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Localized entropy (system disorder) can decrease, but overall entropy always increases
(i.e. systems will spontaneously change from state of lower probability to a state of higher probability)
Working muscle cells for example consume and regenerate as many as 10 million ATP molecules per second.
Enzymes (typical mw 104 – 106) increase reaction rates by a factor of 106 – 1012.
Active site orients substrates in the correct orientation for the reaction.
As the active site binds the substrate, it may put stress on bonds that must be broken, making it easier to reach the transition state.
R groups at the active site may create a conducive microenvironment for a specific reaction.
Enzymes may even bind covalently to substrates in an intermediate step before returning to normal.
Enzymes are unaffected by the reaction and are reusable.
Most metabolic enzymes can catalyze a reaction in both the forward and reverse direction - The actual direction depends on the relative concentrations of products and reactants.
Enzymes catalyze reactions in the direction of equilibrium.
In most cases substrates are held in the active site by weak interactions, such as hydrogen bonds and ionic bonds.
R groups of a few amino acids on the active site catalyze the conversion of substrate to product.
Any factor affecting the three dimensional conformation of the enzymes can influence the activity.
i.e. Temperature, pH...
Catalytic activity of many enzymes are regulated
1. Feedback inhibition
2. Regulatory proteins (inhibit or activate):
e.g. Calmodulin (Calcium sensor in many eukaryotes:
Ca2+ binding to four sites activates the protein.
Activated form binds to many enzymes and proteins,
modifying their activity.
3. Covalent modification
Cofactors: bound permanently to active sites or loosely and reversibly along with the substrate, “help” along with the catalytic activity.
* can be inorganic (e.g. zinc, iron, cooper ions)* can be coenzymes (i.e. organic molecules such as vitamins)
Distinguish between a gamete and a somatic cell.
Compare and contrast mitosis and meiosis.
chromatin: DNA protein material. consists of DNA complexed with histones and other proteins.
-two sister chromatids form
-condense and attach at kineticore
- separated into two separate cells
What is a chromosome? What is a histone? Why is coiling and packing advantageous during cell division?
What event(s) characterizes each of the following cell cycle phases: G1, S, G2 (Interphase), and M. What is the G0 phase?
What percentage of time does the cell spend in interphase (G1, S, G2) versus mitosis?
What type of eukaryotes have centrosomes (and centrioles)? What type of eukaryotes do not?
Motor proteins on the kinetochores “walk” the chromosomes along the microtubules towards the poles by depolymerization at the kinetochores.
How does cytokinesis differ between animal and plant cells?
Where are the important signaling molecules for cell cycle regulation found in the cell?
How is entry into the mitotic cycle regulated? What role do each of the following play: cyclins, cyclin-dependent kinases (cdk), mitosis-promoting factor (MPF)? How does the concentration of cyclin change over the course of the cell cycle (see figure)? How is MPF activated and deactivated?
What might occur if the regulatory molecules controlling the checkpoints are defective?
the checkpoint may fail and cells may start dividing in an uncontrolled fashion.
What is p53? What does it do when it is functional? What happens when it is damaged?
What is cancer? How do cancers arise?
What type of defects lead to cancerous cells? What changes must occur in a cell in order for it to become cancerous?
polypeptides or small proteins released by cells that stimulate division in other cells (paracrine signaling).
The karyotype is the number and types of chromosomes present in an organism. Can be used to identify chromosomal disorders
replicated chromosome of each homologous pair have separated but sister chromatids of replicated chromosomes are still attached.
What is interkinesis? What does NOT occur during interkinesis?
List and describe three mechanisms that increase genetic diversity in sexually reproducing organisms.
The genetic variation introduced during meiosis (crossing over and independent assortment) ensures that even during self-fertilization, where gametes from the same individual combine, the offspring will be genetically different from the parent.
Humans, with a haploid chromosome number of 23, can produce 223 (~ 8.4 million) different combinations of chromosomes in gametes.
70.6 x 1012 genetically distinct offspring. (8.4 million x 8.4 million)
Describe three hypotheses that suggest why sexual reproduction (meiosis and fertilization) exists.
refers to the failure of chromosomes to separate correctly during meiosis – the chromosomes from the parent cells will not be properly distributed to each daughter cell.
What is the relationship between meiotic errors and genetic predispositions? maternal age?
Describe DNA's primary structure. What is meant by DNA having directionality?
The primary structure of DNA has two major components:
DNA has directionality—one end has an exposed hydroxyl group on the 3′ carbon of deoxyribose, and the other end has an exposed phosphate group on a 5′ carbon.
The molecule thus has a 5′ end and a 3′ end.
Describe DNA's secondary structure. Who was responsible for discovering this structure?
Describe complementary base pairing. What connect did Watson & Crick draw between complementary base pairing and DNA replication?
the parental molecule serves as a template for the synthesis of an entirely new molecule.
the parental DNA strands separate and each is used as a template for the synthesis of a new strand. Daughter molecules each consist of one old and one new strand.
cuts, swivels, and rejoins the DNA downstream of the replication fork, relieving this tension.
attach to the separated strands to prevent them from closing.
Primase is the enzyme that synthesizes a short RNA segment that serves as a primer for DNA synthesis.
active in body cells that produce gametes but somatic cells normally lack telomerase. adds more repeating bases to the end of the lagging strand, catalyzing the synthesis of DNA from an RNA template that it carries with it.
Name some ways in which DNA can be damaged outside of DNA replication. What repair system is used to fix damaged DNA? What happens when repair mechanisms are defective (see Xeroderma Pigmentosum example and cancer)?
DNA can be broken or altered by various chemicals and types of radiation. The nucleotide excision repair system recognizes such types of damage.
Its enzymes (nucleases) remove the single-stranded DNA in the damaged section.
is synthesis of RNA using information in the DNA.
the synthesis of a polypeptide using the information from the transcribed RNA.
Describe how protein synthesis is a 'change in language'.
In protein synthesis – DNA monomers must be transcribed then translated into protein monomers
How many amino acids are there? How can four DNA bases encode so many amino acids? What is a codon?
act as translators, transferring amino acids from the cytoplasmic pool to a growing polypeptide in the ribosome.
thus they are made in the nucleus.
They travel out of the nucleus to the cytoplasm where translation occurs.
Yes, a tRNA molecule can be used repeatedly.
When the amino acid is bonded to the tRNA it is called an aminoacyl tRNA or charged tRNA
Name the three steps of translation. Be able to describe the process of RNA translation.
The idea that the genetic material from the two parents blends together (blue + yellow paint blend to make green).
The idea that parents pass on discrete heritable units (genes).
Unlike blending hypothesis, can explain the reappearance of traits after several generations (i.e. traits skipping generations).
Genes can be shuffled and passed along and traits will not be diluted.
supported by Mendel's work
discrete heritable units that consist of specific nucleotide bases.
The genetic makeup, or set of alleles, of an organism is called the genotype.
The observable traits of an organism, which are determined by the genotype, is called the phenotype.
a heritable feature that varies among individuals.
2) Identical vs Nonidentical Alleles
3) Some alleles can mask others
4) Alleles for a particular gene are NOT inherited together (law of segregation)
breeding the “mystery individual” with a homozygous recessive (pp) individual.
If any offspring display the recessive phenotype, the mystery parent must be heterozygous.
List and describe some situations in which inheritance of characters via a single gene may not follow simple Mendelian patterns?
When alleles are not completely dominant or recessive.
When a gene has more than two alleles.
When a gene produce multiple phenotypes
phenotypes of the heterozygote and dominant homozygote are identical.
phenotype of F1 hybrids is somewhere in between the phenotypes of the two parental varieties. (blending)
two dominant alleles affect the phenotype in separate, distinguishable ways.
· What is the relationship between dominance and the frequency of the trait in the population?
· What type of dominance system is the ABO blood groups an example of?
Pleiotropic alleles are responsible for the multiple symptoms of certain hereditable diseases, such as cystic fibrosis:
a gene at one locus masks or modifies the phenotypic expression of a gene at a second locus.
those that vary in the population along a continuum.
an additive effect of two or more genes on a single phenotype.
Example: skin color
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