Preschool

Front 1

Bases in DNA

Back 1

Adenine
Cytosine
Guanine
Thymine

Front 2

Bases in RNA

Back 2

Adenine
Cytosine
Uracil
Guanine

Front 3

sugar in DNA and how differs from RNA

Back 3

deoxyribose (no OH at 2' carbon)

Front 4

sugar in RNA

Back 4

ribose

Front 5

Where phosphate group is attached on sugar

Back 5

5' carbon

Front 6

Where purine or pyrimidine base is attached on sugar

Back 6

1' carbon

Front 7

Characteristics of Pyrimidine:
# Carbons and shape

Back 7

smaller molecule, bigger name
shaped like benzene
aromatic
inflexible
stacks in water because of hydrophobic interactions
attaches to sugar at 1st nitrogen

Front 8

Characteristics of Purine

Back 8

Attaches to sugar at #9 position (a nitrogen)

Front 9

Purines

Back 9

Adenine
Guanine

Bonds to pyrimidines
A bonds to T (2 hydrogen bonds)
G bonds to C (3 hydrogen bonds)

Front 10

Pyrimidines

Back 10

Thymine
Cytosine
Uracil (RNA only - bonds to A)
Bonds to purines
T bonds to A
C bonds to G

Front 11

Nitrogenous bases

Back 11

Purines: Adenine, Guanine
Pyrimidines: Cytosine, Thymine, Uracil

Front 12

Nucleoside composition

Back 12

Nitrogenous base plus sugar

Front 13

Nucleotide composition

Back 13

Nitrogenous base, sugar, AND phosphate

Front 14

Conformation of ribose

Back 14

B-Furanose
(insert structure)

Front 15

At which carbons is the flexibility in the ribose, allowing it to be in different conformations?

Back 15

C2 and C3

Front 16

5-Methylcytidine

What is it?
What's the structure?

Back 16

minor pyrimidine base
methylated
methyl group attached directly to 3rd atom in chain
(insert structure)

Front 17

N6-methyladenosine

Back 17

minor purine base

Methyl group attached to a side chain

R-C-NH-CH3

The 6 is the number of the carbon in the chain

Front 18

Purpose of methylation

Back 18

methyl groups get added in order to activate DNA

around 5% is methylated to control gene expression

Front 19

structure of Adenosine 5'-monophosphate

Back 19

One phosphate group attached to 5' carbon. Adenine is attached to 1' carbon (at 9' atom because it's a purine)

Front 20

alpha, beta, gamma phosphate

what do they mean?

Back 20

Alpha has one phosphate attached at 5' carbon (e.g., ribonucleoside monophosphate, AMP)

Beta has 2 phosphates attached by ester bond - second phosphate (the beta) is attached to alpha phosphate (e.g, ribonucleoside diphosphate, ADP

gamma - gamma phosphate is attached to beta phosphate (eg in ATP)

Front 21

Phosphodiester linkage structure

Back 21

(insert structure)

One part is attached to the 5' carbon, the other to the 3' carbon of the next ribose

5' end is PHOSPHATE
3' end is a hydroxyl group

Front 22

5' ----- 3' ends: characteristics

Back 22

5' end is always phosphate
3' end is a hydroxyl

Front 23

Why won't DNA hydrolyze?

Back 23

Because it doesn't have the OH group at the 2' carbon, it isn't susceptible to nucleophilic attack by a free -OH.

This makes it more stable than RNA.

Front 24

Hydrolysis of RNA under alkaline conditions - mechanism

Back 24

OH group at 2' carbon is attacked by -OH ion --> 2', 3'-cyclic monophosphate derivative and water --> reacts with water to form mixture of 2' and 3' monophosphate derivatives

Front 25

Two common cyclic nucleotides that result from RNA hydrolysis

Back 25

1)Adenosine 3', 5'-cyclic monophosphate (cAMP)

(insert structure)

Phosphate linking in position 3' and 5'

2) Guanosine 3', 5'-cyclic monophosphate (cGMP)

(insert structure)

Front 26

Absorption spectra of nucleotides: how does it work and what's it used for

Back 26

Different nucleotides absorb UV light most strongly at different frequencies. Can be used to quantify amount of DNA or RNA you have in sample.

Front 27

Kinds of bonds and how many of these link the different nucleotides

Back 27

Hydrogen bonds

3 h-bonds in C-G
2 h-bonds in A-T or A-U (weaker)

Front 28

4 Stabilizing features of DNA

Back 28

1) Hydrogen bonds
2) Hydrophilic sugar-phosphate backbone is external; hydrophobic bases are internal
3) Base stacking (e.g, bases on same strand) due to rigidity of aromatic bases
4) cations neutralize negatively charged phosphates

Front 29

Chagroff's rules

Back 29

Same amount of A and T, and C and G

A+C = T+G

Front 30

Watson-Crick model of DNA

Back 30

(insert structure)

major and minor grooves

major groove is where proteins bind by recognizing sequence

34 Angstroms per rotation

Front 31

Types of double stranded helices

Type A

Back 31

RNA/RNA or DNA/RNA interaction
Found in solutions with little water
right-handed
strongest interaction

Front 32

Types of double stranded helices

Type B

Back 32

Most common in cells
DNA/DNA in solution
Right-handed

Front 33

Types of double stranded helices

Type Z

Back 33

Double strand DNA at alternating purine-pyrimidine sequences.

Left-handed

Front 34

Distance between bases in B DNA

Back 34

3.4 Angstrom

Front 35

Distance in one turn of B DNA

Back 35

34 Angstrom

Front 36

Weakest nucleotide interaction

Back 36

DNA/DNA

Front 37

Strongest nucleotide interaction

Back 37

A form

RNA/RNA

Front 38

Common DNA sequences (mostly in regulatory regions)

Palindrome

Back 38

TTAGCAC GTGCTAA
AATCGTG CACGATT

Opposite strand is same backwards as other strand is forwards

Front 39

Common DNA sequences (mostly in regulatory regions)

Mirror repeat

Back 39

TTAGCAC CACGATT
AATCGTG GTGCTAA

On SAME STRAND

Front 40

Hairpin structure

Back 40

(insert structure)

necessary for binding of transcription factors in RNA and possibly DNA

Front 41

Cruciform structure

Back 41

(insert structure)

Front 42

Characteristics of RNA

Back 42

1)U instead of T
(in tRNAs, some Us are converted to T or dihydro U, or Psi (pseudouridine))

2) Intramolecular stem loops (double strand helices) form. For example, tRNAs can form cloverleaf that is further folded into higher-order L shaped structure)

3) 2' -OH of ribose makes it unstable in alkaline pH

Front 43

Difference between replication, transcription, and translation

Back 43

DNA-----> DNA = replication

DNA-----> RNA = transcription

RNA -----> protein = translation

Front 44

Monocistronic vs. Polycistronic mRNA

Back 44

Monocistronic: one open reading frame, or cistron, for a peptide (one mRNA -> one protein)

Polycistronic: multiple open reading frames (cistrons), found in bacteria, sets of genes that regulate one process (operons)
(one mRNA -> multiple proteins)

Front 45

Helix rise in Angstrom per base pair

Back 45

3.4 angstrom

Front 46

Helix per complete turn

Back 46

34 Angstrom

Front 47

Promotes denaturation of DNA strands

Back 47

Low salt (cation) concentration can't keep the neg charged phosphates from separating.

Higher (alkaline pH)

Organic solvents

Heat

Front 48

Hyperchromic Shift

Back 48

when arrive at Tm, get an increase in absorption because bases are more free to absorb

Front 49

Mutation defn

Back 49

Permanent change in nucleotide sequence

Front 50

Point mutation defn

Back 50

Permanent change of ONE nucleotide

Front 51

Long term DNA mutation rate and significance of

Back 51

1% / million years.

Forms basis of evolutionary process.

Front 52

Short term DNA mutation rate and significance of

Back 52

more frequent, acct for 20% of death in Western hemisphere.

CANCER - most cancers are clones of cells with mutated DNA

Front 53

Gain of Function mutation

Back 53

When protein acquires new function; can lead to cancer

Front 54

Protecting somatic cell DNA protects _________

Back 54

Individuals

Front 55

Protecting germline cell DNA protects _______

Back 55

the species

Front 56

Depurinations:

Definition and Frequency

Back 56

Spontaneous hydrolysis of beta N glycosidic bonds due to heat fluctuations in nucleus

Screws up base-to-ribose bond
C1 - N9 in purines
C1 - N1 in pyrimidines
5000/cell/day

Front 57

Deaminations

Back 57

hydrolysis reaction: oxidizes nucleotides to another nucleotide

http://upload.wikimedia.org/wikipedia/commons/a/a9/DesaminierungCtoU.png

Front 58

Product of deamination of cytosine

Back 58

uracil

Front 59

Product of deamination of adenine

Back 59

HX (hypoxanthine)

Hypoxanthine, in a manner analogous to the imine tautomer of adenine, selectively base pairs with cytosine instead of thymine. This results in a post-replicative transition mutation, where the original A-T base pair transforms into a G-C base pair.

Front 60

Product of deamination of guanine

Back 60

X (xanthine)

Xanthine, in a manner analogous to the enol tautomer of guanine, selectively base pairs with thymine instead of cytosine. This results in a post-replicative transition mutation, where the original G-C base pair transforms into an A-T base pair.

Front 61

Product of deamination of 5-methylcytosine

Back 61

Thymine

This is the most common single nucleotide mutation. In DNA, this reaction cannot be corrected because the repair mechanisms do not recognize thymine as erroneous (as opposed to uracil), and, unless it affects the function of the gene, the mutation will persist.

Front 62

Alkylation

Back 62

can include methylations and larger adducts such as benzoapyrene from cigarette smoke

Front 63

Pyrimidine dimers

Back 63

UV-induced covalent bonds between adjacent pyrimidines on the same strand

ex: Thymine dimers

Front 64

Transition mutation:

definition and implication

Back 64

Type of POINT MUTATION

Purines converted to other purine (A->G) OR
Pyrimidine converted to other pyrimidine (T->C)

After a round of replication, A-T pair becomes G-C

Front 65

Transversion mutation:

definition and implication

Back 65

Type of POINT MUTATION

Purine converted to pyrimidine
and vice versa

ex. (A->C) After round of replication, A-T pair becomes C-G

Front 66

Possible effects of point mutations within protein coding region

Back 66

When transitions or transversions occur in open reading frame, the possible consequences:

neutral/silent: no change in amino acid sequence because of redundancy in amino acid codons

missense: substitution of ONE amino acid

nonsense: when change causes a stop codon. Leads to short protein, can be very serious

Front 67

Start codon

Back 67

AUG

Front 68

Stop codons

Back 68

UGA, UAG, UAA

Front 69

Frameshift

Back 69

Result of single base insertion/deletions; changes the way the codons are read

Only happens when deletions/insertions amt is not divided by 3

Front 70

Two general ways to think about DNA repair

Back 70

1) Remove entire damaged segment and replace

2) Reverse chemical modification "find hole and plug it"

Front 71

Direct repair: DNA Photolyase system

Back 71

active in prokaryotes, NOT in humans

cofactor absorbs light and passes it on to FADH cofactor. Causes reversal back to normal.

Front 72

Simple reversal example: O(6)-methyl-guanine. What happens?

Back 72

Carbonyl group in guanine changes to O-methyl group --> can't form H bonds

O(6)-alkyl-guanine is the major carcinogenic lesion in DNA induced by alkylating mutagens. This DNA adduct is removed by the repair protein, O(6)-methylguanine-DNA methyltransferase.

Called a "suicide enzyme" bc entire protein is used to to take methyl out of DNA

Front 73

Direct repair

Back 73

Part of base taken out and fixed "plugged the hole"

Front 74

Base-excision repair

Back 74

Entire base taken out

"replaced the radiator"

DNA glycosylase recognizes and removes wrong base. Then AP endonuclease nicks phosphodiester backbone. DNA Polymerase I (in bacteria, DNA Pol B in humans) then adds new base onto chain. DNA ligase seals.

Front 75

DNA glycosylases

Back 75

Enzyme that recognizes mutated base and removes as part of Base-Excision Repair

Do it by cleavage of beta-N-glycosidic bond

Front 76

AP Site

Back 76

Location in DNA that is missing a base

Apurinic or apyramidinic site

Front 77

AP endonuclease

Back 77

create a nick in the phosphodiester backbone of the AP site created when DNA glycosylase removes the damaged base

part of Base Excision Repair

Front 78

DNA Polymerase Beta

Back 78

Replaces nucleotide as part of Base Excision Repair

Front 79

Nucleotide Excision Repair

Back 79

Required for removal of bulky lesions (e.g., pyrimidine dimers, cyclobutane rings)

1) excinuclease makes single cut in two places

2) DNA helicase unwinds double helix (either 13 mer long in E. coli or 29 mer long in humans)

3) DNA poly I (bacteria) or DNA pol epsilon (human) resynthesizes from 5' -> 3'

4) DNA ligase seal final phosphodiester bond

Front 80

Mismatch Repair

Back 80

Corrects errors left by DNA poly III during replication and missed by proofreading activities. ONLY works just after replication - NOT in resting cells.

Fixes mismatches (e.g., C=T) or short insertions/deletions caused by errors in DNA poly

Front 81

How does E. coli determine which strand is the correct (wild-type) and which is the mutant?

Back 81

Dam methylase adds methyl group to A of all randomly occurring sites with GATC sequence shortly after each replication (approx 1/256 nucleotides)

Before the new strand gets methylated, mismatch repair complex senses the methylated template strand and repairs the erroneous new strand

Front 82

Names of E. coli proteins that bind, recognize problem, bend entire DNA and make cleavage on new strange OPPOSITE of methyl group, part of Mismatch Repair

Back 82

MutS

MutL

MutH

Front 83

How does mismatch repair occur in humans?

Back 83

Same process as E. coli, except no DAM methylation. We don't know how cells recognize old strand from new.

Front 84

Translesion DNA synthesis (TLS)

Back 84

Emergency system; if extensive damage, have expression of new enzymes.

DNA damage tolerance process that allows the DNA replication machinery to replicate past DNA lesions such as thymine dimers or AP sites.[24] It involves switching out regular DNA polymerases for specialized translesion polymerases (e.g. DNA polymerase V), often with larger active sites that can facilitate the insertion of bases opposite damaged nucleotides.

Front 85

Recombinational DNA repair

Back 85

Emergency system; if extensive damage

Front 86

Mutations in hMSH2 and hMLH correlate with which cancer?

Back 86

hereditary non-polyposis colon cancer

Front 87

Mutations in BRCA1 and BRCA2 correlate with which cancer?

Back 87

breast

80% chance

decreased rate of homologous recombination repair

Front 88

Xeroderma pigmentosum caused by a failure of what DNA repair system?

Back 88

Xeroderma pigmentosum is a genetic disease causing UV hypersensitivity, skin cancer due to a failure in nucleotide excision repair (NER).

Front 89

Hereditary nonpolyposis colorectal cancer is related to failure in which DNA repair system?

Back 89

Mismatch repair

Front 90

2+6

Back 90

8