BIOLOGY 1A03 Lecture Notes - Lecture 1: Single-Nucleotide Polymorphism, Noncoding Dna, Tandem Repeat

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crimsonbat46

3 Sep 2018

School

McMaster University

Department

Biology

Course

BIOLOGY 1A03

Professor

Alastair Tracey Rosa Da Silva

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BIOLOGY 1A03 Full Course Notes

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The human genome contains the complete set of instructions that codes for life. As we have seen though, exons and regulatory elements that code for proteins make up a relatively small portion of the genome in many eukary organisms. We know that amongst protein coding genes, there are also noncoding and repeated sequences that serve a function of their own. In addition to noncoding rna and single-copy genes, we can also have a variety of different repeated nucleotide sequences such as tandem repeats or even simple-sequence repeats that are repeated over and over throughout a dna sequence stretch. Tandem repeats can be up to several thousands nucleotides in length and be present next to each other in multiple identical or near identical copies. Simple-sequence repeats which are repeats as short as 2 nucleotides. All these different possible sequences that are spread throughout the genome can result in genetic variation both within and across organisms.

Related Questions

QUESTION 1

A mutation caused by exposure to gamma rays is called a spontaneous mutation

	a.	True
	b.	False
	c.	Sometimes, depending on the type of base change
	d.	Gamma rays do not cause mutations

QUESTION 2

A recessive mutation affecting an essential biochemical pathway can be detected________

	a.	when the organism is heterozygous for that mutation.
	b.	when the organism is homozygous for that mutation.
	c.	in either homozygous or heterozygous conditions.
	d.	only by sequencing (recessive mutations never show a phenotype).

QUESTION 3

During DNA replication, the newly synthesized chain grows by adding

	a.	nitrogenous bases
	b.	the sugar-phosphate backbone
	c.	nucleosides
	d.	dNTPs

QUESTION 4

During replication, the DNA strand 5â- AAGTCTAGCCTAG -3â will serve as a template for the polymerization of:

	a.	5â- CTAGGCTAGACTT -3â
	b.	5â - TTCAGATCGGATC -3â
	c.	5â - GATCCGATCTGAA -3â
	d.	3â - AAGTCTAGCCTAG -5â

QUESTIOn 5

Given the following DNA sequences, select which statement(s) is(are) correct.

Sequence 1:

5â-TGGACGCTAA-3â

3â-ACCTGCGATT-5â

Sequence 2:

5â-AATCGCAGGT-3â

3â-TTAGCGTCCA-5â

Sequence 3:

5â-ACCTGCGATT-3â

3â-TGGACGCTAA-5â

	a.	Sequences 1 and 2 are the same
	b.	Sequences 1 and 3 are the same
	c.	Sequences 2 and 3 are the same
	d.	Sequences 1, 2 and 3 are all different

QUESTION 6

Repetitive sequences in the genome are hotspots for:

	a.	Deamination
	b.	Depurination
	c.	Thymine dimer formation
	d.	Replication errors

QUESTION 7

Select which statement(s) about the Ames test is(are) correct

	a.	it has been designed to understand mutation repair systems in Salmonella typhimurium
	b.	it uses mammalian liver extract
	c.	it allows to study whether chemical compounds or their enzymatic breakdown products are mutagenic
	d.	it is based on whether a chemical compound causes reversion mutations from his+ to his-
	e.	two of the above are correct
	f.	three of the above are correct

QUESTION 8

Select which statement(s) is(are) correct.

	a.	All DNA strands have a direction, and it is specified by the carbons in the sugar backbone.
	b.	All DNA strands have a direction, and it is specified by hydrogen bonds between nucleotides.
	c.	In order to form proper base pairs in a double stranded DNA molecule, the two strands must run in opposite directions.
	d.	A and C are correct.
	e.	B and C are correct.

QUESTION 9

Studies of gene mutation frequencies have shown that:

	a.	mutations are rare, and genomes are generally stable.
	b.	mutation frequencies differ among organisms and also between genes, suggesting certain genes are more susceptible to mutation.
	c.	mutation frequencies are consistent between organisms, and each region of DNA is equally susceptible to random mutations.
	d.	Both A and B are correct.
	e.	Both A and C are correct.

QUESTION 10

The compound 5-bromodeoxyuridine (BrdU) is a derivative of uracil, and if BrdU becomes incorporated during DNA replication, it pairs with adenine. This compound is best classified as which type of mutagen?

	a.	base analog
	b.	base inducer
	c.	intercalating agent
	d.	oxidative agent
	e.	alkylating agent

QUESTION 11

The rate of mutation of the fruit fly is higher than the rate of mutation of Algae

True

False

QUESTION 12

Thymine dimers are most commonly caused by which of the following?

	a.	X-rays
	b.	Alkylating agents
	c.	U.V. irradiation
	d.	DNA intercalating agents

QUESTION 13

What chemical group is found in the 3â end of a DNA strand?

	a.	an alcohol
	b.	a hydroxyl
	c.	a methyl
	d.	a phosphate

QUESTION 14

What chemical group is found in the 5â end of a DNA strand?

	a.	an alcohol
	b.	a hydroxyl
	c.	a methyl
	d.	a phosphate

QUESTION 15

Which is the correct order of molecules binding to DNA during DNA replication?

	a.	Helicase, SSB, primase, DNA pol III, DNA pol I, ligase
	b.	SSB, DNA pol I, ligase, helicase, DNA pol I, primase
	c.	primase, helicase, DNA pol III, ligase, DNA pol I, SSB
	d.	SSB, helicase, primase, DNA pol III, DNA pol I, ligase

QUESTION 16

Which statement(s) is(are) correct about strand slippage?

	a.	It can cause disorders such as Huntingon disease.
	b.	It is a process that causes mutations altering the number of DNA repeats.
	c.	It is a process that incorporates nucleotide base analogs and trinucleotide repeats.
	d.	a and b are correct.
	e.	b and c are correct.
	f.	a, b and c are correct.

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QuestionGroup: #21 Gene expression 2

Assigned as

Homework

The direct end result of gene expression is which of the following?

Amino acids

Translation

Proteins

Carbohydrates

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QuestionGroup: #22 Mutation

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Homework

Which of the following is the ways in which nucleotide mutations lead to altered proteins?

One nucleotide is substituted by another nucleotide, which can cause an early stop codon to be incorporated into the amino acid sequence resulting in a truncated protein.

One nucleotide is replaced by another nucleotide, which can change an amino acid in the protein sequence

Nucleotides are inserted into a nucleotide sequence causing a frameshift in the sequence.

All three choices may cause mutations.

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QuestionGroup: #23 Mutation 2

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Mutations are the result of which of the following?

Change in the normal nucleotide sequence in the DNA directly resulting in different carbohydrates

Change in the normal nucleotide sequence in the DNA directly resulting in different proteins

Change in the order of transfer RNA to messenger RNA so that the transfer RNA take over the role of Messenger RNA

Primarily an alteration in the sequence of nucleotides in the abnormal proteins

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QuestionGroup: #24 Cell division

Assigned as

Homework

There are two major kinds of cell division. Which of the following plays a major role in promoting genetic diversity?

Meiosis since it causes the cells to make more daughter cells than mitosis

Mitosis since it causes the cells to duplicate and eventually have mutations

Meiosis since it causes the DNA sequences to be separated into new patterns in the daughter cells.

Mitosis since it essential for the ovaries in humans to separate and duplicate

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QuestionGroup: #25 Cancer

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Homework

Genes that slow down or stop the cell cycle are called...

Apoptotic genes

Oncogenes

Restriction genes

Tumor suppressor genes

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QuestionGroup: #26 Cancer2

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The common theme in the development of all cancers is...

Mutation

Evolution

Infection

Syncopation

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QuestionGroup: #27 Genetics

Assigned as

Homework

Punnett's square is which of the following?

Example of all possible combinations of alleles

Example of all possible combinations of chromosomes

Example of only certain combination of alleles since some will not be expressed.

Example of all possible combinations of DNA

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QuestionGroup: #28 Embryo development

Assigned as

Homework

Which of the following is the end of the cleavage phase?

A fetus

Formation of a blastocyst

Implantation to the lining of the uterus

Fewer number of cells

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QuestionGroup: #29 Development of organ system

Assigned as

Homework

For organs to be differentiated, which of the following is the first step?

Stem cells trigger the development of differentiated cells

Tissues assemble into organ systems such as blood

Tissue specific genes in stem cells are triggered

Differentiated cells form tissues

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QuestionGroup: #30 Development and society

Assigned as

Homework

A pregnant mother ingests a chemical which her mother said would be great for the baby. When the baby was born, it had a large head and flippers for arms. What caused this phenotype?

The chemicals were teratogens which influenced oxidative phosphorylation causing the changes in the phenotype.

The chemicals influenced the expression of different stem cells.

There is no way to assume the chemicals caused the phenotype since we have no data on other mothers who took this medicine. It could have been purely by chance.

The chemicals were teratogens which caused the baby to show early signs of evolution.

The bacterium E. coli, which is a major model system for the study of genes and DNA, has a singular circular chromosome of about 4x106 bp. In contrast, human diploid cells have __1__ chromosomes, of __2__ different types (donât forget that the X Â¹ Y!). The total amount of DNA found in a haploid cell such as a sperm or egg is called the organismâs âC-valueâ; the human C-value is __3__.

Also in contrast to the E. coli circular chromosome is the fact that eukaryotic chromosomes are not circular, but instead are __4__. Eukaryotic chromosomes are complexed heavily with protein to form a DNA-protein complex generically called __5__. The proteins found can be considered to fall into two general classes: __6__ and __7__. The first class is made up of 5 major proteins called __8__, __9__, __10__, __11__, and __12__. On a weight to weight basis, these proteins make up about __13__% of the total mass of a chromosome. Since these proteins must associate relatively non-specifically with DNA, they are rich in the basic amino acids __13__ and __14__, which gives the proteins a net __15__ charge.

One goal of packaging the DNA into chromatin is to compact the genome so it will fit into a nucleus. The basic unit of chromatin structure is the __16__, which has __17__ base pairs of DNA wrapped around a âcore particleâ composed of __18__ copies each of the core histones. Each nucleosome is separated by a stretch of âlinkerâ DNA so that the repeating unit is approximately 200 bp. Lets do a little arithmetic: If we consider that the nucleosome is approximately __19__ nm in diameter, that there is about 200 bp in this structure, and that 200 bp of DNA would normally occupy __20__ nm if stretched out straight (recall that each base is spaced about 0.34 nm from the next), we can see that the nucleosome alone allows for a __21__-fold compaction ratio.

The nucleosome structure is further compacted by histone __22__, which is not a part of the core particle. Instead, this histone __23__ (does what?) to cause the nucleosomal 10 nm fiber to condense into a higher-order structure referred to as the __24__ nm fiber. In the nucleus, chromosomes do not just float around freely: they are tethered to a proteinaceous structure called the __25__ at specific DNA regions called âSARsâ, which stands for __26__. SARs are rich in topoisomerases, to allow the winding and unwinding of the DNA that accompanies replication and transcription to occur, despite this constraint.

The 30 nm fiber discussed above is the form in which transcriptionally active DNA is believed to exist in the nucleus; however, further condensation leads to a highly condensed inactive form called __27__; in this terminology, the active form is referred to as __28__. The inactive condensed form can be divided into two types: one type is essentially invariant between cell types, and since it is âon all t timeâ, it is referred to as __29__. The other type comes and goes, depending on the expression of the genes present in that region of the chromosome; it is referred to as __30__.

Eukaryotic chromosomes carry the genes, of course, but also have other functional regions. One such region is the place where the spindle apparatus attaches during mitosis and meiosis; this region of the chromosome is called the __31__. Another important part of the linear eukaryotic chromosome is the ends; these are called __32__. In humans, the end of each chromosome is composed of many repeats of the short sequence __33__. One more type of functional region on each chromosome is the place where DNA replication starts; in humans, each chromosome has several of these __34__. Thus, eukaryotic chromosomes carry several different types of functional sequences, which together allow for their __35__ during S phase, __36__ during mitosis and meiosis, and the __37__ of their genes

BIOLOGY 1A03 Lecture Notes - Lecture 1: Single-Nucleotide Polymorphism, Noncoding Dna, Tandem Repeat

BIOLOGY 1A03 Full Course Notes

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