DNA history,relication, transcription and translation

Question 1

Why do scientist though proteins were more likey DNA material

Answer 1

Proteins were made of 20 amino acids and give different codes

Question 2

Griffith’s Transformation experiment, 4 step, what it told us

Answer 2

s.pneumonia strains smooth cells (s) with a slime layer coating and rough cells (r) without coating
experiment:
take s cells, inject to mouse, muse dies from pneumonia
take r cell, inject t mouse, sick mouse lives
take heat killed s cells, inject to mouse, sick mouse lives
take dead s cell ad living r cells, inject to mouse, mouse dies and find living smooth cells
tells us about horizontal gene transfer, dead s cells were transformed.

Question 3

hershy and chase

Answer 3

Radioactive sulfur (give radioactive protein) and phosphorus (give radioactive DNA)
when phages infected, DNA lit up.
esult: genetic material was fund to be radioactive. Confirmed DNA is the genetic material passed, not proteins.

Question 4

Avery McacLeod and McCarty 3 steps and result

Answer 4

Heat killed strep cells with only RNAm DNA, and Proteins
added enzymes to digest one of each of those 3 and insert it into R cells
only transformation when DNA was in the R cell.
told us: transformation requires DNA

Question 5

Watson and Crick- what were the 3 main competing models? what was their model and how did it fit with Chargoff’s rule?

Answer 5

Semi-conservative - strands separate, each being a template for new strand synthesis. One template one new strand.
dispersive: two template strands, each mixed with new DNA.
conservative. After replication, two template strands come together and two new Dna strands come together. Each is it’s own.

Watson and crick suggested the semi-conservative. the structure of DNA- has a double helix, with phosphate backbone, and nitrogenous bases facing inside (CR)
Bases are equal in amount to each other

Question 6

How did Meselson and Stahl (1958) identify the correct model? And which one was it?

Answer 6

• Bacteria grown in heavy nitrogen and bacteria grown in lighter nitrogen
• Cells grown in heavier media, transferred to light media and allowed one generation to produce. A second generation was later produced.
• Generally, 3 results could occur: conservative, dispersive, or semi-conservative.
• Able to tell which is which by looking at combinations of bands
• 1 band in the first replication, two bands in second generation (semi-conservative)

Question 7

Topoisomerase

Answer 7

Reduces supercoils when being unwind

Question 8

Helicase

Answer 8

Separates two stands by breaking apart hydrogen bond

Question 9

SSBP’s

Answer 9

Stabilizes isolated strands. Protect two strands from cleavage and prevents them from snapping back together.

Question 10

DNA poly 1

Answer 10

removes primer and replaces it wih DNA material

Question 11

Primase

Answer 11

Adds RNA primers-needed to bigin DNA replication

Question 12

DNA ligase

Answer 12

spaces in between Okazaki fragments. seals nick after primer is replaced with DNA

Question 13

DNA POLY 3 . Lagging strand vs leading strand

Answer 13

Will attach to where RNA primer is and adds nucleotides in the 5’ to 3’ directions

Leading strand: RNA polymerase runs in the 5 to 3 direction even though the template runs from 3 to 5. goes along the template. Only needs one primer to continuously add

Lagging strand: will still attach at 5 to 3 direction in the opposite side. Will need more primase for DNA poly III to add nucleotides. Not continuous

Question 14

Where does energy come from to power DNA synthesis

Answer 14

ATP

Question 15

What does DNA poly 3 use to power

Answer 15

ATp, GTP, dNTP

Question 16

How does the current model, the Trombone Model, work for a complete Replication Fork?

Answer 16

Trombone models: lagging strand forms a loop so that the lagging and leading stand replication proteins are in contact of one another
Helicase and DNA poly 3 are in contact
More efficient

Question 17

Be able to briefly describe how scientists deciphered the genetic code

Answer 17

synthetic mRNA with multiple units of uracil to instruct amino acids to add phenylalanine. Poly U sequence served as a messenger for protein synthesis. Demonstrated that mRNA transcribes genetic information from DNA

Question 18

Key point of gentic code

Answer 18

aminoa cids are encoded by three nucleotides (codon)
most amino acids have more than one codon
variability comes from third position of the “wobble”
- allows for silent mutations and genetic engineering
is universal

Question 19

Three codes that dont have assigned amino acid and which one is unambiguous

Answer 19

UAA, UAG , UGA
AUG always codes for Methionine, and UUU for Phenylalanine

Question 20

Transcription is

Answer 20

gene specific

Question 21

RNA Polymerase vs DNA polymerase

Answer 21

○ RNA Pol does not require a primer (sort of like Primase in that way – but then it just keeps going)
○ RNA POL utilizes UTP rather than TTP, and NTP’s in general instead of dNTP’s
○ There is Topoisomerase both ahead and behind the RNA POL to relieve or build back in supercoiling.
○ No need for Helicase or SSBP’s
○ Synthesis is still 5’ -> 3’
○ Termination of Transcription in Eukaryotes follows transcription of the AAUAAA sequence known as the Polyadenylation signal.

Question 22

role of 5’-Cap and 3’-Poly-A tai

Answer 22

• 5 prime cap: modified guanine added to first nucleotide in transcript. Protects transcript from being broken down and help ribosomes attach to mRNA. the pass that allows mRNA out of nuclues
  
  • Poly A tail: Sequence called polyadenylation signal shows up , nuclear proteins chops the rna. Another enzyme adds adnine nucleotided to the cut end and from ploy a tail. Tail makes transcript more stable and help it exported to cytosol
  • Both protect mRNA and guide to cytoplasm

Question 23

5’-Cap and 3’-Poly-A tail are formed,

Answer 23

Poly A
1. RNA poly synthesizing new strand.
2. Codes polyadenylation signal (termination signal)
3. Nuclear proteins bind to RNAP and cut later on in sequence.
4. enzymes add poly a tail

Question 24

What are the roles of snRNP’s and snRNA’s in the process

Answer 24

Spliceosomes had small nuclear RNA and binds to proteins to form a complex. This complex snRNP identify and remove introns
- snRNA are specific for each protein

Question 25

How do different tissues create different mRNA’s (and therefore different proteins) from the same preRNA.

Answer 25

Alternative splicing different mRNA molecules from same transcript. Leads to different expressions

Question 26

Be able to identify the 5’ UTR (untranslated region) and 3’UTR, and explain why they are there.

Answer 26

to make room for small unit on ribosome to bind

Question 27

Be able to describe the basics of tRNA structure.

Answer 27

Has functional DNA, a shuttle that carries amino acids. Small sequence, hydrogen bodies hold together, has anticodon and amino acid attachment site.

Question 28

Be able to describe Aminoacyl-tRNA Synthetases, and the mechanism of tRNA charging.
What provides the energy to charge tRNA’s? Why is this step critical for the proper assembly of proteins?

Answer 28

• Amino acid attaches (one for every amino acid) to Aminoacyl-tRNA Synthase active site. ATP powers sythase.
  
  • Now amino acid and what is now AMP form a bond in sythase.
  • AMP will fall off and now tRNA will come and bind to amino acid in sythase.
  • activated tRNA molecules created and falls off Aminoacyl tRNA

Question 29

Mitochondrial Ribosomes, where do the rRNAs come from?

Answer 29

have their own ribosomes

Question 30

where do Mitochondrial Ribosomes proteins come from

Answer 30

nuclear genome

Question 31

The mitochondrial chromosome is barely larger than our plasmids in lab. What are the three main types of genes encoded within that chromosome?

Answer 31

mrRNA, tRNA, electron transport

Question 32

If Eukaryotic Ribosomes are generally larger, have more and bigger rRNA, and more proteins than Prokaryotic Ribosomes, how do they compare to mammalian Mitochondrial Ribosomes?

Answer 32

Mitochondrial robosomes are mcuh smaller than mammalian. However, their proteins in the bigger and smaller unit are the same. THe rRNA in the mitochondria is also smaller uncleotides.

Question 33

Initiation
What are the major players at each point?
What is the sequence of events?
What energy is required, and when

Answer 33

Small subunit separated from big subunit through initiation factors
tRNA-MET binds to P site on small subunit.
mRNA binds to small subunit through 5’ccap
Once subunit scans start codon(AUG) GTP is hydrolyzed and kicks out initiation factor. Big subunit joins back

Question 34

Elongation
What are the major players at each point?
What is the sequence of events?
What energy is required, and when

Answer 34

a second tRNA-AA (Aminoacyl-tRNA) binds to A site. GTP hydolysis ensures a good match
Ribosome Peptidyl Transferase (ribosome contained in large subunit) transfers MET from its tRNA in the Psite to the amino end of the second tRNA in A site
GTP hydolized to power the movement of of the tRNA in the E site (to exit) and relocate the growing peptide sequence in the P site (to maker room for next tRNA AA)

Question 35

Termination

Answer 35

Ribosome encounters stop codon
no tRNA that matches stop codon, elongation stops
A site filled with release factor (mimics a tRNA)
peptidyl Transferase passes on peptide chain where tRNA leaves and chain is cut free

Question 36

In Prokaryotes, there is no nuclear membrane to separate Transcription and Translation, what effect does that have on Signal Amplification and timing?

Answer 36

multiple ribosomes can translate the same mRNA at the same time. In bacteria, transcription and translation can happen at the same time

Question 37

In general terms, after a protein is synthesized, why might it not be fully functional yet

Answer 37

can be in wrong part of the cell, may need more modification, or help achieving final conformation. Cappersons need to help these to guide folding