Descent with Modification: A Darwinian View of Life

1) Explain some of the Pre-Darwinian Views of Life!

Greek Philosophers: Plato (organism perfectly adapted to the environment), Aristotle(Scala Naturale - a scale of increasing complexity

Fixed Spicies Concept: the Creator had designed each and every species for a particular purpose

Catastrophism: fossils related to current life (Georges Cuvier); fossils were remains of species lost due to a catastrophe

Gradualism - Hutton: profound change is the product of slow, but continuous processes

Uniformatarianism - Lyle: geological processes à operated at the same rate over the Earth’s history à the Earth must be very old!

Lamarck's Theory: life changed to complex from simple over time
a) use/disuse - body parts used to survive become larger and
stronger; body parts not used to survive deteriorate
b) acquired characteristics - modifications acquired by use/disuse
are passed on to offspring

2) What are endemic species?

Species found at certain geographical locations and nowhere else.

3) What are some signs for evolution?

biogeography, fossils, taxonomy, comparative anatomy, comparative embryology,molecular biology...

Facts:

- Lamarck recognized that species evolve, though his explanatory mechanism was flawed.

- Fossils provide evidence for the theory of evolution.

- Evolution is change in species over time.

- Heritable variations exist within a population.

- These variations can result in changes in the genetic composition.

Summary:

Evolution includes changes over time, and is continuous (still occurs).

Ideas about change over time include fossils, paleontolgy, catastrophism, uniformitrarianism. Lamarck first provided with his hypothesis. Later, Charles Darwin defined the natural selection and supported his ideas.

Many evolutions that have to do with ancestors and environments have been contemplated and discovered.

Extra:

Evolution (of dance) video

Genomes and their Evolution

1) What is genomics?

The study of the whole set of genes and their interactions.

2) What is a homebox?

Homebox is a 180-nucleotide sequence that specifies a 60-amino-acid homeodomain in the encoded proteins.

3) Explain the whole-genome shotgun approach to genome sequencing!

The whole genome is cut into many small, overlapping fragments that are sequenced; computer software then assembles the complete sequence. Correct assembly is made easier when mapping information is also available.

Facts:

- Websites on the Internet provide centralized access to genome sequence databases, analytical tools and genomerelated information

- Only 1.5% of the human genome codes for proteins or gives rise to rRNA or tRNA; the rest is noncoding DNA, including repetitive DNA

- Genomes vary in size, number of genes, and gene density

- Biologists in the field of evo-devo compare developmental processes of different multicellular organisms

- Duplication, rearrangement, and mutation of DNA contribute to genome evolution

Summary:

Sequencing the human genome is the most ambitious mapping project. It officially began as the Human Genome Project in 1990, in major, going through three stages: genetic mapping, physical mapping, and DNA sequencing. Humans have 20,488 genes and we can make 75,000 polypeptides. Humans and other mammals have the lowest gene density and the number of genes is not correlated to genome size.

It seems that the rate of duplications and inversions have accelerated about 100 million years ago.

Extra:

DNA Genechip

DNA Technology and Genetics

1) What is biotechnology?

The manipulation of organisms or their components to make useful products.

2) List some methods of biotechnology!

1.Bacteria Transformation

2.Restriction Enzymes

3.cDNA

4.DNA Sequencing

5.PCR

6.RFLP

3) What are the steps for plasmid use?

1. Get the DNA for the trait.

2. Insert DNA into the plasmid.

3. Bacterial Transformation.

4. Identification of the new trait.

Facts:

- The practical applications of DNA technology affect our lives in many ways.

- DNA cloning and other techniques, collectively termed DNA technology, can be used to manipulate

and analyze DNA and to produce useful new products and organisms.

- Restrictive enzymes cut DNA at specific nucleotide sequences called “restriction sites”

- Markers are inherited in a Mendelian pattern and can show relationships (Pedigree studies).

- PCR can produce many copies of a specific target segment of DNA, using primers that bracket the

desired sequence and a heat-resistant DNA polymerase.

Summary:

DNA cloning yields multiple copies of a gene or other DNA segment. DNA technology allows us to

study the sequence, expression, and function of a gene. The DNA practical applications of DNA

technology affect our lives in many ways.

Extra:

The PCR song

Viruses

1) What is a capsid?

A capsid is a protein shell that surrounds the genetic material.

2) How are the viruses that infect bacterial cells called?

Bacteriophages (Phages)

3) What does limited host range mean for viruses?

Viruses have a limited host range. This means they can infect only a very limited variety of hosts. Ex. human cold virus infects only cells of the upper respiratory tract.

Facts:

- Researchers discovered viruses in the late 1800s by studying a plant disease, tobacco mosaic disease.

- The genome of a virus can be single or double stranded DNA or RNA

- Phages can reproduce two alternative mechanisms: the lytic cycle and the lysogenic cycle.

- Viruses can reproduce only within cells

- Viroids are naked RNA molecules that infect plants and disrupt their growth.

Summary:

Viruses are particles of nucleic acids, proteins, and, in some cases, lipids. It is in common to all viruses that they enter living cells and, once inside, use the machinery of the infected cell to produce more viruses. Viruses are parasites, not considered to be living things because they are not made up of cells. Once the virus is inside a host cell, two different processes may occur and they are lytic infection and lysogenic infection.

There are viruses that cause diseases and they are called pathogens.

Extra:

HIV virus structure video

Regulation of Gene Expression

1) What makes an operon?

- an operator (controls the access of RNA polymerase to the genes)

- the promoter (where RNA polymerase attaches here)

- genes of the operon (the entire strech of DNA required for all the enzymes produced by the operon)

2) The zygote undergoes transformation through three interrelated processes. What are these?

1. cell division
2. cell differentiation
3. morphogenesis

3) What controls differentiation and morphogenesis?

1. cytoplasmic determinants
2. cell-cell signals

Facts:

- Cells control metabolism by regulating enzyme activity or the expression of genes coding for enzymes.

- An operon site on the DNA switches the operon on or off; resulting in coordinate regulation of genes.

- Cells differ in structure and function not because they contain different portions of a common genome, but because they express different portions of a common genome.

- Differentiation is heralded by the appearance of tissue-specific proteins, which enable differentiated cells to carry out their specialized roles.

[Drosophila - gradients of morphogens encoded by maternal effect genes determine the body axes]

- A hyperactive version of a protein in an stimulatory pathway, such as Ras (a G protein), functions as an oncogene protein.

Summary:

The controls that act on gene expression are much more complex in eukaryotes than in prokaryotes. In bacteria, genes are clustered into operons (gene clusters that encode the proteins necessary to perform coordinated function).

During normal growth on a glucose-based medium, the lacrepressor is bounded to the operator region of the lac operon, preventing transcription. However, in the presence of an inducer of the lac operon, the repressor protein binds the inducer and is rendered incapable of interacting with the operator region of the operon.

The trp operon encodes the genes for the synthesis of tryptophan. Since the activity of the trp repressor is enhanced in the presence of tryptophan, the rate of expression of the trp operon is graded in response to the level of tryptophan in the cell.

Extra:

lac operon video

From Gene to Protein

1) What is gene expression?

It is the process by which DNA directs the synthesis of proteins.

2) What are the three steps of transcription?

Initiation, Elongation, and Termination.

initiation stage of translation

3) Define mutations and point mutations!

Mutations are alterations in the genetic material of the cell.

Point mutations are are alterations of just one base pair of a gene. They come in two basic types: 1. base-pair substitutions; 2. insertions and deletions

Facts:

- DNA controls metabolism by directing cells to make specific enzymes and other proteins

- Genes specify proteins via transcription and translation

- Eukaryotic cells modify RNA after transcription

- Genetic information is encoded as a sequence of nonoverlaping base triplets (codons)

- Ribosomes coordinate the three stages of translation

Summary:

The information content of DNA is in the form of specific sequences of nucleotides along the DNA strands. The DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins. Gene expression, the process by which DNA directs protein synthesis, includes two stages called transcription and translation. Proteins are the links between genotype and phenotype. For example, Mendel’s dwarf pea plants lack a functioning copy of the gene that specifies the synthesis of a key protein, gibberellin. Gibberellins stimulate the normal elongation of stems.

Extra:

translation rap video

The Molecular Basis of Inheritance

1) How was it proved that DNA (not protein) is the genetic material?

In 1952, Alfred Hershey and Martha Chase answered this question utilizing bacteriophages (viruses that infect bacteria). They used a radioactive isotope of phosphorous to tag the DNA in one culture of bacteriophages and radioactive sulfur to tag the protein in a second culture. The results showed that only DNA entered the bacteria infected by the virus. --> DNA must be the genetic material!

2) What is the basic structure of DNA?

1. double helix
2. nitrogenous bases - A, C, T, G
3. the strands are termed antiparallel

3) List some of the bacterial DNA replication proteins and their functions.

- helicase - unwinds parental double helix at replication forks

- topoisomerase - relieves "overwinding" strain ahead of replication forks by breaking, swiveling, and rejoining DNA strands

- primase - synthesizes an RNA primer at 5' end of the leading strand of each Okazaki fragment of lagging strand

- DNA ligase - joins 3' end of DNA that replaces primer to rest of leading strand and joins Okazaki fragments of lagging strand

Facts:

- DNA must be the genetic material

- DNA is a double helix, built up from 4 nitrogenous bases (A,T,C & G) with antiparallel strands

- A & T always pair as well as do C & G

- DNa polymerase can add nucleotides only to the 3' end of a molecule

- As DNa becomes more highly packaged, it becomes less accessible to transcription enzymes

Summary:

In 1950s, Harshey and Chase proved that DNA is the actual genetic material. The next big discussions in this area were based on the DNA structure. It is now known that DNA is a double helix, built up from 4 nitrogenous bases (A,T,C & G) with antiparallel strands.

Replication is the making of DNA from an existing DNA. The replication occurs in six major points:

1) it begins at origins of replication

2) replication bubble formation

3) DNA polymerases catalyze the elongation of the new DNA

4) DNA polymerase adds nucleotides to the growing chain (5' to 3')

5) continuous replication from 5' to 3' strands

6) Okazaki fragments (lagging strand) sealed together by DNA ligase

Extra:

DNA replication non-melodical song! :D