Structure Of Dna & Rna Lecture 2

Front 1

What is a nucleic acid?

Back 1

-macromolecule composed of chains of monomeric nucleotides

-located w/in cells and form structures

Front 2

what is the basic unit of nucleic acid?

Back 2

NUCLEOTIDE

Front 3

Nucleic acid are based on what? And what two categories do Nucleic Acid fall in?

Back 3

-Based on diff. pentose sugars & nitrogenous base

-1.) DNA Deoxyribonucleic acid

2.) RNA ribonucleic acid

Front 4

What is DNA?

Back 4

the genetic material that has all the info. to direct every cellular process is carried w/in DNA

Front 5

What is RNA?

Back 5

participate in several cellular processes involved in the formation transfer from the DNA to protein synthesis.

-the info. in DNA & RNA is encoded in the order of bases

Front 6

Nucleic acid are based on functions, RNA falls into 3 categories which are?

Back 6

1.) mRNA

2.) rRNA

3.) tRNA

Front 7

What is mRNA, rRNA & tRNA?

Back 7

-mRNA: template of DNA, carries info from DNA to ribosomes

-rRNA: protein manufacturer

-tRNA: rRNA & tRNA are involved in protein synthesis (transport genetic code)

Front 8

Nucleic acid are composed in three parts name them?

Back 8

1.) Nitrogenous base: aromatic ring of Carbon & nitrogen

2.) Pentose Sugar: 5 carbon sugar in ring form

3.) Phosphate group: acidic in nature

Front 9

nitrogenouse base, pentose sugar & phosphate group make what?

Back 9

nucleotide

Front 10

Nitrogenous bases are in two categories which are?

Back 10

1.) Purine

2.) Pyrimidine

Front 11

What is a purine?

Back 11

-fused 5-6 member ring

-AG (adenine & guanine)

Front 12

What is pyrimidine?

Back 12

-6 member ring

- C, U, T (cytosine, uracil, thymine)

Front 13

What is the difference btw Thymine and Uracil?

Back 13

-There is a METHYL group at C5 on Thymine, which uracil does not.

Front 14

what are the two sugars?

Back 14

Ribose & 2-deoxyribose

-2-Deoxoyrbions has no OH on C2'

Front 15

What are phosphate groups?

Back 15

-phosphorous occur mainly in the form of acidic phosphate groups, they are always negatively charged

-DNA & RNA are neg. charged cuz Phosphate is negatively charged.

Front 16

Nitrogenous bases is linked to what?

Back 16

1 ' carbon of sugar

Front 17

Nucleoside includes what parts?

Back 17

Nitrgoenous base + sugar

-glycosidic bond from N1 to pyrimidines or N9 of purines

Front 18

Phosphate groups is attached to what?

Back 18

5 ' carbon of sugar

Front 19

Nucleotide include what parts?

Back 19

nitrogenous base + sugar + phosphate

Front 20

DNA is a long molecule made up of what?

Back 20

polynucleotide

Front 21

one nucleotide has three parts which are?

Back 21

nitrogenous base + pentose sugar (2'-deoxyribose) + phosphate grp

Front 22

DNA molecule contains 4 nitrogenous bases which are ?

Back 22

A, T, C, G

Front 23

What is the DNA structure?

Back 23

-a polymer of nucleotides w/a long, flexible, threadlike structures

-constant diameter w/regulary spaced & repeated structures

-phosphodiester bonds link 5 ' phosphate of one nucleotide to the 3 ' OH of another

Front 24

DNA is usually what?

Back 24

-two single-stranded nucleic acids held together by base pairing through hydrogen bonds in anti-parallell orientation called double stranded, the DNA DOUBLE HELIX

Front 25

What forms the backbones of the DNA structure?

Back 25

-sugar & phosphate residues in each strand

Front 26

How does the backbone of the DNA structure run?

Back 26

-run anti-parallel (in opposite directions) to each in the 5' to 3'

Front 27

The two strands of the double helix are held together by what?

Back 27

base paring in anti-parallel orientation

Front 28

1.) A : T are held together by what?

2.) C : G are held together by what?

Back 28

1.) 2 hydrogen bonds

2.) 3 hydrogen bonds

Front 29

The two chains of double helix have what?

Back 29

-complementary sequences that goes 5' to 3' (on one chain) & 3' to 5" (opposite chain)

Front 30

What is the fundamental feature of the double helix?

Back 30

hydrogen bonds btw the complementary bases

Front 31

Double helix has 2 external grooves called what?

Back 31

major and minor grooves

Front 32

What is a groove?

Back 32

the space btw the strands

Front 33

Each complete twist of DNA is how long in length?

Back 33

3.4 nm

Front 34

The major groove is _____ wider than the minor groove and rich in what?

Back 34

50% ; chemical info.

Front 35

The sugar-phosphate backbone circles around where?

Back 35

outer surface of DNA

Front 36

DNA is usually right-handed double helix or left handed helix?

Back 36

Right handed double helix

Front 37

Left handed double helix is only what?

Back 37

alterative purine & pyrimidine

Front 38

DNA structure image of right-handed vs left-handed doubles helix. Look at image!

Back 38

Front 39

Double helix has 3 forms which are?

Back 39

1.) B DNA right handed (flower)

2.) A DNA right handed (donut)

3.) Z DNA left handed (ball)

Front 40

Look at the pic of the 3 forms of DNA double helix.

Back 40

Front 41

which one is the most common double helical structure?

Back 41

- B DNA

Front 42

What is the B form DNA?

Back 42

-observed at high humidity

-vast majority of the DNA in the cell = B form

-right-handed

- ~ 10 nucleotides per turn

-contains a major & minor groove

-Major groove is wider than minor groove

Front 43

What is A form of DNA?

Back 43

-observed under low humidity

-observed in certain DNA-protein complexes, RNA- DNA and RNA-RNA helices.

-right handed

- ~ 11 nucleotides per turn

-contains a major & minor groove

-Major groove is narrower, much deeper than B form

-minor groove is broader & shallower

Front 44

What is the Z form of DNA?

Back 44

-observed in DNA containing alterative purine & pyrimidine

-left handed

-helix w/ zigzag look

Front 45

DNA double helix can separate which is called, define it?

Back 45

Denature/ DNA melting

-heat to near 100 C

-High PH

Front 46

DNA double helix can reassociate is called, define it?

Back 46

renature

-single strands often meet their complementary strands & reform regular double helixes when heated solution of denatured DNA are slowly cooled.

Front 47

What is hybridization?

Back 47

-artificial hybrid DNA to be formed by slowly cooling mixtures of denatured DNA from 2 diff. Sources. (the basis of several molecular techniques)

Front 48

(Denature of DNA )

-when DNA is heated to 80 degrees and up, its UV absorbance is what and increases to what?

Back 48

260 nm ; 30-40%

Front 49

(DENATURE of DNA)

The hyper chromic shift reflects on what?

Back 49

the unwinding of the DNA double helix

Front 50

(denature of DNA)

When temperature is lowered, the ______ drops, reflecting the ___________.

Back 50

absorbance ; re-estabilishment of stacking

Front 51

(Denature of DNA)

What is Tm?

Back 51

melting temperature: a point which exactly half of a double stranded sequence becomes single-stranded.

Front 52

What is DNA supercoiling structure?

Back 52

-occurs in closed structure when ends are not free to release torsion on molecule

-in duplex, DNA 10 bp per turn of helix, circular DNA sometimes has more or less than 10 bp per turn.

Front 53

What are topoisomerase or gyrases?

Back 53

-removes supercoils

Front 54

DNA has type types of supercoiling which are?

Back 54

1.) positive supercoiling

2.) negative supercoiling

Front 55

What is positive supercoiling?

Back 55

- when DNA is supercoiled in the same direction as the intrinsic winding of helix

-tightens the structure

-increase the rotation per base pair

-overwound

Front 56

DNA is said to be overwound is called?

DNA is said to be underwound is called?

Back 56

-Positive supercoiling

-negative supercoiling

Front 57

Microorganisms that lived under high extreme high temps such as hot springs have what kinda of supercoiled DNA?

Back 57

-positive supercoiled DNA

Front 58

what is DNA negative supercoiling?

Back 58

-twists dada about its axis in the opposite direction rom the clockwise turn of the right-handed double helix

-loosens the winding of the 2 strands

-reduces the rotation per base pair

Front 59

Circular DNA from bacterial and eukaryotes are usually what type of supercoiling?

Back 59

-negative supercoiling

Front 60

look at the structures of DNA supercoiling?

Back 60

Front 61

DNA supercoiling requires what?

Back 61

-energy to introduce supercoil and to separate DNA strands for replication or transcription

-does not occur spontaenously

Front 62

Molecules without supercoiling is said to be what?

Back 62

relaxed

Front 63

DNA supercoiling is important for what? and required for what?

Back 63

-DNA packaging w/in the cell

-DNA/RNA synthesis

Front 64

Supercoils results as....

Back 64

result of the undwinding of DNA for DNA/RNA polymerase action

-Topoisomerases

Front 65

DNA supercoiling structure can be separated by what technique?

Back 65

-gel electrophoreiss

- the more compact the Dna, the fasted it is able to migrate through the gel

Front 66

what is topoisomerase?

Back 66

-enzyme that catalyzes the reversible breaking and rejoining of DNA strands (relieves the strain of twisting)

-maintains supercoling by acting as a swivel

Front 67

what are the two types of topoiosomerase?

Back 67

1.) Type 1: make transient single-strand breaks (NO ATP)

2.) Type 2: make transient double-strand breaks ( REQUIRE ATP)

Front 68

what topoisomerase type is this?

Back 68

Type 1

Front 69

what topisomerase type is this?

Back 69

type 2

Front 70

What is RNA?

Back 70

-long molecule made up of polynucleotide

-single stranded

- nucleotide w/ 3 parts

- 4 nitrogen bases: A, U, G, C

-contains 10 times more RNA than DNA

-URACIL in place of THYMINE

Front 71

RNA has 3 primary classes which are?

Back 71

1.) rRNA- 3-4 different types

2.) tRNA - 50 different types

3.) mRNA - > 1000 different types

Front 72

For RNA, a nucleotide contains what?

Back 72

nitrogenous base

sugar (RIBOSE)

phoshpate group

Front 73

RNA chains fold back on themselves to form diff. structures what are they?

Back 73

a. hairpin

b. bulge

c. Loop

Front 74

label these.

Back 74

a. hairpin

b. bulge

c. loop

-Theses are stem-loop structures

Front 75

what is a stem-loop structure?

Back 75

non complementary sequences become "looped out" to form different structure.

Front 76

what is this?

Back 76

pseudoknot

Front 77

what is a psedoknot?

Back 77

formed by base pairing take place btw noncontiguous complementary sequences

Front 78

what is this?

Back 78

C(UUCGG)G TETRALOOP

Front 79

what is a C(UUCG)G TETRALOOP?

Back 79

SPECIAL bise stacking interactions in the loops

Front 80

what is this?

Back 80

tertiary structure G : U

Front 81

what is this?

Back 81

tertiary structure, U : A : U base triple

Front 82

what is this?

Back 82

-secondary structure, enzyme

-Hammer head ribozyme

Front 83

What does hammer head ribozyme do?

Back 83

cleavesRNA by the formation of 2', 3' cyclic phosphate

Front 84

Some RNA's can be what?

Back 84

enzymes (RIBOZYMES) ex: RNase P & RNA Self-splicing

Front 85

what is this?

Back 85

tertiary strcture