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Biology Final
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325
Biology
Undergraduate 1
11/30/2010

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Term
Chromosome Theory of Inheritance
Definition
Mendelian genes have specific locus on the chromosomes.
Chromosomes undergo segregation and independent assortment.
Morgan used Drosophila as a model system and demonstrated gene chromosome relationships.
Morgan demonstrated that linked genes tend to be inherited together because they are near each other on the same chromosomes.
Term
Genetic Linkage
Definition
Independent assortment does not always occur.
Independent segregation of chromosomes during meiosis I leads to independent assortment.
Independent assortment leads to recombination.
Term
Recombination
Definition
Any process that leads to combinations of genotypes not seen in the parents
Term
Recombination Gametes
Definition
Gametes that display a recombinant genotype.
Term
Recombination Offspring
Definition
Offspring whose phenotype reveals that they inherited genes from a recombinant gene.
Term
Linked Genes
Definition
Genes that are on the same chromosome may not sort independently.
Term
Crossing Over
Definition
Breaks linkages between genes.
The further apart two genes are, the more likely they are to have crossing over occur between them (thus leading to genetic combination).
Term
Genetic Maps of Chromosomes
Definition
Percentage of crossing over or recombination is calculated from 100 times the number of recombinant offspring divided by the total number of offspring.
Term
Map Unit
Definition
By convention, one map unit = 1% recombination (the term cM or centiMorgan is sometimes used for map units, in honor of a pioneer in gene mapping)
Term
Map Distances
Definition
Between genes on the same chromosome are measured in map units.
Term
Linkage Group
Definition
All genes on a particular chromosome; tend to be inherited together.
Term
Genetic Mapping
Definition
Placement of a gene into a position in a linkage group.
Map distances get less meaningful as they get large.
As genes get further apart, the odds of multiple crossing over events between them increase.
When distances approach 50 map units, the genes appear essentially unlinked.
Many chromosomes have an overall map length of well over 50 map units.
Genetic maps are useful in locating the actual physical location of genes.
Term
Sex Determination Varies Between Species
Definition
Hermaphroditic Organisms have both sexes in the same individual.
Many animals have sex determined in response to environmental signals.
Most animals have sex determined by genetic inheritance; sex chromosomes are involved.
Term
Homogametic Sex
Definition
Has a pair of similar sex chromosomes; all gametes that individual produces get that kind of sex chromosome.
The sex chromosome found in the homogametic sex is considerably larger.
Term
Heterogametic Sex
Definition
Has two different sex chromosomes, and makes gametes with two different types of sex chromosome.
The shorter sex chromosome found only in the heterogametic sex has few genes.
Term
Autosomes
Definition
All the other non-sex chromosomes
Term
Klinfelter Syndrome
Definition
XXY humans are male.
Term
Turner Syndrome
Definition
X_ humans are female.
Term
XXX females
Definition
Likely to give birth to a XXY child
Term
Jacob's Syndrome
Definition
XXY humans are male.
Term
Sex-Linked Traits
Definition
Genes on sex chromosomes show inheritance patterns that do not fit traditional Mendelian ratios that describe what happens to genes on autosomes.
A number of inherited diseases in humans are located in sex chromosomes. Examples: Hemophilia, color blindness.
Term
X-Linked
Definition
In humans (and other species with XY sex determination), a gene found only on the X chromosome.
Recessive X-Linked alleles are expressed more often in males than in females.
X-linked alleles are written with superscripts.
Term
Dosage Compensation
Definition
A mechanism for equalizing the overall expression of a sex-linked genes in both males and females.
Some organisms (like fruit flies) ramp up X-linked gene expression in the heterogametic sex.
Some (like humans and other mammals) use inactivation of most of one of the X-chromosomes.
Term
Barr Body
Definition
Condensed, mostly inactivated X chromosome visible during interphase in most mammalian cells.
Term
Variegation or Mosaicism
Definition
Mixes in phenotypic appearance in an organism due to expression of X-linked genes and variable, random inactivation patterns for X chromosomes. (Example: Calico Cat)
Term
Aneuploidy
Definition
Nondisjunction of homologous chromosomes during meiosis may lead to formation of an embryo with one extra chromosome called trisomic (2n+1) or less chromosomes called monosomics (2n-1)
Term
Alterations in Chromosomes Structures
Definition
Deletion or loss of a part of chromosome - usually lethal. Loss of a piece of chr 5 leads to a child with cri-du chat (cries of a cat) syndrome.
Translocation of a part chromosome to another site
A piece of chromosome 9 to chromosome 22 is associated with CML leukemia.
Fragile sites - thin chromosomes at a particular point.
Fragile X has a CGG repeats more than 1000 times leading to break in X chromosomes.
Term
Asexual Reproduction
Definition
Creates offspring that are genetically to each other and to the parent cell (clones).
Only mitotic cell division, or something very similar, is required.
The parent may split, bud, or fragment; sometimes, this involves mitotic cell division with unequal partitioning during cytokinesis (cellular budding).
Asexual reproduction is typically rapid and efficient compared to sexual reproduction.
Term
Sexual Reproduction
Definition
Occurs when specialized sex cells called gametes fuse to form a single cell called a zygote.
Usually the gametes that fuse are produced by different individuals, but they may be produced by the same individual.
In plants and animals the gametes are called the egg and the sperm.
The offspring are not genetically identical to their parents.
This genetic recombination may render the offspring better adapted to the environment than either parent, or it may be more poorly adapted than either parent.
Sexual reproduction must contain a mechanism to half the number of chromosomes at some point. Halving the chromosomes number is accomplished through meiosis.
Term
Diploid Cells Give Rise to Haploid Cells During Meiosis
Definition
The somatic cells of animals and higher plants are diploid cells.
The partners are called homologous chromosomes.
The partners are called homologous chromosomes.
One member of each pair came from the father (paternal homolog), and one from the mother (maternal homolog)
Diploid (2n) Haploid (n)
Term
Meiosis reduces chromosome number, producing up to 4 haploid cells from one diploid cell.
Definition
Meiosis has two successive cell divisions after only one DNA replication.
The two cell divisions are called meiosis I and meiosis II
Homologous chromosomes separate during meiosis I.
Sister chromatids separate during meiosis II
Meiosis is best understood by following the chromosomes (and their kinetochores)
Term
Prophase I
Definition
Chromatin condenses to form chromosomes, and homologous chromosomes pair.
Term
Tetrad
Definition
The resulting structure, with 4 total chromatids (two sisters from each homologous chromosome)
Term
Synapsis
Definition
The process of homologous chromosomes pairing lengthwise.
Term
Synaptonemal Complex
Definition
What the tetrad is held together by during early prophase I.
Term
Sister Chromatids
Definition
In mitosis, sister chromatids are held together at centromeres and have kinetochores, but their kinetochores are side-by-side and attach to spindle fibers from the same pole.
Term
End of Prophase I
Definition
The spindle has formed
The nuclear membrane has vesicularized
Nucleoli have disintegrated
Homologous chromosomes are attached by their kinetochores to spindle fibers from opposite poles.
Homologous chromosomes are held together only at chiasmata, the sites where crossing-over occurred.
Term
Metaphase I
Definition
Tetrads line up along the midplane of the cell - the presence of tetrads (bundles with 4 total chromatids) is the key distinguishing feature of metaphase I of meiosis.
Term
Anaphase I
Definition
Homologous chromosomes separate and are moved toward opposite poles.
Each pole gets one set of homologous chromosomes.
The initial "maternal" or "paternal" chromosome sets are mixed and distributed randomly (crossing-over largely blurs such identity anyway)
Term
Telophase I
Definition
After anaphase is completed, generally:
The spindle fibers disintegrate
The chromosomes partially decondense
Nuclear membranes may form around the genetic material.
Cytokinesis occurs.
Term
Interkinesis
Definition
The period between meiosis I and meiosis II, varies in length and distinctiveness.
Interkinesis differs from interphase because there is no S phase (no DNA replication).
Typically, interkinesis is brief (some cells skip it altogether)
Term
Prophase II
Definition
Of meiosis is similar to prophase of mitosis, but is usually very short because the chromatin did not completely decondense after meiosis I.
Term
Metaphase II
Definition
Similar to metaphase of mitosis.
Chromosomes line up along the midplane of the cell.
Sister chromatids are connected by their kinetochores (now on opposite sides) to spindle fibers from opposite poles.
Term
Anaphase II
Definition
Like mitotic anaphase, sister chromatids segregate toward opposite poles.
Term
Telophase II
Definition
Much like mitotic telophase:
The spindle is disintegrated.
The chromosomes decondense.
Nuclear membranes reform around the genetic material to form nuclei.
Nucleoli reappear, and interphase cellular functions resume.
Cytokinesis usually begins during telophase II and ends shortly thereafter.
Term
Key Differences Between Mitosis and Meiosis
Definition
Mitosis has one DNA replication and one division, resulting in two genetically identical daughter cells; homologous chromosomes do not pair, do not cross-over, and are not segregated.
Meiosis has one DNA replication but two divisions (reductive division), resulting in up to four genetically distinct daughter cells; in the process, homologous chromosomes pair (synapsis), cross-over (homologous recombination), and segregate during meiosis.
Term
Aerobic Respiration
Definition
A generally efficient process that requires O2; most, but not all, organisms can use a form of this process at least some of the time; also called cellular respiration.
A redox process.
The most efficient form of cellular respiration, is used by most organisms.
Nutrients (typically glucose) are catabolized to water and carbon dioxide, and energy is stored in ATP.
Yields 36 or 38 ATP molecules from one glucose molecule.
Term
Anaerobic Respiration
Definition
Processes similar to aerobic respiration but that do not use O2; used mainly by bacteria that live in anaerobic (O2-deficient) environments.
Not as efficient as aerobic respiration.
Term
Fermentation
Definition
Generally inefficient processes used mainly when other pathways cannot be used or when ATP is needed quickly; fermentation processes do not use O2.
Involves no electron transport chain.
Inefficient; net is 2 ATP per glucose molecule (only glycolysis works).
Term
Substrate-level Phosphorylation
Definition
Coupled Reactions that directly phosphorylate ADP or GDP.
Term
Dehydrogenation Reactions
Definition
Redox reactions that transfer hydrogen to NAD+ or FAD
Term
Decarboxylation Reactions
Definition
Carboxyl groups are removed; CO2 is released.
Term
Preparation Reactions
Definition
Molecules are rearranged to prepare for other reactions.
Term
Glycolysis
Definition
Occurs in the cytosol (both in prokaryotes and eukaryotes).
Glucose is converted to 2 pyruvate molecules (a 3-carbon molecule).
Released energy is stored in a net yield of 2 ATP and 2 NADH molecules.
Occurs under both aerobic and anaerobic conditions (no O2 required).
A series of ten reactions, each catalyzed by a different enzyme; broken into 2 phases (energy investment and energy capture).
Term
First Phase of Glycolysis
Definition
Requires energy investment.
Phosphorylation, using two ATP, charges the sugar with two phosphates.
2 molecules of G3P are formed.
Term
Second Phase of Glycolysis
Definition
The energy payoff phase yields private and energy captured in ATP and NADH.
Each G3P is converted to pyruvate.
Aside: -ate and -ic acid forms are essentially equivalent in cells.
Produces 4 ATP (net of 2 ATP)
Produces 2 NADH + H+
Term
Formation of Acetyl Coenzyme A From Pyruvate
Definition
Pyruvate is sent to the mitochondria in eukaryotes.
Set of three enzymes catalyze the reactions, grouped together in the pyruvate dehydrogenase complex.
Oxidative Decarboxylation: A carboxyl group is removed from pyruvate.
Remaining 2-carbon fragment is oxidized (loses 2 electrons); NADH is produced.
Remaining 2-carbon fragment, an acetyl group, is joined to coenzyme A.
Term
Citric Acid Cycle
Definition
A.K.A tricarboxylic acid cycle, TCA cycle, Krebs cycle.
Still in mitochondria of eukaryotes.
Series of 8 enzyme-catalyzed steps, and one side reaction where GTP+ADP->GDP+ATP
Glucose has ben completely catabolized, yet only 4 ATP have been formed; the rest of the energy is stored in NADH and FADH2.
Term
Oxidative Phosphorylation: The Electron Transport Chain and Chemiosmosis
Definition
Occurs in mitochondria of eukaryotes, and on membrane surface in prokaryotes.
Electrons from NADH and FADH2 are transferred to a chain of membrane-bound electron acceptors, and eventually passed to oxygen.
Hydrogen ions are pumped across the inner mitochondrial membrane, creating a concentration gradient with high proton concentration gradient with high proton concentration in the intermembrane space.
Chemiosmosis produces ATP.
Energy from oxidation of NADH yields ~3 ATP
energy from oxidation of FADH2 yields ~2 ATP
Term
Regulation of Aerobic Respiration
Definition
ATP/ADP balance regulates much of oxidative phosphorylation.
ATP synthesis continues until ADP stores are largely depleted.
Rapid use of ATP leads to excess ADP, and thus speeds up aerobic respiration.
Term
Phosphofructokinase
Definition
The enzyme for one of the earliest steps in glycolysis, is highly regulated.
ATP, though a substrate, also serves as an allosteric inhibitor.
Citrate is also an allosteric inhibitor.
AMP serves as an allosteric activator.
Term
Alcohol Fermentation
Definition
Produces ethanol, CO2, and NAD+
Pyruvate is converted to ethanol and CO2 to regenerate NAD+
Ethanol is potentially toxic waste product, and is removed from cells.
Yeast (and many bacteria) perform alcoholic fermentation in low oxygen environments.
Used in making alcoholic beverages and baking.
Term
Lactic Acid Fermentation
Definition
Produces lactate and NAD+
pyruvate is reduced to lactate to regenerate NAD+
Performed by some bacteria and fungi, and by animals (when muscles need energy fast).
Used in making cheese, yogurt, and sauerkraut.
Term
Basic Rules of Inheritance were first demonstrated by Mendel
Definition
At the time of Mendel's work, most thought that parental traits were fluids that "blend" in offspring.
Mendel recognized that this model did not explain what he observed.
Term
Model System that Mendel chose that Carefully Established Testing Conditions
Definition
He used pea plants that he could outcross or allow to self-fertilize.
He chose traits that had two clear possible outcomes (yellow or green seeds, etc.)
He established true-breeding or "pure" lines to use for genetic crosses.
Term
P Generation (P1)
Definition
Parental Generation
Term
F1 Generation
Definition
First generation offspring (from filial)
Term
F2 Generation
Definition
Second generation offspring.
Term
Phenotype
Definition
Appearance or characteristic of an organism.
Term
Genotype
Definition
Genetic Makeup of an organism, determines phenotype. (Aa, AA, aa)
Term
Gene
Definition
Unit of heredity; controls a trait that determines a phenotype.
Term
Locus
Definition
The location of a particular gene on a chromosome.
Term
Alleles
Definition
Alternative versions of a gene.
Term
Dominant
Definition
Allele that dominates over others in determining phenotype.
Term
Recessive
Definition
Allele whose phenotypic expression is "hidden" when a dominant allele is present.
Term
Hybrid
Definition
Offspring from a cross between two "pure" lines of different, competing phenotypes.
Term
Law of Segregation
Definition
Individuals normally carry two alleles for each gene, these alleles must segregate in production of sex cells.
Mechanism for segregation: the pairing and subsequent separation of homologous chromosomes during meiosis.
Term
Rules of Probability
Definition
Govern genetic inheritance.
The likelihood of a sex cell carrying a particular allele is determined by probability, its expected frequency of occurrence.
The combination of sex cells to form a zygote is generally ruled by probability as well.
The rules of probability govern genetics.
Term
Product Rule
Definition
When independent but not mutually exclusive events are combined, you multiply their individual probabilities to get the overall probability of the result.
Term
Sum Rule
Definition
If there is more than one way to obtain a result (mutually exclusive events), you add their individual probabilities to get the overall probability of the result.
The sum of all probabilities is one (no more, no less).
Term
Test Cross
Definition
Mating an individual that has the dominant phenotype for a trait with an individual with the recessive phenotype; this often will reveal the genotype of the dominant parent, or at least give some idea of the probably genotype.
Term
Monohybrid Cross
Definition
Cross between individuals that are both heterozygous for the gene that you are following; note that these give a 3:1 phenotype ratio and a 1:2:1 genotype ratio.
Term
Dihybrid Cross
Definition
Cross between individuals that are both heterozygous for two different genes that you are following.
When Mendel performed dihybrid crosses he found phenotype ratios of 9:3:3:1, which is expressed by the product rule.
Term
Law of Independent Assortment
Definition
Segregation of any one pair of alleles is independent of the segregation of other pair of alleles.
We now know that this is also a consequence of events in meiosis.
This doesn't hold perfectly true for all genes.
Term
Incomplete Dominance
Definition
The heterozygote has a phenotype that is intermediate between the two homozygous states.
Really, the term dominance has no true meaning here.
Example: red, pink, and white snapdragon flowers.
Term
Codominance
Definition
The heterozygote expresses characteristics of both alleles; very much like incomplete dominance.
Not an intermediate form, instead you see each allele distinctly expressed.
Roan cattle, expressing both red and white hairs, are a good example. (The difference between incomplete dominance and codominance is essentially a case of splitting hairs.
One of the best examples of codominance is the ABO human blood type, which will be covered below.
How to spot codominance or incomplete dominance: monohybrid crosses with a 1:2:1 phenotype ratio.
Term
Multiple Alleles
Definition
It is very common for there to be more than two allele types for a given locus; anytime there are three or more allele types involved, we say that there are multiple alleles.
Dominance relationships can vary between multiple alleles.
Example: Rabbit coat color is influenced by a gene that has four known alleles.
example: human ABO blood types
Term
Pleiotrophy
Definition
One gene, many phenotypes.
One gene affects more than one characteristic.
Usually only one gene product is directly involved, and its status affects many things.
Many disease genes are pleiotrophic (examples: cystic fibrosis, sickle cell anemia).
Term
Gene Interactions
Definition
Two or more genes interact to produce a novel phenotype.
Examples: rooster combs; coat color in Labrador retrievers.
Hallmark of gene interactions: exactly 4 phenotypes are found, and certain crosses will produce a 9:3:3:1 phenotype ratio in offspring (thus indicating that they are a dihybrid cross)
Term
Epistasis
Definition
One gene influences the phenotype that a second gene usually controls, masking any effects of alleles at the second gene; the name literally means "stopping" or "standing upon"
example: albinism is generally epistatic
spot epistasis by modification of dihybrid cross results, getting ratios like 9:7 or 9:3:4 instead of 9:3:3:1
Term
Polygenic Inheritance
Definition
Multiple, independent genes have similar, additive effects on a characteristic.
When plotted out for a population, polygenic traits produce a normal distribution curve if mating is random with respect to the trait.
Examples include height and skin color in humans.
Most economically important traits are polygenic (cow milk production, cattle weight, corn crop yield, etc.)
Polygenic traits don't fall easily into distinct categories; instead, they usually are measured traits.
Term
Autosomal Recessive Genetic Disorders
Definition
Most genetic disorders are inherited as autosomal recessive traits.
The recessive allele is usually a nonfunctional (or poorly functional) copy of a gene whose product is needed in metabolism.
Much genetic research with model organisms (mouse, fruit fly, etc.) uses such traits to determine gene identities and functions.
Term
Gene Therapy
Definition
Considered to be a promising possibility for treatment of many disorders.
The problem is how to get the gene delivered to the cells where it is needed - sometimes a virus is used to infect cells, with the virus actually carrying and expressing the desired gene.
In some cases, particularly if blood is involved, it appears that blood stem cells may be able to be removed from the patient, transformed (have new genetic material inserted), and then returned to the patient's body.
The most promising transformation mechanism uses embryonic stem cells and cloning.
Perform a technique to the gene you want into the cells, then select for the cells that do what you want.
Grow those cells in culture, treat them with hormones that cause them to differentiate into the cell type that you want, and put those cells into the patient.
Term
Phenylketonuria (PKU)
Definition
Most common in those of western European descent; occurs in about 1 in 12,000 human births in the U.S.
Phenylalanine (an amino acid) is not metabolized properly, leading to a buildup of a toxic compounds that can lead to severe mental retardation.
Treated with a diet that dramatically reduces phenylalanine consumption; potential gene therapy target.
Term
Sickle Cell Anemia
Definition
Most common in those of African descent; about 1 in 500 of African-Americans have it.
Caused by a mutation in hemoglobin that makes it tend to crystallize when oxygen is not bound to it.
Treatments have increased life expectancy, including stimulating fetal hemoglobin production and bone marrow transplants; work continues on gene therapy.
The heterozygous condition actually leads to increased resistance to malaria, and thus is favored when malaria is present - about 1 in 12 African-Americans are heterozygous and thus "carriers" for sickle cell anemia
Term
Cystic Fibrosis
Definition
Most common in those of European descent.
Abnormal mucus secretions, particularly in the lungs, due to a defect in Cl- ion transport.
Life expectancy short (about 30 years); treatments are limited - has been a target for gene therapy trials.
Heterozygous carriers may be less likely to die from diarrhea-inducing diseases (based on mouse model studies involving cholera)
Term
Autosomal Dominant Genetic Disorders in Humans
Definition
Severe dominant genetic disorders are not common, because they are usually not passed on to the next generation.
Those that do exist typically have late onset of disorder symptoms.
Term
Huntington's Disease
Definition
The best known autosomal dominant disorder.
Occurs in about 1 in 10,000 human births in the U.S.
Affects central nervous system, leading to sever mental and physical deterioration.
Onset of symptoms usually in 30s or 40s.
One of at least 9 known "trinucleotide repeat disorders" in humans.
Term
Karyotyping
Definition
Many genetic problems occur on the large-scale, chromosomal level.
Studies of karyotypes are often done to test for such problems.
A karyotype display reveals the composition of chromosomes for an individual.
Term
Human Genome Project
Definition
Sequencing the human genome provides a means to greatly accelerate studies of human genetics.
The underlying genetic causes for gene-based traits can be studied more easily.
Sequence variations can be readily analyzed.
More sophisticated genetic testing can be performed, leading to the potential for genetically tailored medical treatment.
Term
What must genetic material do?
Definition
The genetic material must be able to replicate itself.
Must be able to control living processes.
Term
A Model of Genetic Inheritance Was in Place in the Early 1900s:
Definition
Mendel's "laws" of genetics - inherit one copy of each gene from each parent.
Chromosomes as locations/carriers of genes.
Distribution of chromosomes in making sex cells explains Mendel's laws.
Term
Chromosomes are predominately made of which two things?
Definition
Protein and DNA
Term
Studies by Griffith in the 1920s of Pneumococcus in Mice
Definition
smooth (S) strain killed mice, rough (R) strain did not.
heat-killed S strain did not kill mice, but heat-killed S+R strain killed mice.
Some "transforming principle" from the heat-killed S strain changed the R strain to make it deadly.
Term
Hershey-Chase Experiments
Definition
Viruses inject DNA into bacteria and take them over.
Viruses that infect bacteria are called bacteriophages.
Viruses execute a "genetic takeover" of cells.
Hershey and Chase concluded that phage injected DNA into bacteria to infect them.
Term
Structure of DNA
Definition
Deoxynucleotide has 5-carbon doxyribose sugar, phosphate, and nitrogenous base.
Bases are the purines adenine (A) and guanine (G), and the pyrimidines thymine (T) and cytosine (C).
Nucleotides are linked by a 3',5' phosphodiester linkage.
Resulting chain has a 5' end and a 3' end.
The phosphates and sugars are collectively called the "backbone" of the strand.
Term
Chargaff and colleagues found that...
Definition
Amounts of A=T and C=G.
Term
X-Ray Diffraction Studies by Rosalind Franklin and Maurice Wilkins Indicated a Helical Molecule.
Definition
Molecule has three repeating patterns that any model of its structure must account for.
The data indicated a double helix.
Franklin and Wilkins inferred that the bases are stacked like rungs of a ladder.
DNA was envisioned as a twisted ladder, with the sugar-phosphate backbone forming the sides and basepairs forming the rungs.
Term
The Accepted Model for the Structure of the DNA Double Helix was Published by James Watson and Francis Crick in 1953.
Definition
Double helix and antiparallel strands.Each strand a nucleotide chain held together by phosphodiester linkages.
Strands held together by hydrogen bonds between the bases (basepairs).
A paired with T, with 2 hydrogen bonds predicted.
C paired with G, with 3 hydrogen bonds predicted.
The strands were described as complementary: the sequence of one had to have an appropriate, complementary sequence on the other for the molecule to hold together.
The double-helix model strongly suggested a way to store information in the sequence of bases, which indeed appears to be true.
Term
DNA Structure Suggests an Obvious Replication Mechanism
Definition
Watson and Crick noted that "specific basepairing...immediately suggests a possible copying mechanism for the genetic material"
The model suggested that each strand could serve as a template for making a complementary strand, so-called semiconservative replication.
One strand old, one new.
Term
Experiments with E. coli supported the semiconservative replication model
Definition
Meselson and Stahl used nitrogen isotopes to mark old vs. newly synthesized DNA strands.
Bacteria grown in medium with 15N were transferred to medium with 14N; thus, old DNA strands had 15N and new ones 14N.
Isolated DNA after one generation: DNA molecules all had roughly equal amounts of 15N and 14N - disproved conservative replication.
Later generations: Some 14N only, some still with roughly equal amounts of 15N and 14N - disproved dispersive replication.
Term
Overview of DNA replication
Definition
DNA replication requires the coordinated activity of many enzymes and other proteins.
Also requires the presence of nucleotide triphosphates.
Term
Origins of Replication
Definition
DNA replication begins at specific sites.
Synthesis generally proceeds in both directions from an origin, creating a "replication bubble."
There is usually only one origin of replication in the circular bacterial DNA.
Eukaryotic chromosomes usually have several origins of replication each.
Both strands are replicated at the same time on both sides of the replication bubble, producing Y-shaped replication forks on each side; the forks move as synthesis proceeds.
Term
Unwinding and Opening DNA
Definition
The twisted double helix must be unwound and the basepair bonds broken ("opening" the DNA molecule)
DNA helicase does the unwinding and opening.
Single-strand DNA binding proteins keep it open (also called helix-destabilizing proteins)
Topoisomerases break and rejoin strands, resolving knots and strains that occur.
Term
Direction of Synthesis
Definition
DNA polymerases direct synthesis of new strands.
Synthesis proceeds by adding nucleotides onto the 3' end of a strand.
Thus, synthesis can only proceed in the 5'->3' direction.
The nucleotide added is from a deoxynucleotide triphosphate; two phosphates are released in the process.
Term
Priming New Strands
Definition
DNA polymerase can only add onto an existing strand, so it can't start the strand.
Primase starts the strand by making an RNA primer that is a few (usually about 10) ribonucleotides long.
DNA polymerase can then add nucleotides starting at the end of the RNA primer.
The RNA primer is later degraded and (usually) replaced with DNA.
Term
Leading and Lagging Strands
Definition
The 5'->3' directionality of synthesis complicates the replication activity.
One strand being synthesized, the leading strand, has its 3' end at the fork; thus, its synthesis can proceed continuously, in the direction that the fork moves.
The other, lagging strand has its 5' end at the fork; it must be synthesized in the "opposite direction"from the leading strand.
The lagging strand is thus made in short 100-1000 nucleotides Okazaki Fragments.
Fragments are later joined by DNA ligase.
Term
DNA proofreading and DNA repair
Definition
DNA polymerase proofreads: initial error rate about 1 in 100,000; final rate about 1 in 100,000,000.
Cells have DNA repair mechanism to fix most mistakes that get through as well as to fix most damaged DNA.
Term
The Dead End: Problem at the Telomeres
Definition
The ends of chromosomes are called telomeres.
They present special problems for DNA replication: the 5' end RNA primer cannot be replaced with DNA, creating 5' end gaps.
This leads to shorting of chromosomes at the ends with each cell generation.
In some cells, special telomerase enzymes can generate longer telomeres - telomerase is required in germ-line cells, and active in cancer cells as well.
Term
The DNA Molecule is Too Long if Not Folded
Definition
Bacteria have much less DNA in their cells than eukaryotes do, but even so the length of their DNA molecule if stretched out would be 1000x the length of the cell itself.
Thus, even in the bacteria DNA must be "packaged", folded and coiled to make it fit in the cell.
Eukaryotes have even more DNA, and use somewhat elaborate means to package the DNA even when it is in "decondensed" chromatin.
Term
Nucleosomes
Definition
Nucleosomes are the main packaging mechanism for eukaryotic DNA.
The nucleosome is made up of 8 protein subunits, acting like a "spool" for the DNA "thread"
The proteins are called histones
Histones are positively charged, and thus able to associate with the negatively charged phosphates of the DNA backbone
The 8 proteins in a nucleosome are 2 each of 4 different histones.
Nucleosomes are linked together with "linker DNA" regions, parts of the continuous DNA molecule that are not wound on histones.
Overall this gives an appearance of nucleosomes as "beads" on a DNA "string."
Nucleosome packaging of DNA is found throughout the cell cycle, except when DNA is being replicated.
Term
Further Packaging: Histone H1 and Scaffolding Proteins
Definition
Even during interphase, most of the DNA is packed tighter than just being wound on nucleosomes.
This next packing step uses another histone, H1, that associates with the linker DNA regions.
H1 binding leads to packing of nucleosomes into a chromatin fiber that is 30nm wide.
Those fibers form loops that are often held together by non-histone scaffolding proteins.
More complex packing stpes occur when chromosomes are fully condensed for cell division.
Term
Work By Beadle and Tatum in the 1940s
Definition
Found mutant genes in the fungus Neurospora that each affected a single step in a metabolic pathway.
Developed the "one gene, one enzyme" hypothesis.
Later work by Pauling and others showed that other proteins are also generated genetically.
Also, some proteins have multiple subunits encoded by different genes.
This ultimately led to the "one gene, one polypeptide" hypothesis.
Term
RNA (ribonucleic acid)
Definition
RNA serves mainly as an intermediary between the information in DNA and the realization of that information in proteins.
Term
RNA Has Some Structural Distinctions from DNA
Definition
Typically single-stranded
Sugar is ribose; thus, RNA polymers are built from ribonucleotides.
Uracil (U) functions in the place of T.
Term
Three Main Forms of RNA are used: mRNA, tRNA, and rRNA
Definition
mRNA or messenger RNA: copies the actual instructions from the gene.
tRNA or transfer RNA: links with amino acids and brings them to the appropriate sites for incorporation in proteins.
rRNA or ribosomal RNA: main structural and catalytic components of ribosomes, where proteins are actually produced.
All are synthesized from DNA templates.
Term
Central Dogma of Gene Expression:
Definition
DNA->RNA->protein
The gene is the DNA sequence with instructions for making a product.
the protein (or protein subunit) is the product.
Term
DNA -> RNA is ...
Definition
Transcription.
Making RNA using directions from a DNA template.
Transcribe = copy in the same language.
Term
RNA->Protein is ...
Definition
Translation.
Making a polypeptide chain using directions in mRNA.
Translate = copy into a different language.
Term
Transcription: Making RNA from a DNA Template...
Definition
RNA is synthesized as a complementary strand using DNA-dependent RNA polymerases.
Process is somewhat similar to DNA synthesis, but no primer is needed.
Bacterial cells each only have one type of RNA polymerase.
Eukaryotic cells have three major types of RNA polymerase.
RNA polymerase I is used in making rRNA.
RNA polymerase II is used in making mRNA and some small RNA molecules.
RNA polymerase III is used in making tRNA and some small RNA molecules.
Term
Only One Strand is Transcribed, with RNA Polymerase Using Ribonucleotide Triphosphates (rNTPs, or just NTPs) to build a strand in the 5'->3' Direction.
Definition
Thus, the DNA is transcribed in the 3'->5' direction.
The DNA strand that is read is called the template strand or sense strand.
Upstream means toward the 5' end of the RNA strand, or toward the 3' end of the template strand (away from the direction of synthesis).
Downstream means toward the 3' end of the RNA strand, or toward the 5' end of the template strand.
Term
Transcription Has Three Stages:
Definition
Initiation, Elongation, and Termination.
Term
Initiation Requires a Promoter - Site where RNA Polymerase Initially binds to DNA
Definition
Promoters are important because they are needed to allow RNA synthesis to begin.
Promoter sequence is upstream of where RNA strand production actually begins.
Promoters vary between genes; this is the main means for controlling which gnes are transcribed at a given time.
Bacterial Promoters.
Eukaryotic Promoters (for genes that use RNA polymerase II).
Regardless of promoter specifics, initiation begins when RNA polymerase is associated with the DNA.
Term
Elongation
Definition
RNA polymerase continues building the RNA strand in a linear fashion, unwinding and opening up the DNA along the way.
The newly synthesized RNA strand easily separates from the DNA and the DNA molecule "zips up" behind RNA polymerase, reforming the double helix.
Term
Termination
Definition
The end of RNA transcription.
In prokaryotes, transcription continues until a terminator sequence is transcribed that causes RNA polymerase to release the RNA strand and release from the DNA.
Termination in eukaryotes is more complicated and differs for different RNA polymerases.
Term
The Genetic Code
Definition
The actual information for making proteins.
Based on codons, always written in 5'->3' fashion.
AUG is the "start" codon.
Genetic code is universal.
Term
mRNA Coding Region
Definition
Codes for protein synthesis.
The coding region ends when a stop codon is reached.
the mRNA strand prior to the start codon is called the 5' untranslated region or leader sequence.
the mRNA strand after the stop codon is called the 3' untranslated region or trailing sequence.
Term
Translation
Definition
Using information in mRNA to direct protein synthesis.
In eukaryotes, mRNA is moved from the nucleus to the cytoplasm (in prokaryotes, there is no nucleus so translation can begin even while transcription is underway).
Term
The Site of Translation is the Ribosome
Definition
Ribosomes are complexes of RNA and protein, with two subunits.
Ribosomes catalyze translation.
Term
Peptide Bonds Must Be Created Between Amino Acids to Form a Polypeptide Chain
Definition
Recall that peptide bonds are between the amino group of one amino acid and the carboxyl group of another.
Primary polypeptide structure is determined by the sequence of codons in mRNA.
The ribosome acts at the ribozyme that catalyzes peptide bond formation.
Term
tRNAs Bring Amino Acids to the Site of Translation
Definition
tRNAs are synthesized at special tRNA genes.
tRNA molecules are strands about 70-80 bases long that form complicated, folded 3-dimensional structures.
tRNAs have attachment sites for amino acids.
Each tRNA has an anticodon sequence region that will form a proper complementary basepairing with a codon on an mRNA molecule.
tRNA is linked to the appropriate amino acid by enzymes called aminoacyl-tRNA synthetases.
Term
The mRNA and aminoacyl-tRNAs Bond at the Ribosome for Protein Synthesis
Definition
The large ribosome subunit has a groove where the small subunit fits.
mRNA is threaded through the groove.
Term
The Large Ribosomal Subunit has Two Depressions Where tRNAs Attach
Definition
The E site is where uncharged tRNA molecules are moved and then released.
The P site is where the completed part of the polypeptide chain will be attached to tRNA.
The A site is where the new amino acid will enter on an aminoacyl-tRNA as a polypeptide is made.
Term
Restriction Enzymes
Definition
Molecular scissors with a twist.
Also called restriction endonucleases, are enzymes that cut DNA molecules in specific places.
Hundreds of different kinds of restriction enzymes are known.
Recognized sequence length varies.
Placement cut varies; some lave sticky ends, others blunt ends.
Pallindromic.
Term
Making Recombinant DNA
Definition
Restriction enzymes are used to cut up DNA of interest and a vector into which you want to place the DNA, making restriction fragments.
Particularly when sticky ends are involved, the target DNA restriction fragment can form basepairs with the vector.
DNA ligase is then used to join the DNA strand backbones.
Term
Cloning
Definition
The process of making many genetically identical cells from cell containing recombinant DNA.
The gene piece introduced in the recombinant DNA is said to be the DNA that is cloned.
Recombinant DNA is introduced to cells by a vector; the vector is usually maintained in the altered cell line.
Term
Vector
Definition
A means of delivering recombinant DNA to an organism.
Combined Foreign DNA + Vector = recombinant DNA
Vectors must have a way of getting into the host organism (transformation).
Vectors must have some way of being propagated.
Vector DNA sequence must be known enough so that restriction sites can be accurately predicted and used.
Viruses are vectors.
Viruses infect cells with their DNA; recombinant DNA in a virus can thus be transferred into cells.
Some of this "transduction" occurs naturally, but genetic engineers control and exploit the process.
Term
Plasmids
Definition
Plasmids are vectors.
Plasmids are the most commonly used vectors.
They are small, circular DNA molecules with at least one replication origin.
Term
Yeast Artificial Chromosomes (YAC)
Definition
Vectors.
Eukaryotes can support and maintain larger pieces of DNA as chromosomes.
YACs have the required elements of chromosomes (centromere, telomeres) and can be used as vectors for large segments of recombinant DNA in some eukaryotes.
Term
Screening
Definition
Often many clones are made with various DNA pieces inserted.
Screening is used to find the DNA of interest; typically:
A selectable marker is used to ensure that the vector is present.
A second type of selectable marker is tested to ensure that the vector contains inserted DNA.
Cells from cell colonies that pass the screens to this point are used as sources for making large numbers of cells.
Term
DNA Libraries
Definition
The first step in working with the DNA of a species is to break the whole genome into manageable bits for study; this is done by creating DNA libraries.
Vectors serve as the "books" in a DNA library - each "book" has a different piece of inserted DNA.
Two main types of libraries are genomic libraries and cDNA libraries.
Term
Genomic Libraries
Definition
Raw genomic DNA is broken into fragments.
The broken DNA pieces are put into vectors and then the vectors into host cells.
Cells lines are maintained for each library piece.
The cell lines are given unique identifiers, and DNA probing techniques can be used to determine what lines carry particular cloned DNA sequences.
Term
cDNA Libraries
Definition
A more refined approach than genomic libraries, this type of library is based mainly on the coding regions of DNA.
mRNAs are isolated from a cell and converted into complementary DNA using the enzyme reverse transcriptase.
the cDNA is then inserted into vectors and the library is made and maintained just like a genomic library.
Different types of cDNA libraries can be made, reflecting the conditions under which cells made the original mRNAs.
DNA probing techniques are used to find which lines have a cDNA of interest.
Term
DNA sequence amplification: PCR (polymerase chain reaction) is used to get enough DNA to work with
Definition
DNA polymerase can build a DNA strand provided there is a template strand, a primer, and dNTPs.
Term
Denaturation
Definition
Heating a DNA molecule will eventually denature (melt) the double strands into separate single strands, breaking the hydrogen bonds between A-T and C-G basepairs; this can provide potential template strands.
Term
Annealing of Primers
Definition
When the DNA cools, basepairs will reform; if small, specific DNA primers are added in excess compared to the amount of target (template) DNA molecules, the DNA primers will tend to bind to the target DNA strands and keep the original double helices from reforming.
Term
Primer Extension
Definition
ENA polymerases can add dNTPs to make a complementary DNA strands, starting at the 3' ends of the primers.
Term
DNA Gel Electrophoresis
Definition
The overall DNA molecule is negatively charged, and will migrate through a viscious material such as a gel if a voltage difference is supplied (moving toward the positive pole).
The speed of migration through a gel will be determined in part by the size of the DNA molecule; the longer the molecule, the slower it moves.
Relative migration rate through a gel can be used to determine the approximate size of a DNA fragment.
This mostly holds true for RNA as well, but different conditions must be used to prevent degradation of RNA.
Term
Probing
Definition
DNA and RNA fragments can be transferred to a filter, denatured, and incubated with probe molecules that will hybridize with specific sequences.
The probe molecules can be made with some nucleotides that are either radioactive or fluorescent, thus "labeling" the probe - and, when the probe is used, labeling the sites on the filter where the probe is able to hybridize.
if DNA is on the filter and being probed, this is called a Southern blot or DNA gel blot.
If RNA is being probed, this is called a Northern blot or RNA gel blot.
An analogous process with proteins is called a Western Blot.
Term
DNA Sequencing
Definition
A DNA sequence can be determined using special nucleotides and migration differences of DNA strand through a gel based on size.
Special ddNTPs are used for sequencing.
When a ddNTP is incorporated into a growing DNA strand, it prevents further elongation of the DNA strand.
Sequencing typically involves 4 polymerization mixtures.
Term
Restriction Fragment Length Polymorphisms (RFLPs)
Definition
DNA cut by restriction enzymes and run on a gel can produce distinguishable DNA bands.
Sequence differences between organisms can result in different bands.
DNA sequencing is the most reliable means of identification, and as it becomes cheaper and more available it is replacing some uses of RFLP analysis; however, RFLP analysis likely will always be quicker and cheaper than sequencing, and is still used heavily.
Term
Membranes Separate Aqueous Environments, so that Differences can be Maintained
Definition
The plasma membrane surrounds the cell and separates the interior of the cell from the external environment.
Membrane-bound organelles have their interior region separated from the rest of the cell.
Passage of substances across membranes is generally regulated, helping to establish and maintain appropriate environments in the cell even as the outside environment changes.
Term
Membranes Provide a Surface on Which Many Chemical Events Occur.
Definition
Enzymes embedded in membranes catalyze many chemical reactions, and the locations of reactants and products on one side or the other of the membrane is often used to help control reaction rates.
Proteins and glycoproteins embedded in membranes are used for chemical recognition and signaling.
Term
Physical Properties of Cell Membranes
Definition
The lipid bilayer and the fluid mosaic model.
Biological membranes are lipid bilayers with associated proteins and glycoproteins.
Most of the lipids involved are phospholipids, although others like cholesterol and various glycolipids are also present.
Phospholipid molecules spontaneously form bilayers in aqueous environments due to their amphipathic nature and overall cylindrical structure.
Term
Amphipathic Molecules Have Distinct Hydrophobic and Hydrophilic Regions
Definition
Hydrophilic "head" and hydrophobic "tails" of phospholipids.
Tails come from two chains of fatty acids linked to glycerol.
Head comes from a polar organic molecule linked via a phosphate group to the glycerol backbone.
The two tails combine with the head to give a roughly cylindrical shape to the phospholipids molecule, a shape that favors the formation of lipid bilayers over lipid spheres.
There are other amphipathic molecules, such as detergents that come to a point at their single hydrophobic tail, thus tending to form spheres instead of bilayers.
Detergents can "solubilize" lipids to varying degrees; high enough concentrations of detergents will disrupt cell membranes.
Term
The Fluid Mosaic Model
Definition
Describes the structure and properties of cell membranes.
While a structural model including a lipid bilayer was proposed in the 1930s, early models sandwiched the lipid bilayer with membrane-associated proteins.
EM data after the 1950s showed that membrane bilayers are uniformly about 8nm thick, too thin for the sandwich model; also, isolated membrane proteins were often found to have a globular nature that did not fit the sandwich model.
In 1972, the fluid mosaic model was proposed where some proteins are imbedded in lipid bilayers that act as two-dimensional fluids; this model explained the existing data and made two key predications that have been verified:
Materials, including embedded proteins, can be moved along the membrane due to its fluid properties.
Digestion of certain "transmembrane" proteins applied to one side of a membrane will produce protein fragments that differ from those found if digestion is done only on the other side.
Term
Biological Membranes Act us Two-Dimensional Fluids, or Liquid Crystals.
Definition
Free to move in two dimensions, but not in the third, the molecules of the membrane can rotate or move laterally.
Molecules rarely "flip" from one side of the membrane to the other (that would be movement in the third dimension).
Term
The Fluidity of a Membrane is a Function of Both Temperature and the Molecules in the Membrane
Definition
Cells need membranes to be within a reasonable range of fluidity - too fluid and they are too weak, too viscous and they are more like solid gels.
At a given temperature, phospholipids with saturated fats are less fluid than those with unsaturated fats.
In an unsaturated fat, a carbon-carbon double bond produces a "bend" that causes the phospholipids to be spaced further away from its neighbor, thus retaining more freedom of motion.
The upshot is: At colder temperatures, unsaturated fats are preferred in cell membranes; at higher temperatures, saturated fats are preferred.
Other lipids, such as cholesterol, can stabilize membrane fluidity.
Term
Organisms Control Membrane Fluidity By Several Means
Definition
By regulating their temperature.
By changing the fatty acid profile of their membranes.
By adding fluidity modifiers or stabilizers like cholesterol.
Term
Biological Membranes Resist Having Open Ends
Definition
A lipid bilayer will spontaneously "self-seal"
Usually, this results in nearly spherical vesicles with an internal, aqueous lumen.
The spherical tendency can be modified with structural elements, such as structural proteins.
Winding membrane surfaces must be kept far enough apart and structurally supported to prevent them from self-sealing.
Vesicle formation takes advantage of self-sealing as regions of membrane are pinched off by protein contractile rings.
Term
Fusion of Membrane Surfaces Can Occur When They are in Close Proximity
Definition
Fusion is common between vesicles and various organelles.
Contents of two separate membrane-bound lumens are mixed when fusion occurs.
Fusion of vesicles with the plasma membrane delivers the material in the vesicle lumen to the outside of the cell.
Term
Integral Proteins
Definition
Amphipathic proteins that are firmly bound to the membrane, and can only be released from the membrane by detergents.
Some integral proteins are transmembrane proteins, extending completely across the membrane.
Hydrophobic alpha-helices are common in the membrane spanning domains of transmembrane proteins.
Some wind back-and-forth across the membrane, but most only span the membrane once.
Term
The Protein Profile of One Membrane Side Typically Differs from that of the Other Side
Definition
Many more proteins are on the cytoplasmic side of the plasma membrane, as revealed by freeze-fracturing plasma membranes.
The types of processing that a protein receives differs depending on the target side, or if it is integral.
Membrane proteins perform several functions, including acting as enzymes, regulating transport across the membrane, and in cell signaling.
Term
Cell Membranes are Selectively Permeable
Definition
Some substances readily pass through, others do not.
Most permeable to small molecules and lipid-soluble substances.
water and other small molecules like CO2 and O2 can pass through easily.
Some examples of molecules that do not pass through easily; amino acids, sugars, ions.
Some passage across the membrane is assisted with special channels to allow or speed up the passage.
The specific selectivity can vary depending on the membrane.
Term
Diffusion
Definition
Particles move by random motion (kinetic energy); over time, the concentration across a membrane will tend to equalize.
Diffusion is the net movement of particles from an area with high (initial) concentration to an area with a low (initial) concentration; a difference in concentrations establishes a concentration gradient, which provides the energy for diffusion.
Given enough time, equilibrium will be reached.
Often equilibrium is never reached due to continual removal and/or continual production of a substance.
Rate of diffusion is a function temperature and of the size, shape, and charge nature of the substance.
Term
Osmosis
Definition
Diffusion of a solvent across a membrane.
In biology, the solvent is typically water.
Solutes do not travel across membranes with water, but they affect movement by affecting the concentration of water.
Term
Osmotic Pressure
Definition
Determined by the amount of dissolved substances in a solution; it is the tendency of water to move into the solution.
When two solutions have the same osmotic pressure, they are isotonic.
When a solution has a higher osmotic pressure than another, it is hypertonic to the other solution; water will tend to flow into the hypertonic solution.
Conversely, a hypotonic solution has a relatively lower osmotic pressure; water will tend to flow out of the hypotonic solution into the hypertonic solution.
Term
Turgor Pressure
Definition
Hydrostatic pressure in cells with a cell wall.
A cell wall enables cells to take in extra amounts of water without bursting.
The cells take in water and push against the cell wall, which pushes back.
Many cells use turgor pressure as part of maintaining structure; thus, if they lose turgor pressure, plants wilt.
Term
Facilitated Diffusion
Definition
When net transport follows a concentration gradient, but proteins are needed to assist in transport.
The carrier protein often provides a regulated channel or pore through the membrane.
Typically used to transport ions and large molecules like glucose, although water channels also exist.
Added energy is not required (concentration gradient provides the energy), and in some cases is harvested during transport.
Term
Carrier-Mediated Active Transport
Definition
Requires energy to work against a concentration gradient.
Energy is often supplied by ATP powering a protein "pump" that moves a substance against a gradient.
Term
Linked Cotransport
Definition
Can also provide the energy for active transport.
Na+, K+, or H+ is transported down its gradient, providing energy.
Another substance is transported at the same time against its gradient, using the energy.
The Na+, K+, or H+ gradient is often produced by active transport via a pump that uses ATP.
Term
Endocytosis
Definition
Fusion of vesicles or vacuoles bud into the cell from the plasma membrane, bringing materials into the cell.
Term
Phagocytosis
Definition
Large solid particles are ingested (including whole cells in some cases)
Term
Pinocytosis
Definition
Smaller regions of dissolved materials are ingested.
Term
Receptor-Mediated Endocytosis
Definition
Receptor proteins in the plasma membrane bind to specific molecules, causing protein conformational (shape) changes that lead to the formation of a coated vesicle.
Typically lysosomes bind with vesicles or vacuoles formed via phagocytosis or receptor-mediated endocytosis.
Term
Exocytosis
Definition
Fusion of vesicles or vacuoles with the plasma membrane that results in secretion outside the cell or discarding waste outside the cell.
Term
Signal Reception
Definition
Special protein receptors in the cell membrane bind to signaling molecules outside the cell.
Term
Signal Transduction
Definition
The receptor, now activated, changes shape in some way and transfers information to the interior of the cells (often though a series of protein activations and eventual formation of cAMP on the cytosolic side of the cell membrane)
Term
All Living Organisms are Composed of Cells
Definition
Smallest "building blocks" of all multicellular organisms.
All cells are enclosed by a surface membrane that separates them from other cells and from their environment.
Specialized structures with the cell are called organelles; many are membrane-bound.
Today, all new cells arise from existing cells.
Term
All Presently Living Cells Have a Common Origin
Definition
All cells have basic structural and molecular similarities.
All cells share similar energy conversion reactions.
All cells maintain and transfer genetic information in DNA.
The genetic code is essentially universal.
Term
Cell Organization and Homeostasis
Definition
Plasma membrane surrounds cells and separates their contents from the external environment.
Cells are heterogeneous mixtures, with specialized regions and structures (such as organelles).
Term
Cell Size is Limited
Definition
Surface area to volume ratio puts a limit on cell size.
Food and/or other materials must get into the cell.
Waste products must be removed from the cell.
Thus, cells need a high surface area to volume ratio, but volume increases faster than surface area as cells grow larger.
Cell shape varies depending both on function and surface area requirements.
Term
Most Cells are Large Enough to Be Resolved From Each Other With Light Microscopes (LM)
Definition
Cells were discovered by Robert Hooke in 1665; he saw the remains of cell walls in cork with a LMs, at about 30x magnification.
Modern LMs can reach up to 1000x
LM resolution (clarity) is limited to about 1um due to the wavelength of visible light.
Small cells are about 1um across, just on the edge of resolution.
Some modifications of LMs and some treatments of cells allow observation of subcellular structure in some cases.
Term
Resolution of Most Subcellular structure require Electron Microscopy (EM)
Definition
Electrons have a much smaller wavelength than light.
Magnification up to 250,000x or more and resolution over 500,000 times better than the human eye.
Includes transmission (TEM) and scanning (SEM) forms.
Term
Transmission (TEM)
Definition
Electron passes through sample; need very thing samples (100 nm or less thick); samples embedded in plastic and sliced with a diamond knife.
Term
Scanning (SEM)
Definition
Samples are gold-plated; electrons interact with the surface; images have a 3D appearance.
Term
Cells Can Be Broken and Fractionated To Separate Cellular Components For Study
Definition
Cells are broken (lysed) by disrupting the cell membrane, often using some sort of detergent.
Grinding and other physical force may be required, especially if cell walls are present.
Term
Centrifugation
Definition
Used to separate cellular components.
Using a centrifuge, samples are spun at high speeds, resulting in exposure to a centrifugal force of thousands to hundreds of thousands times gravity.
Results in a pellet and supernatant; cell components will be in one or the other depending on their individual properties; intact membrane-bound organelles often wind up in pellets, depending on their density and the centrifugal force reached (more dense=more likely in pellet).
Special treatments can determine whether a component ends up in the pellet or supernatant.
Density Gradients can also be used to subdivide pellet components based on their density; this can be used to separate organelles from each other, for example Golgi apparatus from ER.
Term
Eukaryotic Cells
Definition
Have internal membranes and a distinct, membrane-enclosed nucleus; typically 10-100um in diameter.
Term
Prokaryotic Cells
Definition
Do not have internal membranes (thus no nuclear membrane).
Main DNA molecule (chromosome) is typically circular; its location is called the nuclear area.
Other small DNA molecules (plasmids) are often present, found throughout the cell.
Plasma membrane is typically enclosed in a cell wall.
Often the cell wall is enclosed in an outer envelope or outer membrane.
Do not completely lack organelles; the plasma membrane and ribosomes are both present and are considered organelles.
Term
Cytoplasm
Definition
Compartment in Eukaryotic Cells.
Everything outside the nucleus and within the plasma membrane.
Contains fluid cytosol and organelles.
Term
Nucleoplasm
Definition
Compartment in Eukaryotic Cells.
Everything within the nuclear membrane.
Term
Membranes Separate Cell Regions
Definition
Have nonpolar regions that help form a barrier between aqueous regions.
Allow for some selection in what can cross a membrane.
Term
Nucleus
Definition
The "control center" of the cell.
Typically large (~5um) and singular
Term
Nuclear Envelope
Definition
Double membrane surrounding the nucleus.
Term
Nuclear Pores
Definition
Protein complexes that cross both membranes and regulate passage.
Term
Chromatin
Definition
DNA-protein complex.
Have granular appearance; easily stained for microscopy ("chrom-"=color).
"Unpacked" DNA kept ready for message transcription and DNA replication.
Proteins protect DNA and help maintain structure and function.
Term
Chromosomes
Definition
Condensed or "packed" DNA ready for cell division
("-some"=body)
Term
Nucleoli
Definition
Regions of ribosome subunit assembly.
Appears different due to high RNA and protein concentration (no membrane).
Ribosomal RNA (rRNA) transcribed from DNA there.
Proteins (imported from cytoplasm) join with rRNA at a nucleolus to form ribosome subunits.
Ribosome subunits are exported to the cytoplasm through nuclear pores.
Term
Ribosomes
Definition
The sites of protein synthesis.
Granular bodies with three RNA strands and about 75 associated proteins.
Two main subunits, large and small.
Perform the enzymatic activity for forming peptide bonds, and serve as the sites of translation of genetic information into protein sequences.
Term
Prokaryotic Ribosome Subunits are Both Smaller Than the Corresponding Subunits in Eukaryotes
Definition
In Eukaryotes:
The two main subunits are formed separately in the nucleolus and transported separately to the cytoplasm.
Some are free in cytoplasm while others are associated with the endoplasmic reticulum (ER).
Term
Endomembrane System
Definition
A set of membranous organelles that interact with each other via vesicles.
Includes ER, Golgi apparatus, vacuoles, lysosomes, microbodies, and in some definitions the nuclear membrane and the plasma membrane.
Term
Endoplasmic Reticulum (ER)
Definition
Membrane network that winds through the cytoplasm.
Winding nature of the ER provides a lot of surface area.
Many important cell reactions or sorting functions require ER membrane surface.
Term
ER Lumen
Definition
Internal aqueous compartment in ER.
Separated from the rest of the cytosol.
Typically continuous throughout ER and with the lumen between the nuclear membranes.
Enzymes within lumen and imbedded in lumen side of ER differ from those on the other side, thus dividing the functional regions.
Term
Smooth ER
Definition
Primary site of lipid synthesis, many detoxification reactions, and sometimes other activities.
Term
Rough ER
Definition
Ribosomes that attach there insert proteins into the ER lumen as they are synthesized.
Ribosome attachment directed by a signal peptide at the amino end of the polypeptide.
A protein/RNA signal recognition particle (SRP) binds to the signal peptide and pauses translation.
At the ER the assembly binds to an SRP receptor protein.
SRP leaves, protein synthesis resumes (now into the ER lumen), and the signal peptide is cut off.
Proteins inserted into the ER lumen may be membrane bound or free.
Proteins are often modified in the lumen (ex, carbs or lipids added).
Proteins are transported from the ER in transport vesicles.
Term
Vesicles
Definition
Small, membrane-bound sacs.
Buds off of an organelle (ER or other).
Contents within the vesicles (often proteins) transported to another membrane surface.
Vesicles fuse with membranes, delivering contents to that organelle or outside of the cell.
Term
Golgi Apparatus
Definition
A stack of flattened membrane sacs (cisternae) where proteins further processed, modified, and sorted [the "post office" of the cell].
Not contiguous with ER, and lumen of each sac is usually separate from the rest.
Three areas: cis, medial, and trans
Term
Cis (golgi)
Definition
Near ER and receives vesicles from it; current model (cisternal maturation model) holds that vesicles actually coalesce to continually form new cis cisternae.
Term
Medial (golgi)
Definition
As a new cis cisterna is produced, the older cisternae mature and move away from the ER.
In this region proteins are further modified.
Maturing cisternae may make other products; for example, many polysaccharides are made in the Golgi.
Some materials are needed back at the new cis face and are transported there in vesicles.
Term
Trans (golgi)
Definition
Nearest to the plasma membrane; a fully matured cisterna breaks into many vesicles that are set up to go to the proper destination, taking their contents with them.
Term
Lysosomes
Definition
Small membrane-bound sacs of digestive enzymes.
Serves to confine the digestive enzymes and their actions.
Allows maintenance of a better pH for digestion (often about pH 5).
Formed by budding from the Golgi apparatus; special sugar attachments to hydrolytic enzymes made in the ER target them to the lysosome.
Used to degrade ingested material, or in some cases dead or damaged organelles.
Ingested material is found in vesicles that bud in from the plasma membrane; the complex molecules in those vesicles is then digested.
Can also fuse with dead or damaged organelles and digest them.
Digested material can then be sent to other parts of the cell for use.
Found in animals, protozoa; debatable in other eukaryotes, but all must have something like a lysosome.
Found in animals, protozoa; debatable in other eukaryotes, but all must have something like a lysosome.
Term
Vacuoles
Definition
Large membrane-bound sacs that perform diverse roles; have no internal structure.
Distinguished from vesicles by size.
In plants, algae, and fungi, performs many of the roles that lysosomes perform for animals.
Term
Central Vacuole
Definition
Typically a single, large sac in plant cells that can be 90% of the cell volume.
Usually formed from fusion of many small vacuoles in immature plant cells.
Storage sites for water, food, salts, pigments, and metabolic wastes.
Important in maintaining turgor pressure.
Term
Tonoplast
Definition
Membrane of the plant vacuole.
Term
Food Vacuoles
Definition
Present in most protozoa and some animal cells; usually bud from plasma membrane and fuse with lysosomes for digestion.
Term
Contractile Vacuoles
Definition
Used by many protozoa for removing excess water.
Term
Microbodies
Definition
Small membrane-bound organelles that carry out specific cellular functions.
Lysosomes could be considered a type of microbody.
Term
Peroxisomes
Definition
Sites of many metabolic reactions that produce hydrogen peroxide (H202), which is toxic to the rest of the cell.
Peroxisomes have enzymes to break down H2O2, protecting the cell.
Peroxisomes are abundant in liver cells in animals and leaf cells in plants.
Normally found in all eukaryotes.
Example: detoxification of ethanol in liver cells occurs in peroxisomes.
Term
Glyoxysomes
Definition
In plant seeds, contains enzymes that convert stored fats into sugar.
Term
Energy Converting Organelles
Definition
Energy obtained from the environment is typically chemical energy (in food) or light energy.
Mitochondria are the organelles where chemical energy is placed in a more useful molecule, and chloroplasts are plastids where light energy is captured during photosynthesis.
Term
Mitochondria
Definition
The site of aerobic respiration:
sugar+oxygen->carbon dioxide+water+energy
The "energy" is actually stored in ATP
Term
Mitochondria Have a Double Membrane
Definition
Space between membranes = intermembrane space.
Inner membrane is highly folded, forming cristae; provides a large surface area.
Inner membrane is also a highly selective barrier.
The enzymes that conduct aerobic respiration are found in the inner membrane.
Inside of inner membrane is the matrix, analogous to the cytoplasm of a cell.
Term
Other Functions of Mitochondria
Definition
They have their own DNA, and are inherited from the mother only in humans.
Mitochondria have their own division process, similar to cell division; each cell typically has many mitochondria, which can only arise from mitochondrial division.
Some cells require more mitochondria than others.
Mitochondria can leak electrons into the cell, allowing toxic free radicals to form.
Mitochondria play a role in initiating apoptosis (programmed cell death)
Term
Plastids
Definition
Organelles of plants and algae that produce and store food.
Include amyloplasts (for starch storage), chromoplasts (for color, often found in petals and fruits), and chloroplasts (for photosynthesis).
They have their own DNA.
Derive from undifferentiated proplastids, although role of mature plastids can sometimes change.
Numbers and types of plastids vary depending on the organism and the role of the cell.
Chloroplasts get their green color from chlorophyll, the main light harvesting pigments involved in photosynthesis.
Term
Chloroplasts Have a Double Membrane
Definition
The region within the inner membrane is the stroma; it is analogous to the mitochondrial matrix.
Inner membrane is contiguous with an interconnected series of flat sacks called thylakoids that are grouped in stacks called grana.
The thylakoids enclose aqueous regions called the thylakoid lumen.
Chlorophyll is found in the thylakoid membrane, and the reactions of photosynthesis take place there and in the stroma.
Carotenoids in the chloroplast serve as accessory pigments for photosynthesis.
Term
Endosymbiont Theory
Definition
States that mitochondria and plastids evolved from prokaryotic cells that took residence in larger cells and eventually lost their independence.
The cells containing the endosymbionts became dependent upon them for food processing, and in turn provide them with a protected and rich environment (a mutualistic relationship)
Term
Cytoskeleton
Definition
A dense network of protein fibers that provides needed structural support.
A scaffolding for organelles.
Cell movement and cell division
Transport of materials within the cell.
Composed of three types of protein filaments: microtubules, microfilaments, and intermediate filaments.
Term
Microtubules
Definition
The thickest filaments of the cytoskeleton.
Hollow, rod-shaped cylinders about 25 nm in diameter.
made of alpha-tubulin and B-tubulin dimmers.
Cilia and Flagella are made of microtubules.
9+2 Arrangement
(9*3 Structure)
replicates itself.
Term
Microfilaments
Definition
Solid Filaments are about 7 nm in diameter.
Linker proteins cross-link the actin chains with each other and other actin associated proteins.
Actin monomers can be added to lengthen the microfilament or removed to shorten it; this can be used to generate movement.
Important in muscle cells; in conjunction with myosin, they are responsible for muscle contraction.
Term
Intermediate Filaments
Definition
Typically just a bit wider than microfilaments, this is the catch-all group for cytoskeletal filaments composed of a variety of other proteins.
The types of proteins involved differ depending on cell types and on the organism; apparently limited to animal cells and protozoans.
Not easily disassembled, thus more permanent.
Form the most insoluble part of the cell.
Term
Glycocalyx
Definition
Polysaccharides attached to proteins and lipids on the outer surface of the plasma membrane.
Typically functions in cell recognition and communication, cell contacts, and structural reinforcement.
Often works thorugh direct interaction with the ECM.
Term
ECM
Definition
A gel of carbohydrates and fibrous proteins; several different molecules can be involved.
Main structural protein is tough, fibrous collagen.
Term
Fibronectins
Definition
Glycoproteins in the ECM that often bind to both collagen and integrins.
Term
Integrins
Definition
Proteins in the plasma membrane that typically receive signals from the ECM
Term
Anchoring Junctions
Definition
Hold cells tightly together; one common type in animals is the desmosome.
Desmosomes form strong bonds between cytoskeletons, of adjacent cells and hold them together.
Materials can still pass in the space between cells with anchoring junctions.
Not involved in the transport of materials between cells.
Term
Tight Junctions
Definition
Between some animal cells, are used to seal off body cavities.
Cell plasma membranes are adjacent to each other and held together by a tight seal.
Materials cannot pass between cells held together by tight junctions.
Not involved in the transport of materials between cells.
Term
Gap Junctions
Definition
Between animal cells act as selective pores.
Proteins connect the cells.
Those proteins are grouped in cylinders of 6 subunits.
They cylinder can be opened to form a small pore (less than 2nm), through which small molecules can pass.
Term
Plasmodesmata
Definition
Act as selective pores between plant cells.
Plant cell walls perform the functions of tight junctions and desmosomes.
Plant cell walls form a barrier to cell-to-cell communication that must be breached by the functional equivalent of a gap junction.
Plasmodesmata are relatively wide channels (20-45nm) across the cell wall between adjacent cells; they actually connect the plasma membranes of the two cells, and allow exchange of some materials between the cells.
Term
Living Organisms Require Energy To Do Work, Any Change in State or Motion of Matter
Definition
Energy can be expressed in units of work (kJ) or heat energy (kcal); 1 kcal = 4.184 kJ
Energy can change forms (energy conversion)
Organisms carry out transformation in energy forms between potential energy and kinetic energy.
Organisms commonly use chemical bonds for storage and transfer of (potential) energy.
Work is required for the processes of life.
Term
First Law of Thermodynamics
Definition
The total amount of energy (+matter) in a closed system remains constant (principle of conservation of energy)
The universe is a closed system.
Living things are open systems.
Term
Second Law of Thermodynamics
Definition
In every energy conversion, some energy is converted to heat energy that is lost to the surroundings, and thus cannot be used for work.
Every energy conversion increased the entropy of the universe.
Energy converted to heat in the surroundings increases entropy (spreading of energy).
No energy conversion is 100% efficient.
Organisms must get a constant influx of energy because of energy is lost in conversions.
Term
Metabolism
Definition
The sum of chemical activities in a organism.
Can be divided into anabolism and catabolism.
Term
Anabolic Reactions
Definition
Processes that build complex molecules from simpler ones.
Term
Catabolic Reactions
Definition
Processes that break down complex molecules into simpler ones.
Term
Free Energy
Definition
Energy available to do work in a chemical reaction (such as: create a chemical bond).
Free energy changes depend on bond energies and concentrations of reactants and products.
Term
Bond Energy
Definition
Energy required to break a bond; value depends on the bond.
Left undisturbed, reactions will reach dynamic equilibrium when the relative concentrations of reactants and products is correct.
Forward and reverse reaction rates are equal; concentrations remain constant.
Cells manipulate relative concentrations in many ways, so that equilibrium is rare for key reactions.
Term
Exergonic Reactions
Definition
The products have less free energy than reactants.
The difference in energy is released and is available to do work.
Exergonic reactions are thermodynamically favored; thus, they are spontaneous, but not necessarily fast (more on activation energy later).
Catabolic reactions are usually exergonic.
ATP+H20->ADP+Pi highly exergonic in cellular conditions.
Term
Endergonic Reactions
Definition
The products have more free energy than the reactants.
The difference in free energy must be supplied (stored in chemical bonds).
An endergonic reaction is coupled with an exergonic reaction to provide the needed energy to drive an endergonic reaction.
Together, the coupled reactions must have a net exergonic nature.
Anabolic reactions are usually endergonic.
Term
ATP
Definition
The main energy currency in cells.
A nucleotide with adenine base, ribose sugar, and a chain of 3 phosphate groups.
Making ATP involves an endergonic condensation reaction.
ATP is typically created in catabolic reactions and used in anabolic reactions, linking those aspects of metabolism.
Cells maintain high levels of ATP relative to ADP.
Overall concentration of ATP is still very low.
Term
Redox Reactions
Definition
Used for energy transfer.
As the electron is transferred to an acceptor molecule, it releases free energy that can be used for other chemical reactions.
Term
Enzymes
Definition
Regulate chemical reactions in living organisms.
An enzyme is an organic molecule (typically a protein) that acts as a catalyst.
Enzymes only alter reaction rate.
Enzymes only catalyze reactions that are occurring anyway.
Enzymes work by lowering the activation energy of a reaction.
Enzymes lower activation energy by forming a complex with the substrates.
Many enzymes require cofactors to function.
Each enzyme has an optimal pH.
Term
Inhibitors
Definition
Reduce or eliminate catalytic activity.
Term
Activators
Definition
Allow or enhance catalytic activity.
Term
Allosteric Site
Definition
A receptor site on an enzyme where an inhibitor or activator can bind.
Term
Feedback Inhibition
Definition
Where the last product in a metabolic pathway binds to an allosteric site of an enzyme in an early step of the pathway (often the first) and inhibits activity of the enzyme.
Term
Irreversible Inhibition
Definition
Enzyme is permanently inactivated or destroyed; includes many drugs and toxins.
Term
Reversible Inhibition
Definition
If inhibitor is removed, the enzyme activity can be recovered.
Term
Competitive Inhibition
Definition
Inhibitor is similar in structure to a substrate; competes with substrate for binding to the active site.
Term
Noncompetitive Inhibition
Definition
Binds at allosteric site, alters enzyme shape to make active site unavailable.
Term
Biological Species Concept (for sexual organisms)
Definition
A species is one or more populations whose members are capable of interbreeding and producing fertile offspring, and whose members are reproductively isolated from other such groups.
Not always clear-cut, because some can interbreed under "artificial" conditions but don't appear to do so in nature.
Sometimes, "race" and "subspecies," and "strain" designations are used, but often different specific epithets are used when there are clear morphological differences involved.
Term
Asexual Species
Definition
Definition based on biochemical (think DNA sequence) and morphological differences; no solid rules.
Also includes use of "race," "subspecies," and "strain" designations.
In asexual species, microevolution over time directly leads to macroevolution (speciation).
Term
Phylogenetic Species Concept or Evolutionary Species Concept
Definition
A species is a single line of descent (lineage with a unique genetic history) that maintains its distinctive identity from other lineages.
This is a more comprehensive concept (it works for both sexual and asexual species)
But, it can be hard to clearly define and agree upon "distinctive identity"
The basis of macroevolution in sexual species is microevolution coupled with reproductive isolation.
Term
Reproductive Isolation Can Occur in a Variety of Ways
Definition
Reproduction isolation is any means of preventing gene flow between species; for a new species to evolve from an existing (sexually reproducing) species, there must be a reproductive isolating mechanism in place.
Reproductive isolating mechanisms can be classified as either prezygotic or postzygotic.
Term
Prezygotic Barriers
Definition
Prevent fertilization (zygote formation) between gametes from two species.
Term
Habitat Isolation (or ecological isolation)
Definition
Isolation by differences in habitat occupied at the time of mating; examples: some garter snakes; some flycatchers.
Term
Temporal Isolation
Definition
Isolation by differences in timing of mating; examples: mating seasons in some skunks; flowering time in some plants; mating time in some fruit flies.
Term
Behavioral Isolation
Definition
Differences in behavior that cause reproductive isolation; examples: mating calls, courtship patterns, and other mating rituals; can be an aspect of sexual selection (selective pressure that comes from mating choices).
Term
Mechanical Isolation
Definition
Differences in physical aspects make successful mating impossible; examples: many flower species; dragonflies may attempt interspecies mating, but the physical structure of their genitalia prevents successful mating.
Term
Gametic Isolation
Definition
Mating occurs, but the sperm and egg can not fuse; examples: sperm cannot penetrate the egg of the different species, such as between sea urchins species, as well as in many other animal species; in plants, often pollen grains do not get the proper signal to germinate when on a stigma of a different species.
Term
Postzygotic Barriers
Definition
Reproductive isolation after fertilization has occurred.
Term
Hybrid Inviability
Definition
(The most common type of postzygotic barrier) normal development of the zygote formed from the mating of two species does not occur and the embryo is aborted, or if development is completed the offspring is very frail; examples: crosses between different iris species, cross between bullfrog and leopard frog; crosses between some salamander subspecies.
Term
Hybrid Sterility
Definition
A zygote of a hybrid proceeds through normal development, but is reproductively sterile.
Sometimes due to other barriers such as behavioral isolation.
Most often due to problems in meiosis.
Term
Hybrid Breakdown
Definition
A zygote of a hybrid proceeds through normal development, and the interspecific hybrid reproduces, but the F2 generation and beyond have problems with reproduction; examples: crosses between sunflower species result in 80% hybrid breakdown in the F2 generation; crosses between some rice strains.
Term
Anagenic Speciation
Definition
The gradual change of one species into a new form, with the "new" species form replacing the "old" form; this is essentially microevolution on the whole species level - the number of species does not change.
Term
Cladogenic Separation
Definition
Branching evolution. Occurs when two or more species are present where only one existed before; these species share a common ancestor.
Term
Clade
Definition
A cluster of species that share a common ancestor is a clade.
Cladogenic speciation increases the number of species.
Two separate species are said to diverge from the point where they shared a common ancestor - the gene pools of these species are separated from the point of divergence on.
Term
Cladogenic Speciation Occurs When a Population is Different Enough From its Ancestral Species so That No Genetic Exchange can Occur Between Them
Definition
The appearance of a reproductive isolating mechanism produces two or more species where once there was one.
The question of macroevolution becomes, what creates reproductive isolation?
There is no easy way to define when cladogenic speciation is complete - often some level of hybridization can persist when there is essentially no gene flow between the "species" or "subspecies" involved.
Term
Allopatric Speciation
Definition
One population becomes geographically separated from the rest of the species.
The separated population encounters different selective pressures from the rest of the species, and also is usually subjected to a genetic bottleneck.
After a long period of time, the population has diverged enough from the parent species that it is reproductively isolated from the parent species if they come in contact.
Likely the most common means of cladogenic speciation.
Term
Sympatric Speciation
Definition
A species achieves reproductive isolation and evolves in the same geographic location as its ancestral species.
Polyploidy (extra sets of chromosomes) is a major factor in sympatric speciation in plants.
Term
Autopolypoidy
Definition
Multiple sets from one parent species; example - plants around Agent Orange sites.
Term
Hybridization + Allopolyploidy
Definition
Closely related species produce a hybrid that must double its chromosome number to reproduce successfully; a new, viable hybrid species is thus formed.
Term
Disruptive Selection
Definition
When disruptive selection occurs, hybrids are selected against.
There is thus strong selective pressure for the development of reproductive isolation mechanisms.
Term
Adaptive Radiation
Definition
Most easily produced by a combination of allopatric speciation and sympatric speciation.
Term
Macroevolution Involves Both Rapid and Gradual Divergence
Definition
Darwin's original theory suggested that evolution occurs gradually.
There is some fossil evidence for this, but in many cases there is a lack of transitional forms.
The fossil record by its very nature is incomplete, which would explain some of the lack of transitional forms, but there is an alternative: punctuated equilibrium.
Term
Punctuated Equilibrium Theory
Definition
States that evolutionary change can be rapid, and that this rapidity explains much of the lack of transitional forms in the fossil record.
Rapid change means that the transitional forms are around for only a short time, and thus are far less likely to be preserved as fossils.
Between periods of rapid change are long periods of relative stasis, with little evolutionary change and thus little change in form; these long periods greatly increase the likelihood of such forms being preserved as fossils.
First advanced by Stephen Jay Gould and Niles Eldredge in 1972.
Term
Divine Design and Perfection Model
Definition
Espoused by Aristotle whose ideas on biology dominated most thinking on the subject until the renaissance.
Species were viewed on a scale from simple to complex.
All organisms were seen as moving toward perfection.
Based on divine intervention and design.
Now discredited in biology, but still part of the social consciousness.
Term
Fossils
Definition
Fossils were known for centuries before Darwin.
Fossils reveal organisms unlike any living today, and the idea that some fossils represent species that had become extinct was recognized even by Leonardo da Vinci.
Term
Fossils
Definition
Fossils were known for centuries before Darwin.
Fossils reveal organisms unlike any living today, and the idea that some fossils represent species that had become extinct was recognized even by Leonardo da Vinci.
Term
Acquired Traits
Definition
Mostly associated with Lamarck.
Still focused on a model of organisms driven toward complexity, but involved an explanation with natural causes.
Postulated that changes or "acquired characteristics" during an organism's life could be passed on to offspring.
Term
Birth of Modern Geology
Definition
Lyell, uniformitarianism, and the ancient Earth.
Prior to the early 1800s, the world view of most was that the Earth is very young (around 6000 years old).
In the early 1800s, geologists began to apply scientific reasoning to studies of geological processes, and quickly recognized that these processed require that the Earth be very old to occur naturally.
This "uniformitarian" model influenced Darwin.
Uniformitarian model is the basis of geology today.
Term
Darwin's Theory
Definition
Evolution occurs by natural selection.
Darwin proposed that species evolve by natural selection; his theory of evolution was based on four general observations: overproduction, variation, competition, and differential reproductive success.
Term
Overproduction
Definition
Each species produces more offspring than will survive to maturity.
Term
Variation
Definition
Individuals in a population vary, and some of the variation is heritable.
Term
Competition
Definition
There is competition among the individuals of a population for limited resources.
Term
Differential Reproductive Success
Definition
Individuals that possess more favorable characteristics are more likely to survive and reproduce ; those with less favorable characteristics are less likely to survive and reproduce.
Term
Fossils Provide Direct Evidence for Change Over Time
Definition
Fossils range from mineralized casts or imprints to actual body parts preserved in bogs, tar, amber, or ice.
Fossils provide evidence of intermediates between extant and extinct forms.
Many relatively complete examples of transitions in body forms are known, such as the evolutionary lineage of horses and the transition of terrestrial species to modern whales.
The fossil record provides tests of evolution as an explanation for the history of life on Earth.
Term
Fossils Most Commonly Form In Sedimentary Rocks in Aquatic Environments
Definition
The fossil record is biased toward organisms with hard parts that lived in aquatic or arid environments, where decay is slow and incorporation in rocks can occur with reasonable speed.
Organisms that lived in places of rapid decay are thus biased against in the fossil record.
Term
Dating Fossils
Definition
Relative position in rock layers.
Sedimentary layers most commonly have the youngest layers nearer the surface, and are progressively older as you go deeper.
Large-scale geological events can be used to correlate rock strata from different sites; other dating methods are also used to correlate rock strata.
Association with index fossils that have been dated by other means from other locations.
Term
Radioisotope Dating
Definition
Each radioisotope has characteristic, constant rates of decay.
Some allow for measurement of when a rock was formed or when an organism died.
Example: potassium-40 decaying to argon-40.
Once the rock hardens, the radioactive clock begins - potassium-40 in the rock decays to argon-40.
Half-life of 1.3 billion years: used for fossils tens of millions to billions of years old.
Term
Binary Fission
Definition
A prokaryotic cell divides by this, splitting into two nearly equal halves.
Term
Chromatin
Definition
Each chromosome is made of chromatin, a long DNA molecule with associated proteins.
Chromatin is packaged into dense chromosomes during cell division.
Protects the DNA
Helps assure proper distribution of DNA during cell division.
The dense bodies can be stained and show up well under light microscopy.
Term
Genes
Definition
Each chromosome contains hundred to thousands of genes.
Genes are the functional units of heredity.
typically, a gene contains the instructions to make a protein or RNA molecule.
The complete DNA sequence for an organism is the genome; it contains the complete set of instructions for that organism.
Humans apparently have ~20,000 genes in the now-sequenced human genome.
Term
Interphase
Definition
Divided into three parts, defined with respect to DNA replication. S phase, G1 phase, and G2 phase.
Term
S phase
Definition
Synthesis phase.
The DNA is completely replicated.
Term
G1 Phase
Definition
Gap phase.
The period before the S phase.
Most cellular growth occurs in this phase.
This phase is usually the most variable with respect to time, and its typically longest.
Cells that do not divide become arrested in this phase, then called G0.
Term
G2 Phase
Definition
The period between the S phase and cell division.
The G2 phase is usually short; cells in this phase are committed to and preparing for cell division.
Term
Mitosis
Definition
The process that distributes a complete copy of the duplicated genetic information to each daughter cell.
PMAT
Term
Cytokinesis
Definition
The process of dividing the cytoplasm into two separate cells.
Begins in telophase and ends shortly after.
Some cells have mitosis without cytokinesis (most common in fungi and slime molds).
Term
Prophase
Definition
Chromatin condenses to form chromosomes.
Each chromosome forms a pair of sister chromatids.
Sister chromatids are joined at a centromere by protein tethers.
Centromeres contain a kentochore where microtubules bind.
The nuclear membrane has disappeared by the end of prophase.
The nucleoli have disintegrated.
Term
Metaphase
Definition
Chromosomes line up along the midplane of the cell.
Chromosomes are most condensed, most visible, and most distinguishable during metaphase.
The mitotic spindle, now complete, has two types of microtubules.
Term
Anaphase
Definition
Sister chromatids separate and are moved toward opposite poles.
The protein tethers at the centromere between the chromatids are broken.
Each former sister chromatid can now be called a chromosome.
Model for the mechanism that moves chromosomes to the poles.
This process assures that each daughter cell will receive one of the duplicate sets of genetic material carried by the chromosomes.
Term
Telophase
Definition
The processes of prophase are reversed.
The mitotic spindle is disintegrated.
The chromosomes decondense.
Nuclear membranes reform around the genetic material to form two nuclei, each with an identical copy of the genetic information.
Nucleoli reappear, and interphase cellular functions resume.
Term
Cleavage Furrow
Definition
In animals, a cleavage furrow develops during cytokinesis, usually close to where the metaphase plate was.
A microfilament (actin) ring contracts due to interactions with myosin molecules, forming a deepening furrow.
Eventually, the ring closes enough for spontaneous separation of the plasma membrane, resulting in two separate cells.
Term
Cell Plate
Definition
In plants, a cell plate develops during cytokinesis, usually close to where the metaphase plate was.
Vesicles that originate from the Golgi line up in the equatorial region.
The vesicles fuse and add more vesicles, growing outward until reaching the plasma membrane and thus separating the cells.
The vesicles contain material for making the primary cell wall and a middle lamella.
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