BIOL 3010 Exam 1 Vocab

denaturation

first step of PCR- double-stranded DNA broken into two separate strands

-hydrogen bonds are broken

annealment

second step of PCR- hydrogen bonds formed between complementary bases

-joining of the template strand and the primer

elongation

final step of PCR- polymerase extends the amplified strand of DNA based on complementary template strand

segregation

separation of alleles in gamete formation

-one allele of each gene goes to the gamete

-one of Mendel’s laws:within one gene

independent assortment

random distribution of different alleles of different genes in gamete formation

ex. the gene for smooth v wrinkled will be passed down separately from the gene for green v yellow

-between genes!

locus

designated location on a chromosome

-sometimes refers to a gene

allele

alternative forms of a single gene

selection

eliminates individuals whose fitness is low and chooses individuals of high fitness to be the parents of the next generation

fitness

based on fecundity and survivorship: the relative advantage or disadvantage a particular genotype gives to an individual

inheritance/heredity

way genes transmit physiological, physical, and behavioral traits from parents to offspring

preformationism

the pre-Mendelian idea that organisms develop from a miniature version of themselves

genetic model organism

• Mendelian created the first one with his pea plants

• an organism that is used to understand biological phenomena

dominance

an allele that if present, will result in a particular genotype

recessivity

an allele that if present in BOTH alleles, will show phenotype, but is hidden if paired with a dominant allele

additivity

genes that code fore the same trait and all contribute to the phenotype

continuous v discrete trait

a continuous trait appears in a range of different phenotypes while a discrete trait is one or the other

thermal cycler/ pcr machine

used to amplify DNA through PCR

nucleotide

subunit of DNA or RNA consisting of a phosphate group, nitrogenous base, and a sugar

nucleoside

only the ribose and the nitrogenous base of DNA/RNA

nitrogenous base

components of nucleotides

DNA: adenine, thymine, guanine, cytosine

RNA: adenine, uracil, guanine, cytosine

phosphate group

phosphate bound to four oxygen atoms

-part of a nucleotide

ribose

sugar in an RNA nucleotide - 5 carbons

deoxyribose

sugar in a DNA nucleotide

hydrogen bond

an intermolecular force that holds complementary nucleotides together in DNA

covalent bond

sharing of electrons that result in a sigma bond

antiparallel

the structure of DNA: strands run in opposite directions so that one is 3’ to 5’ (template) and one is 5’ to 3’ (coding strand)

minor v major groove

in a DNA molecule, the minor groove is the smaller gap resulting from the displacement of the backbone whereas the major groove is the larger gap

-each have different reactivites and interactions with other molecules

amino acid

the building blocks of proteins produced during translation

• built from triplets of nucleotides

ribosome

cytoplasmic structures composed of ribosomal RNA and protein; the sites of protein synthesis

ribozyme

RNA molecules that can act as enzymes to catalyze specific chemical reactions

catalysis

the acceleration of a chemical reaction due to a catalyst

RNase

ribonuclease, are enzymes that catalyze RNA into smaller components

DNAse

Deoxyribonuclease are enzymes that catalyze DNA into smaller components

mutagenesis

the process by which an organism's deoxyribonucleic acids (DNA) change, resulting in a gene mutation

haploid

contains one set of chromosome - often used in mutagenesis experiments to isolate certain alleles

ex. haploid yeast in determining transformation of virulence

diploid

two matching set of chromosomes

nonsense mutation

an amino acid codon is changed into stop codon, terminating translation

missense mutation

mutation in a gene that changes a codon for one amino acid to a codon that specifies a different amino acid

collinearity

the length of a DNA sequence in a gene is proportional to the length of the polypeptide encoded by the gene

• the same part of the gene correlated with the location of an amino acid in the polypeptide

transformation

transformation is the genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material from its surroundings through the cell membrane

ex. R form taking up dead S form debris to become virulent

codon

three consecutive nucleotides of DNA/RNA that code for an amino acid

initiation codon

AUG

stop codon

UAG, UGA, UAA

degeneracy

several different codons can code for the same amino acid

sense strand

aka coding or + strand: 5’ to 3’ strand of DNA that is the exact copy of a mRNA to be translated

antisense strand

aka noncoding, template or - strand : 3’ to 5’ strand of DNA that is complementary to the mRNA transcribed

frameshift mutation

insertions or deletions that alter the grouping of nucleotides by the reading frame- results in different amino acids

TSS

transcriptional start site

-The first base of a gene to be transcribed by an RNA polymerase, corresponding to the 5′-most base of the resulting transcript

untranslated region

or UTR, a part of the gene body that is not transcribed occurring before the promoter and after the transcriptional termination site

exon

short regions of DNA that are transcribed to become a part of the mRNA and later translated into protein

intron

part of the gene body that is in pre-mRNA, but is spliced out by spliceosomes before transcription

-important for genetic variation, only in eukaryotes

core promoter

where transcription is initiated

cis-regulatory element

a DNA motif located ON the gene being described that impacts gene expression by interacting with other transcription factors like trans-regulatory proteins

enhancer

cis-acting DNA sequences that promote the transcription of genes

Sanger sequencing

uses DNA sequencing machinery to make a copy of desired template- “first generation”

-extended with oligonucleotide primer and separated by size with electrophoresis

-involves the use of ddNTPs which randomly terminates extension at corresponding nucleotide-varying sizes then separated and read off of a gel

-only feasible with small portions of DNA

dNTP

Deoxynucleotide triphosphates that are building blocks of amino acids

ddNTP

dideoxynucleotide triphosphates used in sanger sequencing

-randomly terminates sequence at the corresponding base by inhibiting DNA polymerase enzyme

bacterial artificial chromosome (BAC)

an engineered DNA molecule used to clone DNA sequences in bacterial cells

flow cell

glass slide coated with oligonucleotides complementary with nucleotides

-single-stranded, adapter-ligated DNA fragments can attach through hybridization

capillary sequencer

a part of improved first gen sequencing

-reactions with ddNTP sent through capillary and the laser separates them by size

dye terminator

eliminated the need to run 4 separate runs of Sanger sequencing by attaching fluorescent dyes to ddNTPs

Moore’s law

based on computer chips, the idea that technological advances doubles every two years

-gave hope to those attempting to sequence the genome that we would have the advances necessary to make it possible

-advances in sequences surpass this

illumina sequencing

“Second generation” sequencing

sequences tethered to a flow cell, adding one nucleotide at a time

-Terminator could be reverse- turned into regular nucleotide and the original dye quenched

contig

stretches of contiguous DNA sequence obtained by computer alignment of sequence reads; each chromosome is a contig

coverage

describes the number of sequencing reads that are uniquely mapped to a reference and “cover” a known part of the genome

-need high coverage to ensure no genes are missing from the sequence

electropherogram

a plot of DNA fragment sizes, typically used for genotyping such as DNA sequencing

pseudogenes

a nonfunctioning gene - originally functioning gene has undergone mutations such that it no longer functions.

transposable elements

DNA segments that move about in the genome

-a barrier to DNA sequencing

transcription factors

cis: on the gene, trans: produced by sites on a different gene (mostly proteins that interact with cis sites to either inhibit or promote transcription)

-protein whose DNA sequence-specific binding to a cis-control element regulates the timing, location, or level of a particular gene’s transcription

chromatin

-DNA must be organized into chromatin in the nucleus- with 1/3 being DNA, histone proteins, and non-histone proteins

-helps condense naked DNA

nucleosome

DNA coiled around histone proteins, refers to particular part of chromatin

euchromatin

“open chromatin” that is more accessible to RNA polymerase and transcription factors

heterochromatin

“closed chromatin” that is more condensed and less accessible to RNA polymerase and transcription factors

acetylation

addition of an acetyl group to histones during histone modification

-takes + charge and neutralizes it so it is no longer as attracted to - charge in DNA → results in more accessible chromatin

histone acetyltransferase

enzymes that acetylate histone tail and opens up chromatin

histone deacetyletransferase

enzymes that removes acetyl group from histone tail and condenses chromatin

methylation

addition of a methyl group on the histone tail that usually closes up chromatin but can have both effects

Protein arginine methyltransferase (PMRT)

enzyme that methylates arginine

histone methyltransferases (HMTs)

enzyme that methylates histone tails, impacting chromatin structure

histone mark

places where histones are modified

Chromatin immunoprecipitation

chip sequencing used to locate histone marks

-antibodies of the protein are incubated with the protein, unattached DNA is washed out, and you are left with the fragments that contain the modification of interest

pioneer transcription factor

can weasel in to relatively condensed chromatin that other transcription factors cannot

-bind DNA sequence to permit binding of other transcription factors, histone variants, and chromatin remodelers

pre-initiation complex

aka PIC, a complex of proteins that is formed before the transcription

-includes RNA polymerase 2 and other transcription factors

-important for RNA pol 2 recruitment, also opens DNA helix, through DNA translocase XPB so transcription can be initiated

mediator

promotes PIC assembly and helps pol 2 to be localized in the correct spot

acts as a bridge between the promoter DNA sequence bound to an enhancer or silencer, and RNA polymerase II at the initiation site

TATA-box

-a sequence of DNA found in the core promoter region of genes

• a part of the PIC and determines the side where transcription begins

initiator

A site, upstream from a structural gene, for attachment of a protein that stimulates initiation of transcription

general transcription factor

proteins that help to position Pol II correctly on the promoter, a part of the PIC

pre-mRNA

the initial form of mRNA that still includes introns

mRNA

messenger RNA, the product of transcription that is then sent out into the cell to be translated

eRNA

enhancer RNAs result from RNA pol2 attaching to an enhancer instead of a promoter due to their similarities

uaRNA

antisense RNA, transcribed upstream instead of downstream

DNA binding domain

independently folded protein domain that contains at least one structural motif that recognizes double- or single-stranded DNA

transactivation domain

contains binding sites for other proteins such as transcription coregulators.

cofactor (coactivators and repressors)

-lack DNA binding domains

bound to a protein (usually an enzyme) and is required for the protein's biological activity

Bridge activators to basal transcriptional apparatus

ex. mediator complex

coactivator promotes transcription while corepressors inhibit it

DNA methyltransferase

methylates CpG islands (not to be confused with histone methyltransferase!!)

• removes transcription factor off of the promoter to inhibit transcription

• leads to histone methylation

• Methylated cytosines recognized by methyl-CpG binding proteins (meCPs) - leads to chromatin condensation

CpG island

large number of CpG nucleotide repeats often near the promoter - can be methylated, leading to the inhibition of transcription

epigenetic silencing

non mutational gene inactivation that can be passed down to daughter cells

ex. methylation of CpG islands

ATP-dependent chromatin remodeler

alters chromatin structure by sliding, displacement, modification

-share affinity for nucleosome, domains to recognize histone modifications/other proteins, and similar ATPase domains for overcoming nucleosome-DNA interactions

-exposes DNA for DNA binding protein to access, allows accessibility for transcription factors to interact with cis-regulatory elements

phosphorylation

-A process in which a phosphate group is added to a molecule, such as a sugar or a protein.

-changes chromatin state

cancer driver mutation

changes in the DNA sequence of genes that cause cells to become cancer cells and grow and spread in the body

-dysregulation of gene expression