Module 2 Concept Questions

CH 5, 6, 7

T/F DNA is made of protein

F

What carbon atom in deoxyribose does the nitrogenous base attach to in a nucleotide?

1’ carbon

What carbon atom in deoxyribose doe the hydroxyl group attach to in a nucleotide?

3’ carbon

What carbon atom in deoxyribose does the phosphate group attach to in a nucleotide?

5’ carbon

If adenine makes up 20% of the bases in a species’ genome, what percent of the bases are guanine?

30%

How many hydrogen bonds are formed between adenine and thymine?

2

How many hydrogen bonds are formed between cytosine and guanine?

3

What does it mean to say that the two strands of the double helix are antiparallel?

the two complementary strands run in opposite directions from each other in terms of their chemical structure

Does DNA control the cell?

DNA is a library, it controls the cell in the sense that the information defines the range of structures the call can build and the activities it can perform

Bacterial/Eukaryotic chromosomes?

What is a function of the protein component of chromosomes?

packages the DNA strands

When Griffith injected heat-killed infectious bacteria mixed with live harmless bacteria, he found that the mice died because

the live harmless bacteria were transformed into infectious bacteria

the type of bond that holds together neighboring subunits in a single strand of DNA is a

phosphodiester bond

the consistent diameter of the DNA double helix arises because of which property?

base pairing of pyrimidines with purines

If one end of a DNA strand has a phosphate group on it, the chemical group on the other end must be

hydroxyl

the part of the DNA molecule that carries the information for producing proteins is

the order of the nucleotide bases

the structural feature of DNA that hints at the mechanism for its replicaiton is the

complementary base pairing

Which of the following is found only in eukaryotic genomes, and NOT in prokaryotic genomes?

telomeres

The technique whereby human chromosomes are stained and identified is called a

karyotype

What describes the chromosomal makeup of a somatic cell of a human biological male?

22 pairs of autosomes + 1 X chromosome + 1 Y chromosome

_____ is a sequence of DNA that contains the information required for making a particular functional RNA or protein

a gene

What is the relationship between genome size and organismal complexity?

more complex organisms generally have larger genomes but there are many notable exceptions

Which of the following is true about “junk DNA”?

portions of junk sequence are conserved between species and thus may be functional

Which of the following specialized DNA sequences provides an attachment point for the segregation of duplicated chromosomes?

centromeres

What is the function of the nucleolus?

to assemble ribosomal RNA and proteins into ribosomes

When are chromosomes in their most compacted form?

during mitosis

What type of bonds are formed between histone proteins and DNA to form nucleosome core particles?

electrostatic interactions

How does methylation of histone tails affect the accessibility of DNA?

it can have different effects depending on the location

In an interphase chromosome, which region is most likely to contain the highest density of genes?

the euchromatin between the telomere and centromere

Heterochromatin can spread along a chromosome until it encounters a

barrier DNA sequence

What can happen if heterochromatin spreads inappropriately into an area with active genes?

the active genes can become silenced

After replication, each new DNA double helix consists of

one old strand and one new strand

The leading strand is assembled in the ____ direction in _____ piece

5’ to 3’, continuous

The lagging strand is assembled in the ____ direction in _____ which are then joined together

5’ to 3’, many segments

What are some limitations of DNA polymerase that complicates the process of DNA replication?

-must have a template strand to guide it

-can attach new nucleotides only in the 5’ to 3’ direction

-must begin synthesis by building onto the end of an existing DNA strand or RNA primer

How does primase differ in its abilities from DNA polymerase?

-no proofreading ability

-can start making a new strand without the need for a primer or 3’ end to extend

-assembles RNA nucleotides

Why does the proofreading ability of DNA polymerase require that the enzyme work only in the 5’ to 3’ direction?

The high-energy triphosphate groups which power the linking of nucleotides are on the 5’ carbons of the incoming dNTPs. Removing the last (mismatched) nucleotide on the 3’ end of the DNA strand allows another dNTP to be added like usual

What protein unwinds and separates the DNA double helix?

helicase

What protein prevents supercoiling ahead of the replication fork?

topoisomerase

What protein holds the separated strands of DNA apart during replication?

Single-stranded binding proteins

What protein manufactures an initial 10-12 base segment of RNA?

primase

What protein is responsible for the majority of DNA replication?

DNA polymerase

What protein attaches adjacent Okazaki fragments, forming a continuous DNA strand?

ligase

What protein keeps DNA polymerase attached to the template?

sliding clamp

T/F Most illustrations depicting DNA replication are highly simplified and flattened out for clarity. Many of the proteins involved actually join together in a large multi-protein replication machine.

T

What are functions telomeres? (4)

-mark the ends of chromosomes so they’re not mistaken for double-strand breaks by repair enzymes

-may protect against cancer by limiting the number of cell divisions

-extends telomeres of germline and other stem cells, as well as cancer cells

-protect the ends of chromosomes from premature wear

How does telomerase extend telomeres?

A strand of RNA within the telomerase serves as a template to synthesize new repeats of the DNA telomere sequence

T/F Repair mechanisms make sure an organism’s genome remains unaltered, because change is always bad

F

T/F Most cases of mutation and damage can be repaired, but few always slip through

T

T/F When mutations happen, cells have very little ability to repair them

F

T/F Excision and repair enzymes can repair the majority of spontaneous and environmentally caused mutations and breakage

T

T/F DNA polymerases have proofreading ability to correct most nucleotide mismatches

T

_____ quickly rejoins double-strand breaks, but “cleaning” of the ends results in deletion of a few base pairs.

nonhomologous end-joining

_____ uses newly-made sister chromatid as a template for perfect double-strand break repair

homologous recombination

Meselson and Stahl performed a classic experiment to explore three models for the mechanism of DNA replication. Which of the models held that two parental strands would remain associated after replication?

conservative

What is the name of the DNA sequence where replication begins?

replication origin

The sequence at which DNA replication begins tends to have which characteristic?

AT-rich

In which direction, and on which strands does DNA replication proceed from a replication origin on a chromosome?

in both directions, on both strands

What are the bonds that link two DNA strands together?

Hydrogen bonds

What is the energy for the polymerization reaction in DNA synthesis powered by?

The breaking of high-energy phosphate bonds in the deoxynucleotides

How does polymerase help maintain the accuracy of DNA replication?

DNA polymerase can cut out improperly base-paired nucleotides and add the correct one during synthesis

How are the primers from the start of DNA synthesis different from the DNA itself?

The primers are made up of RNA not DNA

What enzyme fills the sequence gaps after primers are removed from a newly synthesized DNA strand?

repair polymerase

What protein that binds the two separated DNA strands to keep them from base pairing again before they can be replicated?

single-strand binding protein

What is the function of a topoisomerase in DNA replication?

It relieves the tension in DNA strands

What strand does telomerase elongate?

template of lagging strand

What are three common sources of DNA damage for cells in our bodies?

Uv light, spontaneous loss of amino groups on cytosine, replication fork problems

What type of damage is caused by an improperly paired base in the DNA?

mismatch

What is the first step that must occur to repair damage on one strand of the double helix?

the damaged region must be removed

In bacteria, how does the cell recognize which strand is the newly synthesized strand and thus contains the mismatch?

the newly synthesized strand is unmethylated

Which double-strand break repair mechanism is a simple ligation mechanism?

nonhomologous end joining

Single nucleotide changes from unrepaired DNA damage that leads to uncontrolled cell division can contribute to which condition?

cancer

What is an example of gene expression?

mouse fur color results from pigment formed by gene-encoded enzymes

_____ refers to assembly of messenger RNAs by enzymes using instructions from DNA

transcription

_____ refers to assembly of proteins by ribosomes using instructions from messenger RNAs

translation

mRNA is complementary to _____

the template strand of DNA

What role does the sigma factor play in transcription?

Sigma factor joins with other subunits of bacterial RNA polymerase and recognizes the -35 and -10 sequences in the promoter. After transcription begins, sigma factor is released so that elongation can proceed

Where does the process of eukaryotic transcription initiation begin?

promoter

Unlike DNA polymerase, RNA polymerase has no proofreading ability. Why does this not pose any major problem?

Even with genes which are expressed at low levels, many copies of its mRNA are produced. Even if a few are flawed, there will still be plenty of usable copies

How is pre-mRNA processed before leaving the nucleus? (3)

-certain segments are removed and degraded, and the remaining segments are spliced together

- a 7-methylguanosine cap is added to the 5’ end

several hundred adenine nucleotides are added to the 3’ end

What are the coding regions of eukaryotic genes which are translated?

exons

What are the noncoding regions of eukaryotic genes which are removed from their mRNAs before translation

introns

Many eukaryotic genes code for more than one protein. How is this accomplished?

alternative splicing

What is a ribozyme?

A segment of RNA which can act as a chemical catalyst

The term genetic code refers specifically to ____

the amino acids specified by each 3-nucleotide codon in messenger RNA

T/F The genetic code is nearly universal in the DNA of every living thing on Earth, from bacteria to mammals, with only a few very minor exceptions

T

Structure of tRNA molecule (5)

-its conformation is held together by complementary base pairs between its own bases

-it has a cloverleaf shape overall, with 3 stem loops

-anticodon on one end

-amino acid attached to one end

-several chemically modified bases

Complementary base-pairing between codons and anticodons serves what function?

Using genetic instructions to link amino acids in a specific sequence to build a protein