BIO SCI 98 Midterm: Midterm Study Guide

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blushmammoth506

19 Jun 2018

School

UC-Irvine

Department

Biological Sciences

Course

BIO SCI 98

Professor

RAZORENOVA/INLAY/MORRISETTE

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Lecture 1 Central Dogma

Be able to state the Central Dogma and why the exceptions mentioned in class go against it.

-DNA → RNA → protein:

-Telomerase

-Telomerase is used to make DNA from RNA in order to regenerate telomeres and keep

the genome complete. This violates the dogma because it goes RNA → DNA

-RNA Viruses

-Similar to Telomerase, RNA viruses go from RNA to DNA. They do this by using reverse

transcriptase to create DNA molecules

-Prions

-Prions induce other proteins to change their shape. This happens without interaction with

DNA or RNA, violating the dogma. An example is mad cow disease

Be able to identify the differences between DNA and RNA monomers. Understand why these

differences favor DNA as our genomic information.

Differences DNA RNA

Pentose sugar ❌-OH on 2' C ❌ -OH on 2' C

Phosphate Ester bond between 5' C and phosphate, glycosidic bond between 1'

C and base

Base Thymine (T) Uracil (U)

Be able to list the characteristics of the DNA double helix and why they contribute to DNA being our

genetic information.

-2 DNA strands

-Directionality → antiparallel strands

-Sugar phosphate backbone outside of helix

-H-bonded bases inside the helix

Lecture 2 DNA as genetic info

Be able to explain how the experiments discussed in lecture helped to confirm DNA as the

hereditary material and how they worked (not just memorizing the steps of the experiment).

-Frederick Griffith: transformation experiment

-Something in the smooth strain is capable of transforming rough strain into smooth strain

-Oswald Avery: transformation experiment

-Remove DNA/RNA/protein using DNAse,RNAse, or protease

-Treating virulent bacteria with DNAse killed bacteria → mouse lives

-Treating virulent bacteria with RNAse or protease → mouse dies bc DNA is still there

-Hershey/Chase experiment

-Only protein and DNA in bacterial capsid

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-Radioactively labeled protein coat and DNA core

-Blend bacteria and centrifuge culture of bacteria and phage

-Only phosphorus was detected in the infected bacteria → DNA is hereditary

material

-https://www.youtube.com/watch?v=BXhFDh15hhg

Be able to explain why the Watson/Crick model explains how DNA is a good fit for the hereditary information

of a cell.

Be able to define a gene in a clear, concise manner

-DNA: promoter sequence, ends at signal of polyAdenilation

-pre-mRNA contains both exons and introns

-Splicing → introns cut out to get mature RNA

-Start codon AUG and stop codon

-5' UTR and 3' UTR (untranslated region)

Be able to describe the different types of DNA found in the genome. Understand the role of repetitive DNA in

our cells and in DNA testing.

-Genome: the sequences that make up an organism

-Chromosomal, DNA/RNA, protein/RNA coding sequences

Lecture 3 Chromatin &

Chromosomes

Be able to diagram how our DNA fits inside of our nucleus including the contributions of the DNA,

histones and other protein components.

Chromosomes Chromatin

Tightly packaged DNA

Found only during cell division

DNA is not being used for macromolecule

synthesis

Unwound DNA

Found throughout interphase

DNA is being used for macromolecule synthesis

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Be able to explain the different components of the chromosome and understand how the function of

each was experimentally demonstrated.

-Chromosomes

-Histones: DNA wraps around histones to form condensed nucleosomes

-Origin of replication: replication proceeds in both direction of replication fork

-Without ORI, replication does not occur

-Centromere: segment of each eukaryotic chromosome for proteins to attach to link

chromosomal to mitotic spindle during metaphase (cell division)

-Mitotic segregation is bad without centromere

-Telomere: protective ends of chromosomes

-Without telomeres, linear plasmid is unstable

Lecture 4 DNA replication

Be able to explain the Meselson-Stahl experiment and how it confirmed that DNA

replication occurs in a semi-conserved mechanism. Be able to extend the results to

explain what would be observed during the multiple rounds of DNA replication.

-Meselson-Stahl

-Grew E coli in heavy 15 N → all nitrogenous bases of bacterial DNA

labeled with 15N

-Bacteria switched to light 14N medium

-Used centrifugation to separate DNA molecules into bands + form density

gradient

-Semi-conservative mechanism: each strand in DNA serves as template for synthesis of

new complementary strand

-If it was dispersive model . . .

-Each replicated DNA would be a patchwork of new + old DNA

-Would produce patchwork molecules with heavy and light sections

-A fuzzy band would appear higher and higher with decreasing density

- If it was conservative model . . .

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Document Summary

Be able to state the central dogma and why the exceptions mentioned in class go against it. Telomerase is used to make dna from rna in order to regenerate telomeres and keep the genome complete. This violates the dogma because it goes rna dna. Similar to telomerase, rna viruses go from rna to dna. They do this by using reverse transcriptase to create dna molecules. Prions induce other proteins to change their shape. Be able to identify the differences between dna and rna monomers. Understand why these differences favor dna as our genomic information. Ester bond between 5" c and phosphate, glycosidic bond between 1" Be able to list the characteristics of the dna double helix and why they contribute to dna being our genetic information. Be able to explain how the experiments discussed in lecture helped to confirm dna as the hereditary material and how they worked (not just memorizing the steps of the experiment).

Related Questions

In addition to identifying the genetic material, the experiments of Avery, MacLeod, and McCarty with different strains of Streptococcus pneumoniae demonstrated that

	DNA is a double helix.
	DNA may be taken up by bacterial cells and be active.
	DNA is present in bacteriophage T2.
	eukaryotic cells may be genetically transformed.
	DNA binds to the cell wall of the bacterium.

In order to show that DNA in cell extracts is responsible for genetic transformation in Streptococcus pneumoniae, important corroborating evidence should indicate that _______ also destroy transforming activity.

	temperatures high enough to kill cells
	enzymes that hydrolyze proteins
	enzymes that hydrolyze DNA
	enzymes that hydrolyze polysaccharides
	enzymes that hydrolyze RNA

Based on what you have learned about the experiments conducted by Griffith and Avery and colleagues with bacteria, which of the following would result in transformation of living R cells?

	Pure RNA from S cells
	Cell-membrane extracts from S cells
	A mixture of pure RNA and protein from S cells
	Cell-free extracts from S cells
	Pure protein from S cells

A-T base pairs in a DNA double helix

	form three hydrogen bonds with each other.
	are more heat-stable than G-C base pairs.
	are of a substantially different length than G-C base pairs.
	are not accessible to DNA binding proteins.
	are chemically distinct from G-C base pairs.

If 23 percent of the bases in a sample of double-stranded DNA are adenine, what percentage of the bases are uracil?

	27
	50
	0
	73
	23

The uniform diameter of the DNA structure provides evidence for

	antiparallel DNA strands.
	a right-handed helix.
	a double-stranded helix.
	3â² end phosphorylation.
	purineâpyrimidine pairing.

If a sequence of one strand of DNA is 5â²-TGACTATC-3â², what is the complementary strand?

	5â²-ACTGATAG-3â²
	3â²-TGACTATC-5â²
	3â²-ACTGATAG-5â²
	3â²-ACTGATAG-3â²
	5â²-TGACTATC-3â²

What structural aspect of the DNA facilitates dissociation of the two DNA strands for replication?

	3â² end phosphorylation
	Purineâpyrimidine pairing
	Antiparallel DNA strands
	Covalent bonds between sugars and phosphate groups
	Hydrogen bonding between paired bases

If the MeselsonâStahl density gradient experiment had resulted in two bands of DNA molecules after only one round of replication, one containing only ¹⁵N and the second only ¹⁴N, this result would have indicated that replication was

	unidirectional.
	dispersive.
	conservative.
	bidirectional.
	semiconservative.

10.

The nucleoside analogue acyclovir, which is used to treat herpes simplex virus (HSV) infections, lacks a 3â² hydroxyl group (âOH). Predict what will happen if the host cell DNA polymerase incorporates a molecule of acyclovir into an elongating strand of HSV DNA.

	The replication complex will no longer bind to origins of replication.
	The DNA polymerase will only incorporate acyclovir molecules.
	Acyclovir will bind single-strand binding proteins.
	DNA polymerase will not be able to link a successive nucleotide.
	Acyclovir will block the activity of the DNA helicase.

11.

Which of the following does not demonstrate the stability of the DNA double helix?

	Single-strand binding proteins are required to keep the strands apart.
	Paired bases form hydrogen bonds.
	High temperatures are required to denature it.
	DNA synthesis requires energy.
	DNA helicases require ATP.

12.

What effect would a primase inhibitor have on DNA replication?

	DNA polymerase would not be able to add bases to the DNA.
	Primase would be blocked from joining the DNA replication complex.
	Primase would not be able to provide primers for DNA polymerases.
	DNA polymerase would not be able to use DNA as a template.
	There would be no effect on DNA replication.

13.

To replicate their DNA in a timely manner, most eukaryotic chromosomes

	normally have uncoiled DNA.
	have multiple origins of replication.
	contain linear molecules of single-stranded DNA.
	have two replication forks that move in the same direction.
	are composed entirely of DNA.

14.

Which statement about DNA replication is false?

	Okazaki fragments are synthesized as parts of the leading strand.
	Error rates for DNA replication are reduced by proofreading of the DNA polymerase.
	The sliding clamp increases the rate of DNA synthesis.
	Replication forks represent areas of active DNA synthesis on the chromosomes.
	Ligases and polymerases function in the vicinity of replication forks.

15.

In many eukaryotes, there are repetitive sequences called telomeres at the ends of chromosomes. After successive rounds of DNA replication, the _______ strand becomes shorter. In some cells, an enzyme called _______ repairs the shortened strand.

	leading; telomerase
	lagging; telomerase
	lagging; DNA polymerase I
	leading; DNA polymerase I
	leading; replicase

16.

A researcher studies normal human fibroblast cells. They can be maintained in culture but die off after about 30 cell generations. Unexpectedly, a colony of cells continues to survive and divide past 30 generations. Which scenario is most likely true for these cells?

	DNA polymerase is constantly active.
	Primase is able to extend the telomeres.
	The mismatch repair system is extra efficient.
	The telomerase gene is being expressed.
	The cells do not need the ends of their chromosomes.

17.

If DNA polymerase III introduces an incorrect nucleotide, what is the first corrective action made by the DNA repair system?

	The replication complex excises the incorrect nucleotide.
	The excision repair proteins remove the incorrect nucleotide.
	The mismatch repair system scans for base-pairing mismatches.
	There is no correction, because nucleotide errors by DNA polymerases are not repaired.
	DNA ligase connects the correct nucleotide.

18.

Choose the correct order of the following four events in the excision repair of DNA:
(1) Base-paired DNA is made complementary to the template.
(2) Damaged bases are recognized.
(3) DNA ligase seals the new strand to existing DNA.
(4) Part of a single strand is excised.

	1, 2, 3, 4
	2, 1, 3, 4
	3, 4, 2, 1
	2, 4, 1, 3
	4, 2, 3, 1

19.

Six complete cycles of PCR should result in a _______-fold increase in the amount of DNA.

	64
	32
	12
	128
	6

20.

When double-stranded DNA is heated to temperatures above 90Â°C, it denatures. Denaturation is a process that

	breaks covalent bonds.
	hydrolyzes DNA.
	separates double-stranded DNA into two single strands.
	causes new hydrogen bonds to form.
	irreversibly destroys the double helical structure.

__________ are fairly small organelles that provide a safe place within the cell to carry out certain biochemical reactions that generate harmful, highly reactive oxygen species. These chemicals are both generated and broken down in the same location.

Lysosomes

Endosomes

Peroxisomes

Nucleosomes

Biologists cannot possibly study all living species. Instead, they try to understand cell behavior by studying a select subset of them. Which of the following characteristics are useful in an organism chosen for use as a model in laboratory studies?

rapid rate of reproduction

all of the above

ability to grow under controlled conditions

amenability to genetic manipulation

By definition, prokaryotic cells do not possess __________.

ribosomes.

a nucleus.

membrane bilayers.

replication machinery.

Cell biologists employ targeted fluorescent dyes or modified fluorescent proteins in both standard fluorescence microscopy and confocal microscopy to observe specific details in the cell. Even though fluorescence permits better visualization, the resolving power is essentially the same as that of a standard light microscope because the resolving power of a microscope is limited by the __________ of light.

intensity

absorption

wavelength

filtering

Choose the phrase that best completes this sentence: Microtubules ____________ and are required to pull duplicated chromosomes to opposite poles of dividing cells.

generate contractile forces

can rapidly reorganize

are found in especially large numbers in muscle cells

are intermediate in thickness

Despite the differences between eukaryotic and prokaryotic cells, prokaryotes have proteins that are distantly related to eukaryotic actin filaments and microtubules. What is likely to be the most ancient function of the cytoskeleton?

cell division

cell motility

vesicle transport

membrane support

DNA and RNA are different types of nucleic acid polymer. Which of the following is true of DNA but not true of RNA?

It contains thymine.

It has 5'-to-3' directionality.

It is single-stranded.

It contains uracil.

Double covalent bonds are both shorter and stronger than single covalent bonds, but they also limit the geometry of the molecule because they ____________________.

prevent additional bonds from being formed with the bonded atoms.

limit the rotation of the bonded atoms.

create a new arrangement of electron shells.

change the reactivity of the bonded atoms.

Drosophila melanogaster is a/an __________. This type of animal is the most abundant of all animal species, making it an appropriate choice as an experimental model.

mammal

amphibian

bird

insect

10.

If the isotope 32S has 16 protons and 16 neutrons, how many protons, neutrons, and electrons will the isotope 35S have, respectively?

16, 19, 17

16, 19, 15

16, 19, 16

16, 20, 15

11.

Living systems are incredibly diverse in size, shape, environment, and behavior. It is estimated that there are between 10 million and 100 million different species. Despite this wide variety of organisms, it remains difficult to define what it means to say something is alive. Which of the following can be described as the smallest living unit?

cell

organelle

protein

DNA

12.

Macromolecules in the cell can often interact transiently as a result of noncovalent interactions. These weak interactions also produce stable, highly specific interactions between molecules. Which of the factors below is the most significant in determining whether the interaction will be transient or stable?

the concentration of each molecule

the size of each molecule

surface complementarity between molecules

the rate of synthesis

13.

Many of the mechanisms that cells use for maintenance and reproduction were first studied at the molecular level in bacteria. Which bacterial species had a central role in advancing the field of molecular biology?

E. coli

S. pombe

C. elegans

D. melanogaster

14.

Many types of cells have stores of lipids in their cytoplasm, usually seen as fat droplets. What is the lipid most commonly found in these droplets?

cholesterol

isoprene

triacylglycerol

palmitic acid

15.

Mitochondria contain their own genome, are able to duplicate, and actually divide on a different time line from the rest of the cell. Nevertheless, mitochondria cannot function for long when isolated from the cell because they are __________________.

anaerobes.

viruses.

parasites.

endosymbionts.

16.

Mitochondria perform cellular respiration, a process that uses oxygen, generates carbon dioxide, and produces chemical energy for the cell. Which answer below indicates a correct pairing of material âburnedâ and the form of energy produced during cellular respiration?

17.

Polar covalent bonds are formed when the electrons in the bond are not shared equally between the two nuclei. Which one of these molecules contains polar bonds?

BIO SCI 98 Midterm: Midterm Study Guide

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