Question 1

The argument that mitochondria and chloroplasts originally were self-sufficient bacteria is supported by the presence of what protein-DNA structure?

Accepted Answer

A) nucleoids 
B) chromatin 
C) importins 
D) chromatids 
E) nucleosomes 
A) nucleoids 
B) chromatin 
C) importins 
D) chromatids 
E) nucleosomes A

Question 2

Show the product of the following restriction digest. PstI has a restriction site of CTGCA$\downarrow$G. P- indicate the 5' phosphate, -OH indicates the 3' hydroxyl.
P-T C A C T G C A G C C T-OH
HO-A G T G A C G T C G G A-P
+ PstI $\rarr$

Accepted Answer

P-T C A C T G C A-OH P-G C C T-OH
HO-A G T G-P HO-A C G T C G G A-P

Question 3

For a restriction enzyme with a 6-base recognition site, what is the average number of base pairs between occurrences of the site?

Accepted Answer

A) 1296 base pairs 
B) 4096 base pairs 
C) 46656 base pairs 
D) 16777216 base pairs 
E) none of the above 
A) 1296 base pairs 
B) 4096 base pairs 
C) 46656 base pairs 
D) 16777216 base pairs 
E) none of the above B

Question 4

What proteins, responsible for specific protein kinase activation, are major control elements in the cell cycle?

Accepted Answer

A) Rb proteins 
B) cyclins 
C) p53 
D) cohesins 
E) nonhistone chromosomal proteins 
A) Rb proteins 
B) cyclins 
C) p53 
D) cohesins 
E) nonhistone chromosomal proteins

Question 5

BamHI has a restriction site of G$\downarrow$GATCC while HpaI has a restriction site of GTT$\downarrow$ACC. Based upon this, BamHI produces __________ and HpaI produces __________.

Accepted Answer

A) a 5'overhang; a 3'overhang 
B) a 5' overhang; a 5' overhang 
C) a 5'overhang; blunt ends 
D) a 3'overhang; a 5' overhang 
E) a 3'overhang; blunt ends 
A) a 5'overhang; a 3'overhang 
B) a 5' overhang; a 5' overhang 
C) a 5'overhang; blunt ends 
D) a 3'overhang; a 5' overhang 
E) a 3'overhang; blunt ends

Question 6

Which of the following represents the correct order of steps usually taken in a Southern analysis?

Accepted Answer

A) electrophoresis $\rarr$ restriction digest $\rarr$ nitrocellulose transfer $\rarr$ hybridization 
B) electrophoresis $\rarr$ hybridization $\rarr$ restriction digest $\rarr$ nitrocellulose transfer 
C) hybridization $\rarr$ restriction digest $\rarr$ electrophoresis $\rarr$ nitrocellulose transfer 
D) restriction digest $\rarr$electrophoresis $\rarr$ hybridization $\rarr$ nitrocellulose transfer 
E) restriction digest $\rarr$electrophoresis $\rarr$ nitrocellulose transfer $\rarr$hybridization 
A) electrophoresis $\rarr$ restriction digest $\rarr$ nitrocellulose transfer $\rarr$ hybridization 
B) electrophoresis $\rarr$ hybridization $\rarr$ restriction digest $\rarr$ nitrocellulose transfer 
C) hybridization $\rarr$ restriction digest $\rarr$ electrophoresis $\rarr$ nitrocellulose transfer 
D) restriction digest $\rarr$electrophoresis $\rarr$ hybridization $\rarr$ nitrocellulose transfer 
E) restriction digest $\rarr$electrophoresis $\rarr$ nitrocellulose transfer $\rarr$hybridization

Question 7

What does a yeast artificial chromosome (YAC)allow one to do?

Accepted Answer

A) selective analysis of yeast replication and transcription 
B) incorporation of eukaryotic genes into prokaryotic cells 
C) sequence analysis of DNA fragments up to 106 base pairs in size 
D) analysis of chromosomal-sized DNA in the absence of centromeres and telomeres 
E) all of the above 
A) selective analysis of yeast replication and transcription 
B) incorporation of eukaryotic genes into prokaryotic cells 
C) sequence analysis of DNA fragments up to 106 base pairs in size 
D) analysis of chromosomal-sized DNA in the absence of centromeres and telomeres 
E) all of the above

Question 8

The alteration in chromatin structure that occurs within the centromere is brought about by the replacement of which histone protein?

Accepted Answer

A) H1 
B) H2A 
C) H2B 
D) H3 
E) H4 
A) H1 
B) H2A 
C) H2B 
D) H3 
E) H4

Question 9

A typical size for a viral genome is ______ nucleotides per haploid genome while a typical size for a bacterial genome is ______ nucleotides per haploid genome.

Accepted Answer

A) 2*106; 4*108 
B) 8*104; 5*107 
C) 1*103; 9*104 
D) 5*104; 4*106 
E) 3*104; 5*109 
A) 2*106; 4*108 
B) 8*104; 5*107 
C) 1*103; 9*104 
D) 5*104; 4*106 
E) 3*104; 5*109

Question 10

Where in the following DNA sequence is the start of a 6-base type II restriction site? Every fifth nucleotide is indicated with a bold letter using the top strand for numbering. 5' A C T T C A G A A T T C C T T A C G A A G T T A T C 3'
3' T G A A G T C T T A A G G A A T G C T T C A A T A G 5'

Accepted Answer

A) 1 
B) 7 
C) 10 
D) 18 
E) there is no restriction site in this sequence 
A) 1 
B) 7 
C) 10 
D) 18 
E) there is no restriction site in this sequence

Question 11

The combination of histone proteins with DNA gives rise to what structure?

Accepted Answer

A) cohesins 
B) telomeres 
C) centromeres 
D) nuclear scaffold 
E) nucleosomes 
A) cohesins 
B) telomeres 
C) centromeres 
D) nuclear scaffold 
E) nucleosomes

Question 12

What technique is used to amplify portions of DNA, usually about 500 base pairs in size?

Accepted Answer

A) DNA sequencing 
B) polymerase chain reaction 
C) cloning 
D) restriction digestion 
E) electrophoresis 
A) DNA sequencing 
B) polymerase chain reaction 
C) cloning 
D) restriction digestion 
E) electrophoresis

Question 13

In the event of DNA damage during mitosis, p53 is phosphorylated and prevents mitosis from continuing until the damage is corrected. If the damage cannot be corrected, what happens?

Accepted Answer

A) cell returns to G1 and mitosis stops with excess DNA being degraded 
B) cell repeats S phase 
C) cell repeats G2 phase 
D) cell proceeds through mitotic division and the daughter cell with the damaged DNA is destroyed 
E) apoptosis 
A) cell returns to G1 and mitosis stops with excess DNA being degraded 
B) cell repeats S phase 
C) cell repeats G2 phase 
D) cell proceeds through mitotic division and the daughter cell with the damaged DNA is destroyed 
E) apoptosis

Question 14

Which histone protein is associated with the linker DNA and therefore not actually part of the nucleosome?

Accepted Answer

A) H1 
B) H2A 
C) H2B 
D) H3 
E) H4 
A) H1 
B) H2A 
C) H2B 
D) H3 
E) H4

Question 15

What is the term used to describe genetic variation that occurs among individuals of the same species resulting in gain or loss of restriction sites that can be detected by Southern analysis?

Accepted Answer

A) polymorphism 
B) hybridization 
C) clone 
D) epigenetic variant 
E) none of the above 
A) polymorphism 
B) hybridization 
C) clone 
D) epigenetic variant 
E) none of the above

Question 16

What is a haplotype?

Accepted Answer

A) a collection of polymorphisms that occur by insertions 
B) a collection of polymorphisms that occur by deletions 
C) a collection of polymorphisms that occur by repetition of short sequences 
D) a collection of polymorphisms that occur by single base changes 
E) a collection of polymorphisms that display a distinct pattern that arises from the use of similar modifications to the area of the genome in question 
A) a collection of polymorphisms that occur by insertions 
B) a collection of polymorphisms that occur by deletions 
C) a collection of polymorphisms that occur by repetition of short sequences 
D) a collection of polymorphisms that occur by single base changes 
E) a collection of polymorphisms that display a distinct pattern that arises from the use of similar modifications to the area of the genome in question

Question 17

What term is used to describe a collection of cloned genomic fragments?

Accepted Answer

A) sequence 
B) repository 
C) fragmented genome 
D) library 
E) none of the above 
A) sequence 
B) repository 
C) fragmented genome 
D) library 
E) none of the above

Question 18

A linear DNA molecule was treated with PstI and gave two fragments with sizes of 2150 and 3420 base pairs. The same DNA was treated with BamHI and gave three fragments of 1250, 1930 and 2390 base pairs. Finally, the DNA was treated with both enzymes at the same time and gave fragments of 900, 1250, 1490 and 1930 base pairs. Provide a map of the DNA molecule clearly indicating the restriction sites.

Accepted Answer

The answer of A linear DNA molecule was treated with...

Question 19

What is the typical percentage of lysine + arginine in histone proteins?

Accepted Answer

A) 35% 
A) 35%

Question 20

What structure is responsible for linking the centromeres to the spindle fibers during mitosis?

Accepted Answer

A) metaphase plate 
B) nucleosome 
C) kinetochore 
D) centromere scaffold 
E) none of the above 
A) metaphase plate 
B) nucleosome 
C) kinetochore 
D) centromere scaffold 
E) none of the above

Exam 24: Genes, Genomes and Chromosomes

The argument that mitochondria and chloroplasts originally were self-sufficient bacteria is supported by the presence of what protein-DNA structure?

Show the product of the following restriction digest. PstI has a restriction site of CTGCA ↓\downarrow↓ G. P- indicate the 5' phosphate, -OH indicates the 3' hydroxyl. P-T C A C T G C A G C C T-OH HO-A G T G A C G T C G G A-P + PstI →\rarr→

For a restriction enzyme with a 6-base recognition site, what is the average number of base pairs between occurrences of the site?

What proteins, responsible for specific protein kinase activation, are major control elements in the cell cycle?

BamHI has a restriction site of G ↓\downarrow↓ GATCC while HpaI has a restriction site of GTT ↓\downarrow↓ ACC. Based upon this, BamHI produces __________ and HpaI produces __________.

Which of the following represents the correct order of steps usually taken in a Southern analysis?

What does a yeast artificial chromosome (YAC)allow one to do?

The alteration in chromatin structure that occurs within the centromere is brought about by the replacement of which histone protein?

A typical size for a viral genome is ______ nucleotides per haploid genome while a typical size for a bacterial genome is ______ nucleotides per haploid genome.

Where in the following DNA sequence is the start of a 6-base type II restriction site? Every fifth nucleotide is indicated with a bold letter using the top strand for numbering. 5' A C T T C A G A A T T C C T T A C G A A G T T A T C 3' 3' T G A A G T C T T A A G G A A T G C T T C A A T A G 5'

The combination of histone proteins with DNA gives rise to what structure?

What technique is used to amplify portions of DNA, usually about 500 base pairs in size?

In the event of DNA damage during mitosis, p53 is phosphorylated and prevents mitosis from continuing until the damage is corrected. If the damage cannot be corrected, what happens?

Which histone protein is associated with the linker DNA and therefore not actually part of the nucleosome?

What is the term used to describe genetic variation that occurs among individuals of the same species resulting in gain or loss of restriction sites that can be detected by Southern analysis?

What is a haplotype?

What term is used to describe a collection of cloned genomic fragments?

What is the typical percentage of lysine + arginine in histone proteins?

What structure is responsible for linking the centromeres to the spindle fibers during mitosis?

The Scope of Biochemistry

The Matrix of Life: Weak Interactions in an Aqueous Environment

The Energetics of Life

Nucleic Acids

Introduction to Proteins: the Primary Level of Protein Structure

The Three-Dimensional Structure of Proteins

Protein Function and Evolution

Contractile Proteins and Molecular Motors

Carbohydrates: Sugars, Saccharides, Glycans

Lipids, Membranes and Cellular Transport

Enzymes: Biological Catalysts

Chemical Logic of Metabolism

Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

Citric Acid Cycle and Glyoxylate Cycle

Electron Transport, Oxidative Phosphorylation, and Oxygen Metabolism

Photosynthesis

Lipid Metabolism I: Fatty Acids, Triacylglycerols, and Lipoproteins

Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates

Lipid Metabolism Ii: Membrane Lipids, Steroids, Isoprenoids, and Eicosanoids

Metabolism of Nitrogenous Compounds I: Principles of Biosynthesis, Utilization, and Turnover

Metabolism of Nitogenous Compounds II: Amino Acids, Porphyrins, and Neurotransmitters

Nucleotide Metabolism

Mechanisms of Signal Transduction

DNA Replication

DNA Restructuring: Repair, Recombination, Rearrangement, Amplification

Information Readout: Transcription and Post-Transcriptional Processing

Information Decoding: Translation and Post-Translational Protein Processing

Regulation of Gene Expression

Filters

Show the product of the following restriction digest. PstI has a restriction site of CTGCA $\downarrow$ G. P- indicate the 5' phosphate, -OH indicates the 3' hydroxyl. P-T C A C T G C A G C C T-OH HO-A G T G A C G T C G G A-P + PstI $\rarr$

BamHI has a restriction site of G $\downarrow$ GATCC while HpaI has a restriction site of GTT $\downarrow$ ACC. Based upon this, BamHI produces and HpaI produces .

A typical size for a viral genome is nucleotides per haploid genome while a typical size for a bacterial genome is nucleotides per haploid genome.