exam 1 Flashcards
Genomics
- The study of an organism’s complete set of genetic information.
- Coding and non-coding DNA.
- Genome: complete genetic info of an organism.
Proteins
Proteins are polymers of amino acids (AA).
Protein Coding regions
The genetic code specifies the relationship between the sequences of the bases of the DNA and the sequences of AA
Open Reading Fram (ORF)
A region of DNA sequence that begins with an initiation code (ATG) and ends with a stop codon.
Non-coding DNA
Does not provide instructions for making proteins.
Non-coding RNA
Translation, transformation, splicing
Introns
Nucleotide sequence within a gene. Removed by RNA splicing as RNA matures. Not expressed in the final product. (skinny line on the gene.)
Exons
Nucleotide sequence within a gene. covalently bonded to one another to create mature RNA. (Thick = coding & thin = non-coding)
Splicing
Pre-mRNA is made into mature mRNA, by the removal of introns and the joining together of exons.
Alternative splicing
A single gene can contain numerous exons and introns, and the exons can be spliced together in different ways.
Can produce different forms of a protein from the same gene.
The different forms of the mRNA are called transcript variants, splice variants, or isoforms.
5’
5’ exon starts with a transcription start point, the promotor site comes before the start of transcription. (TATA Box)
3’
The ending of transcription (AG splice site) is followed by a poly A site. (downstream)
Why sequence non-human genomes?
They help us to understand the functions of different regions of the
human genome
An important principle is that if evolution conserves something it is
essential
Conserved sequences
identical or similar sequences in nucleic acids (DNA and RNA) or proteins
across species
Single nucleotide polymorphism (SNPs)
Substitution of a single nucleotide that occurs at a specific position in the genome. Biological markers
Mutation
The changing of a structure of a gene results in a variant form. Alterations to single base units in DNA or change of larger sections of genes.
Haplotypes
Refers to a set of DNA variants along a single chromosome that tends to be inherited together.
SNP’s
Genome editing
Making specific changes to the DNA of a cell or organism. It can be used to add, remove or alter DNA in the genome.
High-throughput sequencing
Technologies that sequence DNA and
RNA in a rapid and cost-effective
manner
Sanger Sequencing
- Denatures DNA
- Makes multiple copies of a segment
- Attaches a primer
- Added to polymerase solutions (color)
- Grows complementary strand until termination dye.
- Dentatures the new strand
- Electrophorese the chains
Pseudogenes
degenerate genes that have become non-functional due to accumulation of mutations
Genome
Contains genes that code for proteins and non-coding RNAs (other than mRNAs),
control regions, pseudogenes, and a variety of repetitive sequences.
“jumping genes” or transposons
sequences of DNA that move (or jump) from
one location in the genome to another.
The Human Genome Project
Global scientific effort whose signature goal was to generate the first sequence of the human genome.
How many pairs of human chromosomes?
23 pairs
Short Tandem Repeats (STRs)
repeated DNA sequences that involve a repetitive unit of 1-6 bp (1), forming series with lengths of up to 100 nucleotides (nt).
Variable Number Tandem Repeats (VNTRs)
short repetitive nucleotide sequences are
specific for a person. 10-60 bp
DNA Fingerprinting
Identifying differences in some
specific regions in DNA
sequence called repetitive
DNA
Satellite DNA
The bulk DNA forms a major peak and the other small peaks are referred to as satellite DNA.
Restriction enzymes
Used to cut DNA into
smaller fragments. The cuts
are always made at specific
nucleotide sequences. (shape matching)
Found in bacteria
restriction enzyme pt 2
EcoRI was the first restriction enzyme isolated from Escherichia coli strain RY13, whereas HindIII was the third enzyme
isolated from Haemophilus influenzae strain R d.
Blunt ends
Straight edge
Sticky ends
Staggered ends, are easier to bind to complementary strands.
PCR
Amplify STRs
Mitochondrial DNA
Mitochondrial DNA is the circular chromosome found inside the cellular organelles called mitochondria. Located in the cytoplasm, mitochondria are the site of the cell’s energy production and other metabolic functions. MOTHER
Genome Mapping
used to identify and record the location of genes and the distances between genes on a
chromosome.
Genetic Mapping
looks at how genetic information is shuffled between chromosomes or between different regions in the same chromosome during
meiosis (a type of cell division). A process called recombination or ‘crossing
over’.
Physical Mapping
looks at the physical distance between known DNA sequences (including genes) by working out the number of base pairs (A-T, C-G) between them.
Centimorgan or cM
is a measurement or rate of how often recombination occurs during meiosis. One centimorgan is equal to a 1% chance that two markers on a chromosome will become separated from one another due to a
recombination event during meiosis
Cytogenetic map
the visual appearance of a chromosome when stained and examined under a microscope.
Genetic Markers
for tracking inheritance of characteristics or
diseases through several generations of a family.
Genetic Mapping Examples
SNPs, VNTRs, Satellite
Restriction Mapping
A restriction map shows all the
locations of that particular restriction
site throughout the genome.
Fingerprint mapping
comparing the patterns from all the fragments of DNA to find areas of
similarity. Those with similar
patterns are then grouped
together to form a map.
Optical Mapping
Optical mapping uses single molecules of
DNA that is stretched and held in place
on a slide.
Fluorescent in situ hybridization
(FISH) mapping
This uses fluorescent probes to detect the
location of DNA sequences on chromosomes.
Sequence-tagged site (STS)
mapping
This technique maps the positions of short DNA sequences (between 200-500 base pairs in length) that are easily recognizable and only occur once in the genome.
Traits
Traits are “written” into specific areas, called genes, within the large, continuous DNA molecules called chromosomes.
Three major experiments led to the conclusion that DNA is the
the genetic material in cells.
Frederick Griffith (hereditary info can be transferred), Oswald Avery (can be DNA), Hershey and Chase (concluded that its only DNA)
Transformation
a change in genes that is caused when cells take up genetic material from outside sources.
The structure of DNA was discovered largely by these three experiments:
-James Watson &
Frances Crick (Nobel prize for being the first to correctly model DNA structure.)
-Erwin Chargaff (Provided the mathematical data to support Watson & Crick)
-Rosalind Franklin & Maurice Wilkins (Provided the visual evidence to support Watson & Crick.)
Chargaff’s rules
-A, T, C, and G were not found in equal quantities (as some models at the time would have predicted)
-The amounts of the bases varied among species, but not between individuals of the same species
-The amount of A always equaled the amount of T, and the amount of C always equaled the amount of G (A = T and G = C)
Deoxynucleoside triphosphate
(dNTP)
3rd C has the OH group
2nd C has the H
ATGC
Dideoxynucleoside
3rd C has the H without the O
2nd C has the H without O
dATP=
dTTP=
dGTP=
dCTP=
A
T
G
C
When there is a dd present in the sequence=
reaction terminates
