Nucleic Acids: Main Themes Notes

Question 1

How does DNA/RNA differ?

Answer 1

DNA:
-Sugar: deoxyribose
-Pyrimidines: thymine
-usually, two helical strands coiled around a common axis

RNA:
-sugar: ribose
-pyrimidines: uracil
-single strand but can fold to form elaborate structures

Question 2

How is DNA/RNA similar?

Answer 2

-Purines: adenine and guanine
-Pyrimidines: cytosine

Question 3

How can you identify purine and pyrimidine nitrogenous bases? What about removing a base?

Answer 3

-purine (two carbon rings)
-pyrimidine (one carbon ring):

Loss of bases from a DNA double helix is called depurination (loss of purine bases) or depyrimidination (loss of pyrimidine bases)

Question 4

Why is DNA more stable than RNA

Answer 4

1. Base-Catalyzed hydrolysis
   -ribose deprotonation leads to nucleophilic attack
2. photodegradation
   -Uracil more photosensitive than thymine

Question 5

How does the hydrophobic effect impact DNA’s structure?

Answer 5

-nonpolar nitrogenous bases: Interior of double helix stabilized by van der Waals interactions and hydrogen bonds
-polar phosphate groups: exterior stabilized by hydrogen bonds

Question 6

Why is DNA damage a concern? What types of damage can occur?

Answer 6

-may prevent nucleic acid synthesis or result in daughter strands with different sequences

-may induce cell transformation (loss of cell division), metastasis, or cell death
-metabolic dysfunction
-repair systems recognize damage and restore the nucleic acid to its undamaged form

Question 7

How do prokaryotic and eukaryotic chromosomes differ?

Answer 7

Prokaryotic: store DNA on a single circular chromosome

Eukaryotic: store DNA across multiple pairs of linear chromosomes

Question 8

How are dietary nucleic acids digested? Do humans store the nitrogenous bases?

Answer 8

-Digestion is completed by digestive enzymes that cleave covalent bonds
1. Mouth: saliva does not contain any enzymes for NA’s
2. Stomach: acidic environment denatures NA’s
-pepsin cleaves NAs into oligonucleotide fragments

-nitrogenous bases are not stored for later use

Question 9

PP2: Nitrogenous base metabolism generates B-alanine, B-amino isobutyrate and uric acid. What happens to each of these products? Can any major metabolic intermediates be generated from them?

Answer 9

-Nitrogenous base metabolism occurs in the liver
-final products can be excreted from the body in urine

-b-alanine converted into malonyl CoA (Fatty acid synthesis intermediate)

-b-amino isobutyrate converted into succinyl CoA (cellular respiration)

Question 10

What is unusual about the pentose phosphate pathway

Answer 10

there is no ATP produced or used

Question 11

How do pentoses (like ribose and deoxyribose) enter cellular respiration? check

Answer 11

1. during the non-oxidative phase, ribose 5 phosphate is converted into fructose 6-phosphate and glyceraldehyde 3-phosphate (products directed into glycolysis: ATP or gluconeogenesis: glucose)
2. sugar cleaved by DERA that generates acetaldehyde and glyceraldehyde 3-phosphate (intermediate of alcoholic fermentation and glycolysis)

Question 12

PP3: Do cells perform DNA synthesis constantly? If not, when?

Answer 12

No they do not, they replicate when cell repro is needed.

Question 13

How is DNA replicated? What happens at each stage?

Answer 13

• replication requires denaturation (requires all four activated deoxyribose nucleotides and Mg2+)
  -new DNA strand has a complementary sequence to the template DNA strand
  -strands must be separated for cellular machinery to access nucleic acids

-Helicase denatures DNA via ATP hydrolysis
-to begin, DNA polymerase requires a primer
-errors can be corrected by DNA polymerase during proofreading
-Initiation, elongation and termination

Question 14

Eukaryotic DNA polymerase alpha has “intrinsic primase activity.” What does that mean?

Answer 14

enzyme that creates primers during cellular DNA replication

Question 15

Define telomere. Are telomeres present on prokaryotic chromosomes?

Answer 15

Telomere: repetitive regions of non-coding nucleotides at ends of chromosome

Prokaryotes lack telomeres because they are circular with no endings. The chromosome should be straight or linear to identify its start or end. Telomeres are only found in eukaryotes because eukaryotes have straight, linear chromosomes that can be identified by their final segment or end

Question 16

How does a translesion polymerase differ from a “standard” DNA polymerase?

Answer 16

-translesion polymerase are deployed during strand breaks
-has a larger active site and lower fidelity
-specialized for replication of damaged or abnormal templates

Question 17

Are all genes on a single chromosome expressed at the same time?

Answer 17

-transcription occurs on a per-gene or small group of genes basis
-Only a fraction of the genes in a cell are expressed at any one time.

Question 18

How is RNA synthesized? What happens during each stage?

Answer 18

PROKARYOTIC BASICS
-requires all four activated ribonucleotides and Mg2+ and Mn2+
-new RNA strand has a complementary sequence to the template DNA strand
-errors generally not corrected by RNA polymerase, little proofreading
EUKARYOTIC BASICS
-the abundance of enhancers sequences
-RNA product further processed/ edited
-an abundance of “junk DNA”

Question 19

Prokaryotic RNA polymerase has “intrinsic helicase activity”, what does that mean

Answer 19

it separates the helicase by itself

Question 20

most eukaryotic DNA is non-protein coding. What purposes does it serve?

Answer 20

-regulatory sequences (like promoters and enhancers)
-protection from exonucleases (telomeres)
-DNA that generates other transcribed products (tRNA/rRNA)

Question 21

Which modifications (to histones or DNA) increase versus decrease gene expression?

Answer 21

PROMOTE:
-acetylation of histone amino-terminal tail reduces affinity with nucleic acid
-histone phosphorylation also reduces affinity with nucleic acid, as modification promotes acetylation
-these modifications promotes chromatin remodeling (condensed to accessible state)

HINDER
-ubiquitination of histone amino-terminal tail associated with gene silencing but mechanism unclear
-DNA methylation causes nucleosome beads to pack more tightly together
-these modifications promote chromatin remodeling (open/accessible to condensed state)

Question 22

Nucleic acid that dictates a protein’s primary structure with its codons

Answer 22

mRNA

Question 23

Nucleic acid that contains a major groove and a minor groove

Answer 23

double-stranded DNA

Question 24

Nucleic acid that forms an ester linkage with an amino acid

Answer 24

tRNA

Question 25

True or false: Nucleic acids are negatively-charged, water-insoluble polymers.

Answer 25

false, DNA is negatively charged but are water soluble

Question 26

Which biochemical role is shared between ribozymes and proteins?

Answer 26

Serving as catalysts in chemical reactions.

Question 27

dCDP

Answer 27

deoxyribose cytosine diphosphate with a pyrimidine nitrogenous base

Question 28

True or false: On a daily basis, double-strand breaks are the most frequent kind of DNA damage.

Answer 28

false, single-strand breaks are the most common

Question 29

Metabolizing deoxyribose with the enzyme ______ will generate glyceraldehyde 3-phosphate (GAP), while synthesizing ribose via the pentose phosphate pathway will generate ______.

Answer 29

DERA, NADPH

Question 30

Some college textbooks state “Prokaryotes do not have chromosomes. Instead, they have circular DNA”. Why do you think that is?

Answer 30

Because prokaryotes lack histone-containing chromatin.

Question 31

Adding salt to a test tube containing DNA and water will alter the nucleic acid’s structure, resulting in a shorter, wider double helix. What do you think is the most logical explanation for this correlation?

Answer 31

Salt decreased the noncovalent interactions between the DNA and the water

Question 32

For each enzyme listed, indicate where in the human body it participates in digestion.

Answer 32

DNase: SI
pepsin: stomach
Nucleosidase: SI
phosphatase: SI

Question 33

True or false: The human body salvages a greater proportion of dietary purines than dietary pyrimidines.

Answer 33

true

Question 34

Does nitrogenous base metabolism involve coenzymes? Select all that apply.

Answer 34

Yes, NADPH in pyrimidine metabolism.

Question 35

Individuals with DERA deficiency produce less of the enzyme than normal. This results in:

Answer 35

Decreased deoxyribose metabolism but no change to ribose metabolism

Question 36

True or false: Circular prokaryotic chromosomes contain telomeres.

Answer 36

false

Question 37

How does eukaryotic nuclear DNA replication differ from prokaryotic DNA replication?

Answer 37

Prokaryotic DNA replication requires a separate primase enzyme, while eukaryotic nuclear DNA replication does not.

Question 38

Why do eukaryotes use replication fork collisions as a termination strategy, but prokaryotes do not?

Answer 38

Because eukaryotic DNA has multiple origins of replication.

Question 39

All of the following statements about transcription are true except:

Answer 39

In eukaryotes, the process occurs within the cytoplasm

TRUE
-In prokaryotes, RNA polymerase denatures a local DNA region.
-The template DNA can form a hybrid helix with the nascent RNA.
-Transcription factors bind to enhancers in chromosomes.

Question 40

To silence a gene, you could:

Answer 40

ubiquitinate histones