Exam 2 Review - Genetics

Enhancer

Regulatory DNA region that binds transcription factors and changes gene expression

Promoter

DNA region where transcription machinery and RNA polymerase are recruited

TATA box

promoter sequence that helps position transcription machinery

TSS

where RNA pol begins making RNA

TTS

where transcription ends

5’ UTR

RNA region before the start codon; transcribed but not translated

start codon

where translation begins

Exon

region retained in mature mRNA after splicing

Intron

region removed from pre-mRNA during splicing

stop codon

where translation ends

3’ UTR

RNA region after the stop codon; transcribed but not translated

Template strand

DNA strand read by RNA pol

Coding strand

DNA strand w/ nearly the same sequence as mRNA

5’ cap

modified structure added to the 5’ end; protects RNA and helps translation

Spliceosome

RNA protein complex that removes introns and joins exons

5’ splice site

signal at beginning of an intron

3’ splice site

signal at end on intron

consensus sequence

showing the most common bases at each position

Alternative splicing

process allowing one gene to produce multiple mRNAs

Splicing isoform

different mRNA produced from alternative splicing

poly-A tail

chain of adenine added to the 3’ end of mRNA

mRNA

full processes and ready to leave the nucleus

Cytoplasm

location where mRNA is translated

UTRs

untranslated region; transc

Transcription

making RNA from DNA template

Translation

making proteins from an mRNA template

Transcription factor

proteins that regulate transcription

Activator

transcription factor that increases transcription

Repressor

transcription factor that decreases transcription

Coding region

portion of mRNA that is translated into protein

ribosome

structure that reads mRNA and builds protein

Exon skipping therapy

treatment that causes a mutated exon to be removed from the mRNA

reading frame

grouping of mRNA nucleotides into codons

premature stop codon

stop codon appearing too early, producing a shortened protein

shock-absorbing domain

dystrophin region that helps absorb mechanical force

Genome

all DNA in an organism

Transcriptome

All RNA expressed in a sample

Bioinformatics

use of computational tools to analyze biological data

Nucleotide sequencing

determining the order or nucleotides

shotgun sequencing

randomly fragmenting DNA, sequencing fragments, and assembling overlaps

Tandem repeat

repeated DNA sequence located next to itself

adapter

DNA sequence added to fragment ends for sequencing

flow cell

surface where sequencing fragments attach

bridge amplification

local copying of fragments to create clusters

index

barcode used to identify a sample

paired end sequencing

reading both ends of a DNA fragment

multiplexing

sequencing multiple samples together using indexes

sanger

very accurate; small number of short fragments

illumina

high-throughput short reads

PacBio

long, highly accurate reads

oxford nanopore

very long reads and portable sequencing

RNA seq

used to study RNA transcripts

RNA abundance

amount of specific RNA transcripts in a sample

novel transcripts

RNA transcript not previously identified

RNA seq library

collection of cDNA fragments prepared for sequencing

SNP

fast, cheap, easier to analyze, useful for large GWAS studies

difference at one nucleotide

limited to the variants on the array

genotype

genetic variant

phenotype

traits

association

relationship b/t two variables

causation

one variable directly produces a change in another

volcano plot

graph shows expression change vs. statistical significance

heat map

color-coded display of expression across genes and samples

rows = genes

columns = samples

color intensity = relative expression

dimension reduction

reducing complex data into fewer dimensions for visualization

PCR

amplification of a specific DNA sequence

qPCR

quantitative PCR; measures amplification as it occurs

SYBR Green

fluorescent dye that binds double-stranded DNA

baseline phase

fluorescence too low to distinguish from background

exponential phase

DNA increases rapidly; best phase for quantificaiton

linear phase

reagents become limiting

plateau phase

little additional product is made

Ct value

cycle at which fluorescence crosses a threshold

standard curve

curve made from samples w/ known concentrations

absolute qPCR

determine actual target amount using standard curve

relative qPCR

compares target expression to a control gene

housekeeping gene

stable control used for relative qPCR

lower Ct

more starting target (DNA or cDNA)

higher Ct

less starting target (DNA or cDNA)

DNA sequencing

reads genome

RNA sequencing

reads transcriptome

qPCR

measures a specific target

Actin binding domain

dystrophin region that connects to actin

Elements not required for basic transcription

enhancers

5’cap

poly A tail

microarrays

measure many known transcripts at once

requires probes for sequences that are already known

cannot easily detect completely new transcripts

PCA plots

each pt = sample

pt close together = similar overall gene expression patterns

PCA separation does not prove that the treatment caused the difference

GWAS Steps

1. traits that can be measured

2. who should participate in it

3. sequence genome

4. look at Manhattan plot

5. figure out whether gene matters

Illumina sequence workflow

1. fragments DNA into smaller pieces

2. library synthesis

3. bind fragments to flow cell

4. bridge amplification

5. sequencing by synthesis

6. read index fragment

7. amplify opposite direction

8. repeat sequence

GO & KEGG

assign biological meaning to changed genes

each term contains group of unrelated genes

useful to make biological interpretations from large gene list

Transgenic

less known consequences of inserted DNA

large burden of proof to demonstrate

Gene edited varieties

makes small insertions or deletion that could occur in nature

easier path towards market use

genetic engineering

process that uses tech to directly alter, delete, or insert DNA into an organism’s genetic makeup

transgenesis

foreign genetic material from one organism is introduced into the genome of another, unrelated organism

mutagenesis

which genetic info. of an organism is altered