Functions And Dysfucntions Of Genomic Regulation DSA

Question 1

What does the central dogma of molecular biology explain?

Answer 1

The flow of genetic info from DNA to RNA to make a functional product,a protein

Question 2

The central dogma state that the pattern of info that occurs most frequently in our cells is what?

Answer 2

From existing DNA to make new DNA (DNA replication)
From DNA to make new RNA (transcription)
From RNA to make new proteins (translation)

Question 3

Describe the DNA backbone

Answer 3

Comprises of five C sugar (pentose) molecules bound to a nucleoside (A, C, G or T)
Pentose molecules are also asymmetrically joined to phosphate groups by phosphodiester bones
Phosphate-deoxyribose backbone

Question 4

Which type of bond stabilizes and forms the double helix structure of DNA?

Answer 4

Hydrogen bonds between complementary nucleotides (G:C or A:T)

Question 5

How many nucleotide pairs are there per helical turn?

Answer 5

10 nucleotide pairs per helical turn

Question 6

What are the three forms of DNA?

Answer 6

B, A and Z form

Question 7

Characteristics of the B form of DNA

Answer 7

10 nucleotide pairs per turn

Right handed

Question 8

Characteristics of the A form of DNA

Answer 8

11 nucleotides per turn

Right handed

Question 9

Characteristics of the Z form DNA

Answer 9

Left handed B form

Actively transcribed DNA

Question 10

The deoxyribonucleotides of DNA are joined by what type of bond?

Answer 10

Covalent phosphodiester bond

Question 11

Where do the phosphodiester bonds form?

Answer 11

Between the 3’-OH groups of the deoxyribose sugar on one nucleotide with the 5’-phosphate groups on the adjacent molecule

Question 12

The 5’ end of one strand is base paired with the 3’ end of the other strand. What stabilizes this?

Answer 12

Noncovalent interactions - H bonds

Question 13

How many hydrogen bonds are between adenine and thymine?

Answer 13

Two

Question 14

How many hydrogen bonds are between guanine and cytosine?

Answer 14

Three

Question 15

How does base pairing in the interior of the helix stabilize the interior of the double stranded DNA?

Answer 15

Because stacked bases repel each other due to their hydrophobic nature

Question 16

What is chromatin?

Answer 16

DNA packaged into a protein-DNA structure which allows it to fit in the nucleus
Consists of very long double stranded DNA molecules, small basic proteins called histones as well as smaller amounts of non-histone proteins and a small quantity of RNA

Question 17

What nucleosomes?

Answer 17

The fundamental organization upon which the higher order packing of chromatin is built
The core consists of a complex of 8 histone proteins with double stranded DNA wound around it

Question 18

What are histones?

Answer 18

A heterogenous group of closely related arginine and lysine rich basic proteins which help them bind tightly to the negatively charged sugar phosphate backbone of DNA
Provide for the compaction of DNA

Question 19

Each nucleosome core consists of what?

Answer 19

Two molecules each of histone H2A, H2B, H3 and H4

Question 20

What separates each nucleosome?

Answer 20

Link histone H1

Question 21

What are the three elements of chromosome structure?

Answer 21

Telomeres, centromeres and multiple origins of replication

Question 22

What are telomeres?

Answer 22

Hexameric DNA repeats found at the ends of chromosomes that serve to protect the chromosome from degradation

Question 23

What are centromeres?

Answer 23

Serve as handles which allow mitotic spindles to attach to the chromosome during cell division
Also serve as a boundary that separates the two chromosome arms

Question 24

Describe multiple origin of replication

Answer 24

In order for DNA in chromosomes to replicate a specific nucleotide sequence acts as a DNA replication origin
They are dispersed throughout its length
At the ORC there is an association of sequence specific double stranded DNA binding proteins with a series of direct repeat DNA sequences

Question 25

What is a gene?

Answer 25

The complete sequence region necessary for generating a functional product/protein

Question 26

Describe the area that the gene takes up on a DNA strand

Answer 26

The area encompasses promoters and control regions necessary for the transcription, processing and translation Genes are concentrated in random areas along the genome,with vast expanses of non coding DNA between them

Question 27

What are the coding regions of the gene called?

Answer 27

Exons

Question 28

What are the noncoding regions of the gene called?

Answer 28

Introns

Question 29

What are the four characteristics of DNA replication/synthesis?

Answer 29

1. Semiconservative with respect to parental strand 2. Bidirectional with multiple origins of replication 3. Primed by short stretches of RNA 4. Semidiscontinous with respect to the synthesis of new DNA

Question 30

Describe the characteristic of DNA replication being semiconservative with respect to the parental strand

Answer 30

When DNA is replicated during the process of cell division one parent or original strand of DNA is distributed to each daughter duplex in combination with a newly organized strand with an anti-parallel orientation At the end of the process each of the two daughter strands has half new DNA and half old DNA

Question 31

Describe how the characteristic of DNA replication being bidirectional with multiple origins of replication

Answer 31

DNA replication is bidirectional and starts in several different locations at once Replication begins at several sites on linear DNA and is completed by the end of DNA synthesis (s phase) of the cell cycle As replication nears completion bubbles of newly replicated NDA come together forming two new molecules

Question 32

Explain the characteristic of DNA replication being primed by short stretches of RNA

Answer 32

Replication requires short stretches of RNA for initiation bc DNA polymerases cant initiate synthesis of a complementary strand of DNA on a single stranded template DNA primase synthesizes short stretches of RNA that are complementary and anti parallel to the DNA template RNA primer is later removed

Question 33

Explain the characteristic of DNA replication being semidiscontinuous with respect to the synthesis of new DNA

Answer 33

``` All DNA polymerases function in the same manner meaning they read a parental strand 3’-5’ and synthesize a complementary strand anitparallel new strand 5’-3’ One strand (leading) is synthesized 5’-3’ and the opposite strand (lagging) is synthesized 5’-3’ but discontinuously ```

Question 34

What are DNA helicases?

Answer 34

A class of motor proteins required to unwind short segments of the parental duplex DNA

Question 35

What is the function of topoisomerases?

Answer 35

Remove the supertwisting of DNA

Question 36

What do single stranded DNA binding proteins do?

Answer 36

Prevent premature annealing of the single stranded DNA to double stranded DNA

Question 37

Which proteins function in parental strand separation during replication?

Answer 37

DNA helicase, topoisomerases and ssDNA binding proteins

Question 38

Which proteins function in DNA synthesis/chain elongation?

Answer 38

DNA primases and DNA polymerases

Question 39

What is the function of DNA primases during DNA synthesis?

Answer 39

Initiate the synthesis of an RNA molecule essential for priming DNA synthesis on both the leading and lagging strands

Question 40

What is the function of DNA polymerases during DNA synthesis/chain elongation?

Answer 40

Function as a complex to initiate DNA synthesis and chain elongation by adding new nucleotides They also have exonuclease activity or proofreading ability that allows them to remove nucleotides that are part of the double helix

Question 41

What enzyme functions in DNA ligation of replication?

Answer 41

DNA ligase

Question 42

What is the function of DNA ligase?

Answer 42

Catalyzes the sealing of nicks (breaks) remaining in the DNA after DNA polymerase fills the gaps left by RNA primers Is required to create the final phosphodiester bond between the adjacent nucleotides on a strand of DNA

Question 43

Describe the telomere/end of chromosome problem

Answer 43

The telomere shortens with every cell division The lagging strands of replicated telomeres undergo shortening after the removal of the last RNA primer from the 5’ ends during each successive cycle of cell division The gap cannot be filled in due to the lack of a primer which leads to shortening of the telomeres Recognized as part of the normal aging process

Question 44

What is the telomere maintenance enzyme?

Answer 44

Telomerase which is an RNA-dependent DNA polymerase which adds TTAGGG repeats to the ends of chromosomes

Question 45

What are the 4 types of RNA?

Answer 45

Ribosomal, transfer, messenger and micro RNA

Question 46

What is the function of ribosomal RNA and which enzyme produces it?

Answer 46

Structure and function of ribosomes | Produced by RNA polymerase I

Question 47

What is the function of tRNA and which enzyme produces it?

Answer 47

Carry aa to ribosomes for protein synthesis | RNA polymerase III

Question 48

What is the function of mRNA and which enzyme produces it?

Answer 48

Carrier of genetic info from genes to ribosomes for protein synthesis Produced by RNA polymerase II

Question 49

What is the function of microRNA and which enzyme produces it?

Answer 49

Regulate mRNA stability and downregulate gene expression | Produced by RNA polymerase II

Question 50

What are the difference regulatory elements in protein coding genes?

Answer 50

Promoter region, splice acceptor and donor sequences (intron) and different regulatory regions

Question 51

Where are promoters located?

Answer 51

Constantly located just before the coding region

Question 52

Where are enhancers and response elements located?

Answer 52

Can be anywhere on the genome upstream and downstream and they can be 1000s of bases away from the transcription units located on the same chromosome

Question 53

What are the three reactions for RNA processing?

Answer 53

Addition of a 5’ cap, addition of a polyA tail and intron removal/splicing