biol 300 1.1-1.6

What is a genome?

all the genetic information within an organism

What are some physical forms of genomes and where can they be seen in?

Physical forms: DNA/RNA

a. Most organisms: ds (double-stranded) DNA

b. some viruses: ss (single-stranded) DNA: ssRNA; dsRNA

What are genes?

a unit of heredity
a DNA sequence that specifies one or more products that can be coding sequences (polypeptide) or non-coding sequences (RNAs)

What is the order from smallest to largest from nucleotide to genome?

Nucleotides → DNA → Gene → Chromatin → Chromosome → Genome

What is each chromosome consist of?

Single DNA molecule + packaging proteins
(aka packaged chromatin)

How is a prokaryotes DNA structured?

one circular DNA = one chromosome

How are Eukaryotes DNA structured?

multiple linear DNA molecules
ex: humans - 23 pairs of chromosomes

What are homologs in chromosomes?

The individual chromosome from a pair.

What is a homologous pair?

Two homologous chromosomes that were paired up from meiosis (2 homologs)

What’s a ploidy?

the number of complete sets of chromosomes in a cell

What do homologous chromosomes have in common with each other?

• Same banding patterns

• Same centromere location

• Almost the same BUT not identical sequences (~1% difference)

• Same loci (gene locations)

• Wild-type, variants, or mutants

What are homologous chromosomes in a DIPLOID organism?

two copies of the same chromosome, one maternal and one paternal copy. sex chromosomes (x and y) are NOT homologous

What are haploid?

the copy number in gametes (half of the zygote/somatic cell )

one copy found in each chromosome

(restored back to diploid by fertilization)

What are monoploids and give examples

a single set of chromosomes

ex: bacteria, male bees, gametes, yeast, algae

What are polyploid and give examples

multiple copies

plants, fish, amphibians

(fatal in birds and mammals)

What is a locus?

physical location of a gene on a chromosome (each having an allelic form such as a specific DNA sequence)

What is genetic analysis?

how changes in DNA seq (genotype) leads to changes in traits (phenotype)

What categories can traits be and provide examples.

• Morphological (appearance) - shapes, colors, etc.

• Physiological (affects function) - development, metabolism, aging, susceptibility to disease

• Behavioral (response to environment/adaptability) - how organisms respond to environment

What are traits controlled by?

They’re controlled by genes and its manifestation of gene products

Name the different complexities of how traits can be controlled

• Simple → 1 trait = 1 gene affected (ex: red-green colorblindness from 1 gene affected)

• Complex → 1 trait = multiple genes (ex: height is affected by multiple genes)

• Pleiotropic → multiple traits = 1 gene (ex: sickle-cell hemoglobin’s various symptoms caused by one genetic mutation)

What are the two different types of genetic variation to DNA at a molecular level?

gene mutation and changes in chromosome structure

Distinguish the difference between gene mutation and changes in chromosome structure

Gene mutation:

• Leads to differences in gene sequences

• results in two or more forms (alleles) of the same gene

Changes in chromosome structure:

• large segments of the chromosome are either:

  • lost, duplicated, or reattached to another chromosome

What is a phenotype?

the observable traits of an organism (physical, behavior, disease susceptibility)

What is a genotype in a broader sense?

the genetic makeup of the organism

What is a genotype in a narrower sense?

the gene combination related to a trait

Does having the same phenotype always mean the same genotype?

No, complex traits are determined by multiple genes + mutations can give rise to similar phenotype

What are traits influenced by?

Genome and environmental factors:

• Nature: genome

• Nurture: environment/lifestyle

What are alleles?

alternate forms of a particular gene

What does it mean when an allele is haplosufficient?

When the wild type allele provides sufficient biochemical activity to result in wild type phenotype
- Allele exhibiting dominance and masking recessive traits

What does it mean when an allele is haploinsufficient?

A single wild type allele does NOT result in enough protein to produce sufficient biochemical activity to result its normal phenotype

What is a hemizygous allele?

If there is only one copy of a gene (often due to deletion)

If there is a..

Change in DNA seq → change in protein amt → too much or too little product..

→What happens to the phenotype?

results in different phenotype

If there is a..

Change in DNA seq → but no change in protein amt..

→What happens to the phenotype?

results in the same phenotype

If there is a..

Change in DNA seq → change in protein seq → but not change in protein function..

→What happens to the phenotype?

results in same phenotype (meaning this amino acid is NOT critical for function)

If there is a..

Change in DNA seq → change in protein seq → change in protein function..

→What happens to the phenotype?

results in a different phenotype (meaning this certain amino acid is critical for function)

What is a loss of function (LOF) mutation?

impledes or completely abolishes function; typically a recessive trait

What is a gain of function (GOF) mutation?

results in new activity or expression pattern or further enhanced expression

• occurs at low frequency

• usually a dominant trait

• an essential force to drive evolution

• most GOF are typically bad for the organism

What is a null mutation?

a complete elimination of a gene function

What is a silent mutation?

no detectable change in phenotype

Name the common dominant mutant alleles and their common traits:

• Gain of Function - could be overexpressed

• Dominant Negative - acts antagonistically to the wild-type; phenotype is altered

• Haploinsufficiency - dominant LOF allele

Dominant mutant alleles are less common than recessive mutant alleles

Name the case study of ABO blood types:

Trait, how many genes, which chromosome, how many alleles, amt of genotypes, amt of phenotypes, primary example of what dominance?

Trait: blood type
Amt of genes: one gene (encodes glucosyltransferase)
Chromosome #9
3 alleles
6 different genotypes
4 different phenotypes
This study is a primary example of codominance

What is Gregor Mendel known for and what did he discover?

“Father of Genetics”

Discovered 7 traits of peas, each with two phenotypes

Created a true breeding cross (both parents are homozygous)

Drew 2 Laws of Inheritance

What is Mendel’s First Law: Principle of Segregation?

heritable traits were controlled by discrete elements called alleles

1. Each individual has two alleles

2. Two alleles segregate equally during gamete formation to be inherited (1:1) = equal chance to be inherited

What is Mendel’s Second Law: Independent Assortment of traits?

Traits are transmitted to offspring independently of one another
(Alleles at separate loci segregate independently during gamete formation)

What are the conditions that need to be met for Mendel’s Principles?

1. Genes for traits should on separate chromosomes or far enough apart on the same chromosome to assort independently

2. Genes should be haplosufficient

What are different ways different alleles can give rise to different phenotypes?

1. Wild type, loss of function, gain of function

2. Dominant/recessive
   (can be complete, incomplete, codominance)

3. Muller’s morphs (interaction of alleles)

What are the five classifications of a mutant allele?

Amorph, Hypomorph, Hypermorph, Neomorph, Antimorph

What symbol is used to represent wild type alleles

+

What is used to represent “unknown” mutant alleles?

M - dominant allele comparing to +

m - recessive allele comparing to +

(letters are NOT wild-type, but for mutants)

What is used to represent deficiency and what kind of mutation happened?

Df = deficiency

a large deletion, removing gene of interest. this is a definitive complete LOF

What is used to represent duplication and what kind of mutation happened?

Dp = duplication

mutant allele carries two or more wild type copies of the gene (increase gene dosage)

What is an amorphic mutation and provide example.

complete LOF (a null allele)

ex: wild type is purple, amorphic is no color, making it a white flower

If the allele is LOF, is it possible to save the allele using a single wild type copy (+)?

Yes, especially for amorphs, hypomorphs, and antimorphs

What is a hypomorph and provide an example.

a partial LOF (weak allele)

ex: A fly’s eye color partially loses its color (phenotypical sensitivity) depending on the allele combos (+/+ = normal, Df/Df = complete loss of color)

almost always recessive to wild type

What is a hypermorph mutation and provide examples.

too much activity/expression which can be bad

ex: duplication (more copies, the more severe), increased protein level/activity (some excessive amts can be fine), constitutively active allele (cannot be turned off)

(wild type copy cannot save this mutation)

What is a Neomorph mutation and provide examples.

A new phenotype that is not observable in wild type OR a new function or same function, but expressed at wrong time/place

ex: an antennae is now expressed as a leg

What is a antimorph mutation and provide examples.

activity is dominant and opposite to the wt function

(LOF allele but cancels out the wild type allele)

ex: dims the amount of protein that’s normally expressed

What are the outcomes of mutations?

positive : drives adaptation and a foundation of evolutionary change

negative : new mutations may be harmful (usually the cause of disease susceptibility)

List the types of mutations

1. Spontaneous (replication error)

2. Induced Mutation (radiation, chemicals, biological)

What are the types of induced mutations and examples?

• Radiation (UV, ionizing radiation (gamma rays))

• Chemicals (base analogs, oxidative agents)

• Biological (pathogens - viruses inserts into host genome)

Types of nucleotide mutations

1. substitution

2. insertions

3. deletions

What are transitions in nucleotide substitution?

purine → different purine or pyrimidine → different pyrimidine changes

What are transversions in nucleotide substitution?

purine → pyrimidine OR pyrimidine → purine changes

What is a point mutation?

changes in a single base pair

• substitution, insertions, or deletion

What is chromosome rearrangement?

large scale mutations caused by

• breakage of dsDNA by rejoining wrong broken ends

name the 4 different mutations that can alter the coding sequence within a gene

Silent - base sub that do not alter the amino acid seq

Missense - base sub that DO alter the amino acid seq

Nonsense - base sub that makes normal codon to stop codon

Frameshift - addition/deletion of the number of nucleotides making new seq