DNA Chemistry and Analysis Flashcards by Adam Purviance

What are the 4 components of a nucleotide?

nitrogenous base (purine or pyrimidine)
sugar (ribose or deoxyribose)
phosphate
rare or minor bases

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

gene expression

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Transfer RNA contains a high percentage of ___ bases

minor

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Ribosomal RNA contains a high percentage of ____ bases

methylated

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What is the most commonly modified base in DNA?

5-methylcytosine

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

B-2-deoxyribose; B-D-ribose

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DNA contains thymine while RNA contains ____ in place of it

Uracil

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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.

phosphodiester

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

true

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

5;3

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

pyrimidine nucleosides, deoxyribose or ribose and phosphate

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

RNA

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

base

note: this is important method for separating DNA from RNA

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

true

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What is the product of base hydrolysis of RNA?

2’ and 3’ nucleoside monophosphates

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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?

true

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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

backbone

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

phosphates

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

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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

van der waals

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

hydrogen; adenine; thymine (and guanine with cytosine)

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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?

true

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

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

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

4 nm; 10 base pairs

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

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

twice (22 A vs 12 A)

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

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

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

lower

What is the hypochromic effect?

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

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

annealing

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

B-DNA

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

9; 3.3 note: not thought to occur in vivo

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

11; 2.8

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

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

hydration; short

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

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

left; right

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

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

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

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

false; it's possible

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

adenine

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

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

blocked

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

coding

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

template

What are three factors that can cause denaturation of DNA?

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

Does denaturation require energy expenditure to occur in vivo?

yes

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

hybridization

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.

Southern blotting

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.

Northern blotting

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

Western blotting

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

hydroxyl

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?

DNA polymerase I

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

endonuclease

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

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

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

palindrome

Restriction enzymes are never palindromic. True or false

false, most are palindromic

_____ 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 ____

recombinant; vector

Describe the process of cloning a human gene into bacteria

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.

What are 3 desirable vector characteristics?

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

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

ligation

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

lambda phage

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

COSmids

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.

highly repetitive

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

highly repetitive

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

moderately repetitive

Haploid human cells contain approximately ____ base pairs of DNA

3.5 x 10^9

About ____ genes are estimated to exist for humans

25,000

In eukaryotic cells, the DNA appears in structures called _____

chromosomes

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

6; 1

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

chromosomes

These proteins package DNA. There are 5 types.

histone

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

arginine; lysine

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

positively; negatively

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

chromatin

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

nucleosome; 200; 2; 1

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 large amount of DNA can be packaged into a small area

Histone H1 proteins interact to form a ____ structure

solenoid

the width of a nucleosome is approximately ___ nm

11 (100 A)

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

30 nm (300 A)

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 ___

core; linker; scaffold

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 _

acetylation; phosphorylation

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

acetylation

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

high-mobility