Moleclar genetics

What does dna do

• hereditary inof

• intructions for making protiens

What are protiens for

To carry out cellular processes

What si dna made of?

Nucleotide

Whta is a nuleotide made of?

Phospahet

Ribose rugar (deocyribose)

Nitorgen base

Whta aare the 4 nitrogen bases and thier differences?

Double ring:
- adenine
- Guanine

Single ring:
- Thymine
- Cytosine

Making the double helix

1. Sugard phospahte backbone: one sugar bonds to the next sugar via the phospahte group

2. the 2 back bones created are bonded to eachother through complimentary nitrogen bases

What are the complimentary bases?

A-t

C-g

In what direction does DNA display?

5’ end to 3’ end (open phospate - empty unbonded phosphate)

Are the backbones prallel?

No anti parallel, right most strand runs 5-3 up to down while left strand runs 3-5 up to down. This allows the nitrogen bases are lined up. (BOTH ARE ATILL READ 5-3)

Differences between RNA and DNA

• double vs single strand

• Sugar molecule is missing na oxygen on carbon2 (both still clasified as ribose)

• Nitrogen base Thymine is Uracil in RNA

Why does DNA prelication need to be almost perfect?

to avoid harmful mutaitons

Process of DNA replication

1. hydrogen bond break and helix opens

2. eahc strand acts as a template for new complimentary strand

3. 2 identicl DNA helices now made (each strand ahs a parent and daughter strand)

What enzyme makes the DNA

DNA polymerase III

What does DNA polymerase need to start building DNA

a primer, starting point signal

Explain how each half of the DNA is made

Leading strand: a continuos peice

Lagging strand: made in smaller peices

Why is the lagging strand made in small peices?

becuase fo the anti parallel nature of the DNA

What enzymes are needed for DNA replicaiton?

1. DNA Polymerase III

2. primase

3. helicase

4. Ligase

What does halicase do

Breakes the hydrigen bonds between the two strands of DNA

Why dont the single strands just bond back together?

Single stranded binding protiens (SSB) stabalize the single strands

Explain the use of primers in DNA replication

Primers are made from Primase. They are Short starnds of RNA that are added to the single DNA strand at the most 5’ end of the seperated DNA

They act as the starting point for DNA polymerase to recognize.

Also knonw as RNA primer

Primer diagram

Are laggign strands made 5-3?

Yes, but back wards. The newly formed Lagging strand runs 3-5 tot eh primase is added part way up and DNA polymerase builds backwards to make the Okazaki fragmanets (Short DNA segments)

Do primers stay in the DNA strand?

No, DNA polymerase I removes it.

What is ligase responsible for

Ligase joins the the okazaki fragments together (becasue fot he primers being removed and spaces left)

What are telomers

Telemors are the non coding regions of the dna that are left after RNA primers are removed.

As they shorten, the cell ages and eventually dies

Why deos DNA get shorter after each round of replication?

as telomers are removd, the dna gets shorter each time

What does DNA polymerase do?

• removes rpimers

• fixes erros: can catch errors in base paring and remove inccorect bases.

• will create a base in between fragments and then ligase fills int he rest of the gaps

How is a protien made?

Dna has the code

code has to get ot ribosome where its built

Describe Crick’s dentral dogma

Dna is slip and RNA is transcribed which leaves the nucleus tot he ribosome where it is translated into amino acids to build the protien

how to RNA code for amino acids?

3 nitrogen bases code fro 1 Amino acid. they are called Codons

Stop codons

The stop result of a codon is a signal for the RNA strad to stop beign rpoduced

What is trancription

the porcess of copying info from dna into an RNA

Does all of the DNA info need to transcribed?

No, only the specific sequences (genes)

How does RNA recognize where to transcribe?

Startign point is called the promoter sequence or Tataa box

what recognizes the tataa box and transcribes the dna info?

Enzyme called RNA polymerase

what does RNA polymerase make?

Pre-MRNA

How does RNA polymerase and the tataa box work together?

RNA polymerase binds to tataa and transcribes the sequecne comign after the taataa box. the RNA strand created is complimentary to thr DNA

In what direction is the RNA polymerase creatign Pre MRNA?

5→3

Compare error managemnt in protien creation vs dna replication

Transcription has NO proofreading so mistakes are made, BUT not always a probelm because fo the redundancy of genetic code

are there okazaki fragments in RNA productions?

no, RNA is single stranded

What is MRNA?

Messenger RNA that is transcribes from DNA

Describe the role of Terminator sequences (STOP) in DNA transcription

Terminator sequences are signals fro RNA polymerase and Pre MRNA to detach from DNA strand. RNA - P recognizes it as a stop

Before makign its way to the cytosol, what happens to MRNA

• Mrna needs to be protected fro the cytosol: A 5 cap and Poly A tail are added to 5’ and 3’ ends right before the Strat codon and aftert the stop codon

• Splicesomes remove introns and reconnect extrons to leave just codons

What is an extron

useful genetic coding sequences

Introns

non coding sequences of RNA

What is needed for RNA translation?

Transfer RNA + Ribosomes + mRNA

what is tRNA

free floating molecules that read the mRNA

mRNA tells the tRNA what amino acid to carry

how does tRNA recognize the codon sequencs of mRNA

using its anti codon that is complimentary to the mRNA codon.

What does Trna do in protien creation?

tRNA anticodon binds to mRNA codon (because complimentary)

3’ end is the attachment site of the amino acid whicht hen unbind and binds tot he next amino acid int he ribosome

Whta is the ribosome is made of

protien rRNA

explain how the ribosome work

Mrna slides in between the two units. tRNA fits into p site where it bind to MRA codons in aticodons. Then another tRNA sits int he a site. amino acid bind to amino acid int he a site. then trna leaves throught eh e site

when does the tranlastion process stop?

when a stop codon ont he mRna is reached an stops mroe amino acids from being created

Release factor free the poly peptide chain (poly peptide start folding and stuff)

Brief summary of protien syntheiss

Transcription

mrna protected

intorns removed - mrna to cytoplasm

mrna in ribosone

trna and mrna make poly petide chain in ribosome

what is a mutation

A permanent change in the genetic material

difference between: germ vs somatic cell mutations

germ: passed on to offsrping - in reproductive cells

somatic: not passsed on to futue offspring passed on to aughter cells - in cell mitosis

what causses a mutation?

Physical or chemical mutagens:

physical - high energy radiation or UV radiation

chemical - carcinogens (molecule that can enter the nucleus and induce mutations)

Type of mutations!

Frameshift: insertion , deletion

Base substitution: missense, silent, nonsense

Frameshit insertion

extra base makes everythign misalign

Frameshift deletion

base removed, makes everythign misalign

Base substitution missense

on randome chaneg creates a diff amino acid

Base substitution silent

one randome base chaneg makes the same amino acid

Base substitution nonsense

one random base change makes a stop codon

why do we care abt determining DNA sequences

• solve crimes

• paternity suits

• fetal creening (genetic disroders)

• research to fidn cures

How to break DNA

restriction enzyme slice the DNA at restiction sites

restiction sites can then be used to isloate specific sequences of interest

what are the 3 steps of studying DNA sequences

break

multiply

sort/analyze

how is dna amplified

bacteria is used as a vector to multiply interseted DNA

what are plasmids

plasmids are the circular portions of DNA (Bacteria vectors)

explaint he process of DNA stuff

rescriction enxyme splits the plasmids at restrction site, same enzyem used on another dna of interest, dna sequence intereted to plsmid to be replicated

how does the restricted dna sequence stick to the split plasmid?

sticky ends of the dna atracted to plasmid are compllimentary. they form hydrogen bonds and ligase fils in any gaps

what is it called when plasmid and target DNA are combined

Recombinant DNA

now how is the dna cloned?

recombinant plasmid is intersted back into the bacteria vecto and multiplies it

What are the diff ways DNA is aomplified?

bacterial vector

PCR

PCR method of amplifying

DNA, primers mucleotied and Taq polymerase are added into test tube

dna heated to 90* to seperate strands

cooled to 37* and primers are added

heated to 70* to activate DNA polymerase makign 2 identical strands

cycle repeats itself

Sortign & analyzing DNA: gel elctophoresis

DNA fragmaents travel trhough a special gel towards a postive charge (dna has a negative charge)

the seperation of fragments creates a patern of bands call DNA fingerprint. Everyones fingerprint is diff

smaller dna fragaments move faster and farther

How is Gel electrophoresis used

perental disputes, matching dna, research for gene diseas)

what is gene expression?

the process of turning on a a gene to produce RNA

why does a cell controll how / when a gene is exressed?

to be mor energentically fabourable

Examplesof egen exrepssion

• lactase

• arctic fox

Gene expression regulation: Eukaryotes

can eb inhibited on protien synthesis pathways (trasncription/translation)

1. trascription control: block / prevent transcription

2. post transcription controll: mRNA dstroyed,

3. Post trancriptopk controll: poly a tail/5cap shortened

4. post translation control: poly peptide degration

5. post translation control: delay of folding

6. RNA transport control: mRNA not allowed out of nucleus (nucleus pore blocked)

Gene expression regulation: prokaryote

ONLY IN TRANSCRIPTION REGULATION. on or off

protiens neede for a specific funtion are encoded togethin blocks of codons called operons. every codon neede for lactase protien will be right after eachtoher int he lac operon

all be cuase prokaryotes are simple and dont have aneclues so both strancriptiona dn trasnlation happens simultaneously

regions of operons

coding regions

premoter / start site (tataa box)

operator ( dna region that determins if trancription hapens) repressor will bind there to block rna polymerase form recognizing the tataa box

What are the molecules that affect the operon?

repressor - binds to operator region and block transcription

activators - recruits RNA polymerase to the promotorer to start transcription

inducers - small molecules that acticate or repress transcription baed on need

what is needed for lac operon to be activated

low/absent glucose elvels

lactose

how does lac operon work

if conditions ar emet, the inducer allolactase binds to lac repressor beating it up so it leaves the fight like the whimp it is. then the RNA polymerase and transcribe

what kind of relationship does th eallolactie and represor rpotien have

ezyme and subtrate

Tooisomerase vs helicases

Helicases are enzymes that separate the nucleic acid strands for replication. Topoisomerases are enzymes that relax the supercoiling in DNA strands

Why are chromosome mutations potentially more serious the gene

because chromosome mutations affect much larger regions of DNA potentially carrying hundreds or even thousands of genes

what are the 4 type sof chromosoem mutations

Deletion

Duplication

Inversion

Translocation

What is agarose gel and how does it work?

used to resolve DNA fragments on the basis of their molecular weight

Where is the DNA placed in the gel electrophoresis apparatus?

wells

Explain why not all the bands in the mother’s or father’s profiles have a counterpart in the baby’s DNA profile.

because the baby gets 50 of each parent

Explain why blood typing may not be a viable method of determining which baby belongs to which parent.

blood typing does not distinguish between people of different genotypes. For example, a person may be Type B blood but that person could either be BO or BB