GEOSCI 110 EXAM 2

Darwin's Dilemma

-Darwin documented numerous examples of variability and inheritance amongst domestic animals
-The two questions were the following:
1. What is the source of this variability?
2. How does heritability work?

Gregor Mendel

-grew 30,000 pea plants
-closely controlled reproduction and kept careful notes on plant traits generation by generation
-applied statistical principles to biology

Blending Inheritance Hypothesis

Mendel refuted this idea
-hypothesis predicts that each hereditary factor is permanently diluted in a hybrid
-WRONG

What did Mendel discover and how did he do it?

-Mendel proposed discrete units of heredity- the genes
-his prediction: each hereditary factor remains unchanged

Genes

a unit of heredity which is transferred from a parent to offspring and is held to determine some characteristic of the offspring
-may be identical or vary slightly

Locus

the position of a gene or mutation on a chromosome

Alleles

alternative forms of the same gene

Alleles: Recessive

-only expressed when homozygous
-type of allele which will not be manifested in an individual unless both of the individual's copies of that gene have that particular genotype

Alleles: Dominant

-expressed even when heterozygous
-a variation of a gene that will produce a certain phenotype, even in the presence of other alleles

Homozygous

2 alleles are identical

Heterozygous

2 different alleles

Chromosomes

-paired except in reproductive cells
-a threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes.

How many chromosomes do humans have? How many pairs?

46 chromosomes; 23 pairs

Mitosis

part of eukaryotic cell division during which the cell nucleus divides

Meiosis

Cell division that produces reproductive cells in sexually reproducing organisms

Punnett Squares

a chart that shows the possible combination of alleles due to fertilization

Number of Phenotypes v Number of Genotypes

in a Gg x Gg Punnett Square:
F1 phenotype ratio 75% Green, 25 % yellow
F1 genotype ratio 50% Gg, 25% GG, 25% gg

5 tenets of Mendelian Genetics

1. Phenotype traits are determined by units of heredity called genes
2. One gene codes for one trait WRONG
3. Some alleles are dominant others are recessive WRONG
4. Principle of Segregation
5. Principle of Independent Assortment WRONG

Principle of Segregation

Each parent contributes one randomly chosen allele of each gene to each offspring

Principle of Independent Assortment

each pair of alleles (gene) behaves independently of other allele pairs

Commonly observed "Non-Mendelian" characteristics of genes or traits

1. incomplete dominance of alleles
2. codominance of alleles
3. many alleles for one gene in a population
4. one gene may have multiple effects
5. one "trait" may be result of input from many genes
6. genes may influence each other

Example for Incomplete dominance between alleles

Snapdragons:
cross of white with red yields pink

Example of Codominance of alleles

human blood type gene has three alleles (A, B, O)
-Both A and B are fully expressed

Example of More than 2 alleles for one gene

Human blood type
-3 alleles for 1 gene

Example of one gene may have multiple effects

allele for albinism (recessive) also associated with crossed eyes and slightly larger body size

Example of One trait may result from input of multiple genes

human skin color results from combination of serval genes

Examples of genes that may influence each other

coat color in labrador retrievers is controlled by 2 genes

4 basic biomolecules of life

1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic Acids (DNA, RNA)

DNA Structure

double helix with anti-parallel strands
-holds information to:
-hold proteins
-direct development

DNA

Deoxyribo-Nucleic Acid

3 Reason why we study DNA

1. DNA is the fundamental basis of variation and change
2. DNA operates the same way in ALL living things
3. Many current issues require understanding DNA

Nucleotide Bases

ATCG

Nucleotide Pairings

A-T
G-C

DNA is what "backbone"

sugar-phosephate

Which way do DNA strands go?

they are anti-parallel strands
-5'-->3' direction v 3'-->5' direction

How many times must your DNA replicate itself during your life time?

In humans, DNA is replicated millions of billions times

DNA Replication

the ultimate team sport for enzymes; roles of Helicase, DNA polymerase

Direction of DNA Synthesis

DNA polymerase writes down 5'-->3' and reads up 3'-->5'

DNA replication

lagging (parent) strand runs 3'-->5' versus leading strands running 5'-->3' direction
1. Unzipping
2. A complementary base hooks up to each unpaired base
3. result is two daughter strands: each strand is half old, half new

Okazaki Fradments for building new lagging strand

short sequences of DNA nucleotides (approximately 150 to 200 base pairs long in eukaryotes) which are synthesized discontinuously and later linked together by the enzyme DNA ligase to create the lagging strand during DNA replication.

DNA replication is "semi-conservative" what does this mean?

during DNA replication, the two strands of nucleotides separate. Both strands then form the template for free nucleotides to bind to to create the two identical daughter strands. Hence each daughter strand has half of the DNA from the original strand and half newly-formed DNA.

Where does DNA replication and bundling into chromosomes happen?

inside the nucleus of the eukaryote cells

Carbohydrates

fast energy

Lipids

long-term energy storage, cell membranes

Proteins

build tissues, muscles, immune systems, and enzymes

Nucleic Acids

DNA, RNA

Amino Acids Structure

-Amino Group
-Carboxyl Group
-"R" group

Where does transcription happen?

nucleus

Where does translation happen?

ribosome

What is shared by ALL living organisms?

1. basic DNA structure, including base pairing
2. the genetic code (any particular codon codes for the same amino acid in ALL organism)
3. ALL organisms share about 500 "immortal genes" that are vital to such essential processes as decoding DNA and RNA, and protein synthesis

What is meant by "immortal genes"? Why are they found in all living things?

-a short portion of the amino-acid sequence of a protein found in all domains of life
-amino acids key to specifying this particular protein

What is different in different organisms?

1. sequence of bases along DNA strand
2. Amount of genetic material
3. number of genes and chromosomes

Size of human genome

6.4 billion nucleobases arranged in 3.2 billion base pairs

Is genome size (ie number of nucleobases) a reliable predictor for organism complexity amongst eukaryotes?

No! Among eukaryotes, the amount of DNA an organism has does NOT correlate well with its complexity

How many chromosomes do humans have?

46 (23 pairs)

Is number of conventional, protein-coding genes a reliable predictor for organism complexity amongst eukaryotes?

No! the correlation between the number of conventional (protein-coding) genes and complexity is poor

Is there a correlation between the amount of non-coding "junk" DNA and organism complexity?

No! Humans have a VERY high percentage of non-coding DNA

What percentage of DNA codes for conventional proteins in humans?

1.5% of human DNA codes for protein synthesis, so 98.5% of our genome is non-coding

Gene regulation

Post-Transcription: RNA interference (RNAi)
the ability of cells to control the expression of their genes

Gene Expression

-pre-transcription: transcription factors bind to DNA and regulate RNA polymerase activity; prevent this from happening for a specific gene and that gene is silenced
-post-transcription: interception of mRNA transcription products prior to their translation into protein by ribosome

Micro-RNA (miRNA)

short interfering RNAs, non-coding RNAs present in all living organisms, have been shown to regulate the expression of at least half of all human genes

Transcription Factors

proteins that bind to specific DNA sequences, and control the activity of transcription of genetic information from DNA to messenger RNA (mRNA)

What percentage of our DNA is from viruses?

8.3%

What is used by humans to make the placenta?

virus protein syncytin

Are viruses living organisms?

No

How do some viruses replicate?

1. Virus attaches to and enters a cell
2. virus releases its genetic material
3. Cell's enzymes copy the viral DNA and transcribe viral DNA to RNA
4. Ribosomes in the cytoplasm translate the RNA into viral proteins
5. Viral proteins and viral DNA recombine to form new virus particles
6. New virus particles escape to infect other cells

Where do some scientists think viruses came from?

evolved from plasmids (pieces of DNA that can move between cells)

Plasmids

small, often circular DNA molecule found in bacteria and other cells
-carry a small amount of genes

Two main sources of variation within a species

1. Mutation
2. Recombination (happens during sexual reproduction)

Which has a higher rate of point mutations: viruses or higher eukaryotes?

Viruses

Types of "point mutations" within a DNA sequence & their consequences

a. Single-base substitution
b. insertion
c. deletion

Insertion

extra nucleotide base is accidentally added to DNA sequence

Deletion

nucleotide base is accidentally omitted from DNA sequence

Is evolution a random process?

No! Because natural selection is the filter. Natural selection is NOT random

Synonymous Codons

mutations that DO NOT change the "meaning" of a triplet

Non-Synonymous Codons

mutations that result in the replacement of one amino acid for another

Ratio of Synonymous codons

-expected ratio of non-synonymous: synonymous 3:1
-in nature, ratio is 1:3

Retrovirus (RNA based)

HIV
-are either RNA or DNA (not both, usually RNA)
-may single- or double-stranded
-may be circular or linear
-variable in size: smallest code for only four proteins largest code for >100 proteins

Mutation of CCR5 ∆32-32 BP

detected in humans and resistance to HIV

Pseudogenes

"fossil" genes conserved within the genome that have been rendered useless by mutations

Chromosomal Mutations

changes in the chromosomes where parts of the chromosomes are broken and lost during mitosis

Within a single chromosome:

-deletion
-duplication
-inversion

Between two different chromosomes during meiosis

reshuffles allele combinations

Recombinant chromosomes (sexual reproduction)

source of variation
-crossing-over
-reshuffling of chromosomes

Homeotic Mutations

lead to the wrong body part forming in the wrong place

Homeobox (Hox) genes

large family of genes that direct and coordinate the formation of body parts during early embryonic development
-they encode proteins (transcription factors) that regulate gene expression in multi-cullular organisms

Regulatory genes

genes that control gene expression

Genetic transplantation and knockout experiments

Geneticists removed HOX gene from MOUSE embryo that codes for eye development, and inserted it into the DNA of a developing FRUIT FLY embryo. However, they activated the mouse eyeball HOX gene in a region of the fly that becomes back leg.
-fly grew fly eyes on its leg

Are hox genes shared (phylogenetically conserved) by all animals?

Yes!

Vestigial features (Structures)

degenerate or undeveloped; reduced in size and function by natural selection as no longer required

Atavistic features

reappearance of a trait lost in evolution
-only occur occasionally

why are some genes no longer expressed in a phenotype?

Natural selection and evolution silenced their action by deactivating them, not snipping them out of the DNA

Does natural selection remove "dead" genes (pseudogenes) from genomes?

No!

Embryology

THE STUDY OF EMBRYOS

Ontogeny

The history of development of an individual organism during its lifetime.

Branchial Arches in embyros

fish embryo has a series of gill arches first arch becomes the jaw the rest become gill structures

Replication

embryology reflects evolutionary history through "adding new stuff to old" principle- what is meant by "adding new stuff to old" principle

Carolus Linneaus

Father of taxonomy

Linnaean Hierarchial Classification

A species is a group of individuals that interbreed or have potential to interbreed in nature, and that do not breed with other interbreeding groups

Binomial Naming System

example homo sapiens
-the two part scientific name of a species is called a binomial
-first part of the name is the genus
-second part is called the species