Biochemistry Exam 2

The base composition of the DNA includes 28% G and 26% A. How much T would be in the RNA synthesized from this DNA template?

0% RNA does not contain T

How many pairs of autosomes does the human genome have?

22

In DNA replication, the new strands always grow in the ______ direction.

5' - 3'

Complete the palindrome. Circle the palindrome sequence and square the mirror set. TCGACGA

5'-TCGACGA TCGTCGA-3' 3'-AGCTGCT AGCAGCT-5' 5'-(TCGACGA) (TCGTCGA)-3' 3'-AGCTGCT AGCAGCT-5' 5'-TCGACGA TCGTCGA-3' 3'-(AGCTGCT) (AGCAGCT)-5' 5'-[TCGACGA] TCGTCGA-3' 3'-AGCTGCT [AGCAGCT]-5' 5'-TCGACGA [TCGTCGA]-3' 3'-[AGCTGCT] AGCAGCT-5'

Helix diameter in A DNA, B DNA, and Z DNA

A DNA: 23 A B DNA: 20 A Z DNA: 18 A

As a result of the rotation about its six bonds, DNA can exist in a variety of forms. Determine whether the properties describe the A form of DNA, the B form of DNA, the Z form of DNA, or all three.

A form: Favored from of dehydrated DNA, Widest helix diameter B form: Most stable under physiological conditions, has a 23.7 A helix diameter, the base pairs are nearly perpendicular Z form: Lefthanded, narrowest All: antiparallel structure, G pairs with C, T pairs with A

The first three bases of the six-base recognition cleavage site of HindIII are AAG. What is the complete sequence of this 6-bp site?

AAGCCT

Biochemist Erwin Chargaff was the first to discover that, in DNA, [A]=[T] and [G]=[C]. These equalities are now known as Chargaff's rule. Using Chargaff's rule, determine the percentages of all of the bases in DNA that is 18% thymine.

Adenine: 18% Cytosine = 32% Guanine = 32%

What statement about the palindromic sequence is right? It is the DNA sequence that reads the same from right to left as it does left to right. It contains a twofold axis of symmetry. It is the specific sequence of four to eight base pairs. A restriction enzyme hydrolyzes hydrogen bonds in this region.

All are correct

Due to what mechanism do many genes encode more than one protein?

Alternate Splicing

The process of DNA renaturation after melting is called ________

Annealing

Write the enzymes and their function in DNA replication

DNA A: bind to 9bp repeats DNA B (Helicase): unwind DNA DNA C: Loads helicase SSB: binds to single strand DNA Gyrase: relieves supercoils Leading Strand: DNA G (Primase): Synthesizes RNA Primers Polymerase 3: Adds dNTPS continuously Lagging Strand Primosome: DNA A and DNA B unwind and prime Polymerase 3: adds dNTPS Polymerase 1: Removes ~10 bp RNA region and replaces with DNA Ligase: Seals Okazaki fragments into continuous strand Topo IV: separates catenenes

What enzyme catalyzes the step by step addition of deoxyribonucleotide units to a DNA strand on the basis of template DNA?

DNA Polymerase

In 1953, the scientists James Watson and Francis Crick published their landmark findings on the structure of DNA. Watson and Crick deduced the structure of DNA by unifying evidence that they collected from several scientists who were also seeking to answer this important question. Identify the pieces of evidence describing the features of DNA that Watson and Crick used to determine the structure of DNA.

DNA forms a right‑handed double helical structure with two polynucleotide chains coiled around a central axis. A purine base forms hydrogen bonds to pair with a pyrimidine base located on the opposite DNA strand. Specifically, A pairs with T, and C pairs with G. The sugar-phosphate backbones of each DNA helix run antiparallel to one another. The diameter of the DNA double helix is 2 nanometers, with each purine-pyrimidine base pair spanning an equivalent distance between the two chains.

What is not included in the PCR mixture

DNA ligase

The process in which two DNA molecules with a strong sequence similarity exchange segments

Homologous recombination

PCP

PCR consists of three steps that are repeated until the desired degree of amplification is achieved: 1. The duplex containing the target sequence and primers is heated briefly to 95 C, to generate a single-stranded DNA template. 2. The mixture is cooled to ~55 C to allow the primers to anneal to the DNA. 3. The mixture is heated to 72C, allowing the polymerase to synthesize the new DNA in a template-directed manner extending from each primer. The three steps are repeated 20 to 30 times.

What are Plasmids? Are plasmids always present in bacteria?

Plasmids are small circular pieces of DNA that replicate independently from the host's chromosomal DNA. Yes. Sometimes in Archaea and Eukaryotes like yeast and plants.

Introns nearly always begin with GU and end with AG that is preceded by the ________

Pyrimidine rich tract

The DNA fragment was inserted into the specific plasmid. What do plasmid and the DNA fragment have in common?

Same Sticky ends

In bacterial mRNA, the initiating AUG codon is preceded several nucleotides away by a purine rich substance called the _______, which base-pairs with a complementary sequence in a rRNA.

ShineDelgarno sequence

Choose the right temperature for each step of the PCR cycle.

Strand separation - heating to 95 C hybridization of primers - cooling to 54 C DNA synthesis - heating to 72 C

Choose the feature of DNA structure that was not deduced by Watson and Crick from the DNA diffraction patterns?

Supercoiling

What is the nucleotide sequence on the DNA template strand that yields the CUA codon for Leucine?

TAG

Why are met and trp often used to design DNA probes from amino acid sequences?

They do not degenerate and have single codons

What advantage can be gained by splicing together portions of two different genes?

This technique allows the creation of proteins with unique characteristics and activities

The temperature at which half of the DNA helical character is lost is referred to as:

Tm

Identify the correct name or abbreviation for the given nucleoside or nucleotide.

UDP

Which artificial chromosome does not have an operon?

Yeast Artificial Chromosome

The composition, in mole‑fraction units, of one of the strands of a double helical DNA molecule is [A]=0.30 and [G]=0.24. This strand is the reference strand. What is the total [T] and [C] for the reference strand? What is the total [A] and [G] for the complementary strand? What is the total [T] for the complementary strand? What is the total [C] for the complementary strand?

[T]+[C]= .46 [A]+[G]= .46 [T]= .3 [C]= .24

What are the common promoter regions found in eukaryotic genes?

a TATA box at about -25 and often a CAAT box found at about -75

Each three-base codon encodes a specific:

amino acid

A non coding region within a gene is known as:

an intron

What bonds link bases to sugars in nucleotides?

beta-glyosidic bond

Identify the correct name or abbreviation for the given nucleoside or nucleotide.

dADP

Although the right-handed double helix is the most well-known DNA structure, DNA can also form

left handed double helix

The enzyme that catalyzes the formation of a phosphodiester linkage at a break in a DNA strand

ligase

Which molecules are used as a template in translation?

mRNA

Classify the descriptions as pertaining to nucleosides, nucleotides, or both nucleosides and nucleotides.

nucleosides: do not contain phosphate group, are the product when a base bonds at Cl or ribose or deoxyribose. nucleotides: contain a base, monosaccharide, and a phosphate group. are the monomers of nucleic acids. can be named adenosine 5' -monophosphate. Both: are found in RNA and DNA. Contain a base and a monosaccharide. may contain either ribose or deoxyribose.

What component is strongly required by DBA polymerases but not needed by RNA polymerase?

primer

Identify two structural features of purines and pyrimidines.

purines: contain four ring nitrogen atoms. contain two heterocyclic rings. pyrimidines: contain one heterocyclic ring. contain only two ring nitrogen atoms.

Ribosomes are composed of

rRNA and protein

What enzyme is capable of synthesizing DNA from an RNA template?

reverse transcriptase, complementary DNA from RNA

How many chiral carbon atoms to ribose and deoxyribose contain in nucleic acids?

ribose: 4 deoxyribose: 3

What statement is correct concerning the adaptor molecule tRNA?

tRNA contains an anticodon sequence that serves as the template recognition site.

What can be used to add nucleotides to the 3' end of DNA?

terminal transferase

What group or atom of the nucleotide base is esterified to a phosphate group to bind that nucleotide to the next one?

the 3'-hydroxyl (3'-OH) group

Ti plasmids stand for:

tumor inducing

Degenerate codon

two codons coding for the same specific amino acid

Which chemical forces that contribute to the stability of the DNA due to the base stacking present in the DNA helix are:

vanderWaals