Exam Ii

Front 1

During DNA replication in eukaryotes, the RNA primers are removed and replaced with DNA by:

Back 1

DNA polymerase I

Front 2

In the famous Meselson-Stahl experiment (1958), after two generations:

Back 2

there were two bands on the CsCl gradient, one half-heavy and one light

Front 3

DNA replication is:

Back 3

Semi-conservative

Front 4

What is located at the Ori C in E. coli

Back 4

DnaA boxes, GATC methylation sites, an A-T rich region, Dam methylase recognition site

Front 5

verlangen, bitten, bestellen

Back 5

pedir (i)

Front 6

Bees determine sex by:

Back 6

The ploidy number of the individual (haploid vs diploid). Males are haploid and females are diploid.

Front 7

A mutant Drosophila fly resulted from the fertilization of an egg that lacked an X chromosome and a sperm that had one. The X this unusual fly inherited from its father carries an X-linked mutation that renders flies blind. This mutant fly has the following sex and phenotype:

Back 7

A blind male. The fly is blind because it inherited an X chromosome with the mutant allele and has no “good” copy of the gene to rescue its phenotype. It is male because the X:autosome ratio is 0.5.

Front 8

Diploid lily cells have a total of six chromosomes. During meiosis II in this species, how many chromosomes line up on the metaphase plate?

Back 8

Cells that undergo meiosis II are haploid. Therefore, only 3 chromosomes can line up on the plate.

Front 9

An organism has the genotype AaBbCc. Assuming that all three genes are located on different numbered chromosomes (i.e. the genes are not linked together on the same chromosome), how many different ways can the homologue pairs line up on the metaphase plate during meiosis I? (Hint: If you don’t know the answer right away, use the back of this sheet of paper to draw it out!)

Back 9

4: ABC on one side and abc on the other; AbC on one side and aBc on the other; ABc on one side and abC on the other; Abc on one side and aBC on the other.

Front 10

In most higher eukaryotes, mitosis is used:

Back 10

For growth and repair.

Front 11

Gregor Mendel performed his genetics experiments with the garden pea:

Back 11

Before chromosomes were discovered and before Morgan began to work with the fly. Mendel performed his experiments in the mid-1800s, chromosomes were discovered in the 1880s, and Morgan began to work with Drosophila in 1910.

Front 12

The DNA polymerase in E. coli cells with mutations in the gene coding for the following polypeptide falls off the template DNA much more quickly than normal.

Back 12

DnaE (the β subunit)

Front 13

The first step in isolating temperature sensitive DNA replication mutants in E. coli is to:

Back 13

Mutagenize a culture of E. coli cells (e.g. with UV light)

Front 14

Unlike prokaryotes, eukaryotes have:

Back 14

Long linear chromosomes, a cell nucleus, sister chromatids, telomerase.

Front 15

A human being with the karyotype XXY is _____ while a Drosophila fly with the same karyotype is _____.

Back 15

Male; female.

Front 16

Which of the following genotypes could explain the phenotype of a rare male tortoise shell cat?

Back 16

XXY. For X-inactivation to occur, the cat must have at least two X chromosomes. To be a male, it must have at least one Y chromosome.

Front 17

Which of the terms below best describes a human male with respect to X-linked genes?

Back 17

hemizygous

Front 18

DNA replication in both prokaryotes and eukaryotes

Back 18

is bidirectional

Front 19

In eukaryotes, the synaptonemal complex forms during

Back 19

prophase of meiosis I

Front 20

Human somatic cells die after about 30 rounds of replication unless

Back 20

the telomerase gene is activated

Front 21

At the end of meiosis I

Back 21

prophase of meiosis I

Front 22

Human somatic cells die after about 30 rounds of replication unless

Back 22

the telomerase gene is activated

Front 23

At the end of meiosis I

Back 23

there are two haploid daughter cells

Front 24

What allows helicase to bind at the forks and initiate the unwinding of the strands in both directions?

Back 24

DnaA proteins bind to the DnaA boxes, aggregate, and torque the double helix.

Front 25

When do sister chromatids segregate?

Back 25

This only occurs during anaphase of mitosis and anaphase of meiosis II.

Front 26

Each day, a fertile human male produces ________________ of sperm.

Back 26

hundreds of millions

Front 27

According to Mendel’s Law of Segregation

Back 27

Each gamete produced by a diploid organism carries only one allele for each gene.

Front 28

Gina and Stephen have identical twin girls, April and May. April has mild symptoms of X-linked muscular dystrophy, while May has no symptoms of the disease. The difference in the phenotypes of these two girls is probably best explained by:

Back 28

a difference in X-inactivation profiles

Front 29

Pseudoautosomal genes

Back 29

Are located on the X chromosome, are located on the Y chromosome, are involved in crossing over, and have an autosomal pattern of inheritanc

Front 30

Mutations in genes controlling male fertility

Back 30

typically disappear from the gene pool in a single generation

Front 31

During replication, __________ heals nicks in the DNA strands.

Back 31

Ligase

Front 32

To view the chromosomes in human white blood cells, the cells are broken open

Back 32

by placing them in a hypotonic solution

Front 33

Each human chromosome

Back 33

has one centromere

Front 34

Okazaki fragments

Back 34

are made of DNA and occur on the lagging strand

Front 35

Marcus has hemophilia, a recessive X-linked blood clotting disorder. (Normal allele = H, disease allele = h). He is also a carrier (heterozygous) for cystic fibrosis, an autosomal recessive disease caused by a mutation in the CFTR gene located on chromosome 7 (normal allele = Cf, mutant allele =cf). Which of the following sperm can Marcus produce via meiosis?

Back 35

Xh,cf and Y,Cf

Front 36

What functions can be performed by eukaryotic nuclear DNA polymerase III?

Back 36

Proof reading, adding a nucleotide to the 3' end of a growing strand of RNA

Front 37

In higher eukaryotes, meiosis is used

Back 37

To produce gametes, to create genetic variation, to half the number of chromosomes in each cell.

Front 38

Sister chromatids

Back 38

Are identical or nearly identical in sequence and segregate from one another during anaphase of meiosis II

Front 39

Homologous chromosomes

Back 39

Have a lot of sequence similarity but often carry different alleles of the same genes, and cross over during prophase I of meiosis

Front 40

After replica plating E. coli colonies that have been growing at the permissive temperature and incubating one of the replica plates at the permissive temperature and one at the non-permissive temperature, colonies that die at the non-permissive temperature but grow at the permissive temperature

Back 40

must have a temperature-sensitive conditional mutation

Front 41

Glen is homozygous for a mutation that changes a phenylalanine to a leucine in the gene coding for alpha- globin. Although alpha-globin is a very important component of hemoglobin and many persons who are homozygous for mutations in the alpha globin gene have anemia, Glen has no symptoms. Which of the following is true of Glen’s mutation?

Back 41

It is a neutral mutation and it is a missense mutation. An amino acid in the polypeptide is changed; therefore, this is a missense mutation. It is also a neutral mutation because there is no phenotype associated with the mutation.

Front 42

Bob’s dog, Spook, has one brown eye and one light blue eye. Spook’s litter mates were all normal, having brown eyes. The fact that Spook’s eyes are different colors is probably due to:

Back 42

A somatic mutation and a mutation during embryogenesis. When a dog (or other animal) has eyes of different colors, it is almost always the result of a mutation in somatic (non-germ-line) tissue during embryogenesis. One cell in the early embryo undergoes a mutation in a gene required for the production or localization of eye pigment. When the mutant cell divides, all of its daughter cells will also carry the mutation. If some, or most of these mutant daughter cells migrate to the tissue of one eye, the eye will lack pigment (i.e. be white or blue). The cells in the other eye, derived from normal cells, will be pigmented.

Front 43

Fur color in Labrador Retriever dogs

Back 43

is governed by two genes

Front 44

Telomerase is active in:

Back 44

Single celled eukaryotes, the female germ-line of animals, the male germ-line of animals, and cancerous tumors.

Front 45

Sister chromatids:

Back 45

Are identical or nearly identical in sequence, segregate from one another during anaphase of mitosis, ignore each other during prophase of meiosis, and segregate from one another during anaphase of meiosis II.

Front 46

What does NOT occur in meiosis?

Back 46

DNA replication

Front 47

What occurs in meiosis?

Back 47

Sister chromatids separate, homologues separate, cytokinesis, crossing over.

Front 48

In mammals, only males produce sperm. This is an example of a trait that is

Back 48

Sex-limited

Front 49

Susan and Mike have a son whose karyotype is XYY. The non-disjunction that caused this:

Back 49

must have occurred in meiosis II. This can only happen if disjunction occurs normally in MI (X and Y chromosomes segregate properly) and nondisjunction occurs in MII in the cell that contains the Y chromosome.

Front 50

Which of the following is the least likely to cause a deleterious phenotype?

Back 50

An inversion of a large region on the long arm of chromosome 19. Unlike the other conditions, inversions do not increase or decrease the amount of genetic material. Therefore, they often have little, if any, phenotypic consequence (except a reduction in fertility).

Front 51

Muscular dystrophy (MD) is an X-linked recessive disease that kills males before they can reproduce. Therefore, almost all children with MD are males. However, Jane is a girl who exhibits mild symptoms. The most likely reason for this is:

Back 51

Skewed x-inactivation.

Front 52

Sydney has Down Syndrome but is very high functioning. Which of the following might explain her mild phenotype?

Back 52

A duplication mutation. High functioning Down Syndrome usually results from a partial duplication of chromosome 21 or somatic mosacism.

Front 53

A human embryo with monosomy of chromosome 1

Back 53

will be miscarried 100% of the time

Front 54

The sickle cell anemia allele:

Back 54

Is a dominant mutation that protects against malaria, it is a recessive mutation that causes a severe illness, it is co-dominant to the wild-type allele at the molecular level, and it is produced when the wild-type allele undergoes a specific missense mutation. All alleles are codominant at the molecular level because both can be detected in a heterozygote. The sickle cell allele is caused by the conversion of amino acid 6 in the beta-globin polypeptide from a glutamic acid to a valine. This is the only mutation that can cause the disease. (Other mutations in the beta-globin gene cause other diseases but not sickle cell.)

Front 55

During the initiation of translation in prokaryotes, the ribosome binding site on the mRNA is recognized by

Back 55

the 16S rRNA in the small ribosomal subunit

Front 56

In the famous Meselson-Stahl experiment (1958), if DNA replication was conservative, what would the researchers have seen after one generation?

Back 56

two bands on the CsCl gradient, one heavy and one light

Front 57

Which of the following enzymes is involved in DNA replication in E. coli?

Back 57

Topoisomerase, DNA primase, DNA polymerase I, and ligase

Front 58

In E. coli, DNA replication begins at a site on the DNA called

Back 58

OriC

Front 59

Which of the following is an example of a genome mutation?

Back 59

A baby is born with three copies of chromosome 13.

Front 60

Which of the following is an example of a silent mutation?

Back 60

A tyr codon is converted to a different tyr codon.

Front 61

Jake’s black dog, Ruff, has a large tuft of white hair on his rump. This phenotype is probably due to

Back 61

a somatic mutation

Front 62

A Drosophila fly exhibits wild-type mating behavior at room temperature but fails to mate when incubated at 30 deg C or above. This fly

Back 62

is a conditional mutant. The fly is a conditional mutant. The “condition” is temperature.

Front 63

At the end of translation initiation, the tRNA that recognizes the start codon is situated at

Back 63

the P site

Front 64

Most mutations

Back 64

are deleterious. Most mutations disrupt the normal function of genes and give rise to polypeptides that are non- functional or work less well than before. Remember when I gave you the analogy of taking a hammer to a washing machine motor? It’s much more likely to damage the motor if you hack on it than to make it work better!

Front 65

Annie carries a recessive mutation in the coding region of the gene coding for insulin. Her mutation is caused by an insertion of a C/G base-pair between nucleotides 345 and 346. One of Annie’s germ-line cells undergoes a second mutation that deletes an A/T base-pair between nucleotides 349 and 340, and the egg carrying this mutation is fertilized by a sperm, giving rise to Annie’s baby, Kathy. The second mutation

Back 65

is an intragenic suppressor. The first mutation will cause a reading frame shift but the second one restores the reading frame. Therefore , this is a suppressor mutation. Since the second mutation is in the same gene as the first, it is an “intrageneic” suppressor.

Front 66

In translation, which of the following occurs immediately before translocation?

Back 66

a peptide bond is formed

Front 67

The mutation that causes Huntington Disease

Back 67

is caused by the expansion of a trinucleotide repeat

Front 68

Ter sequences are

Back 68

important in the termination of replication and located opposite the Origin of Replication on E. coli chromosomes

Front 69

Mammary cells secrete large amounts of the proteins contained in breast

Back 69

Any cell that secretes a lot of proteins will have a lot of rough ER because all proteins that are secreted from the cell have to be co-translationally translocated across the ER membrane. Rough ER is studded with ribosomes (hence “rough) that are involved in this activity.

Front 70

Estrogen

Back 70

causes point mutations in DNA. In class, we talked about the fact that estrogen-like compounds can “feminize” male amphibians. However, since estrogen also induces cells to replicate, and replication can give rise to point mutations, I accepted either d or e. DNA replication does not promote frame-shift mutations; these are usually induced, not spontaneous.

Front 71

Proflavin

Back 71

promotes frame-shift mutations

Front 72

Nitrous acid

Back 72

is a base modifier

Front 73

5-bromouracil

Back 73

is a base analog

Front 74

Peptidyl transferase

Back 74

Is important during translation, joins two amino acids together, is a ribozyme, and is a protein

Front 75

DNA replication

Back 75

is mutagenic

Front 76

DNA primase is

Back 76

a type of RNA polymerase

Front 77

Which is true of eukaryotic nuclear chromosomes but NOT of prokaryotic chromosomes?

Back 77

They become shorter each replication cycle unless telomerase is active, they have centromeres, and they contain multiple origins of replication

Front 78

Which of the following is true of ionizing radiation?

Back 78

It penetrates deeply into the body, it has a shorter wavelength than non-ionizing radiation, it creates chemically reactive free radicals, and it cam cause breaks in chromosomes

Front 79

Which of the following functions can be performed by eukaryotic nuclear DNA polymerase?

Back 79

Proof reading and adding a nucleotide to the 3' end of a growing strand of RNA

Front 80

During translation

Back 80

termination involves release factors, and an mRNA can be read by many ribosomes simultaneously. Even though the 16S rRNA:mRNA interaction does not occur in eukaryotes, RNA:RNA base-pairing is extremely important. The antiocodon on the tRNAs must recognize and base-pair with the codons on the mRNAs, and tRNAs and rRNAs must fold into complex secondary structures that involve RNA:RNA pairing.

Front 81

Spontaneous mutations

Back 81

can be transmitted to offspring, are usually corrected prior to the next round of DNA replication, and occur in both prokaryotes and eukaryotes

Front 82

During DNA replication, lagging strands

Back 82

contain Okazaki fragments, and are synthesized in the direction opposite to that in which helicase is moving

Front 83

Recombination happens

Back 83

at prophase of meiosis I

Front 84

Homologues have

Back 84

different alleles

Front 85

Switching alleles =

Back 85

recombinants. 1/2 of the time it is random.

Front 86

What is the “adaptor hypothesis” and who first proposed it?

Back 86

The adaptor hypothesis was proposed by Francis Crick and Mahon Hoagland. The hypothesis proposed that tRNA has two functions:

1) Recognizing and base pairing to a 3-base codon in mRNA

2) Carrying and amino acid that is specific for that codon

Front 87

Where on a tRNA molecule does amino acyl-tRNA synthetase add on an amino acid? Is this area of the tRNA conserved across all tRNAs? Explain.

Back 87

Acyl-tRNA synthease adds on to the 3’ end of and amino acid by an ester bond. This “charges” the tRNA.

Front 88

What is a “charged” tRNA?

Back 88

A charged tRNA is formed when and amino acid and an ATP bind to an aminoacyl-tRNA synthetase enzyme. AMP is covalently bound to the amino acid and a pyrophosphate is released. Next, the correct tRNA binds to the enzyme and becomes covalently attached, releasing an AMP. Finally an amino acid is attached to the 3’ end by an ester bond which charges the tRNA.

Front 89

Know the mechanism by which amino-acyl tRNA synthetases add amino acids onto tRNAs. What are the three binding sites on the enzyme? What binds to each site and in what order?

Back 89

Aminoacyl tRNA synthetases charge tRNAs in two steps. In the first step, called adenylylation, the amino acid reacts with ATP in a way that adds an AMP molecule (through its phosphate group) to the carbonyl group of the amino acid. This reaction also releases pyrophosphate, which is then hydrolyzed to help drive the overall reaction forward. In the second step, called tRNA charging, the adenylylated amino acid reacts with tRNA, transferring the amino acid to the 3' end of the tRNA (to either the 2' or 3' hydroxyl group), and releasing AMP in the process.

Front 90

What are Aminoacyl-tRNA syntheases?

Back 90

Aminoacyl-tRNA synthetases are enzymes that attach amino acids to tRNAs .There are 20 types, one for each amino acid. These catalyze a two-step reaction involving three different molecules: Amino acid, tRNA and ATP.

Front 91

What are the three functional sites of a ribosome?

Back 91

o Peptidyl site (P site)
o Aminoacyl site (A site)
o Exit site (E site)

Front 92

The translation of the nucleotide sequences in mRNAs into amino acid sequences leads to:

Back 92

the synthesis of polypeptides and, ultimately, to functional proteins

Front 93

Structural genes encode polypeptides and are (blank) into (blank)

Back 93

transcribed into messenger RNA (mRNA)

Front 94

UNDERSTAND THE MESELSON/STAHL EXPERIMENT (1958).! Did their findings support the conservative, semi-conservative, or dispersive model of DNA replication?

Back 94

In 1958, Matthew Meselson and Franklin Stahl devised a method to investigate these models. They found a way to experimentally distinguish between daughter and parental strands.

Their experiment can be summarized as such:

1) Grow E. coli in the presence of 15N (a heavy isotope of Nitrogen) for many generations
• The population of cells had heavy-labeled DNA

2) Switch E. coli to medium containing only 14N (a light isotope of Nitrogen)

3) Collect sample of cells after various times

4) Analyze the density of the DNA by centrifugation using a CsCl gradient

Front 95

DNA replication is “bidirectional.” What does this mean?

Back 95

DNA synthesis begins at a site termed the origin of replication (each bacterial chromosome has only one)

Synthesis of DNA proceeds bidirectionally around the bacterial chromosome

The replication forks eventually meet at the opposite side of the bacterial chromosome and this ends replication

Front 96

What is a replication fork?

Back 96

The replication fork is a structure that forms within the nucleus during DNA replication. It is created by helicases, which break the hydrogen bonds holding the two DNA strands together. The resulting structure has two branching "prongs", each one made up of a single strand of DNA. These two strands serve as the template for the leading and lagging strands which will be created as DNA polymerase matches complementary nucleotides to the templates. The templates may be properly referred to as the leading strand template and the lagging strand template.

Front 97

Which of the following is true of ORI C in E. coli?

Back 97

ORI C contains an A-T rich sequence

Front 98

What is a DnaA box? Is this a DnaA box a DNA sequence or a protein?

Back 98

DnaA box is the replication initiation factor which promotes the unwinding or denaturation of DNA at oriC during DNA replicaion in prokaryotes. The DnaA box is a sequence that binds to the DnaA proteins.

Front 99

How many base-pairs (approximately) are included in ORI C:

Back 99

250

Front 100

When DnaA proteins bind to the DnaA boxes at ORI C, what happens? How does this help with the initiation of replication?

Back 100

DnaA proteins bind to the DnaA box sequences, which stimulate the cooperative binding of an additional 20 to 40 DnaA proteins to form a large complex.

Front 101

What is the role of the following in DNA replication in E. coli?

DNA helicase

Back 101

DNA helicase: separates the two DNA strands by breaking the hydrogen bonds between them. This generates positive supercoiling ahead of each replication fork.

Front 102

What is the role of the following in DNA replication in E. coli?

DNA gyrase

Back 102

DNA gyrase (topoisomerase): travels ahead of the helicase and alleviates the supercoiling

Front 103

What is the role of the following in DNA replication in E. coli?

DNA pol I

Back 103

DNA pol I: removes RNA primers and replaces them with DNA

Front 104

What is the role of the following in DNA replication in E. coli?

DNA pol III

Back 104

DNA pol III: synthesizes DNA in the leading and lagging strands

Front 105

What is the role of the following in DNA replication in E. coli?

Ligase

Back 105

Ligase: catalyzes a phosphodiester bond to connect the DNA fragments; seals the strand

Front 106

What is the role of the following in DNA replication in E. coli?

DNA primase

Back 106

DNA primase: synthesize RNA primers, which prime DNA synthesis

Front 107

What is the role of the following in DNA replication in E. coli?

Single-stranded DNA binding proteins

Back 107

Single-stranded DNA binding proteins: keep the parental strands apart

Front 108

What is an Okazaki fragment? Are these made of RNA or DNA?

Back 108

DNA pol III uses the RNA primers to synthesize small DNA fragments (1000 to 2000 nucleotides each).

Front 109

What limitation of DNA polymerase makes DNA primase necessary?

Back 109

DNA polymerase catalyze the attachments to make new DNA, while primase synthesizes the primers which prime DNA synthesis.

Front 110

KNOW WHY DNA REPLICATION INCLUDES LEADING AND LAGGING STRANDS. UNDERSTAND WHAT THESE ARE AND HOW THEY ARE MADE.

Back 110

The two new daughter strands are synthesized in different ways

Leading strand: One RNA primer is made at the origin then DNA pol III attaches nucleotides in a 5’ to 3’ direction as it slides toward the opening of the replication fork

Lagging strand: Synthesis is also in the 5’ to 3’ direction. However it occurs away from the replication fork. Many RNA primers are required. DNA pol III uses the RNA primers to synthesize small DNA fragments (1000 to 2000 nucleotides each). These are termed Okazaki fragments after their discoverers.

Front 111

Where does the energy come from to add a new nucleotide to a growing DNA strand?

Back 111

DNA pol I removes the RNA primers and fills the resulting gap with DNA. It uses its 5’ to 3’ exonuclease activity to digest the RNA and its 5’ to 3’ polymerase activity to replace it with DNA.

Front 112

In E. coli, what are “Ter” sequences? What is “Tus?”

Back 112

For the termination of replication, opposite to oriC is a pair of termination sequences called ter sequences, which are designated T1 and T2. The protein tus (termination utilization substance) binds to these sequences to stop the movement of the replication forks.

Front 113

What are the three mechanisms that ensure that DNA replication has a high level of fidelity in E. coli?

Back 113

1. Instability of mismatched pairs

2. Configuration of the DNA polymerase active site

3.Proofreading function of DNA polymerase

Front 114

Most DNA polymerases have a “proofreading” function. What does this mean? How does it work?

Back 114

The proofreading function of DNA polymerase:

o If it makes an error and adds on the wrong nucleotide (i.e. covalently links it to the rest of the growing daughter strand) DNA polymerases can identify the mismatched nucleotide and remove it from the daughter strand

o The enzyme uses its 3’ to 5’ exonuclease activity to remove the incorrect nucleotide

o It then changes direction and resumes DNA synthesis in the 5’ to 3’ direction

Front 115

For what three reasons is DNA replication more complex in eukaryotes than in prokaryotes?

Back 115

Eukaryotes have large linear chromosomes, tight packaging within nuclesomes, and more complicated cycle recognition.

Front 116

Why do the ends of linear eukaryotic chromosomes get shorter in somatic cells after each replication cycle?

Back 116

DNA polymerases synthesize DNA only in the 5’ to 3’ direction and cannot initiate DNA synthesis. These two features mean the linear chromosome becomes progressively shorter with each round of DNA replication.

Front 117

Why don’t we pass on shorter and shorter chromosomes to our children?

Back 117

Telomerase contains protein and RNA. The RNA is complementary to the DNA sequence found in the telomeric repeat, which allows the telomerase to bind to the 3’ overhang. This is only true in the case of germ-line tissue, otherwise it can cause cancer in somatic tissues.

Front 118

What is the relationship between telomerase and cancer?

Back 118

If it is activated in somatic tissues it can immortalize cells and cause cancer.

Front 119

How many chromosomes are in a human sperm cell? How many are in a human cheek cell?

Back 119

Sperm cell: 23, cheek cell: 46

Front 120

KNOW THE DIFFERENCE BETWEEN HOMOLOGOUS CHROMOSOMES AND SISTER CHROMATIDS. Which are more alike in DNA sequence and why?

Back 120

Members of a pair of chromosomes are called homologues and the two homologues form a homologous pair. The two chromosomes of a homologous pair are nearly identical in size, have the same banding pattern and centromere location and have the same genes. The DNA sequences are also very similar.

Sister chromatids are a pair of replicated chromosomes. These are more alike because they are identical.

Front 121

What is a “gene locus?”

Back 121

The physical location of a gene on a chromosome is called its locus.

Front 122

Does E. coli reproduce by sexual or asexual means? Explain.

Back 122

E. coli reproduces asexually via cell division and also via conjugation to transfer genetic information.

Front 123

What types of eukaryotic organisms reproduce asexually? Can these organisms also reproduce sexually? If so, under what conditions?

Back 123

A second purpose for asexual reproduction is to produce multi-celled organisms and to enable these organisms to grow and repair damaged tissue. Plants, animals and certain fungi are derived from a single cell that has undergone repeated asexual cell divisions. These organisms reproduce sexually to produce offspring.

Front 124

For what purposes does a multicellular organism undergo asexual reproduction (mitosis)?

Back 124

To grow and to repair tissue.

Front 125

Are eukaryotic chromosomes in the unreplicated or replicated state during the following stages of the cell cycle: G2, G1, Mitosis, Interphase

Back 125

a. G2: replicated
b. G1: unreplicated
c. Mitosis: replicated
d. Interphase: they are in the replicated state at the end of the phase (G2)

Front 126

What do eukaryotic cells do at the end of G1 if their DNA is damaged? Why have they evolved to do this? What are they “protecting”?”

Back 126

The cell cycle will arrest (apoptosis) to prevent replication of damaged DNA and the incorporation of damaged DNA.

Front 127

What is a centromere? What is a kinetocore?

Back 127

A centromere is a region of DNA typically found near the middle of a chromosome where two sister chromatids come in contact. It is involved inc ell division as the point of mitotic spindle attachment. A kinetocore is the protein structure on the chromosomes where the spindle fibers attach during cell division to pull the chromosomes apart. It assembles in the centromere and links the chromosome microtubule polymers from the mitotic spindle during mitosis and meiosis.

Front 128

Does sexual reproduction create new mutations? Explain.

Back 128

Sexual reproduction can create new mutations through nondisjunction.

Front 129

Why are chromosomes only visible under the light microscope during mitosis and meiosis (i.e. not during interphase)?

Back 129

The sister chromatids have not yet condensed into tightly packed chromosomes.

Front 130

What is the difference between a gene mutation, a genome mutation, and a chromosomal mutation? Be able to give an example of a human disease or syndrome caused by each.

Back 130

Chromosome mutations: Changes in chromosome structure. Ex: Cri-du-chat
Genome mutations: Changes in chromosome number. Ex: trisomy 21
Gene mutations: Relatively small changes in DNA structure that occur within a particular gene. Ex: sickle cell anemia

Front 131

What is a point mutation? What is the difference between a point mutation that is a transition and one that is a transversion? Which is more common?

Back 131

A point mutation is a change in a single base pair n It involves a base substitution.

A transition is a change of a pyrimidine (C, T) to another pyrimidine or a purine (A, G) to another purine.

A transversion is a change of a pyrimidine to a purine or vice versa. Transitions are more common than transversions

Front 132

What is the difference between a silent mutation and a missense mutation? Which one can result in a non-functional polypeptide?

Back 132

Silent mutations are those base substitutions that do not alter the amino acid sequence of the polypeptide. This is due to the Due to the degeneracy of the genetic code. Missense mutations are those base substitutions in which an amino acid change does occur. Missense can result in a non-functional polypeptide.

Front 133

What is a neutral mutation? How does it differ from a silent mutation?

Back 133

In a neutral mutation the substituted amino acid does not affect protein function (as measured by phenotype). An amino acid change occurs in this case, but not does not occur in the case of neutral mutations, because of the degeneracy of the genetic code.

Front 134

What is a nonsense mutation? Does it usually result in a short, normal-length, or longer polypeptide than the non-mutant form of the polypeptide? Explain.

Back 134

Nonsense mutations are those base substitutions that change a normal codon to a termination codon.

Front 135

What is a frame shift mutation? What causes a frameshift mutation? Do all deletions and insertions result in a frame shift mutation? Explain.

Back 135

Frameshift mutations involve the addition or deletion of nucleotides in multiples of one or two. This shifts the reading frame so that a completely different amino acid sequence occurs downstream from the mutation.

Front 136

Which of the following mutations is most likely to destroy the function of the polypeptide encoded by the gene? Explain.

Back 136

a. A nonsense mutation in nucleotide 82,788 of a coding region of a gene containing 82,800 nucleotides.

b. An insertion of a single base-pair in exon 1 of a gene containing 4 exons.

c. A silent mutation in codon 2 of gene containing 568 codons.

Front 137

What is the difference between a forward mutation and a reverse mutation? Which is more common? Why?

Back 137

In a natural population, the wild-type is the most common genotype (may be encoded by a dominant or recessive allele). A forward mutation changes the wild-type genotype into some new variation. If it is beneficial, it may move evolution forward, otherwise, it will be probably eliminated from a population. A reverse mutation has the opposite effect. It is also termed a reversion. Forward mutations are more common because it is easier to cause errors rather than fix them.

Front 138

Why do Siamese cats have dark fur on their ears, nose, tail, and paws but white fur everywhere else?

Back 138

Some mutations are called conditional mutants, such as the temperature dependent mutation in Siamese cats. The pointed pattern results from a mutation in tyrosinase, an enzyme involved in melanin production. The mutated enzyme is heat sensitive and fails to work at normal body temperatures, but becomes active in cooler areas of the skin, like the paws.

Front 139

Know the difference between an intragenic supressor mutation and an intergenic supressor mutation. Are supressor mutations forward or reverse mutations?

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Suppressor mutations are classified into two types. In intragenic suppressors the second mutant site is within the same gene as the first mutation. In intergenic suppressors, the second mutant site is in a different gene from the first mutation. These are reverse mutations.

Front 140

The Luria-Delbruck fluctuation test lent support to the hypothesis that

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pre-existing, random genetic variation is the basis for evolutionary adaptation. If a bacterial culture is exposed to penicillin, the bacteria do not respond to the penicillin by mutating. Rather, due to random mutations, some of the bacteria in the culture were already resistant to penicillin prior to exposure. These resistant cells survive in the presence of penicillin once the culture is exposed to it and their resistance genes will pass on to the next generation of cells. This is how organisms evolve to adapt to their environments.

Front 141

During translation initiation, the first tRNA enters the ribosome in the

Back 141

P site

Front 142

What can be caused by a spontaneous mutation?

Back 142

a. depurination
b. deamination
c. transversion
d. transition

Front 143

What can induce mutations in DNA?

Back 143

a. base modifiers
b. ethidium bromide
c. base analogues
d. ionizing radiation

Front 144

Most new germ-line missense mutations

Back 144

Occur during spermatogenesis. Missense mutations are usually caused by the change of a single nucleotide base-pair. Most mutations of this type are caused by errors during DNA replication. Thus, any tissue that undergoes a lot of replication is prone to accumulating missense mutations. In the germ-line, testicular cells replicate throughout the lifetime of a male and are therefore much more susceptible to accumulating missense mutations than ovarian cells.

Front 145

The 5’ end of the coding region of an mRNA codes for the ___________ end of a polypeptide.

Back 145

amino

Front 146

All proteins in a eukaryotic cell

Back 146

All proteins are encoded by genes (one or more of them). However, only proteins with more than one polypeptide have quaternary structure, only a subset are negatively charged, and only a fraction need to be localized through the ER. Moreover, the mRNAs of genes encoded by the mitochondria and chloroplasts are translated inside those organelles (by bacteria-like ribosomes), not in the cytoplasm.

Front 147

An E. coli gene undergoes a mutation that inserts a base-pair into the coding region. A few generations later, one of the descendents of the original mutant cell undergoes a second mutation, three base-pairs down from the original mutation, which deletes one base-pair. The second mutation is called

Back 147

An intragenic supressor mutation

Front 148

Fragile X Syndrome is caused by

Back 148

a trinucleotide repeat expansion mutation

Front 149

A "charged" tRNA

Back 149

Carries and amino acid on its 3' end, is much shorter than a typical mRNA, has double-stranded regions and single-stranded regions.

Front 150

The  white  eye  phenotype  in  fruit  flies  can  be  caused  by  

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a  missing  transmembrane    protein

Front 151

What is the Shine-delgarno sequence? In what section of the mRNA is it located? Where is it located relative to the start codon?

Back 151

The binding of mRNA to the 30S subunit is facilitated by a ribosomal-binding site or Shine-Delgarno sequence. This is complementary to a sequence in the 16S rRNA. IF3 is before it, and then the start codon. IF3 promotes the bindinf of mRNA to the 30S subunit.

Front 152

What role does 16S rRNA play in translation initiation in prokaryotes?

Back 152

It is a component of 30S.

Front 153

In eukaryotic translation initiation, what is “scanning?” What entity does the scanning and what is it scanning for?

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Translation initiation proceeds as follows: A number of initiation factors bind to the 5’ cap in mRNA. These are joined by a complex consisting of the 40S subunit, tRNAmet, and other initiation factors. The entire assembly moves along the mRNA scanning for the right start codon. Once it finds this AUG, the 40S subunit binds to it n The 60S subunit joins and forms the 80S initiation complex.

Front 154

What enzyme catalyzes peptide bonds during translation? Why is the ribosome also called a ribozyme?

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The 23S rRNA (a component of the large subunit) is the actual peptidyl transferase. Thus, the ribosome is a ribozyme.

Front 155

Peptidyl transferase catalyzes bond formation between a growing polypeptide chain and an amino acid being held by a tRNA in the (blank) site of the ribosome.

Back 155

A

Front 156

15. During translocation (which follows bond formation), where does the tRNA in the P site go? Where does the tRNA in the A site go?

Back 156

The tRNA from the P site goes to the E site, and the tRNA from the A site goes to the P site.

Front 157

What is a release factor and what role do release factors play in the termination of translation?

Back 157

Release factors recognize stop codons which terminates translation. Bacteria have RF1-3, and eukaryotes have eRF which recognizes all three stop codons.

Front 158

Can mutations in introns result in non-functional polypeptides? Explain.

Back 158

Yes, if the introns were not removed it would be translated into a nonfunctional polypeptide.

Front 159

What is the difference between a somatic cell and a germ-line cell?

Back 159

Germ-line cells are cells that give rise to gametes such as eggs and sperm, while somatic cells are all other cells.

Front 160

Why do X-ray technicians cover your lower abdomen with a lead sheet when they take X-rays? Why don’t they cover your entire body with lead?

Back 160

To protect from germline cell mutations.

Front 161

Are germ-line mutations caused by errors in mitosis or meiosis? (Which one?) How about somatic mutations?

Back 161

Germ-line mutations are caused by errors in meiosis, while somatic mutations are caused by errors in mitosis.

Front 162

Why do some cats (or dogs, humans, etc.) have eyes that are two different colors?

Back 162

When a dog (or other animal) has eyes of different colors, it is almost always the result of a mutation in somatic (non-­‐germ-­‐line) tissue during embryogenesis. One cell in the early embryo undergoes a mutation in a gene required for the production or localization of eye pigment. When the mutant cell divides, all of its daughter cells will also carry the mutation. If some, or most of these mutant daughter cells migrate to the tissue of one eye, the eye will lack pigment (i.e. be white or blue). The cells in the other eye, derived from normal cells, will be pigmented.

Front 163

April has black hair with a shock of white hair in the middle. Could this be caused by somatic mosaicism?

Back 163

Yes.

Front 164

The N terminal amino acid on all new polypeptides is

Back 164

AUG

Front 165

The N terminus of a polypeptide corresponds to the (blank) end of an mRNA

Back 165

5'

Front 166

After bond formation, is the tRNA in the P site charged or uncharged?

Back 166

Uncharged.

Front 167

During translation initiation, where does the first charged tRNA enter the ribosome? Where do all subsequent charged tRNAs enter the ribosome?

Back 167

The charged tRNA binds to the A site. The subsequent charged tRNAs enter the ribosome through the P site.

Front 168

Translation always begins in the cytoplasm but may not end there. Explain.

Back 168

Co-translational sorting means translation proceeds as it is moved to its appropriate location.

Front 169

What is “Rough ER?” Would you expect a cell that secretes a lot of proteins to have a lot or Rough ER or very little Rough ER?

Back 169

Rough ER synthesizes proteins, so a cell that secretes a lot of proteins will have a lot of rough ER.

Front 170

Once a eukaryotic protein has been translated, how does the cell know where it belongs (e.g. nucleus, mitochondrion, ER, secreted outside the cell, etc.)?

Back 170

Sorting signals direct a protein to its correct location.

Front 171

What signal is needed to target a protein outside the cell? (This is the only signaling system I want you to memorize for the test.)

Back 171

Sorting signal/ traffic signal.

Front 172

UNDERSTAND THE LURIA/DELBRUCK “FLUCTUATION TEST” EXPERIMENT AND WHY IT SUPPORTS THE RANDOM MUTATION THEORY.

Back 172

Salvadore Luria and Max Delbruck studied the resistance of E. coli to bacteriophage T1; tonr (T one resistance). They wondered if tonr is due to spontaneous mutations or to a physiological adaptation that occurs at a low rate? The physiological adaptation theory predicts that the number of tonr bacteria is essentially constant in different bacterial populations after exposure, while the spontaneous mutation theory predicts that the number of tonr bacteria will fluctuate in different bacterial populations. Their test therefore became known as the fluctuation test. If T1 induced mutations happened after plating, there would be an even distribution, whereas is the mutation occurred randomly prior to plating there would be great fluctuation in colonies, which there was.

Front 173

UNDERSTAND THE LEDERBERGS’ REPLICA PLATING EXPERIMENT AND WHY IT SUPPORTS THE RANDOM MUTATION THEORY.

Back 173

The Lederbergs developed a technique to distinguish between the two theories. They pressed a velvet cloth against a colony and then pressed it on a petri plate with T1 phage. The colonies grew in exactly the same spot, so the mutation happened before and was spontaneous rather than induced.

Front 174

Rhonda is a genetics student and has just learned that the sun emits X-rays, gamma rays, U.V. light, and other radiation that can cause DNA in her cells to mutate. Horrified at the thought, she decides to wear a lead-lined suit day and night, which will block out all these forms of radiation. Rhonda gets a sweet contract for a “reality show” and is now making millions, but is the DNA in her cells completely safe from mutagenesis? Explain.

Back 174

No, mutagenesis can occur randomly. Many mutations occur as the results of mistakes made by DNA polymerase during DNA replication

Front 175

What causes cancer? Why does the rate of cancer increase exponentially with age?

Back 175

Cancers develop when one mutation promotes DNA replication and cell division. This promotes additional mutations. Some of the new mutations further promote DNA replication and cell division (or mutate genes that down-regulated replication and cell division). This process continues to produce a malignant tumor.

Front 176

Cancers develop due to somatic mutations. What types of genes are mutated or inappropriately expressed in cancer cells? (I.e. What types of proteins do these genes encode?)

Back 176

The mutation inactivates the tumor suppressor gene -> cells proliferate -> mutation inactivates DNA repair gene -.> etc.

Front 177

Achondroplasia Dwarfism is an autosomal dominant disease caused by a missense mutation in the FGFR3 gene on human chromosome 4. Pablo has the disease but neither of his parents are affected; therefore, the egg or sperm that created Pablo must have carried a new mutation. Do you think it was the egg or the sperm that carried the new mutation? Why?

Back 177

Diseases caused by new point mutations usually come from the father. Testicular tissues undergoes many more rounds of DNA replication than ovarian tissue prior to meiosis.

Front 178

During meiosis, recombinant gametes are produced by two very different mechanisms. What are they and when during meiosis does each occur?

Back 178

Independent assortment: three pairs of homologous chromosomes -> independent assortment of maternal and paternal homologs during meiotic division I, producing recombinant gametes at meiotic division II
Crossing over: exchange of genetic material between one pair of homologous chromosomes during prophase I of meiosis.