Genetics Exam 1 (Rutgers Soliman)

Nucleic Acid

This must be able to contain complex information, replicate, encode the phenotype, be different in phenotypes, and must be complex so it can be carried from one organism to another

DNA

Found in the nucleus and can be found in mitochondria, viral, bacterial, etc. and can exist as double stranded

RNA

Found in the nucleus as a messenger, ribosomal, transfer, anti, etc. and have an Uracil base with single and double stranded

Rough Strain

The nonvirulent form that is unable to invade the immune system due to having no outer capsule

Smooth Strain

The virulent, wild type form that can invade the immune system with an outer capsule

die

When the mice were injected smooth strain bacteria, did they survive or die?

survive

When the mice were injected rough strain bacteria, did they survive or die?

survive

When the mice were injected heated smooth strain bacteria, did they survive or die?

die

When the mice were injected heated smooth strain mixed with rough strain bacteria, did they survive or die?

Transformation

What did Fred Griffith conclude about his results?

Avery, Macleod, and McCarthy

The experiment was meant to prove that DNA was the transforming principle through enzymes like proteases, RNAses and DNAses

Hershey & Chase

This experiment used bacteriophages to examine traces of DNA through replication of those viruses with radioactive sulfur or phosphorous (proved that DNA was genetic material continuously replicating)

Rosalind Franklin

Did her research on DNA structure and gathered an X-ray diffraction image of DNA which concluded that DNA is helical, contains 10 nucleotides and have a diameter of 2 nm

Watson & Crick

Discovered more points about DNA structure and concluded that DNA is double stranded & runs antiparallel and have complementary pairing

Grooves

Meant to make the DNA more visible for protein bidning

Nucleoside Analogs

Can be used to stop cancer cell from dividing through with no OH groups on the end

C-G

This pairing has 3 bonds

A-T

This pairing has 2 bonds

Conservative

When the original strand served as a template for a new molecule of DNA

Dispersive

When both DNA molecules break down like fragments and serve as a new template

Semi-conservative

The original strand unwinds and used as a template to generate a new strand

DNA was semiconservative! As when the 2 different samples of Nitrogen was added, they ended up making a half/half of one another.

In the Meselon & Stahl Experiment, what did they conclude after growing the radioactive Nitrogen?

Theta Replication

A bidirectional step process that takes place in circular DNA like Ecoli

1) Double strand will begin to unwind produce single strands which can function as a template for the new strand at the replication bubble (reminder that the plasmid is melted first)

1st step in Theta Replication

Unwinding is continuous and the bubble gets larger (location where there is unwinding is replication fork)

2nd step in Theta Replication

3) DNA synthesis would occur in the 5’ to 3’ direction

3rd step in Theta Replication

Rolling Circle Replication

Takes place in typically viruses and Ecoli where there would be a single break unidirectionally

A single strand break in 3’ OH & 5’ P group

1st step in Rolling Circle Replication

2) A new strand is added to the 3’ OH break using the inner strand as a template

2nd step in Rolling Circle Replication

The original strand will be displaced and roll off the entire plasmid (and continues until it has several copies) as the linear fragment can be used as another template!

3rd step in Rolling Circle Replication

Intitation

When a DNAa protein will bind to the origin of replication to cause a conformational change to twist and unwind the region

Helicase

Will undo hydrogen bonds

Single Strand Binding Proteins

Will bind to the DNA to stabilize DNA strand once unwound

DNA gyrase (topoisomerase)

Will prevent supercoiling and upstream torsional strain to build up during unwinding

Topoisomerase I

Create single stranded breaks in DNA

Topoisomerase II

Creates double strand breaks in DNA as it passes through double helix and reseals it

Elongation

The addition of new nucleotides on an old template to make a new strand

Primers

Needed for a 3’ OH groups so nucleotides can be added → generated by primase so 10 bps of RNA can be generated

DNA Polymerase III

Replicates DNA using RNA primer (5’ to 3’ for replication and 3’ to 5’ for exonuclease activity)

DNA Polymerase I

Removes the RNA primer and replaces it with DNA (works on lagging strand) with 5’ to 3’ for replication & exonuclease activity to remove primers and replace & 3’ to 5’ for exonuclease activity to backup and check errors

DNA Ligase

Will put together nicks once polymerase I removes and replaces primer

Termination

Two ways that this process can work:

1) DNA can termination once 2 forks meet

2) Some needs the protein tus to bind to the ter sequence so the protein can block replication

Leading Strand

Reads from 3’ to 5 but synthesized from 5’ to 3’ direction since it is continuous and starts from replication bubble

Lagging strand

Reads from 3’ to 5 but synthesized from 5’ to 3’ direction since it is discontinuous and starts from replication fork

Licensing Factor

Like a signal to tell DNA polymerase that DNA replication can intitate in euykaryotes (geminin will bind and remove licensing factors)

DNA polymerase Alpha

Has primase activity in DNA for eukaryotes

DNA polymerase Eplison

After primers are added on, will act on the leading strand

DNA polymerase Delta

After primers are added on, will act on the lagging strand

Trans Lesion Polymerase

This polymerase can bypass error if necessary by adding an incorrect base

Nucleosomes

When histone proteins come together with the DNA wrapped around it (8 histone proteins)

Telomeres

These typically shorten which is part of the normal aging process, but kept when needed for critical genes (if shortened too quickly, this can cause cancer)

Tus Protein

Will bind to this if termination needs to occur (not all DNA needs)

Only one strand (template strand)

How many strands are copied in transcription?

No

Is the promoter transcribed into mRNA?

The promoter needs to be found, with the consensus sequence known as the TATA (bacteria & eukaryotes) or TTGACA in the bacteria

1st step of transcription

pre-mRNA (or mRNA in prokaryotes) will be transcribed by RNA polymerase (RNA polymerase II in eukaryotes) from 5’ to 3’

2nd step of transcription

Rho Independent & Dependent

What are two ways in which transcription can be terminated?

1) RNA polymerase stops at terminator RNA

1st step of Rho Dependent

Rho will attach to a sequence known as Rho ultilization site

2nd step of Rho Dependent

Rho will move to the 3’ end and unwind DNA

3rd step of Rho Dependent

Rho independent terminators

There could be an inverted repeated sequence that causes the formation of secondary structure

Eukaryotic transcription

This type of transcription that has more complexity and uniqueness for genes depending on level of expression as nucleosomes are gripping tightly to DNA

Acetyl Group

Groups that will bind to histones to loosen DNA

RNA polymerase I

Synthesize rRNA

RNA Polymerase II

synthesize mRNA, snRNA, miRNA

RNA Polymerase III

Synthesizes tRNAs, small rRNAs

Use a protein to bind to downstream sequence

How does Poly I terminate?

Works for 100s nucleotides past its stop (Rat1 or xrn1)

How does Poly II terminate?

Transcribing a long strand of Uracils

How does Poly III terminate?

Splicing

This is when a consensus sequence can help form the spliceosome that is responsible for the removal intron

Polyadenylation

Poly-A-Tail (5-20 Adenine) is added to the end thanks to a signal

Guide mRNA

These bind to the mRNA to do last minute editing

AUG

Start codon

UAA, UAG, UGA

Stop codons

Degeneracy & Wobble

Different codons coding for the same amino acid as the first 2 nucleotides pair normally according to watson and crick

Poly-A-Tail, Cap binding proteins (poly A bind to cap binding proteins)

Example of initiation factors in translation

Shine Delgarno sequence

UAAGGAGGU is the what sequence

small subunit in ribosome

What will bind first in the mRNA?

Elongation

Will continue from the A site and elongate from there (only AUG binds to P-site)

Termination

When release factors bind to the ribosome from the A site as the polypeptide is hydrolyzed from the P site

Cis Acting Factors

Factors that will affect transcription but do not move around the cell

Trans Acting Factors

Factors that will affect transcription but move around the cell

Nonsense Mediated mRNA Decay

Will handle premature stops when the ribosome reaches the stop codon as the release factor will bind and junction proteins will sense that there is something wrong with the mRNA and degrade it.

Nonstop Mutation

This mutation can be stopped by having an empty A site in the end, and signaling an enzyme to degrade the mRNA

Enhancers

Can promote direction in transcribing for the lac operon.

Silencers

Have negative control over expression

DNA binding proteins

Will bind to DNA binding domains and recognize them.

Helix Loop Helix

Has the secondary structure that can be crystalized to find the DNA binding domain

Zinc Finger Domain

The DNA binding protein can find this sequence and bind to it so it can carry on positive and negative regulation

Leucine Zippers

Will wrap around the DNA and can control positive and negative regulation

Regulatory Gene (aka Lac I)

Will make the repressor or activator

Promoter

This is where RNA polymerase binds to before it begins transcription

Operator

Will have the repressor bind to it

Lac Z

Can make beta galactosidase that will break down to glucose and galactose

beta galactosidase

break down to glucose and galactose (converts lactose to allolactose)

Lac Y

Encodes permease that permits entrance of lactose into the cell

Permease

Permitting entrance of the cell

Lac A

Forms transacetylase

Glucose

This can help regulate the operon because the operon (lac) prefers this over lactose

CAP (when cAMP binds to CAP protein)

Will bind to a site that will increase transcription in the operon