DNA Chemistry and Analysis

Question 1

What are the 4 components of a nucleotide?

Answer 1

1. nitrogenous base (purine or pyrimidine)
2. sugar (ribose or deoxyribose)
3. phosphate
4. rare or minor bases

Question 2

Methylation is an important modification to a major base because ___ ___ can be controlled by this modification

Answer 2

gene expression

Question 3

Transfer RNA contains a high percentage of ___ bases

Answer 3

minor

Question 4

Ribosomal RNA contains a high percentage of ____ bases

Answer 4

methylated

Question 5

What is the most commonly modified base in DNA?

Answer 5

5-methylcytosine

Question 6

In regards to sugar, DNA contains ____ and RNA contains ____

Answer 6

B-2-deoxyribose; B-D-ribose

Question 7

DNA contains thymine while RNA contains ____ in place of it

Answer 7

Uracil

Question 8

In regards to linkage, mononucleotides are joined together by ____ bridges between the 5’hydroxyl group of one nucleotide and the 3’hydroxyl group of the adjacent nucleotide.

Answer 8

phosphodiester

Question 9

In regards to linkage, the bases are not directly attached covalently to one another. True or false?

Answer 9

true

Question 10

Nucleic acid sequences are always written from left to right: ___’ to ___’ direction

Answer 10

5;3

Question 11

The products of strong acid hydrolysis of DNA or RNA are what?

Answer 11

pyrimidine nucleosides, deoxyribose or ribose and phosphate

Question 12

Base hydrolysis of ____ proceeds through a 2’,3’-cyclic phosphate intermediate

Answer 12

RNA

Question 13

Since DNA doesn’t contain a 2’ hydroxyl group, it is resistant to ____ hydrolysis.

Answer 13

base

note: this is important method for separating DNA from RNA

Question 14

DNA is stable in base and RNA is not stable. True or false?

Answer 14

true

Question 15

What is the product of base hydrolysis of RNA?

Answer 15

2’ and 3’ nucleoside monophosphates

Question 16

In both prokaryotic and eukaryotic cells, DNA exists as a double helix in which two DNA strands are wrapped around the same axis. True or false?

Answer 16

true

Question 17

In regards to the double helix, the phosphodiester bond and the deoxyribose moieties that they link from the ____ of each strand with the nitrogenous base projecting into the interior of the double helix

Answer 17

backbone

Question 18

In regards to the double helix, ____ project to the outside of the double helix where they interact with proteins

Answer 18

phosphates

note: negatively charged phosphates are complexed with cations such as Na, K and Ca - leads to helix stabilization

Question 19

In regards to the double helix, the nitrogenous bases are stacked in the interior of the double helix with the planes of the bases being parallel to each other and perpendicular to the long axis of the double helix. Because of the proximity of the stacked bases ___ ___ ___ attractive forces contribute greatly to the stability of the helix

Answer 19

van der waals

Question 20

In regards to the double helix, bases of one strand form ___ bonds with the bases of the other strand such that ___ always pairs with ____

Answer 20

hydrogen; adenine; thymine (and guanine with cytosine)

Question 21

In any DNA molecule, the amounts of adenine and thymine are always the same while the amounts of guanine and cytosine are always the same. True or false?

Answer 21

true

Question 22

Hydrogen bonding between Adenine and Thymine is ____ than the bonding between Guanine and Cytosine

Answer 22

weaker (double bond in AT vs triple bond in GC)

Question 23

What is the distance of a complete turn of the double helix? How many base pairs are needed for one complete turn?

Answer 23

3. 4 nm; 10 base pairs

note: this is the B form and it is the most abundant

Question 24

The grooves in the DNA provide surfaces to which regulatory proteins can bind. The major groove is almost ___ as wide as the minor groove

Answer 24

twice (22 A vs 12 A)

Question 25

What are the 4 reasons why the double helix is stable?

Answer 25

1. there are hydrophobic and electronic interactions between the stacked bases of each strand 2. the hydrogen bonds that are formed between the complementary bases of the two strands 3. the hydrophobic nitrogenous bases are shielded from the aqueous environment 4. the negatively charged phosphate groups and polar sugar moieties are exposed to the aqueous environment

Question 26

Segments of DNA rich in AT pairs melt at a ____ temperature than GC pairs.

Answer 26

lower

Question 27

What is the hypochromic effect?

Answer 27

Melting of DNA in solution can be followed by an increase in ultraviolet light absorbance when DNA is heated to its melting temperature. The stacked bases in double stranded DNA decreases the UV absorption relative to free nucleotides in solution

Question 28

Hydrogen bond formation allow double strand DNA to form two complementary single strands. This slow step is called what? hint: opposite of melting or denaturing

Answer 28

annealing

Question 29

The most common conformation of DNA (and the one discovered by Watson and Crick) is what?

Answer 29

B-DNA

Question 30

DNA C has ___ base pairs per complete turn of the double helix with the distance of one complete turn being ___ nm

Answer 30

9; 3.3 note: not thought to occur in vivo

Question 31

DNA A has ___ base pairs per complete turn of the double helix with the distance of one complete turn being ___ nm

Answer 31

11; 2.8

Question 32

The nitrogenous bases in DNA A are not perpendicular to the long axis of the double helix but have a tilt of about ___ degrees

Answer 32

20

Question 33

DNA A froms under low ___ conditions and probably occurs in very ___ stretches in DNA and is sequence dependent

Answer 33

hydration; short

Question 34

DNA Z has ___ pairs per complete turn of the double helix. DNA Z has been observed in crystals of synthetic hexanucleotide d and in fibers of the alternating d(GC)n polymers

Answer 34

12

Question 35

Z DNA is in the form of a ___-handed helix who B DNA is in the form of a ___-handed helix

Answer 35

left; right

Question 36

The deoxyribose-phosphate back bone of __ DNA has a staggered zigzag course.

Answer 36

Z

Question 37

Within cells, most DNA is in the B conformation although, regions rich in _-_ base pairs may assume the Z conformation

Answer 37

GC

Question 38

Methylation of deoxycytidine groups in the GC rich regions of DNA may favor ___ DNA formation

Answer 38

Z

Question 39

True or false? It is impossible for a B-Z transition to occur within a segment of DNA without totally separating the two strands

Answer 39

false; it's possible

Question 40

Although not a separate conformation of DNA, it is known that short stretches of ___ residues can cause bending of the DNA helix.

Answer 40

adenine

Question 41

Six adenines in a row can cause a bend of ___ degrees

Answer 41

18

Question 42

The expression of genes is generally ___ in regions of DNA with an A-bending sequence

Answer 42

blocked

Question 43

The nucleotide sequence in the ___ strand is the same as that of the RNA made from the DNA, except uracil will substitute for thymine in the RNA

Answer 43

coding

Question 44

This strand is complementary to the coding strand and also to the RNA which will be synthesized. If the two strands of DNA were separated, the newly synthesized RNA would bind to this strand but not to the coding strand

Answer 44

template

Question 45

What are three factors that can cause denaturation of DNA?

Answer 45

high temperature, high pH, low ionic strength note: low ionic strength is not sufficient to bring about complete denaturation. however, low ionic strength is combination with high pH or high temp is experimentally used to cause denaturation of double stranded DNA

Question 46

Does denaturation require energy expenditure to occur in vivo?

Answer 46

yes

Question 47

The property of self-association of complementary strands has provided the basis of the development of a technique termed _____

Answer 47

hybridization

Question 48

In his type of blotting, a DNA sample is electrophoresed, denatured, transferred to nitrocellulose and hybridized with a radio labeled probe. This technique is often used to see gene structure or gene complexity.

Answer 48

Southern blotting

Question 49

In this type of blotting, an RNA sample is electrophoresed, transferred to a membrane and immobilized, and then hybridized with a DNA probe. This technique is used to measure RNA message levels for genes.

Answer 49

Northern blotting

Question 50

In this type of blotting, protein sample is electrophoresed, transferred to a membrane and then visualized by an immunological procedure

Answer 50

Western blotting

Question 51

A 5' exonuclease must be present with a 5' ___ on the terminal nucleotide to remove it from the polynucleotide chain

Answer 51

hydroxyl

Question 52

A 3' exonuclease must be present with a free 3' OH on the terminal nucleotide to remove it from the chain. What is an example of a 3' exonuclease?

Answer 52

DNA polymerase I

Question 53

these are enzymes which hydrolyze in the interior of a polynucleotide. DNase I is an example which cuts in a nonspecific fashion.

Answer 53

endonuclease

Question 54

____ enzymes are endonuclease that recognize base sequences in double helical DNA and cleave both strands of the duplex DNA.

Answer 54

Restriction note: they are found in a wide variety of bacteria and restrict growth of bacterial viruses

Question 55

____ is a phrase which reads the same way forwards and backwards. "madam i'm adam"

Answer 55

palindrome

Question 56

Restriction enzymes are never palindromic. True or false

Answer 56

false, most are palindromic

Question 57

_____ DNA molecules are created by linking restriction fragments of DNA from one organism with another. Generally the DNA fragments of from the organism of interest are linked to a bacterial ____

Answer 57

recombinant; vector

Question 58

Describe the process of cloning a human gene into bacteria

Answer 58

a fragment of DNA obtained from genomic or cDNA library is introduced into a plasmid. The plasmid is reintroduced into a bacteria (transformation). Bacteria processing the "engineered plasmid" are identified and isolated.

Question 59

What are 3 desirable vector characteristics?

Answer 59

1. multiple enzyme choices 2. bears genes that code for proteins that impart resistance to antibiotics - permits selection of bacteria 3. possesses promoter sequences which permit the insert to be transcribed

Question 60

Through hydrogen bonding, complementary extensions from enemy digestion facilitate joining of DNA fragments by _____

Answer 60

ligation

Question 61

Because the size of the piece of foreign DNA that can be inserted into plasmids is mall, other vectors have been developed. These consist of ____ ___ vectors

Answer 61

lambda phage

Question 62

_____ are plasmids which contain DNA sequences that allow DNA to be packaged into a bacteriophage protein coat. This allows efficient expression of the library.

Answer 62

COSmids

Question 63

This DNA appears to be localized in the centromere region of the chromosome and probably participates in alignment of chromosomes during mitosis and meiosis. These sequences do not appear to be transcribed. Also referred to as satellite DNA.

Answer 63

highly repetitive

Question 64

The Alu I family is an example of what type of DNA

Answer 64

highly repetitive

Question 65

This type of DNA consists of both transcribed and untranscribed sequences.

Answer 65

moderately repetitive

Question 66

Haploid human cells contain approximately ____ base pairs of DNA

Answer 66

3.5 x 10^9

Question 67

About ____ genes are estimated to exist for humans

Answer 67

25,000

Question 68

In eukaryotic cells, the DNA appears in structures called _____

Answer 68

chromosomes

Question 69

Each cell in the human body contains ___ picograms of DNA. If all this DNA were stretched into one linear strand it would stretch ___ m in length

Answer 69

6; 1

Question 70

____ are DNA-protein associations that allow a thousand-fold condensation of DNA in the nucleus

Answer 70

chromosomes

Question 71

These proteins package DNA. There are 5 types.

Answer 71

histone

Question 72

All the histones are very basic proteins due to the presence of high levels of ___ and _____

Answer 72

arginine; lysine

Question 73

At physiological pH, the histones have a large net ___ charge and can bind to ___ charged molecules

Answer 73

positively; negatively

Question 74

The combination of DNA with the histones forms a structure termed ____

Answer 74

chromatin

Question 75

Chromatin contains a repeating unit termed a ____. Each one contains approximately ___ pairs of DNA, ____ molecules of Histones 2A, 2B, 3, 4, and ___ molecule of histone H1

Answer 75

nucleosome; 200; 2; 1

Question 76

In the core particle, eight histone molecules form an octamer forming a sphere. The DNA is wrapped around the exterior of the sphere. What is the advantage of this?

Answer 76

a large amount of DNA can be packaged into a small area

Question 77

Histone H1 proteins interact to form a ____ structure

Answer 77

solenoid

Question 78

the width of a nucleosome is approximately ___ nm

Answer 78

11 (100 A)

Question 79

In a chromosome, the nucleosomes are packaged upon each other to form a structure which is approximately ___ nm at the primary (solenoid) level

Answer 79

30 nm (300 A)

Question 80

The H1 histone, though binding to both the DNA of the ____ particle and the ___ DNA, plays an important role in packaging while the nonhistone proteins help form a ___

Answer 80

core; linker; scaffold

Question 81

In order for DNA to be replicated and transcribed, the binding of histones to DNA must be disrupted. ____ and ____ of N-terminal amino acids in histones alters the histone charge from + to _

Answer 81

acetylation; phosphorylation

Question 82

____ of histones occurs strongly in expressed regions of chromatin (gives rise to R-banding of chromosomes in histology)

Answer 82

acetylation

Question 83

Proteins known as ___-___ group proteins are required for unwinding of nucleosomes to produce regions of DNA that can be transcribed

Answer 83

high-mobility