Dna Structure, Dna Replication, Translation, Transcription

Question 1

What is the difference between the nucleoside and nucleotide?

Answer 1

Nucleoside- nitrogenous group, pentose sugar and no phosphate group
Nucleotide- nucleoside and phosphate group

Question 2

what are the components of a nucleotide?

Answer 2

pentose sugar, nitrogenous base, phosphate group

Question 3

What nitrogenous bases are purines?

Answer 3

“Pure As Gold”- Adenine and Guanine

Question 4

What nitrogenous bases are pyrimidines?

Answer 4

“Cut the Pie”- Cytosine and Thymine

Question 5

How many h-bonds are between each unique purine-pyrimidine pair?

Answer 5

A and T - 2H-bonds
G and C - 3H-bonds

Question 6

List features or structures that are different in RNA compared to DNA?

Answer 6

RNA has ribose pentose sugar and has an OH on C2
RNA uses uracil and not thymine

Question 7

If there are 26% of guanine in a double DNA strand. What percentage is of adenine?

Answer 7

G(26%) = C (26%) G+C = 52%
100= (A+T) + (C+G) = (A+T) + 52%
100% - 52% = 48/2= 24%
There is 24% of adenine

Question 8

If there are 32% of cytosine in a DNA double strand, what percentage is of uracil?

Answer 8

There is no uracil in DNA, therefore 0%

Question 9

If there is 29% of adenine in a DNA double strand, what percentage is of cytosine?

Answer 9

A (29%) = T (29%) –> 58%
100% = (A+T) + (C+G) = 58% + (C + G)
100% - 58% = 42/2 = 21%
There is 21% of cytosine

Question 10

What are nucleosomes composed of?

Answer 10

DNA Wrapped around an octomer of eight histone proteins ( 2 H2A, 2 H2B, 2 H3, and 2 H4).
H1 is not part of the eight histone proteins, but H1 binds to DNA where DNA joins and leaves the histone octomer, locking DNA into place.

Question 11

Name all enzymes and their roles in DNA Replication.

Answer 11

Helicase- Unwinds parental dna strands
Primase- form RNA primer needed by DNA Pol
DNA polymerase- needs a primer (has a 3’ OH for DNA pol to bind) to synthesize nucleotide from 5’ to 3’ using the old/parent strand as a template.
PCNA- a trimer complex that threads onto DNA and prevents the whole complex from falling off the template.
Topiosomerase- relieve tensions by making nicks
Ligases- ligate/connects fragments together to make DNA strands more continuous. Connects ozaki fragments in the lagging strand. Connects strands from neighboring replication bubbles.

Question 12

Explain why DNA Replication is semiconservative.

Answer 12

DNA Replication uses parental DNA as a template to create daughter DNA. Therefore Daughter DNA consists of one parent strand and one new synthesized strand.

Question 13

Explain why DNA Replication is semi-discontinuous.

Answer 13

DNA polymerase requires to bind to 3’OH end of primer in order to synthesize DNA creating lagging strands.

Question 14

Why is DNA Replication concurrent?

Answer 14

It has a leading and lagging strand which are synthesized simultaneously.

Question 15

Name the differences and similarities between Eukaryote and Prokaryote DNA Replication.

Answer 15

Eukaryote- Occurs in the nucleus, Multiple origin of replications, and has linear chromosome.
Similarities- still have leading and lagging strands
Prokaryote- Occurs in the cytoplasm, one origin of replication, circular chromosome.

Question 16

Fill in the Blanks.
BLANK is part of BLANK an BLANK enzyme that synthesizes mRNA from 5’ to 3’ without needing BLANK, and it recognizes the BLANK which is the promoter. Once the complex binds to the promoter, BLANK dissociates and BLANK begins.

Answer 16

SIGMA FACTOR is part of RNA POLYMERASE, a HOLOENZYME enzyme that synthesizes mRNA from 5’ to 3’ without needing PRIMER, and it recognizes the PRIBNOW BOX (-10) which is part of the promoter. Once the complex binds to the promoter, SIGMA FACTOR dissociates and ELONGATION begins.

Question 17

what is the process and where is it found in?

Answer 17

The process is Transcription for prokaryotic organisms located in the cytoplasm.

Question 18

Name all enzymes of Prokaryotic Transcription and their roles.

Answer 18

RNA polymerase- doesn’t require primer to synthesize mRNA strand.
Sigma Factor- associate with RNA polymerase, recognize the Pribnow box and brings RNA polymerase to the promoter. After sigma factor is released elongation occurs.
Pribnow box- a sequence (not and enzyme), that recognized by the sigma factor and is seen in the prokaryotic promoter.

Question 19

What are the relationships between mRNA, coding. strand, and template strand?

Answer 19

• Template and non-template strands are complementary to each other.
• mRNA is complementary to template strand
• mRNA has the same sequence as non-template strand.

Question 20

Name all enzymes of Eukaryotic Transcription and their roles.

Answer 20

Transcription factors- influence expression of other genes
TATA Box binding protein- bind @25 consensus sequences
TFIIA/B- bind at @35 consensus sequences
Mediator- “bridge/connector”
RNA Polymerase- synthesize mRNA strand, replacing T with U no primer needed.

Question 21

How can transcription factor machinery interact with genes and transcribe them?

Answer 21

Histone Tail Modification
nucleosome modeling complex- Acetylation & Methylation

Question 22

What are the roles of transcription factors?

Answer 22

Transcription factors enhance or repress transcription.

Question 23

How does eukaryotes initiate elongation?

Answer 23

CTD is Phosphorylated.

Question 24

what are the types of regulatory sequences?

Answer 24

Enhancers and silencers

Question 25

What are the different types of RNA Processing? Why are they significant?

Answer 25

5’ cap- prevent degradation by 5’ exonuclease
Poly-A-tail- prevents degradation
Splicing- removes introns and combines exons together.

Question 26

Name all enzymes and proteins in translation for prokaryote.

Answer 26

Shine-Dalgarno Sequence- ribosome recognition site near the start codon
Ribosome- Site of protein synthesis
- small subunit: binds to mRNA first
- large subunit: binds to mRNA after tRNA recognizes AUG
tRNA- structure that has anticodon that is complementary to the codon of the mRNA
Release factor- binds to the A site if UAA, UGA, or UAG is the codon. Terminates translation.

Question 27

What are the differences between prokaryotic and eukaryotic translation?

Answer 27

Prokaryotic- Shine-dalgarno sequence, Ribosome 70S, occurs in the cytoplasm
Eukaryotic- 5’cap and poly-a-tail (circularized mRNA to form circularized polyribosome), ribosome 80s, occurs in the cytoplasm.

Question 28

Explain why the genetic code is redundant and not ambiguous?

Answer 28

Not ambiguous because each codon encode for one amino acid
Degenerate or redundant because one amino acid can be encoded by multiple codons

Question 29

What is the wobble hypothesis?

Answer 29

degeneracy seems to be more prevalent for the third position of the codon suggesting that the third nucleotide of the codon is less constraint than the other two.

Question 30

What are the differences between Heterochromatin and Euchromatin?

Answer 30

Heterochromatin- Condensed, Transcription machinery can’t come in, no transcription, methylation promotes condensing, and see more methylated lysine
Euchromatin- Relaxed, transcription machinery can come in, transcription is possible if necessary, acetylation promotes relaxation, and see more acetylated lysine

Question 31

Chromatin state can change between euchromatin and chromatin due to what processes/mechanisms?

Answer 31

Chromatin remodeling complex- Transcription factors and other regulatory proteins alter chromatin structure without altering the chemical structure of the histones directly.
Histone modification complex- modify histone tails to either relax or condense chromatin.

Question 32

What is the histone code?

Answer 32

modifications of histone proteins that encode information affecting how genes are expressed.