BIO 101 - Genetics, Genomics, and Evolution

Chromatid

one of the two identical copies of a chromosome that are formed when the chromosomes duplicates to prepare for cell division

Chromatin

a bunch of nucleosomes wound around histones or other proteins

Chromosome

A structure composed of DNA that is tightly wound around histones

DNA barcoding

• sequencing a specific part of a gene at a specific locus from a sample and comparing that sequence to sequences from specimens where the species identification is already known

• often uses the cytochrome oxidase 1 (CO1) gene

proteins

molecules made up of amino acids responsible for structure, function, and regulation

Amino acid

the fundamental molecule that serves as the building block for proteins

Exons

sections of DNA that code for proteins

Genome

all of an organism's DNA

Histone

protein that DNA coils around, forming a nucleosome

Introns

• Gene sequence sections of DNA that do not code for proteins

• Located between exons

Leading strand

the strand where DNA polymerase can continue to add nucleotides uninterrupted during DNA replication

Lagging strand

• the strand where DNA polymerase cannot add nucleotides uninterrupted during DNA replication, as it must “jump ahead" to travel in the 5’ to 3’ direction

• creates Okazaki fragments

Nucleus

Organelle where where DNA is stored

Mirochondria

• the organelle with the primary function of breaking down other molecules to generate energy in the form of a molecule called ATP (adenosine triphosphate)

• found in most eukaryotic cells

Nucleosome

DNA wrapped around a single histone, the building block of chromatin

Nucleotide

• the basic building blocks of DNA and RNA

• made up of a nitrogenous base (A, G, C, T/U), a sugar, and a phosphate group

Orthologus gene

a gene in different species that evolved from a common ancestral gene through speciation

Okazaki fragment

• Fragments of newly synthesized DNA that occur on the lagging strand during DNA replication

• happen because of DNA polymerase can only add nucleotides in the 5’ to 3’ direction

• are joined by an the enzyme ligase

Sequence alignment

• matching a gene sequence or protein sequence to one or more other sequences of the same type

• hypotheses because there are many possible ways to align a sequence.

• can have "mismatches" and "gaps" in an alignment

Trait

attributes of an organism that are expressed by genes and/or influenced by the environment

Gene

• the fundamental, physical, and functional unit of heredity

• make up sequences of DNA

• changes in these drive evolution and natural selection

Locus

the specific location of a gene on a chromosome

Genotype

the genetic makeup of an organism, an organism’s complete set of genes

Phenotype

the physical or physiological features of an organism, an individual’s observable traits

Population

individuals of the same species living together at the same place and time

Species

A group of closely related organisms that can interbreed

nuclear genome

• made of up linear

• chromosomes are present in pairs called homologues

• diploid

mitochondrial genome

• circular

• many copies per cell

• haploid

diploid

• a cell or organism with two complete sets of chromosomes

• in humans, most cells are _____, meaning they contain 23 pairs of chromosomes, or 46 chromosomes in total

haploid

• a cell or organism with a single set of chromosomes

• in humans, only the gametes (sperm and egg cells) are _____

alternative splicing

• describes the phenomenon in which exons are joined in different combinations

• allows a single gene to produce multiple mRNA transcripts

transcription

• the process of copying the genetic information stored in a DNA strand into a complementary strand of RNA

  1. initiation - RNA polymerase binds to the promoter, DNA is unwound, and forms a transcription bubble

  2. elongation - RNA polymerase facilitates nucleotide base pairing

  3. termination - the hydrogen bonds of the RNA/DNA helix break

• in prokaryotes, occurs in the cytoplasm

• in eukaryotes, occurs in the nucleus

translation

a biological process wherein the genetic code from a strand of mRNA is converted into amino acids

1. initiation - the ribosome binds to the mRNA and the tRNA attaches to the start codon of the transcript

2. elongation - amino acids are brought to the ribosomal site by the tRNAs according to the sequences of codons in the mRNA transcript

3. termination - the stop codon signifies the end, the newly formed protein is folded

promoter

region of DNA upstream of a gene where relevant proteins (such as RNA polymerase and transcription factors) bind to initiate transcription of that gene

central dogma

describes the flow of genetic information

• genetic information from DNA is copied to mRNA

• mRNA is converted into proteins

eukaryote

• any cell or organism that possesses a clearly defined nucleus

• all animals, plants, fungi, and many unicellular organisms

prokaryote

a single-cell organism whose cell lacks a distinct nucleus and other membrane-bound organelles

DNA replication

• the process of copying and duplicating a DNA molecule

  • helicase unwinds the DNA strands

  • primase attaches a primer

  • DNA polymerase extends the primer by adding complementary nucleotides

• semiconservative - the new molecule consists of one original and one newly created strand

DNA polymerase

enzyme that assists in synthesizing chains of nucleic acids

mitosis

• the cellular process where a single cell divides resulting in two identical cells

  1. prophase - the nuclear membrane breaks down, chromatin condenses into an x-shaped structure

  2. metaphase - the chromosomes are aligned in the center of the dividing cell

  3. anaphase - the daughter chromosomes separate and move to opposite poles

  4. telophase - a nuclear membrane forms around each set of chromosomes

PCR (polymerase chain reaction)

laboratory technique for rapidly producing (amplifying) millions of copies of a DNA sample

• ingredients

  • template DNA

  • primers

  • dNTPs (the nucleotides to make DNA copies)

  • DNA polymerase

• steps

  1. denaturing - heat separates DNA into single strands

  2. annealing - the temperature is lowered to allow the primers to base pair to the template DNA

  3. extension -the temperature is raised again and the Taq polymerase enzyme makes a new strand of DNA

primer

short DNA sequence that binds to a specific region of DNA to initiate DNA synthesis

mutations

a change in the nucleotide sequence

two main sources:

• errors during DNA replication

• DNA damage that goes unrepaired

some are synonymous (silent) and some are non-synonymous (missense or nonsense)

• missense - one amino acid is substituted for another

• nonsense - a premature stop coden is coded for, resulting in a shortened or nonfunctional protein

types

• substitutions

  • transition - a purine base is replaced by another purine, or pyrimidine for another pyrimidine (ex. A for G or C for T)

  • transversion - a purine base is replaced by a pyrimidine base (ex. A for C)

• deletions

• duplications

• inversions

• translocations

“on” vs. “off” genes

Gene “on”

• open chromatin

• unmethylated bases

• acetylated histones

Gene “off”

• condensed chromatin

• methylated bases

• deacetylated histones

mRNA

• formed by transcription

• messenger RNA

• carries protein information from the DNA in a cell’s nucleus to the cytoplasm, where it can then be translated into a chain of proteins

tRNA

• formed by transcription

• plays a key role in protein synthesis, linking mRNA and the chain of amino acids

rRNA

• formed by transcription

• structural and functional component of ribosomes, which read the mRNA sequence and translate the genetic code into a string of amino acids

alleles

different versions of a gene

paralogs

gene copies created by a duplication event within the same genome

haplotype

a combination of alleles from multiple loci on a single chromosome, tend to be inherited together

codominance

• neither allele is dominant or recessive, both traits appear

• examples

  • blood type: A and B alleles are _____, when inherited they create the phenotype of AB blood

  • sickle cell: when humans inherit one allele for sickle cell hemoglobin and one normal allele, both proteins are made and create the sickle cell trait

  • flowering plants: some flowering plants show patches of different colors on the same flower

incomplete dominance

• neither allele is completely dominant, resulting in an intermediate phenotype in the offspring

overdominance

a selective process in which the survival and/or fertility of an individual are increased if the individual is heterozygous at a given locus

meiosis

• the process of cell division that results in the production of four haploid daughter cells from a diploid parent cell

• responsible for the production of gametes

• prior to meiosis, the chromosomes in a cell are copied during interphase

• meiosis I

  1. prophase I - the chromosomes condense into X-shaped structures, homologous chromosomes exchange DNA (crossing over), the nuclear membrane dissolves

  2. metaphase I - the chromosome pairs line up along the center of the cell, the spindle fibers attach

  3. anaphase I - the pair of chromosomes are pulled apart by the meiotic spindle, the chromosomes remain together

  4. telophase I - the chromosomes migrate to the spindle poles, nuclear membranes are reformed, daughter cells are seperated

• meiosis II

  1. prophase II - the nuclear envelope disintegrates, the chromatids thicken and shorten

  2. metaphase II - the chromosomes are aligned in the center of the cell

  3. anaphase II - the sister chromatids separate and move towards the poles of the cell

  4. telophase II - four haploid cells are produced, nuclear membranes are fully developed, the cells are completely seperated

mitosis vs. meiosis

mitosis

• produces diploid cells (2n)

• includes one nuclear division

• makes somatic cells

• responsible for asexual reproduction

• no crossing over

• produces two cells

meiosis

• produces haploid cells (n)

• includes two nuclear divisions

• makes gamete cells

• responsible for sexual reproduction

• crossing over

• produces four cells

crossing over

a cellular process that occurs during meiosis during which homologus chromosomes exchange genetic material

results of independent assortment, crossing over, and sexual reproduction

1. new combinations of alleles quickly

2. purging deleterious mutations

why don’t all organisms reproduce via sex if it allows for new combinations?

the energetic costs

• finding/competing for a mate

• secondary sexual characteristics

• exposure to disease and predation

• nuptial gifts

the benefits of sex

1. can unite mutations in a single individual quickly

2. allows an individual to purge deleterious material

mendelian genetics

inheritance patterns where traits are determined by a single gene with clear dominant and recessive alleles

relies on

• complete dominance

• only two possible alleles for a gene

• a trait being determined by just one gene

• independent assortment (the inheritance of one trait does not influence the inheritance of another)

• biparental inheritance

non-Mendelian genetics

• inheritance patterns that do not follow the rules of Mendelian genetics, often involving multiple genes, incomplete dominance, or other complex interactions between alleles

• most traits follow this model because they…

  • have more than two alleles for a given trait

  • are influenced by more than one locus

  • are influenced by the environement

epistasis

a circumstance where the expression of one gene is modified by the expression of other genes

pleiotropy

when one gene impacts multiple traits

horizontal transfer

the movement of genetic material by means other than parent-to-offspring (vertical) inheritance

transposable element (TE)

a piece of DNA that is, or once was, capable of moving or replicating and reinserting in the genome

ploidy

the number of complete sets of chromosomes in a cell

• ex. haploid, diploid, triploid

natural selection

• differential survival and reproduction of individuals due to differences in phenotype

• key force in evolution

random genetic drift

• mechanism of evolution

• characterized by random fluctuations in the frequency of a particular version of a gene (allele) in a population

• strongest effects in smaller populations

assortative mating

mating pattern in which individuals with similar phenotypes or genotypes mate with one another more frequently