Chapter 11. 1

Question 1

Biochemical identification of the genetic material

Answer 1

What is the genetic material?
Four criteria necessary for genetic material:
Information
Replication
Transmission
Variation
Late 1800s – biochemical basis of heredity postulated
Researchers became convinced that chromosomes carry the genetic information
1920s to 1940s – scientists expected the protein portion of chromosomes would turn out to be the genetic material

Question 2

Nucleic acid structure

Answer 2

Levels of DNA Structure:
Nucleotides – the building blocks of DNA and RNA
Strand – a linear polymer strand of DNA or RNA
Double helix – the two strands of DNA
Chromosomes – DNA associated with an array of different proteins into a complex structure
Genome – the complete complement of genetic material in an organism

Question 3

DNA

Answer 3

Formed from nucleotides (A, G, C, T)
Nucleotides composed ofthree components
Phosphate group
Pentose sugar
Deoxyribose
DNA = Deoxyribonucleic Acid
Nitrogenous base
Purines – Adenine (A), Guanine (G)
Pyrimidines – Cytosine (C), Thymine (T)

Question 4

RNA

Answer 4

Formed from nucleotides (A, G, C, U)
Nucleotides composed ofthree components
Phosphate group
Pentose sugar
Ribose
RNA = Ribonucleic Acid
Nitrogenous base
Purines – Adenine (A), Guanine (G)
Pyrimidines – Cytosine (C), Uracil (U)

Question 5

Nucleotide Numbering System

Answer 5

Sugar carbons are 1’ to 5’
Base attached to 1’ carbon on sugar
Phosphate attached to 5’ carbon on sugar

Question 6

DNA strands

Answer 6

Nucleotides arecovalently bonded
Phosphodiester bond – phosphate group links two sugars
Backbone – formed from phosphates and sugars
Bases project away from backbone
Written 5’ to 3’
Example: 5’ – TACG – 3’

Question 7

Solving the Structure of DNA

Answer 7

1953, James Watson and Francis Crick, proposed the structure of the DNA double helix
Watson and Crick used Linus Pauling’s method of working out protein structures using simple ball-and-stick models
Rosalind Franklin’s X-ray diffraction results were crucial evidence, suggesting a helical structure with uniform diameter

Question 8

Base-pairing

Answer 8

Erwin Chargoff analyzed base composition of DNA from many different species
Results consistently showed:
amount of adenine (A) = amount of thymine (T)
amount of cytosine (C) = amount of guanine (G)

Question 9

Watson and Crick

Answer 9

Put together these pieces of information
Found ball-and-stick model consistent with data:
Double-stranded helix
Base-pairing: A with T and G with C
James Watson, Francis Crick, and Maurice Wilkins awarded Nobel Prize in 1962
Rosalind Franklin had died and the Nobel Prize is not awarded posthumously

Question 10

Features of DNA

Answer 10

Double stranded
Antiparallel strands
Right-handed helix
Sugar-phosphate backbone
Bases on the inside
Stabilized by H-bonding
Specific base-pairing
Approximately 10 nts per helical turn

Question 11

DNA Structure - Putting it All Together

Answer 11

Chargoff’s rule:
A pairs with T
G pairs with C
Keeps width consistent
Complementary DNA strands:
5’ – GCGGATTT – 3’
3’ – CGCCTAAA – 5’
Antiparallel strands:
One strand 5’ to 3’
Other stand 3’ to 5’

Question 12

Major and Minor Grooves

Answer 12

Grooves are revealed in the space-filling model
Major groove
Proteins bind to affect gene expression
Minor groove
Narrower

Question 13

DNA Replication: Semiconservative Mechanism

Answer 13

DNA replication produces DNA molecules with 1 parental strand and 1 newly made daughter strand.

Question 14

DNA Replication: Conservative Mechanism

Answer 14

DNA replication produces 1 double helix with both parental strands and the other with 2 new daughter strands.

Question 15

DNA Replication: Dispersive Mechanism

Answer 15

DNA replication produces DNA strands in which segments of new DNA are interspersed with the parental DNA.

Question 16

DNA Replication

Answer 16

The two parental strands separate and serve as template strands
New nucleotides must obey the AT/GC rule
End result: two new double helices with same base sequence as original

Question 17

Molecular mechanism of DNA replication

Answer 17

Origin of replication provides an opening called a replication bubble that forms two replication forks
DNA replication proceeds outward from forks
Bacteria have single origin of replication
Eukaryotes have multiple origins of replication

Question 18

Role and Features of DNA Polymerase

Answer 18

DNA polymerase -Covalently links nucleotides
Uses (dNTPS) Deoxynucleoside triphosphates
DNA polymerase cannot begin synthesis on a bare template strand
Requires a primer to get started
DNA polymerase only works 5’ to 3’

Question 19

Role of deoxynucleoside triphosphates

Answer 19

Deoxynucleoside triphosphates
Free nucleotides with three phosphate groups
Breaking covalent bond to release pyrophosphate (two phosphates) provides energy to connect nucleotides

Question 20

Comparison of the leading and lagging strands

Answer 20

Leading strand
DNA synthesized in as one long molecule
DNA primase makes a single RNA primer
DNA polymerase adds nucleotides in a 5’ to 3’ direction as it slides forward
Lagging strand
DNA synthesized 5’ to 3’ but as Okazaki fragments
Okazaki fragments consist of RNA primers plus DNA
In both strands
RNA primers are removed by DNA polymerase and replaced with DNA
DNA ligase joins adjacent DNA fragments

Question 21

DNA replication is very accurate

Answer 21

Three mechanisms for accuracy
Hydrogen bonding between A and T, and between G and C is more stable than mismatched combinations
Active site of DNA polymerase is unlikely to form bonds if pairs mismatched
DNA polymerase can proofread to remove mismatched pairs
DNA polymerase backs up and digests linkages
Other DNA repair enzymes as well

Question 22

DNA Polymerases Are a Family of Enzymes With Specialized Functions

Answer 22

Important issues for DNA polymerase are:
speed,
fidelity,
Completeness.

Nearly all living species have a than one type of DNA polymerase
Genomes of most species have several DNA polymerase genes due to gene duplication
Independent genetic changes produce enzymes with specialized functions

Question 23

DNA Polymerases: Prokarytotes

Answer 23

E. coli has 5 DNA polymerases
DNA polymerase III – multiple subunits, responsible for majority of replication
DNA polymerase I – a single subunit, rapidly removes RNA primers and fills in DNA
DNA polymerases II, IV and V – DNA repair and can replicate damaged DNA
DNA polymerases I and III stall at DNA damage
DNA polymerases II, IV and V don’t stall but go slower and make sure replication is complete

Question 24

DNA Polymerases: Eukaryotes

Answer 24

Humans have 12 or more DNA polymerases

Designated with Greek letters

DNA polymerase a-its own built in primase subunit polymerase & and -extend DNA at a faster rate

DNA polymerase Y-replicates mitochondrial DNA

When DNA polymerases a, 8 or & encounter abnormalities they may be unable to replicate

Lesion-replicating polymerases may be able to synthesize

complementary strands to the damaged area

Question 25

Telomeres

Answer 25

Series of short nucleotide sequences repeated at the ends of chromosomes in eukaryotes
Specialized form of DNA replication only in eukaryotes in the telomeres
Telomere at 3’ does not have a complementary strand and is called a 3’ overhang

Question 26

DNA replication by telomeres

Answer 26

DNA polymerase cannot copy the tip of the strand with a 3’ end
No place for upstream primer to be made
If this replication problem were not solved, linear chromosomes would become progressively shorter
Telomerase enzyme attaches many copies of DNA repeat sequence to the ends of chromosomes

Question 27

Molecular structure of eukaryotic chromosomes

Answer 27

Typical eukaryotic chromosome may be hundreds of millions of base pairs long
Length would be 1 meter
But must fit in cell 10 to 100 micrometer
Chromosome - Discrete unit of genetic material
Chromosomes composed of chromatin a DNA-protein complex

Question 28

Three levels of DNA compaction

Answer 28

1. DNA wrapping
   DNA wrapped around histones to form nucleosome
   Shortens length of DNA molecule 7-fold
2. 30-nanometer fiber
   Current model suggests asymmetric, 3D zigzag of nucleosomes
   Shortens length another 7-fold
3. Radial loop domains
   Interaction between 30-nanometer fibers and nuclear matrix
   Each chromosome located in discrete territory
   Level of compaction is not uniform:
   Heterochromatin - highly compact chromatin.
   Euchromatin - loosely compact chromatin.