From Gene to Protein_Chapter 17

1. What are the stages of transcription?

2. What is RNA splicing?

3. What are point mutations?

1. Initiation, elongation, and termination are the three stages of transcription.

2. Rna splicing takes places in eukaryotic cells. In rna splicing, large populations of the newly synthesized rna strand are removed. The sections of the mrna that are spliced out are introns, and the sections that remain and spliced together by a splicesome are called exons.

3. Point mutations are alterations of just one base pair of a gene. They come in two basic types. Base pair substituition, and insertation and deletion.

link on rna splicing :

http://www.youtube.com/watch?v=FVuAwBGw_pQ

point mutation:

5 main facts:

. The basic mechanics of transcription and translation are similar in eukaryotes and prokaryotes.

. The initial RNA transcript of any gene is called a primary transcript.

. Several codons may specify the same amino acid, but no codon specifies more than one amino acid.

. Some introns play a regulatory role in the cell. These introns contain sequences that control gene activity in some way.

. A point mutation that results in the replacement of a pair of complementary nucleotides with another nucleotide pair is called a base-pair substitution.

In this chapter we learnt that the information content of DNA is in the form of specific sequences of nucleotides along the DNA strands. The DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins. Gene expression, the process by which DNA directs protein synthesis, includes two stages called transcription and translation. Proteins are the links between genotype and phenotype.

The Molecular Basis of inheritance_Chapter 16

The structure of DNA.

The structure of DNA is double helix, with about 10 nucleotide pairs per helical turn. Each spiral strand, composed of a sugar phosphate backbone and attached bases, is connected to a complementary strand by hydrogen bonding (non- covalent) between paired bases, adenine (A) with thymine (T) and guanine (G) with cytosine (C). Adenine and thymine are connected by two hydrogen bonds (non-covalent) while guanine and cytosine are connected by three. This structure was first described by James Watson and Francis Crick in 1953.

Replication of DNA, and the enzymes.

the video link below describes the replication of dna very well.

http://www.johnkyrk.com/DNAreplication.html

Nucleoid, chromatin, and telomerase.

Telomerase is an enzyme that catalyzes the lenghthening of telomeres in eukaryotic germ cells, so it restores their original lenght abd compensating for the shortening that occurs during the replication. Nucleoid is the dense region of DNA in a bacterium, but is is not bounded by membrane. Eukaryotic DNA is precisely combined with a large amount of protein. Together, this complex of dna and protein, called chromatin, fits into the nucleus through an elaborate, multilevel system of DNA packing.

5 facts on this chapter:

. Nucleic acid strands are always antiparallel, whether it is DNA/DNA or DNA/RNA or R NA/RNA interactions.

. DNA replication is semiconservative.

. The strand that alongs 5' to 3' is called leading strand, and the strand that goes along 3' to 5' is called lagging strand.

. The lagging strand is synthesized in separate pieces called Okazagi Fragments, which are then sealed together by DNA Ligase.

. As DNA becomes more highly packaged, it becomes less accessible to transcription enzymes. This reduces the gene expression.

The Chromosomal Basis of Inheritance_Chapter 15

1. What are the genetic symbols, and their meanings?

Mendel used upper and lower cases.T tall, t short. + means that its wild. (mutant phenotype)

dominant-recessive, dominant is upper case, recessive is lower case. F1 is the first generation, F2 is the second generation from F1 generation.

2. Mutations;

.deletion

.duplication

.inversion

.translocation

3. Human disorders, their results.. (caused by chromosome alterations)

down syndrome: an aneuploid condition that's the result of having an extra chromosome 21. Characteristic facial features, short stature, heart defects, mental retardation.

klinefelter syndrome: an aneuploid condition in which a male possesses he sex chromosomes XXY. males have male sex organs but are sterile.

turner syndrome: a monosomic condition in which the female has just one sex chromosome, an X. sterile female organ.

Video on Chromosome Mutations:

http://www.youtube.com/watch?v=OrXRSqa_3lU

A good website about human disorders due to chromosome alterations:

http://www.biology.iupui.edu/biocourses/n100/2k2humancsomaldisorders.html

Patterns of Inheritance with Sex-Linked Traits

5 main facts on this chapter:

. In humans, there are two types of sex chromosomes. X is for females, Y is for males. Males have one X and one Y.

. Sex linked genes are usually located in X chromosome. So if a boy is hemophilia, that means that his mom has a recessive/dominant hemophilia gene.

. While genes that are on the same chromosome tend to be inherited together, the process of crossing over enables "linked" genes to sort independently. Those that are linked but located farther apart on the chromosome will undergo crossing over more frequently than those located very close together on a chromosome simply because there are more sites between the two genes at which crossing over can take place.

. Turner syndrome is the only known viable monosomy in humans.

. Fertilization restores the diploid number in a sexually reproducing organism. The two major events in the life cycle of sexually reproducing organism are meiosis and fertilization.

Key Terms_ Chapter 9 to 13

Heredity (inheritance) - transmission of traits from one generation to next

Genetics - the scientific study of heredity

Clone - a group of genetically identical individuals

Gametes - reproductive cells

Somatic cells - any cell other than those involved in gamete formation

Karyotype - display of paired chromosomes (map of chromosomes)

Sex chromosomes - x and y, determine the sex

Autosomes - other chromosomes

Diploid cell - any cell with two chromosome sets (2n)

Haploid cell - any cell with a single chromosome set (n)

Autotrophs – self feeders

Heterotrophs – obtain their organic material by the second major mode of nutrition, unable to make their own food

Chlorophyll – the green pigment within chloroplasts

Mesophyll – the tissue in the interior of the leaf

Stroma – the dense fluid within the chloroplasts

Thylakoids – interconnected membranous sacs

Grana – thylakoid coumn

Photophosphorylation – adition of a phosphate group to ADP

Carbon fixation – initial incorporation of carbon into organic compounds

Wavelength – the distance between the crest of electromagnetic waves

Aerobic respiration – the most relevant and efficient catabolic pathway

Anaerobic – no O₂

Cellular respiration – both aerobic and anaerobic processes

Oxidation – loss of electrons and energy

Oxidizing agent – the electron acceptor

Reduction – gain of electrons and energy

Reducing agent – the electron donor

NAD+ - electron carrier/acceptor, oxidizing agent in glycolisis

Chemiosmosis – energy-coupling mechanism

Fermentation – a way of harvesting chemical energy without using either oxygen or any ETC.

Meiosis and Sexual Life Cycles_Chapter 13

1. How does meiosis differ to mitosis?

2. Differences between asexual and sexual reproduction.

3. What are the sexual sources of genetic variations?

1. Meiosis produces cells there differ genetically from their parent cells. Mitosis produces daughter cells that are genetically identical to their parent cell.

Synapsis and crossing over just occur in meiosis, meiosis 1.

At metaphase 1, chromosomes are positioned on the metaphase as pairs of homologs, rather than individual chromosomes, as in metaphase of mitosis.

At anaphase 1 of meiosis, the replicated chromosomes of each homologous pair move toward opposite poles, but the sister chromatids remain attached. In anaphase of mitosis, by contrast, sister chromatids separate.

2. Individuals reproducing asexually transmit %100 of their genes to their progeny, whereas individuals reproducing sexually transmit %50.

Single parent/two parents. Asexual reproduction requires only mitosis, but sexual reproduction is involved by meiosis.

3.Independent assortment = The random distribution of maternal and paternal homologues to the gametes. Crossing over is another mechanism that increases genetic variation is the process of crossing over, during which homologous chromosomes exchange genes. Random fertilization is another source of genetic variation in offspring.

Video on crossing over: http://www.youtube.com/watch?v=op7Z1Px8oO4&feature=related

5 main facts on this chapter :

. Normal human somatic cells are diploid. They have 46 chromosomes made up of two sets of 23.

. 22 homologous pairs of autosomes, each with maternal and paternal homolog. The 23rd pair is the sex chromosome, determines the sex of the person.

. Three events in sexual reproduction contribute to genetic variation in a population..

. Independent assortment happens in meiosis, crossing over during meiosis I, and random fertilization of egg cells by sperm.

. Meiosis I separates homologous chromosomes, while meiosis II separates sister chromatids.

In this chapter, we learnt about meiosis, its different stages, and differences between meiosis and mitosis. We studied origins of genetic variation among offsprings.

The Cell Cycle_Chapter 12

1. How does the interphase work?

2. What are the phases of Mitotic division?

3. Explain the cell cycle control system?

1. Interphase: Interphase is the period in the cell cycle when the cell is not dividing. During interphase, cellular metabolic activity is high, chromosomes and organelles are duplicated, and cell size is may increase. Interphase accounts for $90 of the cell cycle. It has three parts. G1,S, and G2. In G1 part, cell grows. In S part, DNA is synthesized, and chromosomes are replicated. In G2 part, cell is prepared for division.

2. After Interphase, the phases are: Prophase, Prometaphase, Metaphase, Anaphase, Telophase and Cytokinesis.

Video on this mitotic cell division:

http://www.youtube.com/watch?v=vh8JAN8vDeA&feature=fvw

http://nobelprize.org/educational_games/medicine/2001/cellcycle.html

3. The cell cycle has interacting proteins that act as stop and go signals at specific points during the cycle. There are two major CHECKPOINTS. One is just before the cell enters the S phase, and the other is before entering Mitosis. If a cell is too small, or starved, or the environment cannot provide the proteins and energy necessary for the division, control proteins will delay the cell's attempt to duplicate itself. (Gzero) G1 checkpoint. p53 prevents cells with damaged DNA from proceeding to the S phase of the cell cycle. The cell can then attempt to repair the DNA and if succesful, go on to S phase. G2 checkpoint provides a safety gap before the cell plunges into Mitosis. The cell ensures that DNA replication is complete. The G2 checkpoint is similar to the G1 checkpoint in that it is a timing point at the end of g2 where STOP proteins can prevent mitosis until the cell has completed all the required steps for division.

5 main facts about the cell cycle:

. Prophase : In early prophase, the centrosomes move toward opposite poles of the cell, organizing the spindle microtubules between them. The sister chromatids become visible in the nucleus as they condense.

. The chromatids remain lined up between the poles of the cell during metaphase.

. Anaphase begins when the pairs of sister chromatids separate. The separated chromatids are now called chromosomes, and move towards the poles of the cell.

. The chromosomes arrive at the pole and the new nuclear membranes form around them in telophase.

. Division of the cytoplasmic components is called cytokinesis. The parent cell divides into two.

Cell cycle occurs in order to reproduce, grow, and repair the cell. The goal if the cell division is to split the sister chromatids and give one to each new cells. Regulation of cell division must be controlled by checkpoints. If the control system fails, the cancer cells occur. They do not stop dividing.

Cell Communication_Chapter 11

1. The three stages of the cell communication?

2. What are the roles of protein kinases and phosphorylation in signal amplification?

3. What are the membrane receptors?

1. a) Reception : this is the first stage. outside of the cell to inside of the cell. receptor is in the membrane, taking in the signal molecules. the signal molecules are mostly water soluble. they are too large to travel thru membranes, they so uses receptors to get in the cell. receptor molecules are made of protein. they are flexible, depending on the signal molecule.

b) Signal Transduction : when the signal molecule moves to cytoplasm from the receptor. there is phosphorylation during this pathway. uses protein kinases which are enzymes that transfers phosphate groups from ATP to a protein.

c) Response : the signals coming from cytoplasm go to the nucleus. proteins turn specific genes on and off.

2. Protein kinases and phosphorylation in signal amplification :

A protein kinase is a kinase enzyme that modifies other proteins by chemically addingphosphate groups to them (phosphorylation). Phosphorylation usually results in a functional change of the target protein (substrate) by changing enzyme activity, cellular location, or association with other proteins. Up to 30% of all human proteins may be modified by kinase activity, and kinases are known to regulate the majority of cellular pathways, especially those involved in signal transduction.Tyrosine-specific protein kinases phosphorylate tyrosine amino acid residues, and like serine/threonine-specific kinases are used in signal transduction.

3. There are three membrane receptors. G Protein -Coupled Receptors, Receptor Tyrosine Kinases, and Ion Channel Receptors. These are located in the plasma membrane.

Video on cell communication :

http://www.youtube.com/watch?v=U6uHotlXvPo

Some facts about cell communication/signaling :

. Many signal transduction pathways include phosphorylation cascades, in which a series of protein kinases each add a phosphate group to the next one in line, activating it.

. Apoptosis, is a type of programmed cell death.

. Intracellular signals are the proteins in the nucleus or in the cytoplasm that can pass thru the membrane without the help of a receptors. ex. hormones.

. Reception may occur by direct contact, or by indirect contact.

. Two results, cytoplasmic regulation, or transcription regulation in the nucleus.

This chapter is about cell communication/ signaling. Cells communicate in order to respond to the environment, and to regulate themselves. Cells need to control cellular processes by signaling. There are three stages and each stage has its own work, and helpers such as enzymes, receptors, signals etc. There are two types of cellular responses, cytoplasmic regulation, and transcription regulation in the nucleus. It can cause a rearrangement of the cytoskeleton, or activation of new protein synthesis.