Lecture 5

Question 1

Primary structure:

Answer 1

sequence of nucleotides in the linear molecules

Question 2

Secondary structure:

Answer 2

3D arrangement, double helix

Question 3

Tertiary structure:

Answer 3

longer range interactions and supercoiling

Question 4

X-ray diffraction of DNA:

Answer 4

DNA fibers are aligned along their axis. They are exposed to an X-ray beam and photographic film is positioned behind the DNA to capture diffraction of light

Question 5

Diffraction theory:

Answer 5

it is known that a helix gives a cross-shaped pattern. DNA has 10 residues/ turn

Question 6

Diffraction:

Answer 6

the scattering by repeating elements in the structure shows reinforcement of the scattered waves in certain specific directions and weakening in others

Question 7

Constructive diffraction:

Answer 7

reinforce one another

Question 8

Destructive diffraction:

Answer 8

interfere one another

Question 9

Properties of diffraction wavelength:

Answer 9

must be shorter than the regular spacing between the elements of the structure

Question 10

Short spacings in the periodic structure:

Answer 10

large spacings in the diffraction pattern (vice versa)

Question 11

Intensities:

Answer 11

matter

Question 12

Repeat (c):

Answer 12

distance parallel to the helix axis in which the structure exactly repeats itself

Question 13

Reisdue (m):

Answer 13

some number of polymer residues

Question 14

Pitch (p):

Answer 14

the distance parallel to the helix axis in which the helix makes 1 turn

Question 15

When there is an integral number of residues:

Answer 15

the pitch and repeats are equal

Question 16

First diffraction:

Answer 16

parallel to the axis of the stretched fiber

Question 17

Rise (h):

Answer 17

the distance parallel to the axis from the level of one residue to the next (c/m)

Question 18

Layer lines:

Answer 18

lines perpendicular to the fiber axis (inversely proportional to the repeats)

Question 19

Properties of the secondary structure of DNA:

Answer 19

• repeat of 10 nucleotides
• pitch of 3.4 nm
• rise of 0.34 nm between two nucleotides
• stabilize by H-bonds between purines and pyrimidines
• bases are stacked by van der Waals forces
• hydrophilic phosphate backbone
• hydrophobic base pairs

Question 20

Length of base pairs:

Answer 20

each A-T and G-C base pairing has 1.08 nm caused by purine and pyrimidine structure, each rotated at 36 degrees and 0.34 between

Question 21

Chargaff’s rules:

Answer 21

showed that base composition varies from organism to organism: %A=%T and %G=%C

Question 22

Base composition of E. coli:

Answer 22

40 AT, 10 GC

Question 23

Base composition of human:

Answer 23

30 AT, 20 GC

Question 24

Base composition of mycobacterium:

Answer 24

15 AT, 35 GC

Question 25

Base composition of bacterophage:

Answer 25

24 A, 31.2 T, 21.5 C, 23.3 G

Question 26

Most common DNA form:

Answer 26

B-form DNA

Question 27

Properties of B-form DNA:

Answer 27

* backbone outside * bases inside * major groove * minor groove * antiparallel * right-handedness

Question 28

Major groove:

Answer 28

bases can be approached by DNA binding proteins

Question 29

Atoms in DNA:

Answer 29

* oxygen * carbon * phosphorus * carbon-oxygen-nitrogen

Question 30

DNA is antiparallel:

Answer 30

one 5' -OH group at the top, one 3' P group at the bottom (vice versa),

Question 31

DNA chains are held by:

Answer 31

hydrogen bonds between pairs of bases on opposite strands

Question 32

The two DNA strands are:

Answer 32

complementary to one another, and a template for the replication of DNA

Question 33

Conservative model of DNA replication:

Answer 33

one of the daughter duplexes is the conserved original duplex and one is completely new

Question 34

Semi-conservative model of DNA replication:

Answer 34

involves unwinding the two strands and each serves as a template to copy a new strand. The daughter strands contain one of the original template strands and one new material

Question 35

Dispersive model of DNA replication:

Answer 35

parental material is scattered through the structures of both daughter duplexes

Question 36

Meselsohn and Stahl experimental data for semi-conservative replication:

Answer 36

1. *E. coli* grown in 15N or 14N 2. Daughter strands have a density in the middle consistent with semi-conservative replication 3. Another round in light isotope shows daughter strands are solely light, consistent with semi-conservative replication

Question 37

What causes A-DNA form?

Answer 37

* RNA-RNA double helix molecules * DNA-RNA hybrids from helices * DNA in low-humidity environments

Question 38

The difference between B-DNA and A-DNA:

Answer 38

A-DNA has more bp/turn and a shorter rise between successive nucleotides

Question 39

Human mitochondrial tertiary structure:

Answer 39

* relaxed and supercoiled allows for compaction in a cell * circular and double stranded

Question 40

*E. coli* motichondrial tertiary structre:

Answer 40

circular and double-stranded

Question 41

What causes supercoiling:

Answer 41

wrapping around histones

Question 42

Negative and positive supercoils:

Answer 42

overwinding will create a positive supercoil and underwinding creates a negative supercoil

Question 43

Secondary structure of RNA:

Answer 43

* random single stranded RNA * stacked-base structure * "hairpin" structures

Question 44

Secondary structure of viruses:

Answer 44

double-stranded RNA genome

Question 45

Random single stranded RNA:

Answer 45

random coil structure of denatured single strands. There is flexibility of rotation of residues and no specific structure

Question 46

Stacked-base structure:

Answer 46

adapted by non-self complementary single strands under " native" conditions. Bases stack to pull the chain into a helix, but there is no H-bonding

Question 47

"Hairpin" structures:

Answer 47

formed by self-complementary sequences (green and orange regions of the single strand); the chain folds back on itself to make a stem-loop structure

Question 48

Single-stranded nucleic acid base-pairing:

Answer 48

forms stem-loop structures

Question 49

Secondary structure of tRNA:

Answer 49

have extensive regions of double-stranded structures that create an overal 3D structure, important to its function

Question 50

DNA denaturation:

Answer 50

when heated, double-stranded molecules melt into single-strands (disruption of H-bonds and van der Waals). Once cooled, they find their complementary sequences and reassociate (hybridize or anneal)

Question 51

Relative strength of G-C pairs:

Answer 51

stronger than A/T pairs as they have 3 H-bonds instead of 2

Question 52

Energy level between native DNA and denatured DNA:

Answer 52

denatured DNA has higher energy than the double helix because their base pairs are exposed and absorb more energy

Question 53

Free energy of DNA at high temperature:

Answer 53

more favorable at higher temperatures and drives denaturation

Question 54

Free energy of DNA at low temperature:

Answer 54

less favorable at lower temperatures and denaturation does not occur

Question 55

Factors affecting melting temperature:

Answer 55

* length * bonds * composition * ion solution