Biochm T Iii Chpt 8

Front 1

What is the composition of nucleosides?

Back 1

base + pentose

Front 2

What is the composition of nucleotides?

Back 2

base + pentose + phosphate

Front 3

What is pentose?

Back 3

5 member sugar (ribose or deoxyribose)

Front 4

What is the nucleotide base group?

Back 4

either purine or pyrimidine

Front 5

What distinguishes structurally speaking the purines from the pyrimidines?

Back 5

purine = 2 rings
pyrimidines = 1 ring

Front 6

Name the purines

Back 6

Adenine and guanine

Front 7

Name the pyrimidines?

Back 7

cytosine, thymine, uracil

Front 8

Which nucleotide base is in DNA but not RNA?

Back 8

Thymine

Front 9

Which nucleotide is in RNA but not DNA?

Back 9

Uracil

Front 10

4 (abbr.) nucleotides in DNA?

Back 10

AGCT

Front 11

4 (abbr.) nucleotides in RNA?

Back 11

AGCU

Front 12

The 2 pentoses?

Back 12

ribose (RNA) and deoxy-ribose (DNA)

Front 13

Both ribose and deoxy-ribose are what kind of rings?

Back 13

beta furanose rings

Front 14

Each sugar in DNA has one less what then RNA?

Back 14

one less -OH group (see slides, very clear)...you will see H group in RNA where you see an OH group in DNA

Front 15

The nucleoside of adenine associated with RNA?

Back 15

adenosine

Front 16

The nucleoside of adenine assoc. with DNA?

Back 16

deoxyadenosine

Front 17

The nucleoside of guanine assoc. with RNA?

Back 17

guanosine

Front 18

The nucleoside of guanine assoc. with DNA?

Back 18

deoxyguanosine

Front 19

The nucleoside of cytosine associated with RNA?

Back 19

cytidine

Front 20

The nucleoside of cytosine associated with DNA?

Back 20

deoxycytidine

Front 21

The nucleoside of thymine associated with DNA?

Back 21

thymidine or deoxythymidine (thymine is not associated with RNA)

Front 22

The nucleoside of uracil associated with RNA?

Back 22

uridine (uracil not associated with DNA)

Front 23

How many bonds between G and C pairs?

Back 23

three, H-bonds

Front 24

How many bonds between A and T or A and U?

Back 24

2 H-bonds (A=T or A=U)

Front 25

Are A,G,C,T, and U the only bases?

Back 25

No, the are other minor bases in both DNA and tRNA

Front 26

What kind of linkage do you see in RNA and DNA polymers?

Back 26

phosphodiester linkage with 5' to 3' directionality...alternating sugar and phosphate groups form the backbone...in a chain there is usually a phosphate at the 5' end but not the 3'

Front 27

Which carbon is the phosphate usually attached to?

Back 27

5'...but it can also be attached to 2' or 3'...and there are cyclic nucleotides with phosphate attached to C carbons, forming a ring (ex, cAMP)

Front 28

Why is the backbone of DNA and RNA polymers considered hydrophilic?

Back 28

a) because at physiological pH, each phosphate group is negatively charged

b) because of the free -OH groups in RNA

Front 29

Explain the hydrolysis of the covalent backbone?

Back 29

the covalent backbone is subject to hydrolysis...though this is a slow process...But under alkaline conditions (high pH) RNA is rapidly hydrolyzed...BUT DNA is not

Front 30

What is the convention in writing DNA and RNA sequences?

Back 30

with 5' (phosphorylated end) on left and 3' (not phosphorylated end) on right

Front 31

Some different ways to write this nucleic acid sequence: ACGTA

Back 31

pACGTA or see p 278 for schematic showing phosphoro on left and OH on right

Front 32

The 3 key properties of the bases?

Back 32

1. generally flat or close to it

2. maximum light absorbance is at 260nm

3. the bases are mostly hydrophobic at at physiological (near neutral pH)...this leads to [intra-strand] base-stacking)

Front 33

What is base-stacking?

Back 33

property of a nucleic acid...very imp. for their structure...bases are one on top of another because everything else around them is hydrophilic and they are hydrophobic...along with base pairing it is one of the two most important features for maintaining nucleic acid structure.

Front 34

What are the two most important features for maintaining nucleic acid structure?

Back 34

base stacking and base pairing

Front 35

Base pairing?

Back 35

inter strand or in RNA sometimes intrastrand is very important (H-bonding)

Front 36

Watson and crick base pairs?

Back 36

G(3 h bonds)C, A=T, A=U

Front 37

The 3 levels of nucleic acid structure?

Back 37

1. primary = sequence (just order)

2. secondary = local interactions and patterns (helix is most common)

3. tertiary = 3-dimensional, longer-range, possibly involving other mol.s

Front 38

The predominant conformation of DNA? (secondary structure)

Back 38

3-D Watson-Crick model of DNA

1. Right handed double helix

2. H-bonds between bases

3. Major and Minor grooves alternate

4. 2 anti-parallel strands

Front 39

The outside of the watson-crick model is what?

Back 39

the hydrophilic backbone (alternating phophoro-sugar-phosphoro..etc)

Front 40

The inside of the Watson-crick model?

Back 40

stacked bases...perpendicular to helical axis...paired

Front 41

What is Chargraff's rule #4?

Back 41

because G=C and A=T, A + G = T + C...for every G there is a C and same for A and T so A+G(purines) = T+C(pyrimidines)

Front 42

What make DNA replication possible according to the Watson-Crick model?

Back 42

unwrapping and wrapping of paired strands (daughter strands and parent strands etc)

Front 43

The 3 forms of DNA?

Back 43

1. A

2. B

3. Z

Front 44

Describe the A form of DNA?

Back 44

1. R handed like Watson and Crick

2. favored in absence of H2O

3. Wider than B

4. More compact than B

like a compressed spring (short and thick) compared to B

Front 45

Describe B form of DNA?

Back 45

watson and crick model

Front 46

Describe Z form of DNA?

Back 46

1. left handed

2. naturally occuring (found in some stretches of DNA)

3. narrower than B

4. more elongated than B

(like stretched spring)

3.

Front 47

Is A or Z found in lab?

Back 47

A found in lab, Z found in life...A not yet seen naturally

Front 48

Diameters of A vs. B vs. Z?

Back 48

A = 26A

B = 20A

Z = 18A

Front 49

Relative helix rise per base pair A vs B vs Z?

Back 49

A = 2.6A

B = 3.4A

Z = 3.7A

Front 50

Relative distance per turn A vs B vs Z?

Back 50

A = 28

B = 36

Z = 44

Front 51

In vivo what probably plays a role in determining whether a given segment of DNA exists in the B or the Z form?

Back 51

the sequence of nucleotides

Front 52

What is a palindrome?

Back 52

if you turned and flipped it it would be the same (see notes very clear)

Front 53

What is a mirror repeat?

Back 53

just flip it (see notes very clear)

Front 54

What secondary structure can palindromes form?

Back 54

1. hairpins (stemloops) for single stranded

2. Cruciform for Double strand (looks like 2 hairpins)

Front 55

Besides the 1 and 2 strand structures what else probably exists? Are they important?

Back 55

there are also 3 and 4 strand structures found in nature...not common but may be very important...new DNA/RNA drugs in development - combine with the body's DNA/RNA

Front 56

What are Hoogsteen pairs associated with?

Back 56

triple stranded DNA

Front 57

What is H-DNA?

Back 57

triple helix

Front 58

What is mRNA?

Back 58

messenger RNA

Front 59

How is mRNA synthesized?

Back 59

from DNA...transcription

Front 60

What does monocistronic mean relative to mRNA?

Back 60

piece of RNA with only one transcribed gene

Front 61

In terms of mRNA what does polycistronic mean?

Back 61

more than one gene

Front 62

Prokaryotes can have what type of mRNA?

Back 62

mono- or polycistronic

Front 63

eukaryotes mostly have what type of mRNA?

Back 63

monocystronic (this includes humans)

Front 64

Since mRNA synthesized from DNA what can you say about it's structure?

Back 64

right handed helix with base stacking

Front 65

Describe tRNA?

Back 65

transfer RNA....links mRNA and amino acids

Front 66

Describe rRNA?

Back 66

ribosomal RNA...the core of ribosomes (enzymatic role within RNA although they usually make new proteins)

Front 67

What are some "other RNAs"?

Back 67

viruses, ribozymes

Front 68

The RNA is usually what structurally?

Back 68

single stranded with hairpins, bulges, internal loops, and single strands...so folds back on self...imperfect regions....energetically favorable....looped and bulged regions are not part of the paired regions always

Front 69

What can RNA from base pairs with?

Back 69

self...or with other RNA or DNA...G(triple bond)C, A=U, and sometimes G=U

Front 70

In it's double stranded regions what form does RNA most commonly exist in?

Back 70

A form (in secondary structure)(RH helix, with base stacking)...B form not observed...Z form made in lab

Front 71

in RNA their can be extensive what? What else is important?

Back 71

can be extensive secondary structures...and tertiary structure is important (very specific)

Front 72

What are ribozymes?

Back 72

RNA enzymes

Front 73

What is the denaturation of nucleic acids?

Back 73

unfolding

Front 74

What is annealing of nucleic acids?

Back 74

renaturation...tells us that the propensity to come together is inherent within each strand

Front 75

How can you monitor denaturation and renaturation? Why?

Back 75

UV absorption...because it varies as a function of base stacking and pairing, and so can be used to determine whether DNA is paired or denatured

Front 76

When denaturation occurs which bonds break and which do not?

Back 76

H-bonds break...covalent breaks do not

Front 77

Where is the tm (melting point) for denatured DNA?

Back 77

mid-point of a melting curve...different for different DNAs because they have different base concentrations

Front 78

The more G + C DNA has the higher the what?

Back 78

melting point because of H bonds...so harder to pull apart...remember these have 3 h-bonds...you would just look at a graph to figure it out

Front 79

Which is more tightly bound RNA:RNA hybrids or RNA:DNA hybrids or DNA:DNA hybrids?

Back 79

RNA:RNA > RNA:DNA > DNA:DNA

Front 80

Where is hybridization important?

Back 80

in research, medical diagnostic tests, and new drugs

Front 81

Describe chemical transformations of nucleotides and nucleic acids?

Back 81

1. nonenzymatic so very slow/rare

2. cause of mutations

3. 3 types of spontaneous rxns

a. Removal of exocyclic amine (deamination)

b. Breaking the sugar-base bond

c. UV irradiation (dimer formation)

Front 82

Which chemical formations is caused by chemicals such as nitrites and nitrates (nitrosamines, HNO2) and bisulfites?

Back 82

deamination : removal of exocyclic amines...replace it with O2

Front 83

Which chem. transformation involves the breaking of a sugar-base bond?

Back 83

depurination...mostly happens in cells where it doesn't matter

Front 84

Which chm. transformation is caused by UV radiation?

Back 84

dimer formation...mutates DNA, cancer...induced (not chemical)(light)

Front 85

Some deaminating agents?

Back 85

in some foods...nitrites, nitrates, nitrosamines...nitrous acid...bisulfite (preservatives)...in smoked foods

Front 86

What are alkylating agents? ex.

Back 86

reactive chm. that may cause nucleotide or NA transformations...disrupts base pairing...dimethylsulfate...add alkyl (-CH3)

Front 87

What is an oxidative agent?

Back 87

reactive chm. that may cause nucleotide or NA transformation...cells do have defense mechanisms against these

Front 88

DNA methylation is what?

Back 88

a specific type of DNA alkylation...sometimes happens naturally...can provide natural protection

Front 89

What is important for the human genome project?

Back 89

the sequences of DNA strands can be determined

Front 90

2 methods for determining DNA sequences?

Back 90

1. Maxam-Gilbert (degradative, breakdown)

2. Sanger (synthetic, build up)

3. human genome project

Front 91

Can you synthesize DNA in the lab?

Back 91

yes but only up to 70-80 nucleotides...not as long as human genes...can't create whole cells

Front 92

How are nucleotides important in their own right? (stand alone functions)

Back 92

1. energy carriers: ATP->ADP->AMP->adenosine

2. component of enzyme cofactors (coenzyme A, NAD, and FAD)

3. regulatory molecules (cAMP, cGMP, ppGpp)