DNA RNA Lecture

Question 1

3 Domains of Life

Answer 1

Eukaryotes Eubacteria and Archaea

Question 2

Prokaryotes types and general description

Answer 2

Eubacteria and Archaea
Microscopic organisms lacking a nucleus
Ribosomal RNA sequence distinct
Distinct metabolic machinery

Question 3

Eukaryotes examples and general description

Answer 3

Animals, Plants, and Fungi with a defined Nucleus

Question 4

Prokaryotic Genome

Answer 4

Prokaryotic genomes are made of DNA.
Prokaryotic chromosomes can be circular or linear.
very often are linear especially when we talk about e.coli
circular chromosome is important for the mechanism of replication
Prokaryotic cells do not contain organelles (including a separate nucleus).
Genomes float freely inside the cell.
not entirely true because all DNA is captured in a certain area, so tends to sit in one location in the cell

Question 5

Eukaryotic Genomes

Answer 5

The genomes of eukaryotic organisms are made of DNA.
The genomes of eukaryotic organisms are less dense and contain elements in addition to gene coding regions.
many other elements than just the areas that code for genes
such as areas involved in regulation, structure etc.
less efficient than prokaryotic genome
Eukaryotic genomes frequently include several to many linear chromosomes.

DAPI is a dye that can intercalate in DNA and allows us to capture photos

Question 6

Viral Genomes

Answer 6

Some viral genomes are made up of DNA; others are RNA.
Some viral genomes are single-stranded; others are double-stranded.
Some viruses integrate their genetic material into the host cell’s genome; others do not.

Question 7

Bacteriophage Genomes

Answer 7

Bacteriophage are viruses that infect bacteria
not infecting eukaryotes
Head of a phage is a 20- sided protein capsule that contains DNA
Head attached to protein tail and six tail fibers
Phage DNA only replicates once inside the bacterium
it infects

Question 8

3 Separate Chemical Entities that make DNA or RNA

Answer 8

3 Separate Chemical Entities make DNA or RNA
The 3 Separate Chemical Entities assemble
by covalent chemical bonds to make nucleotides

Question 9

What are the sites for Covalent Bonding

to Adjacent Nucleotide’s Phosphate group

Answer 9

The 5’ and 3’ Carbons in Pentose Sugar
are Sites for Covalent Bonding
to Adjacent Nucleotide’s Phosphate group

Question 10

5’-3’ phosphodiester linkage

Answer 10

The 5’ position of each pentose ring is linked to the 3’position of the next pentose ring by a phosphodiester bond. This is called 5’-3’ phosphodiester linkage.

Question 11

polynucleotide.

Answer 11

A single strand chain of nucleic acids
is called a polynucleotide.

Backbone consists of alternating
structures of pentose (sugar) and phosphate residues.
DNA strand has polarity: one end (5’) has a free phosphate group and the other end (3) has a free hydroxyl group available for additional linkage.
Nucleotide bases stick out and are available
for pairing.

Question 12

Chargaff’s rules

Answer 12

Examined nucleotide composition 
in various organisms
Examined nucleotide composition 
in various organisms
Total pyrimidine (T + C) almost always equals 
total purine (A+G)

Question 13

Base Pairing by Hydrogen Bonding

Answer 13

Constant diameter of DNA helix requires specific partners
G-C pair has 3 hydrogen bonds
A-T pair has 2 hydrogen bonds

Question 14

Covalent versus Non-covalent Bonds

Four major forms of non-covalent bonds: (Hint HIVH)

Answer 14

Hydrogen Bonds typical from H in N-H or O-H but not C-H since this is nonpolar

Ionic Interactions from a positive charged ion attraction for a negatively charged ion

Van der Waals Forces from transient dipoles when any two atoms approach each other closely they create weak nonspecific attractive forces as random distribution of electrons

Hydrophobic Bonds non polar molecules cluster and adhere and force any intervening H2O into unstable cage formations

Energy of covalent H-H about 104 kcal/mal
Energy on non-covalent bonds 1-5 kcal/mol
Hydrogen bonds 5 kcal/mol
Hydrophobic bonds 1 kcal/mol

Question 15

Base pairing is central to semi-conservative Replication

Answer 15

Watson and Crick
proposed that DNA 
replicates by the separation 
of the two strands and creation of two daughter strands by pairing of template nucleotides with new nucleotides using the 
A:T and G:C pairing rule.

Question 16

DNA Replication Description

Answer 16

Replication is semi-conservative (each strand can serve as template for making its own partner)
When parental strands separate
Each strand serves as template
Makes a new, complementary strand

Question 17

Structure of DNA Double Helix

Answer 17

There are about 10 base pairs/turn
One complete turn is 0.34nm long (also called 34 Angstroms Å)
The helix is 0.2nm (20 Å) in diameter.
DNA has grooves of 2 sizes, the major and minor groove

Question 18

Major grooves description

Answer 18

major grooves are more open and flat

The bases are more available for bonding

Question 19

DNA is NOT a rigid helix

Answer 19

It twists, turns, writhes, wiggles,

comes apart, and back together

Question 20

Certain base sequences cause bending

Answer 20

Tracts of 4-6 adenines in a row cause DNA to bend. When these tracts repeat every 10-11 bp (a turn of the helix), the DNA bends back on itself and can eventually form a loop.

5’RGCY3’ where R is a purine and Y is a pyrimidine causes DNA to bend.

Question 21

Binding of proteins to DNA and to each other leads to

Answer 21

bending and looping of DNA

Question 22

Palindrome sequences (inverted repeats) can promote

Answer 22

cruciform or hairpin structures
These structures are “strained”

However, they do exist in nature and are often unstable, leading to DNA breakage and small deletions in the region

Question 23

Where in this structure are breaks most likely to happen?

Answer 23

The place where breakages could form is at the loop part of the cruciform

Question 24

DNA helix can take three forms

Answer 24

B-DNA, A- DNA, Z- DNA

Question 25

B-DNA

Answer 25

Right-handed twist with bases stacked.
Occurs in “normal” humidity
Bases in center (no hole)
Phosphates at periphery

Question 26

A- DNA

Answer 26

Right handed twist
Occurs in dehydrated conditions (humidity 75%)
1. Large hole in center
2. Sugar phosphate backbone is at the edge
3. Bases are displaced towards edge

Question 27

Z- DNA

Answer 27

left-handed twist with backbone zigzagged
created by repeats of alternating
purines and pyrimidines
Bases present throughout the matrix of the helix
No exclusive domains for either bases or backbone

Question 28

Triplex DNA structure

Answer 28

When a ds helical structure contains a run of purines on one strand, the structure can accommodate
Pairing with a pyrimidine or purine ssDNA stretch

Each purine pairs with two pyrimidines simultaneously.
Uses BOTH Watson Crick paring and Hoogsteen pairing by hydrogen bonding

Question 29

Quadruplex DNA structure

Answer 29

4 guanines are held by 8 hydrogen bonds
Additional stability comes from a metal cation (Na+ or K+) between stacked quartets

In lower organisms, these structures are rare.
In human DNA these are observed in rDNA, telomeres, immunoglobulin switch regions, some unstable minisatellites, and in first intron of single copy genes

Question 30

Consequences of Quadruplex DNA structure

Answer 30

High thermal stability and can block DNA or RNA polymerase if not resolved.

Helicases are enzymes that catalyze unwinding of dsDNA

The WRN helicase and FANCJ helicase may both act in human cells to relax these structures

Patients defective or deficient in these proteins have diseases related to premature aging and cell death (WRN, Werner’s disease) and blood depletion and cancer predisposition (FANCJ, Fanconi’s Anemia)

Question 31

Denaturation: DNA “Melting”

Answer 31

With heat, noncovalent forces holding DNA strands together weaken and break
When the forces break, the two strands come apart
Temperature at which DNA strands are 50% denatured is the melting temperature or Tm
In addition to heat, DNA can be denatured by:
Organic solvents
High pH
Low salt concentration

GC content of DNA has a significant effect on Tm with higher GC content producing higher Tm

G-C basepairs have three hydrogen bonds to break
A-T basepairs have only two hydrogen bonds to break

Question 32

DNA Renaturation

Answer 32

After two DNA strands separate, under proper conditions the strands can come back together by base pairing
Process is called reannealing, hybridization,renaturation

Requirements for DNA renaturation:
salt concentration must be high (0.15-0.5 M NaCl)
to eliminate electrostatic repulsion between phosphates in the two strands
temperature must be 20-25º below the Tm
allows stable interstrand base-pairing
Renaturation is a slow process compared to denaturation because precise collision between complementary sequences is required

Question 33

What does base stacking mean

Answer 33

Base stacking stabilizes dsDNA

and is cooperative

Question 34

Why does high GC content lead to higher Tm?

Answer 34

more bonds to break

Question 35

What will happen to RNA as the temperature increases?

Answer 35

Intramolecular bonds break

Question 36

You have dsDNA and ssRNA with the same sequence.

You mix them together in a tube, boil, and then cool. What will happen?

Answer 36

different pairs of base pairing, cruciforms,