Biochemistry 1 Ch. 19

RNA, DNA

what are the polymer forms of nucleic acids?

nucleotides

what are the monomer forms of nucleic acids?

Watson and Crick

Figured out structure of DNA was a double helix

double helix

The form of native DNA, referring to its two adjacent polynucleotide strands wound into a spiral shape.

deoxyribose

ribose

dideoxyribose

thymine, uracil, cytosine

pyrimidine bases

guanine, adenine

purine bases

G-C

which DNA/RNA bases pair(s) forms 3 hydrogen bonds?

A-T, A-U

which DNA/RNA bases pair(s) forms 2 hydrogen bonds?

adenosine

the nucleoside formed with adenine

guanosine

the nucleoside formed by guanine

cytidine

the nucleoside formed by cytosine

uridine

the nucleoside formed by uracil

thymidine

the nucleoside formed by thymine

O-H, N-H

what covalent bonds facilitate hydrogen bonding in nucleotides?

-sine

the suffux for the purine nucleotides

-idine

the suffix for the pyrimidine nucleotides

nucleoside

monomer of nucleic acids made up of a 5-carbon sugar and a nitrogenous base

nucleotide

monomer of nucleic acids made up of a 5-carbon sugar, a phosphate group, and a nitrogenous base

They use the energy of splitting of the first two phosphates for the reaction to occur.

Why are new nucleotides used to make DNA and RNA triphosphates?

monophosphate

nucleotide with one phosphate group is considered what?

triphosphate

3 phosphate groups

2

How many phosphate groups break off of a nucleotide when it is synthesized into DNA or RNA?

5 prime

the end of DNA or RNA with the phosphate group

3 prime

The end of DNA or RNA with just ribose

carbon number

what do 3' and 5' refer to?

both, it is amphipathic

is DNA hydrophobic or hydrophilic?

the central nitrogen bases

what region of DNA is hydrophobic?

the phosphate back bone

what region of DNA is hydrophilic?

weak forces

what kind of forces determine the structure of DNA and RNA?

they are strong enough to maintain structure, but weak enough to allow for conformational changes

why is it important that weak forces determine the structure of DNA and RNA?

stacking interactions, hydrogen bonds, hydrophobic effect, charge-charge interactions

what four forces are present in maintaining the structure of DNA and RNA?

stacking interactions

Stacked base pairs form van der Waals contacts

the hydrophobic nitrogen base pairs are buried within the double helix

explain how the hydrophobic effect is present in DNA?

no (it would kill you)

Does denaturation of DNA occur in the body?

melting point

the temperature at which half the DNA has become single stranded is called what?

melting curve

a plot of the change in absorbance of a DNA solution versus temperature is called what?

DNA converts from single stranded to double stranded

What happens at the point that the curve of the melting curve increases sharply?

G-C

The base pair hydrogen bonding of which base pair(s) is the strongest?

A-T, A-U

The base pair hydrogen bonding of which base pair(s) is the weakest?

at pH 7.0 double stranded DNA has an absorbance maximum near 260 nm

single stranded

does single stranded or double stranded DNA absorb more ultraviolet light?

rRNA, tRNA, mRNA, sRNA

what are the four major classes of RNA?

rRNA (ribosomal RNA)

type of RNA that makes up the major part of ribosomes

tRNA (transfer RNA)

The form of RNA that carries each amino acid to the ribosome to form the polypeptide chain (protein)

mRNA (messenger RNA)

The form of RNA which is created as a blueprint from DNA; carries instructions for making a protein

sRNA (small RNA)

RNA that regulates transcription or translation

the - strand of DNA double helix

what do we believe sRNA is transcribed from in DNA?

the + strand of DNA double helix

what do we believe mRNA is transcribed from in DNA?

catalytic activity in association with proteins, process and modify RNA, regulating gene expression

what are the three general purposes of sRNA listed in the book?

15 kJ mol^-1

the resistance of stacking interactions has been measured by atomic-force spectroscopy to be what?

chromatin

granular material visible within the nucleus; consists of DNA tightly coiled around proteins

2.4x10^8 (8cm in B conformation)

How long is the longest human chromosome?

30nm

chromatin exists as fibers that are how long?

packing ratio

The ratio of the length of DNA to the unit length of the fiber containing it.

8000 fold

what is the packing ratio of DNA?

histones

protein molecules around which DNA is tightly coiled in chromatin

H1, H2A, H2B, H3, H4

What are the five types of histones?

lysine, arganine

the numerous positively charged residues in histones that allow it to bind to the negatively charged phosphates of DNA are what?

nucleosomes

Bead-like structures formed by histones and DNA

1, 2, 200

Each nucleosome is composed of \___ molecule(s) of histone H1, \____ molecule(s) each of histones H2A, H2B, H3, H4, and about \_________ base pairs of DNA

H1

which histone is responsible for the higher-order chromatin structures

1.75

DNA wraps around the core particle of a histone about how many times per nucleosome?

histone acetyltransferase (HAT)

Any of a family of enzymes that transfer an acetyl group from acetyl-CoA to the å-amino group of specific Lysine residues on histone tails.

weakens the net positive charge of the histone N-termini and weakens the interactions with other nucleosomes and proteins

what does acetylation do the chromatin?

a loosening up of higher-order structures

what is the net result of acetylation in nucleosomes?

gene expression

what is acetylation of nucleosomes associated with?

Histone deacetylases (HDACs)

A class of eukaryotic enzymes that condense chromatin by removing acetyl groups from histone proteins.

Heterochromatin

Eukaryotic chromatin that remains highly compacted during interphase and is generally not transcribed.

Euchromatin

The less condensed form of eukaryotic chromatin that is available for transcription.

eukaryotes

What class of organism(s) are histones found in?

nucleases

Enzymes that break down nucleic acid phosphodiesters

synthesis or repair of DNA, production or degradation fo cellular DNA

what different things are nucleases responsible for?

RNAase

breaks RNA into nucleotides

DNAase

breaks DNA into nucleotides

exonucleases

Cut DNA from an exposed end of DNA; facilitate repair

endonucleases

Cut DNA backbone within a strand of DNA; facilitate repair and insertions

2' hydroxyl group

what does alkaline hydrolysis of RNA require?

form hydrogen bonds

what can the 2' hydroxyl group of RNA do?

because it lacks the 2' hydroxyl group needed to initiate intramolecular transesterification

why is DNA no hydrolyzed under alkaline conditions?

transesterification

The process that transforms one ester to another when an alcohol acts as a nucleophile and displaces the alkoxy group on an ester.

primary genetic material

The greater chemical stability of DNA is an important factor in its role as the \________, rather than RNA

proximity, acid-base catalysis, transition-state stabilization

what are the three fundamental catalytic mechanisms of RNases?

restriction endonucleases

recognize specific sequences of DNA and break phosphodiester bonds between adjacent nucleotides

specifically destroy incoming bacteriophage DNA

what do restriction endonucleases do in bacteria?

covalent modification

How does the host bacteria protect itself from the restriction endonucleases it releases to destroy phage DNA?

specific methylation of adenine and cytosine residues

what is the covalent modification that protects bacterial DNA from its own restriction endonucleases?

the same sequence as the restriction endonucleases

the methylases that protect bacterial DNA by methylation from its own restriction endonucleases recognize what pattern in DNA?

methylated

Normally all DNA in a bacteria is \______ this protects it from cleavage by restriction endonucleases that the cell makes

Type I restriction endonucleases

catalyze both the methylation of the host DNA and the cleavage of unmethylated DNA at a specific recognition sequence. (bacteria)

Type II restriction endonucleases

only cleave double-stranded DNA at or near an unmethylated recognition sequence, they do not posses a methylase activity (bacteria)

foreign DNA in bacteria

what do restriction enzymes restrict?

hundreds

how many different restriction endonucleases have be characterized?

twofold axis of symmetry (they are palindromes)

in nearly all cases the recognition sites of restriction endonucleases have what kind of axis?

restriction maps

diagram that shows the lengths of fragments between restriction sites in the strand of DNA and is useful for identifying fragments of DNA that contain specific genes

DNA fingerprints

How can restriction enzymes be used on DNA in court cases to provide evidence?

autoradiography

a procedure that locates radioactive substances in a slice of tissue; the radiation exposes a photographic emulsion or a piece of film that covers the tissue

agarose gel

what kind of gel is used to separate DNA that has been digested with restriction enzymes for the purpose of DNA finger printing?