Biochem Exam 3: Synthesis Of Dna

Front 1

Replication of DNA is catalyzed by _____ and requires ______

Back 1

-DNA polymerase
-template - ssDNA
-substrates - dATP, dCTP, dGTP, dTTP

Front 2

DNA undergoes ______, where one DNA is the parental strand, and the other is the new strand

Back 2

semiconservative replication

Front 3

In (prokaryotes/eukaryotes), replication begins at single, unique origin of replication
In (prokaryotes/eukaryotes), replication begins at multiple sites along genomic DNA

Back 3

-prokaryotes
-eukaryotes

Front 4

Origin of replication is usually _____ rich. This makes sense because strands must be ____ at the start site

Back 4

-AT rich
-melted
*AT bonds only form by 2 hydrogen bonds, making it easier to melt

Front 5

When strands replicate, they form a V-like structure called a ____

Back 5

replication fork

*replication is BIDIRECTIONAL!

Front 6

______ protein binds and melts dsDNA
______ unwinds double helix

Back 6

-DnaA protein
-DNA helicase

Front 7

During replication, ssDNA-binding (SSB) proteins bind to ssDNA to:

Back 7

-keep strands separate
-protect from nucleases (nuclease breaks phosphodiester bonds between nucleotide sequences - ssDNA is more susceptible to nuclease)

Front 8

DnaA, DNA helicase, and ssDNA-binding (SSB) proteins, are all part of the ______________________ which unwinds double helix ahead of advancing replication fork and keeps strands separated.

Back 8

Pre-priming complex

Front 9

Unwinding of DNA forms _____ ahead of the fork
The enzyme _____ removes these and facilitates transcription

Back 9

-supercoils
(supercoils can interfere w/ further unwinding)

-DNA topoisomerases

Front 10

DNA polymerase reads DNA in the _____ direction and synthesizes DNA in the ______ direction. Therefore the two newly synthesized chains must grow in opposite directions

Back 10

-3' - 5'
-5' - 3'

Front 11

The _____ strand is copied continuously and the ____ strand is copied discontinously
In the lagging strand, small fragments of DNA, called ______, are copied near the replication fork

Back 11

-leading
-lagging
-okazaki fragments

Front 12

DNA polymerase require ____ to initiate synthesis. Short stretches of RNA complementary to DNA template is synthesized by _____

Back 12

-RNA primer
-primase (a specific RNA polymerase)

Front 13

_____ uses RNA primer to initiate replication

Back 13

DNA polymerase III

Front 14

Elongation is catalyzed by _____
This enzyme stays bound to DNA all the way during synthesis and is responsible for proofreading during replication

Back 14

DNA polymerase III

Front 15

____ synthesizes the lagging strand until it is blocked by RNA primer and _____ locates the space between DNA and RNA and replaces the RNA primer with DNA

Back 15

-DNA pol III
-DNA pol I

Front 16

DNA fragments of lagging strand are linked by _____ enzymes by forming _____ bonds between 3' ____ end and 5' ____ end
This requires _____

Back 16

-DNA ligase
-phosphodiester bonds
-3' hydroxyl
-5' phosphate

-ATP

Front 17

4 steps of lagging strand synthesis:

Back 17

1. RNA primer elongated by DNA pol III until stretch of RNA reached
2. RNA primer excised by DNA pol I (1 nucleotide at a time)
3. Gap (where primer was) filled by DNA pol I
4. Remaining nick sealed by DNA-ligase

Front 18

DNA pol I reads parental DNA in what direction?
DNA pol II?
DNA pol III?

Back 18

DNA pol I
-5' - 3' when filling gap after removal of RNA primer
-3' - 5' when removing RNA primer

DNA pol II
-3' - 5' - DNA repair

DNA pol III
-3' - 5' - replication of DNA, synthesis, and proofreading

Front 19

DNA repair and recombinant DNA techniques use what enzyme?

Back 19

DNA ligase

Front 20

In eukaryotes, the RNA primer is removed by _____

Back 20

RNAse H

Front 21

Eukaryotic Cell Cycle:
Period preceding replication is ____
*Replication occurs during _____
When a cell undergoes rapid growth and prepares for mitosis is ______
Mitosis is the _____
When a cell stops dividing, it is in the _____

Back 21

-G1 phase
-S (synthesis) phase
-G2 phase
-M phase
-G0 phase

Front 22

What are all the different types of eukaryotic polymerases and what are their functions?

Back 22

Front 23

Shortening of DNA is due to inability to fill gap at extreme (3'/5') end

Back 23

-5' end
*results in loss of genetic information and is associated with aging
*Loss of DNA caused by shortening can lead to cell senescence and death

Front 24

The end of the chromosome contains highly repetitive DNA called _____
What is the repetitive unit for human (6 nucleotides long)?

Back 24

-telomere
-TTAGGG

Front 25

What are all the functions of of telomeres?

Back 25

-Serve as a buffer, which is consumed during cell division
-Protect the ends from nucleases
-Limit cells to a fixed number of divisions, in most somatic cells

Front 26

Telomeres can be replenished by _____, which is active in germ, stem, and cancer cells

Back 26

telomerase

Front 27

Exercise has be found to increase _____ in aorta and mononuclear (immune) cells in mice
High levels of vitamin D is also associated with longer ____

Back 27

-telomerase

-telomeres

Front 28

How does telomerase, a ribonucleoprotein (protein and RNA), work?

Back 28

-it's a RNA-dependent DNA polymerase that contains RNA that is complementary to repetitive sequence in telomere
-it uses the 3' end of DNA as a primer and RNA as a template to extend 3-end of parental strand in DNA

Front 29

DNA can be damaged by mutagens. What are some mutagens?

Back 29

-chemicals produced by cell
-chemical from environment
-radiation

Front 30

______ can cause transformation of cells into cancer cells

Back 30

-carcinogens

Front 31

X-rays that produce free radicals from H2O is and example of (direct/indirect) DNA damage
Cigarette smoking is an example of (direct/indirect) DNA damage

Back 31

X-rays-indirect
Cigarette-direct

Front 32

Cigarette smoke contains what carcinogen?

Back 32

-benzo[a]pyrene

(when oxidized in body, forms adducts w/ guanine residues)

Front 33

_____ is an autosomal recessive disease where there is a genetic defect in nucleotide excision repair (NER) system and cells can not repair DNA damage from UV light (skin cancer)

Back 33

-Xeroderma pigmentosum

Front 34

Give an example of:
Direct repair
Nucleotide excision repair
Base excision repair

Back 34

-Direct - E.coli removes thymine dimer by phagoactivating enzymes

-Nucleotide - endonuclease cleaves abnormal chain and removes distorted region. Gap filled by DNA polymerase and joined by DNA ligase

-Base - *DNA glycosylases* recognize distortion and cleaves N-glycoside bond. *AP endonuclease cleaves sugar-phosphate strand at this site

Front 35

What are the four steps to repair DNA?

Back 35

Recognition
Removal
Replacement
Joining

Front 36

How enzymes know which DNA to repair in bacteria and in humans?

Back 36

-Bacteria - adenine bases in parental strand is methylated and newly synthesized strand is repaired

-Humans - unknown

Front 37

During reverse transcription, what happens to RNA after cDNA is made?

Back 37

RNA is degraded

Front 38

Didanosine (ddI) is used for:

Back 38

-inhibition of reverse transcription

(dideoxynucleoside converted to dideoxynucleoside triphosphate in cells, terminates chain growth (elongation) when incorporated into DNA by reverse transcriptase)

Front 39

List the main steps of DNA synthesis in prokaryotes

Back 39

-Replication Fork (divides strands)
-Local separation of strands
-DNA polymerases bind
-New DNA strand synthesized 5'-->3' (on both strands)
-Bidirectional elongation

Front 40

Difference btwn leading and lagging strand synthesis

Back 40

leading- copied in direction of replication fork, continuously
lagging- copied in opposite direction of replication fork, discontinuously (okazaki fragments)

Front 41

describe the mechanism of DNA synthesis in eukaryotes

Back 41

Similar to prokaryotic EXCEPT:
-multiple origins of replication
-RNA primers are removed by RNAse H
-replication and cell division coordinated in cell cycle

Front 42

describe the mechanism of replication at the ends of chromosomes

Back 42

Telomerase contains RNA which is complementary to repetitive sequence of telomere, allowing it to use 3' end of DNA as a primer and RNA as a template to extend 3' end of DNA

Front 43

explain the importance of telomeres to prevent losses of genetic info & the mechanism of extension

Back 43

Importance:
-replication causes shortening at ends, telomeres are located at the end and help prevent loss of necessary DNA by protection from nucleases, limiting cell division, and being consumed (rather than DNA)
Extension:
- uses 3' end of DNA as primer and RNA as a template to extend 3' end of DNA

Front 44

4 main causes of DNA mutation

Back 44

Mutagens:
1. chemicals produced by cell
2. chemicals from environment
3. X-ray radiation
4. UV light radiation
*also by carcinogens and mismatches

Front 45

Properties and functions of reverse transcriptase

Back 45

retroviral enzyme used to synthesize DNA from RNA
-copies RNA template
-degrades RNA
-synthesizes double-stranded cDNA

Front 46

UV light forms covalent dimer between adjacent ______ on DNA strand

_____ dimers are formed in human skin exposed to sunlight

Back 46

thymines


pyrimidines