What did Rosalind Franklin do?

She used X-Ray diffraction to see crystal structure of DNA

What did Watson and Crick do?

They figured out the Double Helix Structure of DNA

What di Erwin Chargaff find?

found that A and T pair and G and C pair

What did Meselson and Stahl discover?

That DNA replicates Semiconservatively. They also found out that it was NOT conservative or dispersive

What did Frederick Griffith discover?

that there is a “Transforming Factor” responsible for heredity

What did Avery and MacLeod suggest?

That DNA was the transforming factor in hereditary material

What kind of expirement did Avery hold?

Recreated Griffith experiments but destroyed (1 at a time) proteins, lipids, RNA, and DNA

Hershey and Chase proved what?

That DNA is hereditary material and is found in viruses too

How did Hershey and Chase prove their theory?

They tagged the Sulfur of a bacteriophage (proteins) and the phosphorus (DNA). Thus phage infected a cell, and all new viruses created had that P tag. NOT the S one.Proving finally that DNA was the genetic material

What does semiconservatively mean?

only one strand of new DNA comes directly from parent molecule

How did Meselsohn Stahl rule out conservative replication?

He labeled both strands of DNA and let it replicate. Through this they discovered that there was one strand of parent DNA in each new molecule

How did Meselsohn Stahl rule out dispersive replication?

By replicating the 2 molecules again and again found there were just the two original strands, and 6 new strands

What did the fred griffith experiments discover?

There was a Transforming Principle responsible for heredity

What were the 3 results from the free griffith experiment?

SIII virus kills mice, RII lets mice live, SIII heat killed lets mice live.

This means that some transforming principle passed from the shocked SIII to the RII

Why does the transforming principle happen a lot in bacteria?

Because DNA is super stable so is hard to get rid of, so in
bacteria if it can jump to a cell with working organelles, it will, and then will become a part of that cell

DNA runs in what direction?

It runs in 2 antiparallel strands. (5'-3')

How are the DNA strands held together?

By hydrogen bonds between A-T and G-C

A-T have how many bonds?

2

G-C have how many bonds?

3

The DNA backbone is held together

phosphodiester bonds

DNA is found in what form?

The B form naturally in living organisms

Base Stacking leads to what?

the turns in the DNA double helix which forms major and minor grooves

In Eukaryotes DNA Replication is what?

Bidirectional and proceeds from multiple replication origins

In bacteria DNA replication is what?

bidirectional but has ONE replication origin

Consensus Sequences are what?

Unique in prokaryotes and eukaryotes, conserved across species, and essentially tell DNA polymerase where to bind and start replication

What does the helicase enzyme do?

It breaks DNA hydrogen bonds and unwinds DNA

These unwound strands are stabilized by what?

SSBs

DNA polymerase is the enzyme that does what?

Extends DNA strands to replicate DNA

DNA polymerase requires what?

RNA Primer made by primase

On bacteria DNA polymerase III is the what?

main replication enzyme

In replication, the 5-3 new strand will always be elongated...

continuously and it makes the leading strand

The 3-5 strand is elongated in short sections called

Okazaki fragments

Okazaki fragments are later joined together by what?

ligase

What does DNA polymerase I do?

its 5-3 exonuclease activity to remove the primer and then its 5-3 polymerase activity to elongate the gaps in the strand

DNA is heavily coiled, so what enzyme helps alleviate the tension during replication?

topisomerase

Telomeres serve as what?

caps at the end of linear chromosomes. They help to combat the shortening of chromosomes in each replication
cycle

Telomeres are fomred by what?

They are formed by T loops and protected by the protein sheltrin

What are the 4 nucleotides of RNA?

adenine, uracil, cytosine, and guanine (no T)

Is RNA double-stranded or single-stranded?

single stranded (so it is way less stable)

RNA includes ribose sugar, what does this mean?

It includes an extra OH on the 2’ carbon

What does Messenger RNA (mRNA) do?

made by protein coding genes and is intermediate between
DNA and proteins

What does Ribosomal RNA (rRNA)?

NOT from protein coding genes...works with proteins to form ribosomes

What does Transfer RNA (tRNA) do?

NOT from protein coding genes...binds to amino acid to add it into growing protein chain

Telomerase RNA does what?

provides template for synthesizing telomeres

Small Nuclear RNA (snRNA) play a role in what?

In mRNA processing and splicing out introns

What does Micro RNA (miRNA) do?

pairs with mRNA to alter stability

Small Interfering RNA (siRNA) is cut from what?

double stranded RNA to also alter mRNA stability

The template Strand is what?

the strand of DNA that RNA polymerase binds to and assembles a complementary strand of nucleotides to

The other strand of DNA is called what?

coding strand. It is where the actual genes being transcribed

True or false. The Promotor Region is immediately upstream of transcription start site (more to the 5’ end)

true

RNA Polymerase is ninds to what?

The promoter region

What does the Transcription Region contain?

sequences to help stop transcription (close to 3’ end)

Describe the process of transcription? (for prokaryotes)

The sigma subunit actually identifies the promotor region and allows RNA Polymerase to bind. The RNA Polymerase holoenzyme complex then unwinds the DNA to form an open promotor complex. After 8-10 nucleotides have been transcribed, the sigma subunit then
dissociates from the complex

What does DNA do in transcription? (for prokaryotes)

the DNA continues to unwind in front of RNA Polymerase and reforms the double helix behind it

What happens in transcription termination? (for prokaryotes)

1. Intrinsic Termination happens in most prokaryotes

2. Rho-Dependent Termination needs the protein rho

What is intrinsic termination?

The termination sequence is a bunch of inverted repeats, followed by a tail of Adenines.

ex: GGGGGGCCCCAAAAAAAAA

What does the rho protein do?

Rho moves up the mRNA, forces it to form a loop, detaching it from the DNA and kicking RNA Polymerase off

In eukaryotic transcription RNA Polymerase I transcribes what?

rRNA

In eukaryotic transcription RNA Polymerase II transcribes what?

mRNA, miRNA, siRNA and snRNA

In eukaryotic transcription RNA Polymerase III transcribes what?

tRNA, miRNA, siRNA one snRNA, and one rRNA

Enhancer sequences can bind what?

proteins around the promotor to enhance the level of
transcription...i.e. gene expression

Silencer sequences bind proteins to bend what?

DNA so it can’t be transcribed as easily...decreases gene expression

What are some of the post-transcriptional modifications for eukaryotes?

1. Capping 5’ mRNA (Guanylyl transferase adds a special Guanine nucleotide to the 5’ end of the mRNA to
serve as a cap)

2. 3’ Poly-A tail (A polyadenylation sequence is at the 3’ end of the mRNA . The mRNA is cleaved after this sequence and then PAP and CPSF then add up to 200 As.)

How does capping 5' mRNA help transcription?

This protects the mRNA molecule from rapid degradation and helps with later translation

How does a 3' poly-a tail help transcription?

This protects mRNA from degradation and helps with translation

What is intron splicing in eukaryotes?

Eukaryotic mRNA is unique in that intronic (non-coding) regions and spliced (cut) out of final transcript. This is important in correct protein formation

Describe intron splicing in eukaryotes?

In splicing, you have a 5’ splice site, 3’ splice site, and a branch
point. Introns are removed by an snRNA - protein complex called a spliceosome. The 5’ end is cut first, then 3’ end. They are then ligated together to form a lariat intron structure

How do we produce alternating proteins?

1. Alternative Intron Splicing

2. Alternative Processing

3. Alternative Polyadenylation

4. RNA Editing and processing

How many amino acids are there?

20 with unique chemical properties

What is the r group of amino acids?

They are distinct and give these amino acids their unique
properties

The ribosome catalyzes the formation of what?

a peptide bond between amino acids which forms a growing polypepetide chain

What is a codon and what does it code for?

A group of 3 nucleotides on an mRNA strand and they code for one amino acid

What are the start and stop codons of translation?

start codon: 5’ AUG (always)

end codon: UGA, UAG, UAA 3’

The starting codon AUG codes for what amino acid?

methionine (met)

What is before or after the start and end codons?

small Untranslated regions (UTRs) on the 5’ and 3’

What are ribosomes?

a combination of rRNA and proteins found in ALL living organisms

What doe ribosomes do?

They bind mRNA, facilitate pairing of correct tRNAs carrying amino acids to catalyze the formation of peptide bonds to
create proteins

Each ribosome has how many sites?

3 (A, P, E)

What is the A site?

where tRNAs carrying amino acids first bind to the ribosome (NOT THE FIRST ONE THOUGH)

What is the P site?

where the ribosome transfers amino acids into the polypeptide chain

What is the E site?

where the tRNA will leave the ribosome after dropping off its amino acid

Eukaryotic ribosomes have __ and ___ subunits to create a ___ ribosome

40s and 60s to create 80s

Prokaryotic ribosomes have ___ and ___ subunits to create a __ ribosome

30s and 50s to create 70s

What provides the energy for translation?

GTP

What are initiation factors (IF)?

proteins that facilitate mRNA and ribosome binding

What are elongation factors (EF)?

They use GTP hydrolysis to help create growing protein chains

What are charged tRNAs?

tRNA molecules WITH an amino acid attached to them

What are release factors?

They bind to the codon in the A site after the stop codon has been reached (basically end translation)

What sequence is in the 5’UTR? ( for prokaryotes)

a Shine-Dalgarno sequence found in all prokaryotic mRNAs

In prokaryotes the first amino acid ONLY is what?

N-formylmethionine (fMET) instead of normal methionine

The tRNA carrying the fMET amino acid will first bind to what site?

the p site (all other tRNAs will first bind to the A site)

For eukaryotes, the small ribosomal subunit (40s here) binds to what consensus sequence?

the Kozak Sequence. (everything else is similar to prokaryotes)

How is a tRNA charged?

aminoacyl-tRNA synthetase binds the correct amino acid to the tRNA with the correct anticodon (this uses ATP)

How does termination occur?

The correct tRNA will have a complementary sequence to the correct codon in its anticodon stem. Once one of the three stop codons binds in the A site, a Release Factor (RF) will bind in the A site as well

How many different codons are for the 20 amino acids.

64 including the 3 stop codons

Our amino acid code is degenerate which means?

more than one codon can code for an amino acid ( but there are 3 exceptions - methionine and tryptophan)

What are the 2 synonymous codons?

methionine and tryptophan (helpful in protecting against mutations)

What is the Wobble Effect?

the third nucleotide in a codon is least important, and has the
flexibility to mutate and still bind the original amino acid

true or false. In prokaryotes, the f-MET amino acid is always removed

true

it is hypothesized that the first 15-20 amino acids act as what?

signal sequences to lead the new protein chain to other organelles for processing or packaging

Fraenkel-Conrat proved that there were no overlapping codes by...

by showing that a single nucleotide substitution only affected one amino acid

How do you read 3 base pairs at a time and what can it lead to?

by looking at the reading frame and it can cause frameshift mutations

What are somatic mutations?

Mutations that occur in somatic, body cells and they can NOT be passed down

What are germline mutations?

mutations that occur in egg/sperm cells and these CAN be passed on

Point mutations occur where?

only one specific place in the DNA (ex: one base pair was deleted)

Substitution Mutations occur when what happens?

when you swap one nucleotide for another

Transitions occur when...

a purine switches with a purine (or pyrimidine for pyrimidine)

Transversions occur when...

a purine and pyrimidine switch places

Frameshift Mutations occur when...

when you insert or delete nucleotides NOT in a multiple of 3 (they change the reading frame of the DNA sequence and can leave it nonfunctional)

What are the types of substitution mutations?

silent, missense, and nonsense

What is a silent mutation?

A nucleotide is substituted, but the amino acid does NOT change (Ex: UUU and UUC both code for Phe)

What is a missense mutation?

A nucleotide is substituted, and the amino acid DOES change
(Ex: UUU codes for Phe but UUA codes for Leu)

What is a nonsense mutation?

A nucleotide is substituted and creates a premature stop codon (Ex: UAU codes for Tyr and UAG is a stop codon)

Regulatory mutations do what?

alter the expression of the protein product but have no affect on the protein coding DNA sequence

What are promoter mutations?

any types of mutations that occur in the consensus sequences in the promotor region. They mainly affect RNA polymerase

RNA polymerase activity correlates to what?

the amount of protein produced

What are splicing mutations?

They occur in the specific splice sites of introns and they can actually change the protein produced

Cryptic Splice Site Mutations will create what?

new splice sites in mRNA, additionally changing the
protein produced (they can accidentally skip some exons)

What does forward mutations mean?

Going from wild type to mutant allele

True Reversion occurs when?

a codon receives a second mutation that restores the original amino acid

Intragenic Reversions are what?

reversions occurring somewhere else in the gene

(a frameshift fixing another frameshift mutation)

Second-Site Reversions occur where? (also known as suppressor mutants)

in a DIFFERENT gene that compensates for the original mutation

true or false. Most mutations in the genome are spontaneous and occur from errors in DNA replication or proofreading

true

What is depurination?

breaks the nucleotide from the backbone, if unprepared is replaced by an A

What is deamination?

occurs when an amino group is lost from a nucleotide