BIO Class 2. Biochemistry Chapter 7

Watson-Crick model of DNA

-right handed -double helix -held together by H bonds -held together by hydrophobic forces between bases -double stranded

prokaryotic chromosome

-singular circular

DNA backbone

-sugar phosphate group. this part is invariant

Why is the stability of RNA unimportant?

because a cell's DNA is necessary for its entire life. RNA is simply transcribed, translated, and destroyed.

annealing

binding of two complementary strands of DNA into a double strand. -another word for it is hybridization

Telocentric

no p

Metacentric

normal

p arms

shorter

Tm

temperature at which a solution of DNA molecules is 50 percent melted

Would the Tm of ATTATCAT and its complementary strand by higher or lower than the melting temperature of ACTCGCAT and its complementary?

the first would be lower bc it has more AT strands

mRNA

the only type of coding RNA! -carries genetic information to the ribosome, where it can be translated into a protein -constantly produced and degraded

Acrocentric

-q is too long, p is too short

Nucleosomes

-DNA wrapped around an octamer of histones -

Phosphoric Acid

-Inorganic (no Carbon) -potential to donate three protons -The Ka's for the dissociation equilibria are 2.1, 7.2, 12.4 -in anionic form at physiological pH

ATP

-RNA precursor. -ribonucleotide (not deoxy)

denaturation

-breaking strands. -also known as melting

genome

-contains sum of all of an organism's genetic info -composed of several large pieces of linear ds-DNA

dNTP

-deoxyriboNucleoSide 5' triphosphate -building block of DNA -N stands for 1 of the 4 basic nucleosides -3 phosphate residues -4 different types depending on the aromatic base

chromosome

-each piece of ds-DNA in a genome -humans have 46, 23 from each parent

Histones

-eukaryotic DNA is wrapped around this -globular protein

Nucleic Acids

-found in nucleus -have many acidic phosphate groups -DNA and RNA are nucleic acids

Phosphodiester Bond

-linkes together nucleotides -between 3' hydroxy group of one sugar and the 5' phosphate group of the next sugar

Deoxyribonucleotides

1. monosaccharide (deoxyribose)(no OH on C2) 2. aromatic nitrogenous base (ATGC) 3. phosphate group

Three reasons why phosphate anhydride bonds store so much energy:

1. negative charges repel each other strongly 2. orthophosphate has more resonance forms and thus a lower free energy than linked phosphates 3. orthophosphate would rather interact with water than other phosphates. -basically a compressed spring that wants to fly open and provide energy

nucleoside

1. sugar. ribose (a deoxunucleoside would be deoxy. not the case here) 2. base. purine or pyrimidine linked to the C1 in a Beta-N-glycosidic linkage

How do we write DNA sequence?

5' to 3'. The end of the chain with the free 5' is taken first, and the last nucleotide has a free 3' hydroxy group.

purine

A G. double ring structure of six and five membered ring

In the Beta-N-glycosidic linkage, where is the aromatic base positioned?

Above the plane of the ribose ring. Remember, "its Better to be Up" -pg 167 in biochem textbook

Anticancer drugs often seek to block the growth of rapidly dividing cells by inhibiting thymine. Why is this an attractive target for cancer therapy?

All cells require RNA production, even if they're not growing, to replenish degraded RNA. Only DNA contains thymine so if it is inhibited, only DNA replication will be stopped and only rapidly dividing cells such as cancer cells will be affected. Unfortunately, hair follicle cells and the lining cells of the gut divide a lot, which explains the side effects of chemotherapy.

Telomeres are guanine rich caps on the ends of each chromosome. Which of the following is the most likely function of a telomere? A. High guanine content stabilizes parental strands to prevent excess tension during DNa unwinding B. To prevent the ends of chromosomes from damage due to incomplete replication C. To provide a site for helices attachment D. To seal the gaps left by Okazaki garments in the lagging strand

B

What is a defining characteristic of heterogenous nuclear RNA? A. It has a methylated guanine cap on the 5' end B. It has a sequence containing introns and eons C. It contains uracil D. It has a poly A sequence on the 3' end

B

Nucleotides and their Structure

Building blocks of nucleic acids(DNA and RNA) -structure: sugar (ribose or deoxyribose), purine or pyrimidine (joined to C1 of ribose ring), and 1-3 phosphate units (joined to C5 of ribose ring). see picture in my notes

G is H bonded to

C -held together by THREE hydrogen bonds

pyrimidines

C T. one six membered ring. cut the py

Packaging a eukaryotic genome involves all of the following structures or steps except: A. wrapping linear portions of DNA around histone proteins B. building an octamer of histories into a nucleoside using gyrase C. providing flexibility by leaving linker DNA between nucleosomes of approx 80. base pairs D. condensing nucleosomes around chromatin

D

DNA

Deoxyribonucleic acid

DNA in the nucleus, from small to large

Deoxyribose -> + base -> nucleoside -> + three phosphates -> nucleotide -> + polymerize with loss of two phosphates -> oligonucleotide -> + polymerize more -> single stranded polynucleotide -> + two complete chains H bonded in antiparallel fashion -> ds DNA chain -> + coiling -> ds helix -> + wrap around histones -> nucleosomes -> + complete packaging -> chromatin

Telomeres

Ends of linear chromosomes -rich in repeats -often TTAGGG -single and double stranded ends -Single stranded DNA at the end loops around to form a knot to stabilize it. -Cap proteins distinguish telomeres from double stranded breaks to prevent any repair pathways -also prevent chromosome deterioration, and prevent fusion with neighboring chromosomes -a disposable buffer -NOT in prokaryotes

Which DNA base pair requires the most energy to break?

GC

Phosphate bond

High energy bond in P-O-P.

Which of the following is/are true about ds-DNA? I. If the amount of G in a double helix is known, the amount of C can be calculated II. If the fraction of purine nucleotides and the total molecular weight of a double helix is known the amount of cytosine can be calculated III. The two chains in a piece of ds-DNA containing mostly purines will be bonded together more tightly than the two chains in a piece of ds-DNA containing mainly pyrimidines IV. The oligonucleotide ATGTAT is complementary to ATACAT.

I, and IV are true I: yes because for every G there is a C II: No. the ratio of purines to pyrimidines is always the same, and we would need to know the ratio of AT to GC pairs III. No. ratio is always the same. BUT if there was more GC pairs then yes because those have 3 hydrogen bonds IV> Yes. strands are antiparallel and the 5' end is always written first.!!!!

Euchromatin

Lighter region of the chromosome. constant and heritable region. higher transcription rates and higher gene activity -looser packing makes the DNA more accessible to enzymes and proteins -lighter stained regions start replication earlier due to the accessibility of the DNA

Is there a correlation between genome size and evolutionary sophistication

No

Will adenine and Thymine H-bond with each other in water?

No. they will bond with water, not themselves. In DNA they interact with each other because DNA coiling places them inside the double helix to interact with each other

What is the backbone of a protein? What is the variable portion?

Peptide bonds R group

The DNA double helix is described as being both complementary and antiparallel. What characteristics generate these properties, respectively?

Pyrimidines hydrogen bond to purines, and a strand in its 5' to 3' direction is paired with a strandd in a 3' to 5; orientation

A is H bonded to

T -held together by TWO hydrogen bonds

If you attached methyl groups to all the acidic phosphate oxygens along the length of a DNA double helix, would the chain have a higher or lower Tm than normal DNA?

Tm would increase -the charged phosphates electrostatically repel each other in DNA. methyl esters will not be charged. the lack of electrostatic repulsion between the methyl ester backbones will increase the Tm and more energy will be needed to separate them

RNA

Unlike DNA, RNA is 1. Single stranded 2. RNA contains URACIL instead of Thymine 3. Pentose ring in RNA is ribose, not 2' deoxyribose, which makes it less stable (the OH can do a nucleophilic attack)

H bonded pair always consists of:

a purine and a pyrimidine. therefore AT and GC take up the same amount of room in the DNA double helix

complementary

bases in each strand can H bond where the strands are oriented in an antiparallel fashion

Linked chromatics with long q arms and short p arms are

acrometric

See pic in my notes of polymerization of nucleotides

also on page 172 of biochem textbook

Are histones acidic or basic?

basic. they must be attracted to the acidic exterior of the DNA double helix. -ARG and LYS are also unusually abundant

Why is the 2 OH' group removed from ribose in order to form the monosaccharide component of DNA?

creates greater stability in the molecule

Heterochromatin

darker region of the chromosome. Rich in repeats. more dense = compact and coiled

Submetacentric

disproportionate.

Kinetochores

fibers attach to the centromere via these -multiprotein complex that act as anchor attachment for spindle fibers

chromatin

fully packaged DNA -composed of closely stacked nucelsomes

hnRNA

heterogenous nuclear RNA -the first RNA transcribed from DNA -an immature precursor to mRNA -adding a cap and tail, as well as splicing, is necessary for hnRNA to become mature mRNA -Only in Eukaryotes!!

DNA gyrase

in prokaryotes to make their single cellular chromosome more compact and sturdy -uses ATP to twist the circular molecule -breaks the DNA and twists the two sides of the circle around each other

Does an enzyme's binding specifity come from ribose and phosphate interactions or purine and pyrimidine interactions?

interactions with the bases. this is the variable part, so specifity comes from here.

q arms

longer

non coding RNA

not translated into a protein -tRNA -rRNA -snRNA: small nucear RNA. help form snRNP -miRNA: micro RNA -piRNAs: PIWI interacting RNAs -Long ncRNAs

nucleotide

phosphate esters of nucleosides. 1-3 phosphate groups joined to the ribose ring by the 5' hydroxy group -linked by phosphodiester bonds

Which reaction is more thermodynamically favorable, polymerization of nucleoside mono phosphates or the polymerization of nucleoside triphosphates?

polymerization of nucleoside triphosphates because pyrophosphate is released and hydrolyzed, driving the polymerizationn reaction forward. the hydrolysis of the high energy pyrophosphate is energetically favorable

supercoil

refers to the twists made by DNA gyrase, since it is already twisting a coil

Centromere

region of chromosome where spindle fibers attach during cell division -made of heterochromatin and repetitive DNA sequences

rRNA

ribosomal RNA -major component of the ribosome -humans have only four different types -gives catalytic function to the ribosome..... like an enzyme.

tRNA

transfer RNA -translates the genetic code -carries amino acids from the cytoplasm to the ribosome to be added to a growing protein -each tRNA must recognize a codon on mRNA. -20 to 61 different types -the third nucleotide of the codon is often not needed for specifity anyways

antiparallel

two long polynucleotide chains are hydrogen bonded this way -5' end of one is paired with the 3' end of the other -reminiscent of the Beta plated sheet, a secondary structure -H bonds are between the bases on adjacent chains

Pyrophosphate

two orthophosphates bound together via an anhydride linkage. Hydrolysis of it is thermodynamically favored