Anthropology Section 3

Ancient DNA

DNA extracted from archaeological materialists to understand population history

Gregor Mendel

Person who discovered the basic principles of heredity in the 1800s

Gene

Unit of inheritance, code for proteins

Locus

Location of a gene on a chromosome

Allele

Different forms of a gene

Dominant Allele

An allele that is fully exposed (A)

Recessive Allele

An allele that is not expressed against a dominant allele

Phenotype

The physical expression of genotypes in an organism

Genotype

The genetic makeup of an organism

Law of Segregation

Mendel's law that states that the pairs of homologous chromosomes separate in meiosis so that only one chromosome from each pair is present in each gamete

Law of Independent Assortment

Each pair of alleles (gene) on separate chromosomes separate independently into gametes, only applies to genes located far away from each other, independent behavior of genes creates unique combination of alleles

Simple Mendelian Diseases

Some (not many) human diseases have Mendelian inheritance, can use pedigrees to track appearance through generations

Pleitrophy

When a single gene affects more than one phenotypic characteristic.

Polygenic Inheritance

combined effect of two or more genes on a single character

Darwin and Mendel

Used observations to find patterns in inheritance, didn't know the mechanism or the physical structure or inheritance

Watson, Crick, and Franklin

Discovered the structure of inheritance which is DNA

DNA structure

Double helix, looks like a twisted ladder, basic of heredity

DNA Backbone structure

Chain of nucleotides bound by phosphodiester bonds.

5' end

the end of the DNA ladder that DNA polymerase is UNABLE to build (phosphate group)

3' end

The end of the DNA ladder that DNA polymerase can add nucleotides to during DNA replication (no phosphate group)

5 carbon sugar, phosphate group, nitrogenous base

Structure of nucleotides

T

A only binds to ...

G

C only binds to ...

DNA chromosome

exists as one long double helix associated with various proteins that regulate genetic activity.

DNA Chromatid

One of the two identical copies of DNA that make up a replicated chromosome

Histones

protein molecules around which DNA is tightly coiled in chromatin, helps control gene expression

Haploid

A single set of unpaired chromosomes

Diploid

Cell contains two complete sets of homologous chromosomes (identical)

DNA Replication Steps

1) Helicase- unwinds the parental double helix

2) Binding Proteins- upstream of helices alleviating torsional strain

3) Single-strand binding proteins (SSBP) stabilize unwound DNA, aided by DNA gyrase.

4) Primase synthesizes a short RNA primer for DNA polymerase to bind to in the 5' to 3' direction to start replication on each strand.

5) DNA polymerase synthesizes the leading strand in 5' to 3' direction while the lagging strand is made discontinuously by primase making short pieces and then DNA polymerase extending these to make Okazaki fragments.

6) DNA ligase joins the Okazaki fragments together

Leading Strand

The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5' to 3' direction.

Lagging strand

The strand in replication that is copied 3' to 5' as Okazaki fragments and then joined up.

Mutuation

any alterations in sequence DNA on a chromosome

Mitosis or Meiosis

Once DNA is replicated, what can we proceed with?

Karyotype

A visual representation of an individual's chromosomes arranged in a standardized format

Mitosis

DNA is copied and allocated equally into two daughter cells (Genomes are exact copies)

Meiosis

Process of cell division that produces gametes (sperm/egg cells)

Meiosis 1: Crossing over and Cell Division

4N chromosomes become 2N chromosomes

Meiosis 2: Second Round Cell Division

2N chromosomes become N chromosome, sister chromatids separate and form two haploid daughter cells, each have one set of chromosomes

Transcription (DNA to RNA)

Unit: stretch of DNA that codes for a polypeptide or RNA (tRNA, rRNA)

RNA Polymerase II: Separates DNA strands and transcribes mRNA. Attaches to promoter (start of gene), stops at terminator (end).

mRNA elongates in 5' - 3'

Uracil replaces thymine when pairing to adenine

Introns

Non coding sections of RNA, important for gene expression

Exons

Coding section of RNA

Alternative Splicing

Splicing of introns in a pre-mRNA that occurs in different ways, leading to different mRNAs that code for different proteins or protein isoforms. Increases the diversity of proteins.

Translation

Process by which mRNA is decoded and a protein is produced

Transfer RNA

type of RNA molecule that transfers amino acids to ribosomes during protein synthesis

Ribosome

Cellular organelle, read the sequence of nucleotides in mRNA, assemble the corresponding sequence of amino acids into a polypeptide chain

Codons

A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code. 64 different combinations.

Start Codon

codon that signals to ribosomes to begin translation; codes for the first amino acid in a protein

Stop Codon

codon that signals to ribosomes to stop translation

DNA Modern Evolutionary Synthesis

Macroevolutionary processes seen in the fossil record are due to microevolutionary (genetic) changes -- combines Darwin's Theory of Evolution by Natural Selection with Mendel's mechanism of inheritance

mutation, gene flow, genetic drift, natural selection

Four Forces of Evolution

Spontaneous Mutation

a random change in the DNA arising from errors in replication that occur randomly

Induced Mutations

refers to those mutations in the DNA resulting from exposure to toxic chemicals or to radiation

Nondisjunction

Error in meiosis in which homologous chromosomes fail to separate.

Point Mutations

chemical changes in just one base pair of a gene

Silent Point Mutation

Point Mutation that does not result in an amino acid change

Non-synonymous Point Mutation

Point mutation that does result in an amino acid change

Missense Mutation

Mutation that changes the codon from amino acid to another

Nonsense Mutation

A mutation that changes the amino acid to a start or stop codon

Frameshift Mutation

Insertion or deletion of a base that results in the rearrangement of sequencing triplets

Transposable Element

Whole genes or portions of genes that are inserted (cut and paste) or copied (copy and paste) into different regions in the genome

Selection

Individuals with advantageous characteristics will survive in higher number and produce more offspring

Directional Selection

Favors extreme form of one trait; over time, allele frequencies shift in one direction

Disruptive Selection

Extreme versions of the trait is favored, results in deviant allele frequencies, over time can produce speciation event

Stabilizing Selection

Favors the average version of the trait, over time less allele frequency variation, and deviance in trait expression

Balancing Selection

Very similar to stabilizing selection, balancing two or more forms of a trait in the population

Frequency-dependent Selection

Fitness of a phenotype depends on how common it is in a population

Sexual Selection

Adaptations to make organisms more likely to attract a mate

Female Choice

Pick mates to increase the survival of offspring, based on looks, behavior, and situation

Male Competition

females are a limiting resource, therefore males will compete with each other to gain access to females

positive assortative mating

Mate with individuals LIKE yourself. Decreases heterozygotes, increases homozygotes

negative assortative mating

Mate with individuals UNLIKE yourself. Increases heterozygotes, decreases homozygotes

genetic drift

A change in the allele frequency of a population as a result of chance events rather than natural selection.

allele frequency

Number of times that an allele occurs in a gene pool compared with the number of alleles in that pool for the same gene

bottleneck effect and founder effect

Causes of genetic drift

Bottleneck effect

A change in allele frequency following a dramatic reduction in the size of a population

Founder effect

change in allele frequencies as a result of the migration of a small subgroup of a population

Positive Selection

natural selection that increases the frequency of a favorable allele

Negative Selection

natural selection that decreases the frequency of a harmful allele

Neutral Theory of Evolution

Genetic Drift is the weakest force, but potentially the most important -- Most mutations are neutral, so selection does not act upon them
Most evolutionary changes occur through genetic drift, not selection

Gene Flow

Movement of alleles between two populations through breeding
Caused by migration (although does not necessarily lead to gene flow in all situations)

Genetic Diversity

Increases genetic diversity within the population (new alleles added)
Increases genetic similarity between two migrating populations (sharing alleles)

Barriers to gene flow

Any factors that prevent the exchange of genetic material between populations of a species, effectively isolating them from each other

Allopatric Speciation

The formation of new species in populations that are geographically isolated from one another.

Adaptive Radiation

When subgroups of a single species rapidly diversify and adapt to fill a variety of ecological niches. EX Lemurs.

Phylogeny

Can be based on morphology, total genomic diversity, or variance within a gene

Primate Genome Project

Understand the evolutionary relationships between the primate clades

Human Genome

3.2 billion base pairs
23 pairs of chromosomes (including 1 pair of sex chromosomes)
Important for understanding:
1. Evolutionary structure and Function
2. Human Population History
3. Impact of lived experience
4. Human Origins

Autosomal DNA

Chromosomes 1-22. Does not include sex-determining chromosomes (X and Y) or mitochondrial DNA (mtDNA). See chromosome.

Identical by descent (IBD)

when two copies of a gene in an individual trace back to the same copy in an ancestor

Single Nucleotide Polymorphisms (SNPs)

Inherited variations in a single nucleotide base in DNA that differ between individuals.

Direct to Consumer (DTC) Genetic Ancestry Testing

Commercial companies will analyze your DNA and return Ancestry Percentages, Disease risk calculations, or find relatives

Reference Genome

Is a digital nucleic acid sequence database, a representative example of a species' complete genetic sequence (genome) in a model organism.

Essentialism

The understanding that individual's characteristics, behaviors, and traits are primarily determined by their genetic makeup

Pros of DTCs

Can tell you what contemporary populations your ancestors approximately 12 generations back were most similar to
But not all past populations
Caveat that populations have changed over time
Can identify genetic relatives

Cons of DTCs

Reference populations may not be representative
Ancestry estimates dependent on number and distribution of SNPs
Only goes back approximately 12 generations
Prone to essentialization due to commercialization

Mitochondrial DNA (MtDNA)

genetic material in the mitochondria of the cytoplasm of a cell; only inherited from the mother

Nomenclature

naming system

Haplotype

Set of DNA variations or genetic markers that are inherited together from a single parent and are located on a single chromosome. Area of linked genetic variations in the human genome

Haplogroup

A group of similar haplotypes, or sets of alleles, that share a common ancestor and a single-nucleotide polymorphism mutation.

Y Chromosome

the sex chromosome found only in males. When paired with an X chromosome from the mother, it produces a male child.