Genetics Vocabulary

EBIO 2070

genotype

the genetic constitution of an individual organism, the set of alleles (alternate forms of genes) possessed by an individual organism (DNA sequence of an individual)

phenotype

the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment

heredity

is the passing on of traits from parents to their offspring

genome

all of the genetic material in an organism

GWAS

Genome-wide Association Study

p-value

a number describing how likely it is that your data would have occurred under the null hypothesis of your statistical test

mendelian genetics

single-gene inheritance

genetic determinism

attributing to genes the formation of human traits at an individual level, perceiving them as having more causal power than what scientific consensus suggests

genetic essentialism

the tendency to infer a person's characteristics and behaviors as based on their perceived genetic make-up

heritability

estimates the degree of variation in a phenotypic trait in a population that is due to genetic variation between individuals in that population, a measure of how well differences in people’s genes account for differences in their traits, a statistical concept (represented as h²) that describes how much of the variation in a given trait can be attributed to genetic variation, percent of the variance in a phenotypic property

norms of reaction

genotypes give different phenotypes in different environments, show the range of phenotypes that can be produced by a genotype when the environment varies; the array of phenotypes that will be developed by a genotype over an array of environments

polygenic expression

a trait that is influenced by multiple genes

allele

An allele is a variation of the same sequence of nucleotides at the same place on a long DNA molecule, one of two or more alternative forms of a gene that arise by mutation and are found at the same place on a chromosome

VP = VG + VE

genetic variance vs environmental variance

H2 = VG / VP

broad-sense heritability

broad-sense heritability

provides a measure of the extent to which phenotypic variation is the result of genetic variation

reaction norm

the array of phenotypes that will be developed by a genotype over an array of environments

genome-wide association study (GWAS)

where scientists look across the entire human genome at genetic differences among people to see whether any of these differences are, on average, associated statistically with higher or lower levels of some outcome

chromosome

structure consisting of DNA and associated proteins that carries and transmits genetic information (23 pairs in humans)

genome

the entire complement of genetic material in a chromosome set (3.2 billion base pairs of DNA in humans)

gene

fundamental units of biological information; a unit of inheritance that gets transcribed and may or may not get translated into protein; often defined at the molecular level as a DNA sequence that is transcribed into an RNA molecule (about 20,000 genes in humans)

allele

one of two or more alternative forms of a gene

genotype

the set of alleles possessed by an individual organism

DNA

two antiparallel sugar-phosphate backbones with paired, complementary bases

Manhattan plot

plots the p-values from association tests of individual SNPs; the significance level is set at a p-value of 5×10^-8 because of the large number of tests

odds

ratio of event occurring to event not occurring

odds ratio

ratio of offs of disease in one group (with a particular allele or genotype) to the odds in another group; effect sizes in case/control data can be expressed as this

effect sizes in GWAS

rare variants with small effects are difficult to detect; common variants with large effects may not exist

Beta

the slope of a regression like that can be used to estimate effect sizes for continuous traits

nucleotide

the building block of DNA; made up of one nitrogenous base (A, T, C, G), a deoxyribose sugar, and a phosphate group

purine nucleotides

two ring nitrogenous bases (A and G)

pyrimidine nucleotides

single ring nitrogenous bases (C and T)

chromatin

1/3 DNA, 2/3 protein; material that makes up chromosomes; each chromosome in eukaryotes is a linear piece of DNA; a flexible and disordered granular chain that is packed together at different concentration densities in interphase nuclei and mitotic chromosomes

nucleosome

the basic unit of chromatin; 147 bp of DNA wrapped around a histone octamer (2 copies each of 4 proteins)

chromosome territories

a particular region of a nucleus occupied by an individual chromosomec

compartments

within each chromosome in a territory we can divide it into two different spatial locations called A and B compartments

B compartment

heterochromatic; attached to the nuclear lamina; darkly staining, tightly condensed, usually inactive in terms of gene expression and transmission; towards the outside of the nucleus

A compartment

euchromatic; lightly staining, loosely-packed, tend to be genes that are active in terms of gene expression and transcription; towards the inside of a nucleus

topologically-associating domains (TADs)

contain sequences that interact more frequently with sites inside than outside the domain; are structural and functional units of chromosomes related to gene expression and DNA replication; reproducible between cells but whether or not they’re in an A or B compartment varies between cells

insulators

DNA sequences that can bind proteins and block interactions between regulatory elements and genes; found at TAD boundaries; insulate regulatory elements in one TAD from coding regions of a gene in another TAD

TAD boundaries

where origins of DNA replication are enriched

cis-regulatory regions

involved in determining whether or not a gene gets transcribed; includes enhancers, promoters, and insulators

transcribed regions

consists of exons (which consist of un-transcribed regions (UTRs) and coding regions) and introns

exons

anything that gets transcribed and left ends up in the mRNA (we want all the parts that code for amino acids in there); all of the protein coding regions are in exons but everything in an exon does not necessarily encode a protein

introns

do get transcribed but they get taken out in the processing that forms the final mRNA

transcription

the process of copying a segment of DNA into RNA

enhancer

a DNA sequence that can be bound by proteins to increase the likelihood that transcription of a particular gene will occur

promoter

a sequence of DNA to which proteins bind to initiate transcription of a single RNA transcript from the DNA downstream of the promoter

pre-initiation complex

assembles on promoters of protein-coding genes to position RNA polymerase II (Pol II) for transcription initiation; made up of general transcription factors, RNA polymerase, and the promoter DNA sequence

transcriptional activators

proteins that bind to enhancers and interact with the proteins of the pre-initiation complex to facilitate transcription/gene expression; also called transcription factors; are how different enhancers have different functions in different locations

chromatin remodeling/nucleosome remodeling

shifting the DNA sequence relative to the histone proteins or moving the nucleosomes to expose enhancers and promoters

SWI-SNF protein

protein that moves the nucleosome during chromatin remodeling

histone modifications

can affect how easy it is to move the nucleosomes/affect chromatin conformation; acetylation and methylation is the covalent modification of histones

acetylation

associated with active or open chromatin

methylation

associated with either active/open chromatin or inactive/condensed chromatin depending on the specific one

pre-mRNA

the primary transcript, needs 3 modifications to make a mature mRNA

ribonucleoproteins

complexes between RNA and proteins

co-transcriptional RNA processing

as we make a transcript, modifications happen before it’s finished; includes 5’ cap, RNA splicing, and addition of poly(A) tail,

5’ cap

added to the 5’ end of a transcript during co-transcriptional RNA processing; 7-methyl guanosine (chemically modified nucleotide) in 5’ to 5’ linkage; is not encoded in the DNA; increases RNA stability, facilitates ribosome binding, and enhances RNA splicing

RNA polymerase II

associated with capping enzymes that carry out modifications, available to put cap on before the end of the transcript is being made

RNA splicing

intron removal; cuts the RNA strand, removes a piece, and rejoins it

spliceosome

complex of multiple small nuclear ribo-nucleo protein particles consisting of proteins and SnRNAs; made up of 5 SnRNPs

SnRNA

involved in catalyzing the cutting of the DNA strand and removal and rejoining of the exons; encoded in the genome and assembles with a set of proteins to form a SnRNP; processes pre-mRNA

SnRNP

small nuclear ribonucleoproteins; RNA-protein complexes that combine with unmodified pre-mRNA and various other proteins to form a spliceosome

alternative splicing

for a given gene, exons can be joined in various combinations; there are exons that in some cases are not in a particular transcript

RNA-binding proteins

facilitate which parts get spliced out and differs between cells

poly(A) tail

added to the 3’ end of a transcript during co-transcriptional RNA processing; increases mRNA stability and facilitates ribosome binding; 50-250 A’s added by poly A polymerase through polyadenylation

post-transcriptional regulation

makes a transcript and then decides not to translate it

amino acid

subunit of a protein; are linked by peptide bonds to create polypeptide chains that form proteins, grow in the amino to carboxyl direction

amino end

5’ end of an amino acid with respect to the mRNA

carboxyl end

3’ end of an amino acid with respect to the mRNA

open reading frame

the protein coding portion of an mRNA, span of DNA sequence between the start and stop codons

tRNA

transfer RNA, encoded by regions of the genome, get transcribed to form the functional tRNA but don’t get translated and instead function in the translation process/apparatus; single stranded RNA molecule but can base-pair with themselves to form regions that would essentially be double-helical with some parts not base-paired; helps incorporate amino acids into polypeptide chain

anticodon

3 nucleotides, complementary and anti-parallel to mRNA/codon, located at one end of the tRNA molecule

aminoacyl-tRNA synthetase

protein that synthesizes a tRNA that is covalently attached to an amino acid; amino acid joined to 3’ end of the tRNA; forms a “charged” tRNA; process is needed for translation

small ribosomal subunit

made up of ribosomal RNAs and proteins; recognizes and attaches to the 5’ cap and scans for a start codon in the proper sequence context moving 5’-3’ relative to mRNA

large ribosomal subunit

made up of ribosomal RNAs and proteins; associates with the small subunit spanning the start codon; after the start codon is found the complete ribosome is assembled

release factor

protein shaped like a tRNA that recognizes/identifies a stop codon and catalyzes the removal of the polypeptide chain from the tRNA

roles of ribosomes

recognize the start codon, stabilize tRNA-mRNA interactions, peptidyl transferase activity (acts as ribozyme), and move along mRNA in 5’-3’ direction

peptidyl transferase

joins two amino acids to begin and continue creating a polypeptide chain

ribozyme

RNA that acts as an enzyme

microRNA (miRNA)

non-coding RNA that seems to be involved in post-transcriptional regulation of gene expression by reducing the amount of translation that occurs; these along with siRNAs and piRNAs are involved in RNA interference (RNAi) by inhibiting the translation of mRNA

transcriptome

which RNAs are present

proteome

which proteins are present

ribosomal RNA (rRNA)

structural and functional components of the ribosome

messenger RNA (mRNA)

carries genetic code for proteins

miRNA-Induced Silencing Complex (miRISC)

binds to an mRNA, preventing or reducing the translation from that particular RNA transcript; binds to the 3’ UTR of a transcript that it’s regulating

endonucleolytic cleavage

break in the covalent bond, clip the transcript, and prevent it from being translated

deadenylation and degradation

removal of the poly(A) tail and subsequent degradation by cellular machinery

development

process of going from a single celled zygote to a trillion (human) celled individual

robustness

despite the fact that individuals might have variation in their genome and despite the fact that there can be random effects on the levels of transcription, similar looking individuals are generated at the end of development despite a multitude of differences around the time of development

invariant output

adult individuals look fairly similar despite them developing in different environments with different genomes

uniform translation

the binding of miRNAs to transcripts takes different transcript levels and makes a uniform output of the protein

DNA replication

semiconservative process, process of producing two identical replicas of DNA from one original DNA molecule

phosphodiester bonds

a covalent linkage between the phosphate of one nucleotide and the hydroxyl (OH) group attached to the 3′ carbon of the deoxyribose sugar in an adjacent nucleotide, forming what is known as the “sugar-phosphate backbone” of DNA

denature

separate

anneal

formation of hydrogen bonds

origin of replication

unique sequence of DNA; always where DNA replication occurs because there are initiator proteins that recognize that sequence and specify where replication starts

DNA helicase

separates/denatures the two strands of the double-helix so they can be used to synthesize a new strand

single-strand-binding proteins

prevent strands from re-associating so they can be used as templates