DNA Lectures - Mega List #3

deoxyribonucleic acid

The backronym of DNA, this macromolecule is a polymer and contains all genetic information that codes for its organism's genes.

central dogma

This is the the theory that describes protein building in this order: DNA to RNA to protein. DNA is transcribed to RNA which is translated to protein. Protein is never back-translated to RNA or DNA; DNA is never directly translated to protein.

nuclear DNA

This is DNA found in the nucleus, shortened to "nDNA." Cells have two copies of this kind of DNA.

mitochondrial DNA

This is DNA found in the mitochondria, shortened to "mtDNA." It is inherited only through mothers. Cells have hundreds to thousands

double helix

This term describes the shape of DNA.

supercoiling

This is the process of how DNA is packed. In this process, DNA is wound tightly around histones to form nucleosomes.

nucleosome

This is formed when DNA is tightly wound around histones.

chromatin

This is densely packed DNA found in the nucleolus of the nucleus.

histone

This is the protein molecule which DNA is tightly coiled around.

chromosome

This is a threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes.

karyotype

This is a display of the chromosome pairs of a cell arranged by size and shape. Humans' consist of 22 pairs of autosomes and a pair of two sex chromosomes.

genome

This is the complete set of instruction for making an organism, consisting of all the genetic material in that organism's chromosomes. It consists of the DNA and all of its chromosomes.

exon

This is the DNA that is expressed to code for proteins. It can be called "extroverted."

intron

This is the DNA that is not expressed to for protein coding. It can be called "introverted."

gene

A segment of DNA on a chromosome that codes for a specific trait, this is known as a "genetic blueprint" and can be passed down from one generation to the next.

genotype

This is the genetic makeup of an organism.

phenotype

This codes for the physical characteristics of an organism.

hybridization

This process occurs when two strands of DNA are linked together.

nucleotide

This is the building block of DNA and RNA, consisting of a pentose sugar covalently bonded to a nitrogenous base and a phosphate group. Adenine (A), guanine (G), cytosine (C), thymine (T, in DNA), and uracil (U, in RNA) are all this type of compound.

nucleoside

This compound is composed of only a nitrogenous base and a pentose sugar.

five

The number of carbons present in a pentose sugar.

deoxyribose

The name of the pentose sugar found in DNA.

ribose

The name of the pentose sugar found in RNA.

hydrogen bond

This kind of bond occurs when individual nucleotides pair up with their complementary bases. It is the easiest bond to break, which is necessary for the process of transcription.

Rosalind Franklin

This scientist provided significant contributions to the understanding of the structure of DNA through the use of X-ray crystallography.

purine

The name for a nitrogenous base that has a double-ring structure. It is one of the two general categories of nitrogenous bases found in DNA and RNA and includes adenine and guanine.

pyrimidine

The name for a nitrogenous base that has a single-ring structure. It is one of the two general categories of nitrogenous bases found in DNA and RNA and includes thymine, cytosine, and uracil.

short tandem repeat

Also known as STR, this is located on the autosomal chromosomes. STRs are important for identification in forensic samples.

non-sex chromosome.

Another name for autosomal chromosomes.

Y chromosome

This sex chromosome is paternally inherited.

somatic cell

This type of cell in a living organism is any cell other than reproductive cells. It is also called a "body cell."

diploid

This is the form of chromosomes in all body cells. It results in two sets of chromosomes per cell, 2n.

6 picograms

The amount of picograms in a diploid cell.

gamete

The type of cell in a living organism is a reproductive cell/specialized sex cell. It is also called a "germ cell" or an "egg" or "sperm."

haploid

This is the form of chromosomes in germ cells. It results in one set of chromosomes per cell, n.

3 picogram

The amount of picograms in a haploid cell.

single stranded

This is a term used to describe RNA because it is not in the shape of a double helix and the nitrogenous bases do not have another strand to pair with unless during transcription or translation.

uracil

The nitrogenous base that replaces thymine in RNA.

miRNA

This type of RNA is a small non-coding molecule that can be used for body fluid identification. It is tissue specific

gene locus

The specific location on a chromosome where a coding region exists. In forensic science, the non-coding region needs to be looked at.

allele

A form of a gene locus or an alternative form of a gene.

homozygote

This word is defined as "two copies of the same allele or form of the gene locus."

heterozygote

This word is defined as "a different allele or form of the gene locus."

loci

The plural form of "locus."

Earth

Our professor used this planet as an analogy for a cell.

continent

Our professor used this landmass as an analogy for a cell nucleus.

state

Our professor used this area of the USA as an analogy for a chromosome.

city

Our professor used this urban area as an analogy for chromosomal DNA.

street

Our professor used this area of a city as an analogy for a locus.

locus

This is the word that a specific STR marker refers to.

size

In forensic science, analysis of DNA evidence does not focus on the DNA code itself, but rather this:

restriction fragment length polymorphism

The backronym of RFLP, this was an early technology of forensic DNA analysis that required a lot of DNA samples and had to be of high quality to provide successful results.

Dr. Alec Jeffreys

This doctor used RFLP.

The Blooding by Joseph Wambaugh

2 young teens in a low crime village are found strangled and sexually assaulted. All able bodied people are told to donate. Some guy talks about how he donated for his cousin cause he is scared of needles. This gets reported and the guy is found, Colin Pitchforke, who is the person who did it.

rape cases

More than 2/3 of these types of cases use forensic DNA analysis.

heme, soil, bones

These substances are are considered inhibitors to polymerase chain reactions (PCRs).

human identity testing

Forensic cases, paternity testing, historical investigations, missing persons investigations, mass disasters, military DNA, and convicted felon DNA databases are all used for this:

circular

This is the shape of mitochondrial DNA.

linear

This is the shape of nuclear DNA.

nDNA testing

Blood, tissue, hair (with root), fresh bone and teeth, body fluids, and stamps and envelopes are all specimens of this type of testing.

mtDNA testing

Old skeletal remains, hair shafts, and fingernails are all specimens of this type of testing.

steps in DNA analysis

Extraction, Quantification, Amplification, Separation, Analysis and Interpretation, Report conclusions (and statistics) are all a part of this.

two steps of extraction

1) Breaking open the organism or cell that contains DNA.
- biological specimen (Human and nonhuman)
- plants, seeds, leaves
- microbial specimen (terrorism)

2) Separation of DNA from other cellular components.
- proteins
- cellular debris and internal cellular structure
- carbohydrate
- lipoproteins
- inhibitors

inhibitors

Heme, humid acid, fulvic acid, calcium and collagen, and melanin are all considered this due to their effect on polymerase chain reactions.

Chelex extraction

This type of extraction produces ssDNA, so it is only good for PCR based testing. It is faster than organic, fewer steps, and there is a lower chance of sample to sample contamination.
-nucleases inactivated
-ion exchange resin
-ions chelate Mg2+ (inactivates nucleases)

FTA extraction

This type of extraction is a card based system.

robotic extraction

This type of extraction utilizes magnetic beads and is simple.

organic extraction

In this type of extraction, DNA will come out double stranded. It is time consuming but provides quality, clean DNA and is considered the "golden standard."

differential extraction

A process by which an analyst can separately isolate male and female DNA from a mixture of female epithelial cells and male sperm cells, such as might be found in sexual assault evidence.

Chelex-100

This compound is an ion-exchange column resin composed of iminodiacetic acid. This compound binds magnesium and removes them from the reaction mixture, stabilizing and preserving DNA. This yields single-stranded DNA, which is then used for STR.

chelate

This is the action of binding ions or molecules to metal ions such as Zn, Mg, and Ca.

metal ion

These molecules (Zn, Mg, Ca) can act as catalysts or co-factors for nucleases, thus helping degrade DNA by the enzymatic degradation of hydrolysis.

intimate source sample

A vaginal swab is considered this type of sample.

quantification

This step in DNA analysis determines the amount of DNA present in the extract to assist in determining the appropriate amount of the extract to add for amplification.
- qPCR = real time PCR
- adding the incorrect quantity can lead to poor results

reagents in differential extraction

Lysis Buffer: chemicals and proteins added to the sample that facilitate lysis of the cell membrane and effective removal of impurities
SDS: sodium dodecyl sulfate (detergent)
Pro K: Proteinase K (digests proteins and chops it up)
DTT: Dithiothreitol (breaks S-S bonds/ breakdown sperm heads)
EDTA: Ethylenediaminetetraacetic acid (chelates metal ions that can degrade DNA and cause hydrolysis of DNA molecule
Buffer/ions: Examples Tris- HCL and NaCl (maintains pH)

lysis buffer

This solution reagent is used in differential extraction to break the cell membrane and release cell contents to remove impurities.

sodium dodecyl sulfate

Backronym of SDS, this detergent reagent is used during differential extraction and results in foaming.

proteinase K

Shortened to Pro K, this enzyme commonly used in differential extraction to degrade proteins.

dithiothreitol

Backronym of DTT, this redox reagent used in differential extraction breaks disulfide bonds, binding the sulfurs to hydrogens, which allows the protein to break apart. This reagent breaks down sperm heads.

ethylenediaminetetraacetic acid

Backronym of EDTA, this acid used in differential extraction to chelate metal ions that can degrade DNA and causes hydrolysis of the DNA molecule. EDTA acts like Chelex.

buffer/ions

Examples of this reagent include Tris-HCl and NaCl. This reagent maintains pH.

polymerase chain reaction

The backronym of PCR, this is the method used for DNA amplification. It is performed by a thermal cycler and works by repeated cycles of heating and cooling.

denature, anneal, extend

The three steps of PCR analysis:

template DNA

A PCR reagent. This is single-stranded.

short primers

A PCR reagent. This substance initiates synthesis of new DNA.

dNTP

A PCR reagent known as "deoxyribonucleoside triphosphate." This is used to add to a growing strand of DNA.

polymerase

A PCR reagent. This is used to to perform synthesis of new DNA.

MgCl₂

A PCR reagent. This chemical is used to activate polymerase.

denature

This step in the DNA amplification process occurs at 95 degrees Celsius and denatures the starting DNA template into two separate strands.

anneal

This step in the DNA amplification process occurs at a range of 50-72 degrees Celsius and binds primers to the separate DNA strands.

extend

This step in the DNA amplification process occurs at 72 degrees Celsius and synthesizes a new strand of DNA from the previously attached primer.

amelogenin

A piece of DNA found in the X and Y chromosomes that determine gender. It is also known as the "sex-determining locus."

Y chromosome

An "X-homologous" amelogenin gene region exists on this chromosome.

complicate

What can these following factors do to DNA analysis interpretation?
- Stutter
- Pull up
- Spikes
- Dye blobs
- Degradation
- Low DNA template amount

Immigration case in Ghana

First DNA case
-Man is detained because the government of the country he was visiting thought he was lying
-They took his blood and matched it with his mom and aunt to prove he was correct

Scientific Working Group of DNA Analysis Methods

The backronym of SWIGDAM.

DNA is the only standard

FALSE, any accredited lab will have other standards

extraction

This is the process of isolating DNA.

three possible conclusions

"Inclusion (must provide stats)," "exclusion," and "inconclusive" are all considered this.

inclusion

The evidence profile and reference profile appear to match. The weight of the match and and a discretion notice must be reported in the conclusion.