DNA Lecture 4

Question 1

Human chromosomes display a one base difference in every ________ bases, on average

Every individual has some differences

Answer 1

1000

Question 2

Base differences may or may not result in difference in amino acid sequences of proteins because

Answer 2

Not all segments of DNA code for proteins

There is more than one codon for most amino acids

Question 3

The DNA sequence changes (single base differences) between individuals can affect recognition sites for

Answer 3

Restriction enzymes

Question 4

Restriction enzyme sites are randomly made and eliminated

If a specific base sequence is present, the restriction enzyme which recognizes it will cleave the DNA molecule at the appropriate site and generate fragments of a specific length. However, if a restriction site is absent due to a base difference, different DNA restriction fragment lengths are formed.

Answer 4

!

Question 5

Base sequence differences between individuals in a population are called

Answer 5

polymorphism

Question 6

The variation in DNA restriction fragments between individuals are known as

Answer 6

Restriction Fragment Length Polymorphisms (RFLP)

Question 7

The analysis of individual differences in RFLPs

In theory, there is a unique DNA fingerprint for every individual, the ____________ fragment pattern for each individual is unique

Answer 7

DNA finger printing

Restriction Enzyme

Question 8

Detection of RFLPs relies on a specialized hybridization technique called

Answer 8

Southern Blotting

Question 9

In DNA fingerprinting, first the DNA must be

Then the DNA must be

Then the DNA fragments must be

Then the DNA must be ______ so that it is single stranded

Answer 9

isolated from the rest of the cellular material in the nucleus

cut into several fragments of different sizes with restriction enzymes

Sorted by size

Denatured by soaking the agarose gel in alkaline solution

Question 10

After the DNA is denatured in fingerprinting, the DNA is blotted onto a nylon membrane. The strands of DNA bind to the positively charged groups in the nylon membrane because of..

Answer 10

The negative charge on the DNA bases

Question 11

After blotting the DNA, the membrane is immersed in a solution of radiolabeled DNA probe.

The probe is a 32P labeled oligonucleotide whose sequence is complementary to a segment of known sequence of DNA.

The oligonucleotide with hybridize to the fragment that contains its

Answer 11

Complimentary Sequence

Question 12

Once the probe is bound to the DNA in DNA fingerprinting, the result is washed and analyzed via autoradiography.

The fragment length is determined from the position on the gel compared to DNA markers of

Answer 12

Known Length

Question 13

Usually DNA fragments resulting from DNA fingerprinting (aka restriction digest) for paternity testing are separately analyzed with several 32P labeled oligonucleotide probes. Combining the use of these makes the test extremely selective.

Answer 13

Each gene fragment analyzed has a different paternity index, from those a combined paternity index is reported. A probability is calculated

Question 14

Many mutations either create a new restriction site in a genome or destroy a previously existing site. If a mutation occurs within or near a particular gene, the restriction fragmentation pattern will change.

This change can be determined by ______ with a sequence that lies in the same region of the genome

Answer 14

Southern blotting

Question 15

This disease has an altered restriction pattern when DNA is probed for part of the gene for the beta-globin subunit, enabling prenatal diagnosis

Answer 15

Sickle cell disease

Other ex:
Cystic Fibrosis, Huntington’s, cancer, manic depression

Question 16

In a classic example of RFLPs, the semen sample obtained from a rape and murder victim was compared with samples from the victim and two suspects. The samples were cleaved by ________ and separated by ___________ and processed by ________

Answer 16

The samples were cleaved by endonucleases and separated by gel electrophoresis and processed by the Southern blotting procedure

Question 17

Name the two disadvantages of the Southern blotting method in a crime scene

Answer 17

Southern blot requires fresh DNA samples and larger amount of DNA than those usually found on a crime scene

Question 18

The need for more sensitive DNA typing methods led to a focus on the _________ and on ______

Answer 18

polymerase chain reaction (PCR) and on STRs

Question 19

Most genetic fingerprinting done today analyzes regions of our genome referred to as _________ that have highly variable repeating sequences

Answer 19

Minisatellites

Question 20

The minisatellites have _______ most commonly 4 bases long that are repeated several times, such as (TAGA)m

Answer 20

Short Tandem Repeats (STRs)

Question 21

____ is observed between the number of repeats (n) in each STR region

Strs represent about ____% of all human DNA

Answer 21

Polymorphism

3%

Question 22

By analyzing the number of repeats in many minisatellites, a unique profile for each individual can be obtained.

_______ is readily applicable to STR analysis

Answer 22

Polymerase Chain Reaction (PCR)

Question 23

This procedure makes it possible to isolate and analyze the DNA in a very small tissue sample (e.g. one human hair, a drop of blood, a small semen sample, or samples that are many years old)

With the increased sensitivity, forensic scientists focused on STRs rather than RFLPs

Answer 23

PCR

Question 24

In this first step of PCR, DNA strands are separated by

In the second step, strands are annealed to an excess of short DNA _____ that flank the region to be amplified

New DNA is synthesize by ____

Answer 24

heating

Primers

Polymerization

Question 25

The DNA sequences flanking STRs are unique to each type of STR and identical in all humans

Answer 25

! Not really sure what this means

Question 26

PCR primers are targeted to the unique flanking DNA and designed to amplify across the STR

The length of the PCR product is the length of the ____ in that sample

Answer 26

STR

Question 27

How many products are there from one person in PCR? Why?

Are they similar or different?

Answer 27

Two, one for each chromosome from each parent

Frequently different

Question 28

The resulting products from PCR are subjected to think capillary _____. The resulting fluorescent bands are scanned by a laser to generate a series of peaks.

The length of the minisatellite and the number of repeats is determined by comparing the capillary gel elution time of the minisatellite DNA to the elution time of DNA strands of known length

Answer 28

PAGE

Question 29

Standardization is required for any forensic analysis. The US forensic STR standard was called the ____ and was established in 1998

Answer 29

Combine DNA Index System (CODIS

Question 30

It is based on 13 well studied STR loci. These must be present in any DNA typing experiment carried out in the US

Answer 30

CODIS

Question 31

The ______ gene, present on human sex chromosomes, is also used as a marker in experiments in addition to the 13 STR loci

It has slightly different flanking on X and Y chromosomes. Different sized products are generated which can reveal the _______ of the DNA donor

Answer 31

amelogen

gender

Question 32

The complete sequence of the human genome (3 billion base pairs) was published in April 2003. Six nations were involved in this collaborative effort.

Answer 32

Human Genome Project

Question 33

In the Human Genome Project, research teams first generated a physical map of the human genome. Then, individual clones were sequenced by shotgun sequencing protocols. Researchers used powerful, new automated sequencers to sequence random segments on a given clone.

The sequence of the entire clone was assembled by identification of

Answer 33

Overlaps

Question 34

A separate commercial initiative sequenced the entire genome by shotgun

The genomes of many organisms have been sequenced and are available in public data bases

Answer 34

cloning

Question 35

We have only _____ to ______ genes

Only ____ to _____ % of our DNA encodes proteins

Answer 35

30,000 to 35,000

1.1-1.4%