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Biochem > DNA Chemistry and Analysis > Flashcards

DNA Chemistry and Analysis Flashcards

1
Q

What are the 4 components of a nucleotide?

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

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

A

gene expression

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3
Q

Transfer RNA contains a high percentage of ___ bases

A

minor

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4
Q

Ribosomal RNA contains a high percentage of ____ bases

A

methylated

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5
Q

What is the most commonly modified base in DNA?

A

5-methylcytosine

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6
Q

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

A

B-2-deoxyribose; B-D-ribose

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7
Q

DNA contains thymine while RNA contains ____ in place of it

A

Uracil

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8
Q

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.

A

phosphodiester

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9
Q

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

A

true

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10
Q

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

A

5;3

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11
Q

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

A

pyrimidine nucleosides, deoxyribose or ribose and phosphate

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12
Q

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

A

RNA

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13
Q

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

A

base

note: this is important method for separating DNA from RNA

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14
Q

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

A

true

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15
Q

What is the product of base hydrolysis of RNA?

A

2’ and 3’ nucleoside monophosphates

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16
Q

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?

A

true

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17
Q

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

A

backbone

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18
Q

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

A

phosphates

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

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19
Q

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

A

van der waals

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20
Q

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

A

hydrogen; adenine; thymine (and guanine with cytosine)

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21
Q

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?

A

true

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22
Q

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

A

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

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23
Q

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

A
  1. 4 nm; 10 base pairs

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

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24
Q

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

A

twice (22 A vs 12 A)

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25
Q

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

A
  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
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26
Q

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

A

lower

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27
Q

What is the hypochromic effect?

A

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

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28
Q

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

A

annealing

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29
Q

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

A

B-DNA

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30
Q

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

A

9; 3.3

note: not thought to occur in vivo

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31
Q

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

A

11; 2.8

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32
Q

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

A

20

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33
Q

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

A

hydration; short

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34
Q

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

A

12

35
Q

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

A

left; right

36
Q

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

A

Z

37
Q

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

A

GC

38
Q

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

A

Z

39
Q

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

A

false; it’s possible

40
Q

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

A

adenine

41
Q

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

A

18

42
Q

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

A

blocked

43
Q

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

A

coding

44
Q

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

A

template

45
Q

What are three factors that can cause denaturation of DNA?

A

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

46
Q

Does denaturation require energy expenditure to occur in vivo?

A

yes

47
Q

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

A

hybridization

48
Q

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.

A

Southern blotting

49
Q

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.

A

Northern blotting

50
Q

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

A

Western blotting

51
Q

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

A

hydroxyl

52
Q

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?

A

DNA polymerase I

53
Q

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

A

endonuclease

54
Q

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

A

Restriction

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

55
Q

____ is a phrase which reads the same way forwards and backwards. “madam i’m adam”

A

palindrome

56
Q

Restriction enzymes are never palindromic. True or false

A

false, most are palindromic

57
Q

_____ 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 ____

A

recombinant; vector

58
Q

Describe the process of cloning a human gene into bacteria

A

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.

59
Q

What are 3 desirable vector characteristics?

A
  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
60
Q

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

A

ligation

61
Q

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

A

lambda phage

62
Q

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

A

COSmids

63
Q

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.

A

highly repetitive

64
Q

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

A

highly repetitive

65
Q

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

A

moderately repetitive

66
Q

Haploid human cells contain approximately ____ base pairs of DNA

A

3.5 x 10^9

67
Q

About ____ genes are estimated to exist for humans

A

25,000

68
Q

In eukaryotic cells, the DNA appears in structures called _____

A

chromosomes

69
Q

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

A

6; 1

70
Q

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

A

chromosomes

71
Q

These proteins package DNA. There are 5 types.

A

histone

72
Q

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

A

arginine; lysine

73
Q

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

A

positively; negatively

74
Q

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

A

chromatin

75
Q

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

A

nucleosome; 200; 2; 1

76
Q

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?

A

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

77
Q

Histone H1 proteins interact to form a ____ structure

A

solenoid

78
Q

the width of a nucleosome is approximately ___ nm

A

11 (100 A)

79
Q

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

A

30 nm (300 A)

80
Q

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 ___

A

core; linker; scaffold

81
Q

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 _

A

acetylation; phosphorylation

82
Q

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

A

acetylation

83
Q

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

A

high-mobility

Biochem (38 decks)

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