Unit 1: DNA Structure

Question 1

1952 Alfred Hershey and Martha Chase

Answer 1

Labelled T2 bacteriophages’ DA with 32P and protein with 35S. Showed that DNA was passed on to virus progeny.

Question 2

Allele

Answer 2

One of several alternative forms of a gene occupying a given locus on a chromosome

Question 3

Chromosome

Answer 3

A discrete unit of the genome carrying many genes. Each consists of a very long molecule of duplex DNA and an approximately equal mass of proteins (in eukaryotes). It is visible as a morphological entity only during cell division.

Question 4

Gene

Answer 4

a sequence of DNA that encodes an RNA, and in protein-coding, or structural, genes, the RNA in turn encodes a polypeptide

Question 5

1928 Griffith

Answer 5

Gave rise to idea that genes have roots in DNA.
Did experiments with mice, “S” bacteria and “R” bacteria. Heat inactivated “S” bacteria and live “R” bacteria still killed mice because of the “transforming principle” (e.g., genes that made “S” bacteria virulent transformed into “R” bacteria making it virulent).

Question 6

linkage

Answer 6

The tendency of genes to be inherited together as a result of their location on the same chromosome; measured by percent recombination between loci

Question 7

Nucleoside

Answer 7

Purine or pyrimidine base linked to the 1’ carbon of a pentose sugar.

Question 8

Nucleotide

Answer 8

A nucleoside linked to a phosphate group on either the 5’ or the 3’ carbon of the (deoxy)ribose.

Question 9

Purine

Answer 9

A double-ringed nitrogenous base, such as adenine or guanine

Question 10

Pyrimidine

Answer 10

A single-ringed nitrogenous base, such as cytosine, thymine or uracil.

Question 11

The ultimate definition of a genome

Answer 11

The sequence of DNA of each chromosome

Question 12

Transfection

Answer 12

In eukaryotic cells, it is the acquisition of new genetic markers by incorporation of added DNA.
Analogous to bacterial transformation.

Question 13

Transforming principle

Answer 13

DNA that is taken up by a bacterium and whose expression then changes the properties of the recipient cell.

Question 14

polynucleotide

Answer 14

a long chain of nucleotides

Question 15

DNA supercoiling

Answer 15

Double helix winds around itself changing overall conformation, or topology, of the DNA molecule in space.

Occurs only in “closed” DNA with no free ends (circular DNA or linear DNA with anchored ends).

Causes tension in DNA. Non supercoiled DNA is said to be in the “relaxed” state.

The reactions to control supercoiling in the cell are performed by topoisomerase enzymes.

Question 16

Positive Supercoiling

Answer 16

The right-handed, double helical form of DNA. Both strands of the double helix coil together in the same direction as the coiling of the strands.

Overwinds the DNA, fewer base pairs per turn.

Results in an increase in the linking number (+ΔL)

Question 17

Negative supercoiling

Answer 17

The left-handed, double-helical form of DNA. Creates tension in the DNA that is relieved by the unwinding of the double helix. The result is the generation of a region in which the two strands of DNA have separated.

Underwinds the DNA, more base pairs per turn.

Results in a decrease in the linking number (−ΔL)

Question 18

Topological manipulation

Answer 18

Topological manipulation of DNA is a central aspect of all of its functional activities (e.g., recombination, replication, and transcription) as well as of the organization of its higher order structure. All synthetic activities involving double-stranded DNA require the strands to separate.

Question 19

Linking number (L)

Answer 19

In a closed molecule of DNA, the number of times one strand crosses over another in space.

Made up of a writhing number (W) and twisting number (T)

The critical feature about the use of the linking number is that this parameter is an invariant property of any individual closed DNA molecule. The linking number cannot be changed by any deformation short of one that involves the breaking and rejoining of strands. A circular molecule with a particular linking number can express the number in terms of different combinations of T and W, but it cannot change their sum so long as the strands are unbroken.

Question 20

Topological isomers

Answer 20

Molecules of DNA that are the same except for their linking numbers (same sequence, different degrees of supercoiling).

Molecules with the same chemical formula but different bond connectivities, thus resulting in different topological structures.

Question 21

Writhing number (W)

Answer 21

In DNA, the turning of the axis of the duplex in space.

Corresponds to the intuitive concept of supercoiling but does not have exactly the same quantitative definition of measurement.

For a relaxed molecule, W = 0, and the linking number equals the twist.

One of two components that make up the linking number.

Question 22

Twisting number (T)

Answer 22

Rotation of one strand about the other.

Represents the total number of turns of the duplex and is determined by the number of base pairs per turn.

For a relaxed closed circular DNA lying flat in a plane, T is the total number of base pairs divided by the number of base pairs per turn.

Question 23

Change in the Linking number equation

Answer 23

ΔL = ΔW + ΔT

The equation states that any change in the total number of revolutions of one DNA strand about the other can be expressed as the sum of the changes of the coiling of the duplex axis in space (ΔW) and changes in the helical repeat of the double helix itself (ΔT). In the absence of protein binding or other constraints, the twist of DNA does not tend to vary—in other words, the 10.5 base pairs per turn (bp/turn) helical repeat is a very stable conformation for DNA in solution. Thus, any ΔL is mostly likely to be expressed by a change in W; that is, by a change in supercoiling.

Question 24

Specific linking difference

Answer 24

σ = ΔL/L0

L0 is the linking number when the DNA is relaxed.

If all of the change in the linking number is due to change in W (that is, ΔT = 0), the specific linking difference equals the supercoiling density.

In effect, σ, as defined in terms of ΔL/L0, can be assumed to correspond to supercoiling density so long as the structure of the double helix itself remains constant.

Question 25

B-form of DNA

Answer 25

The B-form of DNA is a double helix consisting of two polynucleotide chains that are antiparallel.

Right handed - turns run clockwise

Question 26

A-form of DNA

Answer 26

Right handed. Observed when DNA is dehydrated and is shorter and thicker than B-form.

Question 27

Overwound / Underwound

Answer 27

Overwound = DNA has more base pairs per turn (more than 10.4).

Underwound = Fewer base pairs per turn

Question 28

Bent DNA

Answer 28

Series of 8 to 10 adenine residues on one strand can result in intrinsic bending of the double helix.

This structure allows tighter packing with consequences for nucleosome assembly and gene regulation.

Question 29

DNA Helix Measurements

Answer 29

The diameter of the double helix is 20 Å, and there is a complete turn every 34 Å, with 10 base pairs per turn (about 10.4 base pairs per turn in solution).

The double helix has a major (wide) groove which is 22 Å (2.2 nm) and a minor groove (narrow) 12 Å (1.2 nm).

Question 30

Semiconservative replication

Answer 30

DNA replication accomplished by separation of the strands of a parental duplex, each strand then acting as a template for synthesis of a complementary strand.

Question 31

Matthew Meselson and Franklin Stahl in 1958

Answer 31

DNA replication is semi-conservative

Question 32

Semiconservative replication

Answer 32

DNA replication accomplished by separation of the strands of a parental duplex, each strand then acting as a template for synthesis of a complementary strand.

Question 33

DNA Replication fork

Answer 33

The point at which the parental strands are seperated

The point at which strands of parental duplex DNA are separated so that replication can proceed. A complex of proteins including DNA polymerase is found there.

Question 34

DNA polymerase

Answer 34

Enzymes that synthesize DNA

An enzyme that synthesizes a daughter strand(s) of DNA (under direction from a DNA template). Any particular enzyme may be involved in repair or replication (or both).

Question 35

Nucleases

Answer 35

Enzymes that degrade nucleic acids
-DNases
-RNases
Endonucleases or exonucleases

Question 36

Denaturation

Answer 36

A molecule’s conversion from the physiological conformation to some other (inactive) conformation. In DNA, this involves the separation of the two strands due to breaking of hydrogen bonds between bases.

Only a small stretch of the DNA duplex is denature at any moment during replication.

Question 37

Renaturation

Answer 37

The reassociation of denatured complementary single strands of a DNA double helix.

Question 38

Exonuclease

Answer 38

An enzyme that cleaves nucleotides one at a time from the end of a polynucleotide chain; it may be specific for either the 5′ or 3′ end of DNA or RNA.

Remove nucleotide residues on at a time for the end of the molecule, generating mononucleotides.

Question 39

Endonuclease

Answer 39

An enzyme that cleaves bonds within a nucleic acid chain; it may be specific for RNA or for single- or double-stranded DNA.

Breaks individual phosphodiester linkages within RNA or DNA, generating discrete fragments.

Some DNases cleave both strands of duplex DNA whereas other cleave only one of the two.

Question 40

RNA polymerase

Answer 40

An enzyme that synthesizes RNA using a DNA template.

Question 41

Reverse transcriptase

Answer 41

Reverse transcribes RNA into a ssDNA. ssDNA is then converted into dsDNA.

Is a RNA dependent DNA polymerase

Allows a sequence of RNA to be retrieved and used as DNA in a cell