brings AA-tRNA to A site hydrolizes and GTP and EF-Tu leave, leaving AA-tRNA

5)EF-G-GTP moves A site to P site hydrolyzes using GTP EFGGTP and GDP leave with A site open for next

6)RF1/2 recognized stop codon binds in A site transfer peptidyl group to H2O and release polyp chain, RF3-GTP uses GTP to remove RF1/2 and all leave

cAMP regulation of Gene Expression in Euk
Hormone trigger protein kinase which phosphorylates CREB, CBP + Basal Complex bind to CREB-P and transcription starts
Chromatin Remodelling

DNA is packaged so its 50,000x shorter, must remodel to gain access to DNA.


Methylation of Histones silence expression


Acetylation of histons by HAT turns on expression by reduce affinity of histones to DNA by neutralizing positive charge on AA

Eukaryotic Translation

40S with 3 bind with eIF1 and eIF2-GTP-Met-tRNA to form preiniation complex


eIF4 bound to CAP on mRNA bind with pre to form iniation compex


Use ATP everything comes off leaving just 40S, 60s joibs and translation starts

Monofunction of protein kinase HCR

Fe in Heme group activates HCR


HCr uses ATP->ADP to make eIF2->eIF2-P & eIF2B-P





Endo: Target cells are distant from hormone making cell

Para: Target cells are near hormone making cell

auto: hormone maker is targer cell

Translation Process

–Ribosome-binding site (RBS codon) on mRNA allows binding to 30s subunit
–Formylmethionine tRNA binds AUG (start) codon the Formyl group will be removed later
–50s subunit (shell) docks to 30s subunit –fMet-tRNA occupies the “P”site


–Next charged tRNAbinds to “A”site
–Peptide bond forms


–Ribosome moves from one codonto the next and the empty tRNAis released from the “E”site
–Next charged tRNAbinds to empty “A”site

•Process continues until stop codon



trna binds to codon -> ribosome binds at trna to p site and is added to chain -> trna binds to codon at a site-> ribosome move so p->e and a->p -> E codon ejected and new trna binds a site.  read p site to chain

Dihydroorotate -> orotate

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