Chapter 11 - DNA replication

Question 1

what macromolecule did scientists in the early 1900s believe to carry genetic material

Answer 1

proteins because they had the most diversity (20 amino acids vs 4 nucleotides)

Question 2

Four criteria necessary for genetic material

Answer 2

1. information
2. replication
3. transmission
4. variation

Question 3

Describe Griffith’s experiment

Answer 3

• Rough and heat-killed smooth is non-toxic
• Smooth S. pneumoniae toxic because of its capsule
• Rough with heat-killed smooth is toxic
  Conclusion: the genetic material had been transferred from the heat-killed S-type to the R-type
• gave R the capsule-secreting trait that was passed on to their offspring

Question 4

Avery, MacLeod, and McCarty

Answer 4

• used DNase, DNase, and proteases
• only DNase resulted in to transformation
• concluded that DNA is the genetic material

Question 5

genome

Answer 5

complete complement of genetic material in an organism

Question 6

How are the two strands of DNA aligned?

Answer 6

antiparallel in a double helix

Question 7

three components of DNA

Answer 7

1. phosphate group
2. pentose sugar
   - deoxyribose
3. nitrogenous base (a,g,c,t)

Question 8

three components of RNA

Answer 8

1. phosphate group
2. pentose sugar
   - ribose
   - OH at 2’
3. nitrogenous base (a,g,c,u)

Question 9

numbering of nucleotides

Answer 9

• sugar carbons numbered 1’-5’
• base attached to 1’
• phosphate attached to 5’
• exposed 3’ of one sugar attaches

Question 10

backbone of DNA

Answer 10

• made of phosphates and sugars
• phosphodiester bonds
• written: 5’-TACG-3’

Question 11

how was the structure of DNA solved

Answer 11

• Watson and Crick proposed the structure of the double helix using the ball and stick model
• Relied on Rosalin Franklin’s X-ray diffraction findings suggesting a double helix with

Question 12

Erwin Chargoff

Answer 12

• analyzed base composition of DNA
• found that the amount of adenine was always the same as thyme and cytosine the same as gaunine
• supports idea of a uniform diameter

Question 13

features of DNA structure

Answer 13

• right-handed double helix
• antiparallel, complementary strands
• sugar-phosphate backbone
• base pairing on the inside via H-bonding
• consistent distance of about 2nm
• one helical turn is about 10 nucleotides

Question 14

major vs minor grooves

Answer 14

• major grooves are larger and allow proteins to bind to help with gene expression

Question 15

semiconservative model

Answer 15

• DNA replication produces DNA molecules with 1 parent and 1 daughter strand
• discovered by Meselson and Stahl using isotopes
• not conservative or dispersive

Question 16

Meselson and Stahl

Answer 16

• used isotopes of nitrogen to discover the semiconservative model

Question 17

Origin of replication

Answer 17

• sequence that signals the opening of the replication fork
• allows the beginning of DNA replication
• bacteria have one
• eukaryotes have multiple

Question 18

DNA helicase

Answer 18

binds to DNA and travels 5’ to 3’ to separate the strands

Question 19

topoisomerase

Answer 19

• removes knots caused by the helicase

Question 20

single strand binding proteins

Answer 20

hold parent strands open to be replicated

Question 21

DNA polymerase 3

Answer 21

• covalently links nucleotides
• requires primer because it needs something to build off of
• builds 5’ to 3’
• reads 3’ to 5’

Question 22

deoxynucleoside triphosphate (DNTP)

Answer 22

• free nucleotides with three phosphate groups
• two terminal phosphates are broken off for energy in to bind nucleotides together in DNA synthesis

Question 23

how does primer work?

Answer 23

• primate adds and RNA primer must so polymerase can add nucleotides
• DNA polymerase 1 removes the primer after replication and makes it DNA (for okazakis - can’t do this for leading)

Question 24

Leading vs. lagging strand

Answer 24

Leading:
- synthesized 5’-3’ as one long molecule
Lagging:
- synthesized 5’-3’ as Okazaki fragments
- fragments covalently bonded by ligase
both have RNA primer that is later replaced by DNA

Question 25

3 mechanisms for DNA replication accuracy

Answer 25

1. H-bonding between A and T and between G and C is more stable than mismatched combinations 2. DNA polymerase is unlikely to form bonds if the pairs are mismatched 3. DNA polymerase can proofread to removed mismatched pairs - other DNA repair enzymes also exist

Question 26

DNA polymerases

Answer 26

- there are many different types of DNA polymerases that perform different functions - bacteria and human cells have different types of polymerases with different specialized functions

Question 27

telomeres

Answer 27

- series of nonsensical nucleotide sequences at the 3' end of chromosomes - cannot be replicated because there is nowhere for upstream primer to be made - also called the 3' overhang - makes sure that all important DNA can be replicated - progressively shorten

Question 28

how does telomerase work

Answer 28

- makes telomeres - attaches many copies of DNA repeat sequence to the ends of chromosomes

Question 29

what is a chromosome

Answer 29

- discrete unit of genetic material - composed of chromatin - about 1 meter in length

Question 30

three levels of DNA compaction

Answer 30

1. DNA wrapping 2. 30 nanometer fiber 3. formation of loop domains

Question 31

DNA wrapping

Answer 31

- DNA wraps around proteins called histones to form a nucleosome - shortens DNA 7x

Question 32

30nm fibers

Answer 32

- asymmetric, 3D zig zag of nucleosomes - shortens length another 7x

Question 33

radial loop domains

Answer 33

- interactions between 30nm fibers and nuclear matrix - each chromosome located in discrete territory

Question 34

Chromosomes during cell division

Answer 34

- chromosomes compact more during cell division - Euchromatin - not as compact - heterochromatin - more compact

Question 35

how can the charge of histone affect the compactness of chromatin

Answer 35

- DNA is negatively charged - Positive histones favor compactness/heterochromatin - negative histones will favor euchromatin