BIOL1406 LEC Exam 5: Ch. 16, 17, 19

What 2 scientists came up with the DNA model?

Francis Crick & James Watson

DNA Replication (DNA synthesis)

The process of making a copy of DNA.

DNA is the ___________________

genetic material

Transformation

a change in genotype & phenotype due to the assimilation of external DNA by a cell

Who came up with the phenomenon 'transformation'?

Frederick Griffith

Bacteriophage (also called 'phages')

(meaning 'bacteria-eaters')

A virus that infects bacteria.

Are viruses much simpler than cells?

yes

Virus

is little more than DNA (or sometimes RNA) enclosed by a protective coat, which is often simply protein.

What are Chargaff's rules?

1) DNA base composition varies between species

2) for each species, the percentages of A & T bases are roughly equal, as are those of G & C bases

What does a DNA nucleotide monomer consist of?

a nitrogenous base ( A, T, C, G), the sugar deoxyribose, & a phosphate group

Antiparallel

subunits run in opposite directions

DNA Sequences

3'-5' = 5'-3'

Adenine (A) pairs with...

Thymine (T)

Guanine (G) pairs with...

Cytosine (C)

Adenine & Guanine are...

purines

What are purines?

the nitrogen bases that are double ringed

Cytosine & Thymine are...

pyrimidines

What are pyrimidines?

single ring bases

Conservative Model

two parental strands reassociate after acting as templates for new strands, thus restoring the parental double helix

Semiconservative Model

the two strands of the parental molecule separate, and each functions as a template for synthesis of a new, complementary strand

Dispersive Model

each strand of both daughter molecules contains a mixture of old and newly synthesized DNA

Origins of Replication

Sites where the replication of a DNA molecule begins.

Replication Fork

A Y-shaped region on a replicating DNA molecule where new strands are growing.

Helicases

Enzymes that sperate the DNA strands.

Single-Strand Binding Proteins

Bind to the unpaired DNA strands, keeping them from re-pairing.

Stabilize the unwound parental strands.

Topoisomerase

Enzyme that functions in DNA replication, helping to relieve strain in the double helix ahead of the replication fork.

Primase

Synthesizes RNA primer, using the parental DNA as a template.

Helicase

Unwinds & separates the parental DNA strands at replication forks.

DNA Polymerase

Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule.

Leading Strand

The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5' to 3' direction.

Lagging Strand

A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5' to 3' direction away from the replication fork.

DNA Pol III

Using parental DNA as a template, synthesizes new DNA strand by adding nucleotides to an RNA primer or a pre-existing DNA strand.

DNA Pol I

Removes RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides

DNA Ligase

Joins Okazaki fragments of lagging strand; on leading strand, joins 3' end of DNA that replaces primer to rest of leading strand DNA.

Mismatch Repair

repair enzymes correct errors in base pairing

Nuclease

A DNA cutting enzyme that takes out damaged DNA.

Nucleotide Excision Repair (NER)

A DNA repair system in which several nucleotides in the damaged strand are removed from the DNA and the undamaged strand is used as a template to resynthesize a normal strand.

Nucleotide Excision Repair of DNA Damage (steps):

1) Teams of enzymes detect and repair damaged DNA, which distorts the DNA molecule.

2) A nuclease enzyme cuts the damaged DNA strand at 2 points, and the damaged section is removed.

3) Repair synthesis by a DNA polymerase fills in the missing nucleotides, using the undamaged strand as a template

4) DNA ligase seals the free end of the new DNA to the old DNA, making the strand complete.

Telomere

Repeating nucleotide at the ends of DNA molecules that do not form genes and help prevent the loss of genes.

T/F: Telomeres contain genes.

False.

T/F: Normal shortening of telomeres may protect organisms from cancer by limiting the number of divisions that somatic cells can undergo.

True.

Chromatin

Clusters of DNA, RNA, and proteins in the nucleus of a cell.

Histones

Any of a group of basic proteins found in chromatin.

Nucleosome

Bead-like structure in eukaryotic chromatin, composed of a short length of DNA wrapped around a core of histone proteins.

Heterochromatin

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

Euchromatin ("true chromatin")

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

What did Watson & Crick do?

Deduced that DNA is a double helix & built a structural moel.

What does Watson & Cricks model consist of?

2 antiparallel sugar-phosphate chains wind around the outside of the molecule; the nitrogenous bases project into the interior, where they hydrogen-bond in specific pairs A-T, C-G.

Do many proteins work together in DNA replication & repair?

yes.

What does a chromosome consist of?

A DNA molecule packed together w/ proteins.

In his work with pneumonia-causing bacteria and mice, Griffith found that

a. the protein coat from pathogenic cells was able to transform nonpathogenic cells

b. heat-killed pathogenic cells caused pneumonia

c. some substances from pathogenic cells was transferred to nonpathogenic cells, making them pathogenic

d. the polysaccharide coat of bacteria caused pneumonia

c. some substances from pathogenic cells was transferred to nonpathogenic cells, making them pathogenic

What is the basis for the difference in how the leading and lagging strands of DNA molecules are synthesized?

a. the origins of replication occur only at the 5' end

b. helicases and single-strand binding proteins work at the 5' end

c. DNA polymerase can join new nucleotides only to the 3' end of a pre-existing strand, and the strands at the 5' end

d. DNA ligase works only in the 3' → 5' direction

c. DNA polymerase can join new nucleotides only to the 3' end of a pre-existing strand, and the strands at the 5' end

In analyzing the number of different bases in a DNA sample, which result would be consistent with the base-pairing rules?

a. A = G

b. A + G = C + T

c. A + T = G + C

d. A = C

b. A + G = C + T

The elongation of the leading strand during DNA synthesis

a. progresses away from the replication fork

b. occurs in the 3' → 5' direction

c. produces Okazaki fragments

d. depends on the action of DNA polymerase

d. depends on the action of DNA polymerase

In a nucleosome, the DNA is wrapped around

a. histones

b. ribosomes

c. polymerase molecules

d. a thymine dimer

a. histones

E. Coli cells grown on ¹⁵N medium are transferred to ¹⁴N medium and allowed to grow for two more generations (two rounds of DNA replication). DNA extracted from these cells is centrifuged. What density distribution of DNA would you expect in this experiment?

a. one high-density and one low-density band

b. one intermediate-density band

c. one high-density and one intermediate-density band

d. one low-density and one intermediate-density band

d. one low-density and one intermediate-density band

A biochemist isolates, purifies, and combines in a test tube a variety of molecules needed for DNA replication. When she adds some DNA to the mixture, replication occurs, but each DNA molecule consists of a normal strand paired with numerous segments of DNA a few hundred nucleotides long. What has she probably left out of the mixture?

a. DNA polymerase

b. DNA ligase

c. Okazaki fragments

d. primase

b. DNA ligase

The spontaneous loss of amino groups from adenine in DNA results in hypoxanthine, an uncommon base, opposite thymine. What combination of proteins could repair such damage?

a. nuclease, DNA polymerase, DNA ligase

b. telomerase, primase, DNA polymerase

c. telomerase, helicase, single-strand binding protein

d. DNA ligase, replication fork proteins, adenylyl cyclase

a. nuclease, DNA polymerase, DNA ligase

In DNA replication, the next nucleotide is incorporated into the growing polymer at the __________ of the molecule by an enzyme called __________.

a. 3ꞌ (hydroxyl) end; DNA polymerase

b. 5ꞌ (hydroxyl) end; RNA polymerase

c. 3ꞌ (phosphate) end; RNA polymerase

d. 5ꞌ (phosphate) end; DNA polymerase

e. 3ꞌ (hydroxyl) end; topoisomerase

a. 3ꞌ (hydroxyl) end; DNA polymerase

What is the major difference between bacterial chromosomes and eukaryotic chromosomes?

Bacteria have a single circular chromosome whereas eukaryotes have several linear chromosomes.

The experiments of Meselson and Stahl showed that DNA __________.

replicates in a semiconservative fashion

Evidence to support that DNA strands run antiparallel to each other includes all of the following except __________.

a. that the sugar-phosphate backbones are to the inside of the molecule

b. Chargaff's rules

c. X-ray measurement data

d. hydrogen bonding interactions

a. that the sugar-phosphate backbones are to the inside of the molecule

Replication of the lagging strand of DNA is accomplished by repeatedly making __________ followed by 1,000-2,000 nucleotide segments called __________.

a. short RNA primers; Okazaki fragments

b. short DNA primers; Watson segments

c. long RNA primers; Okazaki segments

d. DNA ligase; Watson fragments

a. short RNA primers; Okazaki fragments

The 5ꞌ end of a DNA strand always has a free __________ group while the 3ꞌ end always has a free __________ group.

a. phosphate; amine

b. phosphate; hydroxyl

c. hydroxyl; phosphate

d. amine; phosphate

b. phosphate; hydroxyl

DNA polymerase adds nucleotides to the __________ of the leading strands, and to the __________ of the lagging strands (Okazaki fragments).

3' end; 3' end

The information in DNA is contained in __________.

a. the variation in the structure of nucleotides that make up the DNA molecule

b. the types of sugars used in making the DNA molecule

c. the sequence of amino acids that makes up the DNA molecule

d. the sequence of nucleotides along the length of the two strands of the DNA molecule

d. the sequence of nucleotides along the length of the two strands of the DNA molecule

Why were many of the early experiments on DNA carried out on viruses and bacteria?

They are simple, small, and short generation Times

The role of DNA polymerases in DNA replication is to __________.

attach free nucleotides to the new DNA strand

DNA replication begins at a site called the origin of replication, forming a bubble, which is followed by a __________, where parental strands are unwound by __________.

a. replication fork; helicases

In bacterial DNA replication of the lagging strand, __________ is required for the synthesis of a new DNA strand whereas __________ is required for removing the RNA primer and replacing it with DNA nucleotides.

DNA polymerase III; DNA polymerase I

Which of the following components is required for DNA replication?

d. RNA primer

Telomeres are __________.

a. repeating noncoding sequences at the ends of linear eukaryotic chromosomes

genetic material of a bacteriophage is __________.

dna

Which description of DNA replication is correct?

a. Helicases separate the two strands of the double helix, and DNA polymerases then construct two new strands using each of the original strands as templates.

The overall error rate in the completed DNA molecule is approximately __________.

c. 1 error per 10,000,000,000 nucleotides

A virus that infects bacteria is called a __________, which is made up of the macromolecules __________ and __________.

d. bacteriophage; DNA; protein

The unwinding of DNA at the replication fork causes twisting and strain in the DNA ahead of the fork, which is relieved by an enzyme called __________.

topoisomerase

Proteins that are involved in packaging the eukaryotic chromosome into "beads" called __________ are __________.

a. nucleosomes; histones

b. histones; nucleosomes

c. chromatids; histones

d. a helix; nucleosomes

a. nucleosomes; histones

Avery and his colleagues' 1944 experiment showed that DNA __________.

c. was the substance that transformed the bacteria in Griffith's experiment

Monomers for the synthesis of DNA are called __________.

b. nucleotides

Which of the following techniques was most helpful to Watson and Crick in developing their model for the structure of DNA?

d. X-ray crystallography

The two antiparallel strands of nucleotides that form the DNA double helix are held together by __________.

a. 5' deoxyribose and phosphate bonds

b. covalent bonds between carbon atoms in deoxyribose molecules

c. ionic bonds between guanine and cytosine

d. hydrogen bonds between nucleotide bases

d. hydrogen bonds between nucleotide bases

During the replication of DNA, __________.

d. both strands of a molecule act as templates

At each end of a DNA replication bubble is __________.

d. a replication fork

What enzyme joins Okazaki fragments?

a. DNA ligase

After the formation of a replication bubble, which of the following is the correct sequence of enzymes used for the synthesis of the lagging DNA strand?

c. helicase, primase, DNA polymerase, ligase HPDPL

Which set of enzymes is involved in nucleotide excision repair?

a. nuclease, DNA polymerase, primase

b. DNA polymerase, helicase, primase

c. ligase, nuclease, and primase

d. nuclease, DNA polymerase, and ligase

d. nuclease, DNA polymerase, and ligase

Unlike prokaryotic DNA replication, replication of eukaryotic chromosomes __________.

c. cannot be completed by DNA polymerase

Gene Expression

The process by which information encoded in DNA directs the synthesis of proteins or, in some cases, RNAs that are not translated into proteins and instead functions as RNAs.

The bridge between DNA & protein synthesis is...

the nucleic acid RNA.

What base is different in RNA?

Uracil is used instead of Thymine

T/F: Transcription → Translation

True.

Transcription

"rewritten" from DNA to RNA.

The synthesis of RNA using a DNA template.

Messenger RNA (mRNA)

A type of RNA, synthesized using a DNA template, that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein.

Translation

The synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change of "langauge" from nucleotides to amino acids.

Ribosome

A complex of rRNA and protein molecules that functions as a site of protein synthesis in the cytoplasm; consists of a large and a small subunit.

The sites of translation are:

ribosomes

Primary Transcript

An initial RNA transcript from any gene; also called pre-mRNA when transcribed from a protein-coding gene.

Triplet Code

A genetic information system in which a series of three-nucleotide-long words specifies a sequence of amino acids for a polypeptide chain.

Codon

A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code.