Dental Biochemistry

Front 1

1. How is the 1' C attached to N?

What is a characteristic of this bond?

Due to this bond what can occur?

Back 1

Glycosidic linkage

Can swivel

Errors can come because of this swivel characteristic

Front 2

2. Where do DNA repair enzymes attach?

Back 2

At the 1'C

They cut the glycosidic linkage

Front 3

3. What is special about the 3' C?

What is special about the 5' C?

Back 3

OH has to be there for DNA replication

Where phosphate bonds

Front 4

4. How is a phosphodiester bond?

How is a hydrogen bond?

Back 4

Covalent stable bond between 3' OH and O on phosphate

Weak BUT many of them have a cumulative effect so strong

Front 5

5. Which base pairing is more stable and why?

Back 5

C:G

Because there are 3 H-bonds

Front 6

6. How does chromatin affect transcription?

Back 6

Limits availability of DNA for transcription

Front 7

7. What are the grooves on DNA?

What is the purpose of grooves?

Back 7

Major (wide) and minor (narrow) grooves

Allow enzymes that read DNA to do so w/o having to break open the helix

*readable from outside

Front 8

8. What is the basic reaction carried out by DNA polymerase?

Back 8

(dNMP)n + dNTP -> (dNMP)n+1 + PPi

*Use dNTP as precursoer

*Incorporate dNMP

Front 9

9. What drives the previous reaction?

What is a primer?

What is the template?

Back 9

dNTP - liberating phosphates provides the energy for the reaction

Existing piece of DNA or RNA

Pre-existing info that DNA polymerase copies

Front 10

10. Where does DNA polymerase add to?

Back 10

3' OH

From here DNA polymerase extends

Front 11

11. What do nucleases do?

What are the two types?

Back 11

Tear DNA up
*they have specificity

1. Exonucleases

2. Endonucleases

Front 12

12. Describe exonucleases.

Two points...

Back 12

1. Operate from ends of DNA molecule

2. Breaks phosphodiester bonds down so become dNMP

Front 13

13. Describe endonucleases.

Back 13

1. Operates within the molecule (doesn't start at ends)

2. Nicks or breaks the molecule

Front 14

14. Why is the primer in DNA replication RNA?

Back 14

RNA polymerases and primases are capable of doing de nove synthesis

**De Novo synthesis has lots more errors though

Front 15

15. Where does the primer come from?

Back 15

Primase synthesizes primer at the origin of replication

Have two replication forks at the origin

Front 16

16. How does helicase transverse DNA?

Back 16

It runs up one strand (like a donut)

It unzips the DNA and burns ATP as it does this

Front 17

17. What is left behind as helicase tracks on one of the DNA strands?

What is the problem with this?

Back 17

Single strand DNA template

Single strand is vulnerable to nucleases so cover single strand with single strand binding protein to protect it

Front 18

18. Why are there Okazaki fragments?

Back 18

On the lagging strand, it's the 5' end that's pointing towards the replication fork

Correct this by having short fragments synthesized from 5' -> 3'

Front 19

19. Is one strand really lagging?

Back 19

No, synthesis is coupled so leading strand does not get ahead

Front 20

20. What do the Okaziki fragments run into?

What happens then?

What does ligase do?

Back 20

Bang into back of RNA primer

Exonuclease (5' -3' RNase H) removes RNA from the RNA-DNA hybrid

Another DNA polymerase fills the gaps left from the removal of RNA

Facilitates phosphodiester bonds

Front 21

21. Where is the 5'-3' RNase H located?

Back 21

On DNA polymerase I

*DNA polymerase I has different sites with different functions

Front 22

22. What does 3'-5' DNA exonuclease do?

Back 22

Serves as an edit or proofreading function

Like a back space key and removes wrong bases

Front 23

23. Where is this exonuclease located?

Back 23

On DNA polymerase

What happens is there is a tautomeric shift, remove wrong base, then switch back to DNA synthesis function and continue synthesis in 5' to 3' direction

Front 24

24. What is a retrovirus?

What makes it different?

Back 24

Genome is a single strand of RNA
*longevity and fidelity of replication is not important

RNA strand is converted to DNA

Front 25

25. What is reverse transcriptase?

What does it require?
Three things...

How does is synthesize?

Back 25

Enzyme that makes a DNA copy of the RNA template

1. Template (RNA)
2. Primer (RNA)
3. dNTP's

5' to 3' direction

*Has RNase H function on same polypeptide as DNA synthesis function (like DNA polymerase)

Front 26

26. What is the major difference between reverse transcriptase and DNA polymerase?

What does this result in?

Back 26

Reverse transcriptase does not have a 3' to 5' edit function

Mutates really fast

Mutation frequency driven by poor editing and errors

Front 27

27. What are "long terminal repeats"?

What serves as the primer for reverse transcriptase?

Back 27

Long repeated sequences at each end of the RNA genome

tRNA molecule

Front 28

28. What is the general order of events in retroviral genome synthesis?

Back 28

1. Single strand RNA

2. RNA/DNA hybrid

3. Digest RNA

4. Single strand DNA

5. Double strand DNA
*final DNA integrates with host genome

Front 29

29. Describe the steps in retoviral genome synthesis up to the first recombinational jump.

Back 29

1. tRNA primer binds to PBS (primer binding site)

2. Reverse transcriptase extends tRNA to form DNA copy (5' - 3' direction)

3. RNase H removes hybridized RNA

4. Recombinational jump - DNA hybridizes with remaining RNA and becomes the primer with the 3' OH

Front 30

30. Describe the steps in retroviral genome synthesis after the first recombinational jump.

Back 30

1. DNA strand is extended from 3' end

2. More hybrid RNA is removed by RNase H
*some is left behind as primer for DNA synthesis

3. 3' end of DNA is synthesized, RNA and tRNA are removed

4. Second recombinational jump and both strands are completed by synthesis from 3' end

Front 31

31. What is the dominant or primary mechanism for DNA repair in human cells?

What is this?

Back 31

Homologous Recombination

Genetic exchange between segments of DNA that are homologous (sequence of two exchanging molecules is almost the same)

Front 32

32. What is recombinase?

Back 32

Enzyme that binds single stranded DNA and carries it to homologous double stranded DNA

Carries out invasion of homologous DNA molecule

Front 33

33. How does homologous recombination work?

Six steps...

Back 33

1. Put nick in one of the two duplex DNAs

2. Recombinase searches molecule being invaded for homologous segment

3. Forms a three stranded structure called a "D-Loop"

4. Nicking of invading strand by endonuclease

5. Strands exchange and are ligated forming a "Holliday Junction"

6. Nick and rejoin the crossed strands by resolvase

Front 34

34. What is ultimately formed?

What is the overall goal of recombination?

Back 34

A patch or splice if formed in the recombinant DNA molecules

Put all the damage on one copy and have one copy of DNA that is pristine so can copy

Front 35

35. What is recombinase?

Back 35

An enzyme that binds single stranded DNA and carries it to homologous double stranded DNA

Front 36

36. What is a Holliday Junction"?

What is resolvase

Back 36

Strands of DNA that were nicked are ligated

For every bond that is broken, one is formed

Enzyme that catalyzes the process of nicking and rejoining crossed strands of the Holliday Junction