What is a clade?

A clade is a group that includes the most recent common ancestor of the group plus all of its descendants. The study of cladistics is a subset of PHYLOGENY which is the study of evolutionary relationships. Taxonomy is the study of categorizing living things using the scheme developed by Carolus Linneaus. Phylogeny and taxonomy are often at odds because a taxonomic group that has been created based on appearance does not necessarily agree with a cladistic analysis of the evolutionary history of the group.

More on cladistics here.

Central dogma of cell biology:

DNA > RNA > Protein

This is the most important process in modern biology.

The central dogma involves unwinding of an active portion of DNA that corresponds to a single transcription unit (typically one gene), followed by TRANSCRIPTION of DNA into mRNA and TRANSLATION of mRNA into polypeptides. Polypeptide chains join together to form structural proteins, enzymes or other kinds of protein molecule.

In Eukaryotes, DNA is stored in the cell nucleus. Most of the time it is diffusely scattered through nucleus and many parts of it are being actively transcribed.

During cell division the DNA becomes inactive and condenses into tightly packed chromosomes ready for "shipping" to the new daughter cells.

Want more details? look here, here and here.

Gene:           
A length of nucleotide bases that code for ONE peptide (i.e., a protein) Many proteins are enzymes, hence one gene = 1 enzyme. Often one enzyme= one trait. A gene might be from a few dozen to a few hundred bases long.

Genes are often made up of different functional modules called exons separated by non-coding stretches of DNA called introns.

Genes are turned on an off so that they can be transcribed only when they are needed. Many complex mechanisms are involved in gene regulation, but typically a protein binds to a specifc sequence on a gene in order to block access to the gene so that it cannot be transcribed. When the blocking protein receives a signal to detach from the DNA, the gene may become active.

A simple illustration of this mechanism (found in some bacteria) is the lac operon.

http://vcell.ndsu.nodak.edu/~christjo/vcell/animationSite/index.htm

Chromosome:
A DNA molecule. There are hundreds or thousands of genes on a chromosome. The genes appear in a specific order on the chromosome. The location of a gene on a chromosome is called a locus. Bacteria have just one, circular chromosome. In plants and animals, the chromosomes are sometimes condensed (compressed) and held together with proteins called histones so that they are easier to move during mitosis (cell division).

Alleles:
Different versions of the same gene that occur at the same locus. eg dwarf and normal peas.

Diploid:
Two copies of each chromosome are present. Most animals and flowering plants are diploid. Some plants are triploid or polyploid as a result of hybridization. Evolutionary pressures like to keep reproduction simple and efficient, so redundant chromosomes may eventually be lost, or may fuse with other chromosomes.

Haploid:
One copy of each chromosome is present. Sperm, eggs, pollen, bacteria and some simple plants are haploid.

Genotype:
The specific genetic make up of an organism with respect to the alleles it is carrying. Often considers just one locus for simplicity.

Phenotype:
The characteristics of an organism that are actually displayed. Often considers just one locus for simplicity. In haploid organisms the phenotype is controlled by the single allele that is present. In diploid organisms The phenotype may be determined by solely one of the TWO alleles, partly by both or by some combination of both. (bicycle wheel analogy)

Dominance:
Often misunderstood phenomena where one allele appears to "dominate" another. Actually both alleles are present and both may be functional but the effects of one sometimes mask the effects of the other.

Fixation:
When an allele displaces all other alleles at a given locus in a specific population. For any new allele in a real (non-infinite sized) population, assuming that the allele has no selective advantage or disadvantage, either fixation or loss through chance are the only two possible outcomes given enough time (generations). This means that whenever more than one allele of a particular trait permanently persist in a population, some kind of selection must be acting on one or more of them.

See how the probability of fixation or loss are affected by population size in a simple online simulation here.

Gene frequency:
The proportion of individuals within a population that have a particular gene. Usually expressed as a decimal. 1 = every individual has it. 0.25 = a quarter of all individuals have it. When there is no selection, gene frequencies change randomly from one generation to the next. Nonetheless, one of two fates must befall all genes given enough time; fixation or loss.

Hardy Weinberg law:
States that in a population with two alleles of a particular gene called A and B, if we call their frequencies p and q then, ASSUMING THAT THERE IS NO EVOLUTION, and that the population is infinitely large and randomly mating, then the proportions of individuals who have genotype AA is p squared, the proportion of individuals who are BB is q squared and the proportion of individuals who are AB is 2pq. This distribution should stay constant over time once equilibrium is reached. In practice this does not happen because selection and small population size cause fluctuations from the expected ratio to occur.

NO POPULATION HAS EVER BEEN FOUND THAT IS IN HARDY WEINBERG EQUILIBRIUM !

If you are mathematically inclined, there are a number of other simple simulations that illustrate the mathematics of evolution here. Remember, these are all phenomena that poor Darwin new nothing about because the genetic mechanisms of inheritance were only discovered after his death.

Evolution:
Change in a population's gene frequencies over time.

Factors affecting evolution:
Natural selection
Sexual selection
Population size
Founder effect and genetic drift
Isolation
Co-evolution and symbiosis
Mutator genes
Sex ratio
Mutation rate
Generation time
Ploidy (haploid or diploid)
Genetic exchange (sex, viral transfer, bacterial conjugation and horizontal transfer)
Intensity of competition
Rapid change of environment
Luck
Environment ? (Lamarckian evolution in bacteria)
Cultural evolution
Genetic engineering

Plant cells:

Review the basic structure of a plant cell and make sure you know the functions of the various organelles.

http://micro.magnet.fsu.edu/cells/plantcell.html

http://deepgreen.stanford.edu/