BIO 2A Midterm 2

Central Dogma

DNA → RNA (transcription) → protein (translation) → phenotype

DNA base pairing

A pairs with T and C pairs with G (in RNA, A pairs with U)

Nucleotide

A sugar, a phosphate and a base (A, T, C or G); the order of bases carries the information

Transcription

DNA → mRNA. Happens in the nucleus in eukaryotes. RNA polymerase reads the template strand and builds complementary mRNA

Product of transcription

RNA (RNA polymerase is the enzyme, not the product)

RNA polymerase

The enzyme that builds RNA from a DNA template during transcription

Main base difference between RNA and DNA

RNA uses uracil (U) instead of thymine (T)

Translation

mRNA → protein. Happens on ribosomes in the cytoplasm. tRNAs deliver amino acids as codons are read

Codon

A group of 3 mRNA bases that specifies one amino acid (or a start/stop signal)

tRNA and anticodon

tRNA carries an amino acid; its anticodon pairs with the matching mRNA codon

Start codon

AUG (codes for methionine); translation begins here

Stop codon

A codon that ends translation (UAA, UAG, UGA)

Final product of gene expression

A protein

How a DNA difference becomes a phenotype difference

DNA change → different mRNA → different amino acid sequence → different protein shape/function or amount → different phenotype (plus environment)

Why changes in transcription amount can change phenotype

Transcription level controls how much protein is made, and amount of protein can change the trait

Genome

All the DNA of an organism

Chromosome

One long DNA molecule packaged with proteins; carries many genes

Gene

A stretch of DNA that codes for a product (usually a protein)

Locus (plural loci)

The physical location of a gene on a chromosome

Allele

A version of a gene; different alleles are different sequences at the same locus

Genotype

The alleles an individual carries (e.g., Aa)

Phenotype

The observable trait (e.g., flower color)

Homozygous

Two identical alleles at a locus (AA or aa)

Heterozygous

Two different alleles at a locus (Aa)

How genome, chromosome, gene and allele relate

Genome contains chromosomes, which contain genes, which come in different alleles. The locus is the gene's address

Diploid (2n)

Two sets of chromosomes. Human body (somatic) cells are diploid: 46 chromosomes

Haploid (n)

One set of chromosomes. Human gametes (sperm and egg) are haploid: 23 chromosomes

Chromosome number in a human liver cell vs sperm cell

Liver cell: 46. Sperm cell: 23

Meiosis

Cell division that makes haploid gametes (halves the chromosome number)

Mitosis

Cell division of body cells; daughter cells keep the same chromosome number

Redundancy of the genetic code

64 codons but only 20 amino acids, so several codons can code for the same amino acid

Wobble

Different codons coding for the same amino acid, usually differing at the 3rd position of the codon

Which codon position is most flexible

The 3rd position; mutations there are often silent

Hypothesis for why wobble evolved

It protects against harmful effects of mutation; mutations at the tolerant (3rd) position often don't change the amino acid

Silent (synonymous) mutation

Codon changes but the amino acid stays the same; usually no effect

Missense mutation

A substitution that changes one amino acid; may change protein folding or function

Nonsense mutation

A substitution that creates a premature stop codon; protein is cut short

Frameshift mutation

An insertion or deletion not in multiples of 3 bases; shifts every downstream codon; usually very damaging

Gene deletion

Removing whole genes removes their proteins; likely to change phenotype

Regulatory mutation

Changes when or how much a gene is expressed, not the protein sequence itself

Mutation in non-coding DNA that neither codes for nor regulates anything

Usually no phenotypic effect

Test for whether a mutation produces phenotypic variation

Does it change the amount or the function of a protein?

Law of segregation

The two alleles of a gene separate during gamete formation so each gamete gets one; happens because homologous chromosomes separate in meiosis

Law of independent assortment

Alleles of different genes sort into gametes independently; happens because homologous pairs line up and separate randomly in meiosis (numbering of first/second law varies by course)

Linkage

Genes close together on the same chromosome tend to be inherited together; an exception to independent assortment

Crossing over (recombination)

Homologous chromosomes swap segments in meiosis, creating recombinant gametes

Recombinant offspring

Offspring with new combinations of alleles produced by crossing over

Test cross

Cross an individual of unknown genotype with a homozygous recessive; the offspring phenotypes reveal the unknown parent's gametes

Test cross result for unlinked genes

About 25% each of four phenotype classes (independent assortment)

Test cross result for linked genes

Two large parental classes and two small recombinant classes

Recombination frequency

Percent of offspring that are recombinant; maximum is 50%, which looks like unlinked genes

Recombination frequency and distance

The smaller the recombination frequency, the closer together the genes are on the chromosome

P, F1, F2

P = parents; F1 = first offspring generation; F2 = offspring of F1 × F1

AA × aa offspring

All Aa (100% heterozygous, all show the dominant phenotype)

Aa × aa offspring

1 Aa : 1 aa (1:1 genotype and phenotype ratio); this is a test cross

Aa × Aa offspring

Genotype 1 AA : 2 Aa : 1 aa; phenotype 3 dominant : 1 recessive

Dihybrid cross AaBb × AaBb phenotype ratio

9 : 3 : 3 : 1 (genes on different chromosomes)

Gametes from AaBb

AB, Ab, aB, ab (four types, equally frequent if unlinked)

F1 of two true-breeding parents differing at two genes (BBtt × bbTT)

All BbTt: all heterozygous, all showing the dominant phenotype for both traits

Complete (simple) dominance

The heterozygote looks like the dominant homozygote

Incomplete dominance

The heterozygote is intermediate between the two homozygotes (e.g., red × white gives pink)

Codominance

The heterozygote fully shows both phenotypes at once (e.g., red and white patches)

Why incomplete dominance and codominance matter for HWE problems

Each genotype has its own phenotype, so phenotype frequencies give genotype frequencies directly

Pleiotropy

One gene affects multiple traits

Polygenic inheritance

Many genes affect one trait, often additively; gives continuous variation (e.g., height)

Epistasis

One gene masks or modifies the effect of another gene; changes usual phenotype ratios

Environmental effects on phenotype

The same genotype can produce different phenotypes in different environments; phenotype = genotype + environment

How pleiotropy, polygenic inheritance and epistasis are similar

All make the genotype-to-phenotype map more complex than one gene → one trait

How they differ

Pleiotropy: one gene to many traits. Polygenic: many genes add up to one trait. Epistasis: genes interact and one hides the other

Labrador coat color: B gene

B_ = black pigment; bb = brown pigment

Labrador coat color: E (extension) gene

E_ lets pigment be deposited; ee = yellow regardless of the B genotype

Labrador epistasis ratio from BbEe × BbEe

9 black : 3 brown : 4 yellow

Why two yellow Labs can't produce black puppies

Yellow means ee; ee × ee can only produce ee offspring, which are always yellow

Yellow Lab hidden genotype

A yellow Lab can carry B or b alleles that are hidden by ee

Blood type alleles

Three alleles: IA, IB, i. IA and IB are codominant; both are dominant over i

Blood type phenotypes and genotypes

A = IAIA or IAi; B = IBIB or IBi; AB = IAIB; O = ii

How to tell dominance from a genotype-phenotype table

If the heterozygote shows both phenotypes, the alleles are codominant; if it shows one, that allele is dominant

What an O child tells you about parents

Each parent contributed an i allele

What an AB child tells you about parents

One parent gave IA and the other gave IB

Additive polygenic trait method

Count the dominant alleles. Find the possible gametes (number of dominant alleles in each), add one from each parent, and each total is a phenotype class

Heterogametic vs homogametic sex

Heterogametic has two different sex chromosomes; homogametic has two matching ones

Sex chromosomes in humans/mammals

Females XX, males XY

Hemizygous

Having only one copy of a gene (males for X-linked genes), so a recessive allele always shows

Carrier

A heterozygous individual who has the recessive allele but doesn't show the disease (e.g., XHXh female)

Hemophilia genotypes

XHXH healthy female; XHXh carrier female; XhXh affected female; XHY healthy male; XhY affected male

Why X-linked recessive diseases are more common in males

Males need only one copy of the recessive allele; females need two

How a son inherits X-linked alleles

His only X comes from his mother; his Y comes from his father

How a daughter inherits X-linked alleles

One X from each parent; her paternal X is always the father's X

Can a father pass an X-linked allele to his sons?

No. Sons get the father's Y, so sons depend on the mother's alleles

Why X-linked probabilities depend on sex of the child

Sons and daughters inherit X chromosomes differently, so always calculate sons and daughters separately

ZW sex determination in birds

Females are ZW (heterogametic); males are ZZ (homogametic)

Inheritance of Z-linked genes

Father gives a Z to all offspring. Mother gives her Z to sons and her W to daughters. A daughter's only Z comes from her father

Probability AND rule

For independent events, multiply the probabilities

Probability OR rule

For mutually exclusive pathways to the same outcome, add the probabilities

Probability an Aa × Aa offspring is aa

1/2 × 1/2 = 1/4 (AND rule)

Probability an Aa × Aa offspring is Aa

(A from mom AND a from dad) OR (a from mom AND A from dad) = 1/4 + 1/4 = 1/2

Dihybrid probability method

Treat each gene separately, then multiply; if more than one genotype combination gives the phenotype, add the pathways

Decomposing ratios like 3/8 or 1/8

Break into products: 3/8 = 3/4 × 1/2 and 1/8 = 1/4 × 1/2, meaning one gene is Aa × Aa (3:1) and the other is Bb × bb (1:1)

Strategy for finding parental genotypes from offspring ratios

Start with the fully recessive offspring; they show which alleles each parent must carry

Chicken comb genetics (standard version)

R_P_ = walnut; R_pp = rose; rrP_ = pea; rrpp = single (two dominant alleles together give a new phenotype)