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vs 307 > Exam 2 > Flashcards

Exam 2 Flashcards

1
Q

a) DNA template

A

codes for the DNA fragments that are being reproduced

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2
Q

DNA primer

A

attaches to the first base in the DNA template to be coded for, signals the polymerase to start copying the designated area of DNA

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3
Q

polymerase

A

protein that copies the DNA sequence to produce identical copies of the DNA

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4
Q

DNA polymerase is used for DNA sequencing. Taq Polymerase is used for PCR reactions. The two enzymes both replicate DNA by copying a single strand template. But DNA polymerase is cheaper. Why do we still use Taq Polymerase for PCR?

A

Taq polymerase is heat resistant. In PCR the DNA is denatured and the double stranded DNA is melted using heat. If polymerase was used for this, it would also be denatured during the heating process

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5
Q

What does the term “genomics” mean (as opposed to genetics)?

A

Genomics is the mapping of a genome . genetics is the study of traits and inherited characteristics.

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6
Q

define linkage

A

Some chromosomes are so close together they are often inherited together. When this occurs, the chromosomes are thought to be “linked”

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7
Q

define polymorphism

A

Continuous genetic variation resulting in the occurance of several different forms or types of individuals among the members of a single species.

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8
Q

when did the horse genome project begin?

A

1995

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9
Q

Describe the steps in a PCR reaction.

A

Add components (DNA template, primer, polymerase, dNTPs and buffers), heat the tube to 95 degrees Cto melt the double stranded DNA, cool to the annealing temperature (55-65C depending on the reaction), reanneal DNA including the primers to the template, heat to 72C for the elongation/synthesis step (polymerase makes the DNA), repeat steps 2-4 at least 30 times to produce billions of copies of DNA target starting from even a single DNA strand

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10
Q

What is the PCR solution to the “needle in the haystack” problem?

A

PCR uses specific primers to find and attach to the specific portion of DNA that needs to be copied. The primer then signals the polymerase to copy the DNA sequence. Since DNA has so many base pairs it is extremely challenging to find a specific segment.

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11
Q

What does the term “haplotype” mean

A

A group of genes within an organism that was inherited together from a single parent

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12
Q

What is the nature of the process referred to as shotgun sequencing?

A

Chromosomes are broken into small fragments, cloned and sequenced . the computer is then used to make alignments and assemble the sequence

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13
Q

what is a SNP?

A

Single nucleotide polymorphism that may be caused by chemical errors, random mutation, radiation etc. Shows variation between individual horses and breeds of horses.

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14
Q

when did the human genome project begin

A

1990

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15
Q

how many genes do mammals have

A

20000

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16
Q

when was the horse genome sequence completed?

A

2006

17
Q

What is shotgun sequencing? Specifically, how does it differ from the “contig sequencing” approach to genome sequencing?

A

In contig sequencing, DNA clones continuous of each other were made. Overlapping BACs were formed and the DNA was assembled using the computer. There was a problem solving gap closure with this method. The shotgun sequence copies overlapping sequences of DNA. The continuous sequences are then aligned to generate the finished sequence.

18
Q

What are the chemical components in a PCR reaction? Specifically, what do you place in the test tube to run the reaction?

A

DNA template, primers, polymerase, dNTPs and buffers

19
Q

What are the steps in running the reaction after you add the chemical components? Specifically define the steps after you mix the ingredients in the tube, giving approximate temperatures at each step.

A

Denature-95C, Anneal-50-65C, Elongate-72C

20
Q

The PCR reaction and the Sanger sequencing reaction are similar. What are two differences in the components or the way the reactions are conducted?

A

Dideoxynucleotides are used in the Sanger sequencing while Taq polymerase is used in PCR. The reaction is heated in PCR, but is not heated in the sanger reaction. PCR uses a single DNA strand and sanger sequencing uses multiple DNA strands

21
Q

what are the products of PCR reactions?

A

many copies of a short target DNA sequence

22
Q
  1. What are the products of a DNA Sanger sequencing reaction?
A

Fragments of DNA with a set terminating each time a di-deoxynucleotide is produced

23
Q
  1. DNA polymerase and Taq polymerase both catalyze the synthesis of DNA. Taq polymerase has a special feature that makes it useful for PCR. What is that feature?
A

This means it is heat resistant and will not denature when the reaction is heated

24
Q
  1. The heat resistant nature of Taq polymerase is a product of its natural origin. Where was Taq polymerase found in nature?
A

Taq polymerase was found in hot springs of yellow stone park

25
Q
  1. Why did Fredrick Sanger win the Nobel Prize? (You have two chances. He won two! One was for the invention discussed in class.)
A

The process of sequencing 200-500 bp lengths of DNA (sanger sequencing)

26
Q

When DNA strands are run through a sequencing gel using electrophoresis, they separate into different bands. What is the physical aspect of the DNA fragments that lead them to separate?

A

The A, T, G, C bases cause the DNA to separate

27
Q
  1. What is the percentage of protein coding genes in mammalian DNA?
A

2%

28
Q
  1. What does GWAS stand for?
A

Geneome wide association studies

29
Q

Describe how GWAS works?

A

Uses SNPs to determine what a gene is responsible for. Horses are tested for at least 50,000 SNPs coming from all chromosomes. The SNPs are not in genes, but close to them. The SNPs that are most similar among horses are the ones closest to the gene being researched.

30
Q

What is a haplotype

A

A group of genes within an organism that was inherited together from a single parent

31
Q
  1. How does genomics differ from genetics?
A

Genomics is the sequencing of genes and genetics is how genes are inherited.

32
Q

what does SNP stand for?

A

Single nucleotide polymorphism

33
Q

how many genes in the mammalian genome?

A

20,000

34
Q

why is PCR reaction run for 30 or more times?

A

The reaction is run for 30 more cycles to create billions of copies of the specific DNA sequence

35
Q

only genes on the same chromosome can be in linkage disequilibrium…Why?

A

Occurs when genotypes at the two loci are not independent of another. Can only happen on the same chromosome , on the same end of that chromosome, close together.

36
Q

If you compared 100 DNA bases and 100 amino acid sequences for a gene for a horse and a human, which would have a higher similarity… protein or DNA?

A

DNA

37
Q

Why do we think that humans started selecting for color differences among horses after domestication?

A

Coat color preferences for the human liking

vs 307 (2 decks)

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