Bio 1A03 Midterm 2

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Housekeeping Genes

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genes required all the time for normal functions, always "turned on"

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Regulated Genes

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genes that can be turned on and off on an as-need basis (ex: genes that code for enzymes and proteins to bring change in growth/division of cell)

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Constitutive Gene Expression

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genes that are always being transcribed and translated allowing for constant maintenance of general cellular activities. For example; housekeeping genes, genes for structural proteins, RNA and DNA polymerase.

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E.Coli

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Glucose is its preferred energy source and it has a unique gene expression mechanism allowing it to switch to metabolizing lactose once glucose is used up.

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Lactose

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Disaccharide made of galactose and glucose with a Beta 1-4 glycosidic linkage

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B-galactosidase

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Enzyme that metabolizes lactose and is produced by the lac operon- production in bacteria dependent on presence of lactose in environment.

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Gene Expression

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The functional product of a gene being made, modified, and activated.

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Francois Jacob and Jaques Monod

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Investigated E.coli production of B-galactosidase and observed that lactose in the growth medium induced expression of the B-galactosidase gene.

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Transcriptional Control

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The control of the amount of messenger RNA produced by the cell. Slowest and most efficient form of regulation. Includes the control of binding proteins to promoter either activating or inhibiting transcription.

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Translational Control

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The control of the rate at which translation occurs-- will affect the amount of protein that is produced (depends on stability of mRNA).

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Post-Translational Control

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Includes control mechanisms that allow polypeptide chain to be folded into a functional 3D structure. Fastest form of control.

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Prokaryotic Cell Division

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Cell division also as reproduction with all elements required for reproduction found within the cell. Making exact copies of genome segregating one copy of each genome to each of 2 daughter cells

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Binary Fission

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Form of asexual reproduction initiated when proteins bind bacterial DNA to inside of plasma membrane- cell elongates until 2 attachment cites are on either end- new cell membrane and wall form- viola two cells!

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Stem cells

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Unspecialized cells that can reproduce indefinitely under the right conditions and can differentiate into specialized cells of one or more types

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Adult Stem Cells

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Cells that are able to replace non-reproducing specialized cells like mammalian adult skeletal muscle cells via satellite stem cells!

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Quiescet

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Non-dividing (ie mature heart cells)

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Process of stem cell into mature muscle cell

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satellite stem cell-->myoblast-->myofiber

quiescent-->activated from G0-->commitment to differentiation-->fusion into myotube-->maturation into myofiber

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Differences between Eukaryotes and Prokaryotes (chromosomes and DNA)

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Eu: larger DNA, DNA organized into linear chromosomes highly condensed into nucleus of cell, requires more regulated control

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Phases of Eukaryotic Cell division

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Interphase (G1 gap 1, S-phase DNA rep, G2 gap 2) and M-phase (mitosis and cytokenesis)

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Interphase

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Preparation for cell division, DNA replication in nucleus, and overall increase in cell size. Different cells take different amounts of time to pass thru this phase (ex: epithelial cells have frequent turnover)

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G0 Phase

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A phase in the cell cycle between M and S-phase. Can last many days to indefinitely. Ex: lenses of eyes, nerve cells, and mature muscle cells. Cells are not dividing in this phase!!

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Mitosis

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Preferentially, Partying, More, At, The (Club)

Prophase, Prometaphase, Metaphase, Anaphase, Telophase.

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DNA Replication

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Exact copies of every chromosome created and left with 2 identical copies of chromosomes called sister chromatids. Occurs during S-phase of Interphase. Centromere is also fully replicated.

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Human chromosomes

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for humans: 22 homologous chromosomes (one maternal and one paternal) and one pair of sex chromosomes. Only recognizable (structure wise) during M-phase

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Prophase

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Duplicated chromosome begins to condense with individual chromosomes visible under a light microscope. (sister chromatids joined together at centromere). Centrosomes begin to radiate long microtubules forming a mitotic spindle.

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Centrosomes

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Duplicated cellular microtubule organizing centres.

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Prometaphase

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Fragmentation of nuclear envelope, microtubules attach to kinetochores or interact with each other.

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Kinetochores

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Specialized protein structures that associate with each one of the two sister chromatids on either side of the centromere.

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Metaphase

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Phase marked by alignment of chromosomes at centre of cell along the metaphase plate facilitated by the kinetochore microtubules.

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Anaphase

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kinetochore microtubules shorten having sister chromatids separate into individual chromosomes towards opposite ends of the cell. Polar microtubules push against each other to help elongate the cell. By the end of this phase, to ends of the cell have equivalent and complete sets of chromosomes.

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Telophase

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Stage in which 2 new daughter nuclei form in the cell because of the nuclear envelope reforming around the chromosomes at opposite poles. Simultaneously, chromosomes begin to de-condense and microtubules depolymerize.

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Cytokinesis

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Post mitosis. Two cells joined together by contractile ring in animal cells or cell plate in plant cells with one centrosome with short microtubules radiating from it in each daughter cell.

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Contractile Ring

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In animal cell cytokinesis, this is made up of motor proteins contracting bundles of actin fibres along the middle of the cell leading to the formation of a cleavage furrow.

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Cleavage Furrow

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This separates 2 animal cells into two distinct daughter cells (cell plate region in plant cells)

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Mitosis Promoting Factor

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A protein/enzyme allowing for the transition from the G2 phase to the M-phase. Ex. CDK

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Tim Hunt

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Measured protein level changes in dividing sea urchin embryos looking for a mitosis promoting factor. Using radioactively labelled met. he took samples every ten minutes and visualized changes in protein levels using gel electro. Found darker protein bands as embryotic development progressed; specifically Cyclin went up and down a lot!!!

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Cyclins

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Enzymes that control kinase proteins. In Cycline Kinase complexes, cyclin will degrade once the complex has fulfilled its purpose.

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Kinases

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Enzymes that activate or deactivate other proteins by phosphorylating key amino acids on target proteins. Stick around in the cell! Usually activated by cyclin.

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G1/S Cyclin-CDK Complex

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Complex needed for transition from G1 to S helping cell prepare for DNA rep. (increasing expression of histone proteins).

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S-cyclin-CDK Complex

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Helps to initiate DNA synthesis (complex)

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M-Cyclin-CDK Complex

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initiates process of mitosis as it is facilitated by phosphorylation of key structural proteins needed for nuclear membrane break down and to regulate assembly of microtubules in spindle

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Cell Cycle Checkpoints and checkpoint times

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DNA Damage checkpoint (end of G1 before S), DNA Replication checkpoint (G2), and Spindle Assembly checkpoint (before anaphase).

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DNA Damage Checkpoint

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End of G1 before S, when DNA is damaged, genes that normally inhibit cell cycle progression turned on. Ex: when there are breaks in the double-stranded backbone, kinases phosphorylate p53 a protein that can inhibit the cell cycle when turned on

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p53 (protein)

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Upon phosphorylation, this protein accumulates in the nucleus and acts as a transcription factor to turn on genes that will produce CDK inhibitor protein to bind to and block G1-cyclin-CDK complex pausing the cycle in G1 and giving it time to repair damaged DNA

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Spindle Assembly Checkpoint

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As early as prometaphase: regulatory proteins associated with spindle assembly monitor degree to which sister chromatids attached to microtubules at kinetochore regions. If unattached a "wait" signal is sent to the proteins which are activated by lack of tension in centromere area. Once enough tension- proteins removed from centromere region and separase breaks sister chromatid attachments

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Watson and Crick Proposal for DNA Rep

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DNA consists of a pair of template strands where prior to rep. H-bonds are broken allowing for unwinding and replicated semi-conservatively (2 new helices with one new and one parental strand)

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“the laser beam experiment”

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Photo-bleached area of the tubules to act as a reference point to see how the chromosomes are going to migrate to the poles. Prediction: the photo-bleached section will still be visible as chromosomes begin to move. Results: the photo bleached section remained visible but the distance between chromosomes and photo-bleached section lessened: microtubules shorten at one end— at the kinetochore!

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Vicristine and Taxol

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Cancer drugs from pacific yew tree’s bark: are anti-microtubule agents, plant extracts inhibit spindle finer formation which results disruption of mitosis

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Discoidermalide

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Cancer drug found in deep water sponges, anti-tumour properties have been found

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Case Study: Emma

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a new mother who has had breast cancer three times whose grandmother passed down the gene to Emma: risk of passing on the gene to her child! human genome sequencer machines are now sequencing genomes of people who have developed cancer

genome extracted from normal cell and cancer cell and both are sequenced and differences are looked for

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Genetically targeted medicine

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“personalized medicine”, should help lessen the negative effects of cancer treatment

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Cancer Drug without Side-Effects

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Targets the potential weakness in some types of cancer cannot repair their DNA properly- exploit that to treat cancer- inhibits ability of cells to repair naturally occurring defects in DNA which would kill cancer cells! would not kill normal cells!

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genome

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complete DNA sequence of an organism

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Genomics

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scientific field that compares, sequences, and interprets whole genomes.

can provide a list of the genes present in an organism

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Functional Genomics

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examines when genes are expressed and how their products interact

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Human Genome Project

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Completed in 2004 by International Human Genome Sequencing Consortium

Took 13 years and 2.7 billion (US) dollars to complete- Mike Stratton (Sanger Institute)

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shotgun sequencing approach

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genome is broken up into a set of overlapping fragments that are sequenced and these sequences are then put in order

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Martin Somerville at the University of Alberta

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Discovered another type of polymorphism

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Connexion40

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A gene expressed in the heart that produces a protein which is part of the gap junctions that hold the cells together as the heart forms during development

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Why do humans have so few genes?

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alternative splicing creates different proteins from the same gene etc.

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Genome Canada

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Organization that coordinates regional, national, and international genome projects

Since 2000 it has overseen 127 projects and over 1.8 billion in grants. Most of these projects are concerned with health issues

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Mytilus

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Constantly bombarded with water but they don’t fall off because they produce Mussel Glue: Fibres holding mussels to rocks are proteins secreted by the muscular foot of the mussel

These proteins have keratin and a resinous protein and other proteins, which form an adhesive known as byssus

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Byssus

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Remarkable underwater adhesive; genetic engineers produce it using muscle genes: generated using the yeast and use it

for metal plates in the knees, titanium screws, holding human parts together etc.

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Spirit Bears

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white subspecies of the American Black Bear whose skin & eyes are pigmented. white fur caused by single nucleotide mutation creating a modified protein product from MC1R gene. aka Kermode Bear

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Kermit Ritland

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• identified single nucleotide mutation in the melanocortin 1 receptor gene (MC1R) (melanin)• Results in the substitution of a cysteine residue for tyrosine at codon 298

MC1R gene encodes for a protein responsible for regulating skin and hair colour in

mammals

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Androgen Insensitivity

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A mutation that changes the nucleotide sequence of a single gene, causing a single type of defective protein to be produced; causes a person who is genetically male (XY) to look like a female (XX) Since no functional androgen receptor proteins, so cells are unable to respond to testosterone

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Eden Atwood

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famous musician-When she was a teen, she wasn’t getting here period so she went to the doctors and they

told he that she had cancer prone twisted ovaries (a lie). Actually was genitically male: androgen insensitivity

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Sophie — teacher that suffered from Cystic Fibrosis

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Hours of physio to remove mucus from her lungs: Even if she does everything right (exercise, physio, medicine…)

and infection can still come in and effect her: Went to the Welcome Collection in London: One of the genes is the CFTR Gene — everyone has it but it is mutated in CF patients

• Four letters of the gene are wrong causing CF

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Treatment for Cystic Fibrosis

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Gene Therapy — identify a single mutated gene that is not working properly and insert a

healthy gene into the cell to do the job instead: they can inject CFTR gene to make

effective CFTR protein making the mouse be born without CF — be born normally

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Professor Adrian Thrasher-

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gene therapy of Reese Evans — one of the first patients they treated with gene therapy-- born without a working immune system removed a small amount of his bone marrow and inserted

cells with healthy copy of gene. He then injected the marrow back into Reese

• The healthy genes could repopulated immune system

• 9 years after the therapy, he has a working immune system

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Mutations that keep the lactase gene permanently on

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Mutations arose randomly in adjacent regulatory gene (MCM6) and once it

arose gave distinct advantages to these populations (enhances LCT

transcription)- frequent in Swedish, Danish, and pastoralist African populations

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Lactose Intolerance

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congenital lactase deficiency Results in

excessive lactose in intestine attracts water molecules which prevents water from being properly absorbed into the bloodstream, Intestinal bacteria act on lactose (via fermentation), Leads to bloating, gas,

cramps, nausea and diarrhea

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Galactosemia

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Brought about by inherited mutations in the GALT, GALE, GALK1 and genes on chromosomes 9; genes code for the important enzymes that process galactose into glucose; Mutations alter single amino

acids or lead to polypeptides that

are too short

• Almost completely eliminate

enzyme activity

Results:

• Toxic accumulation of galactose

which can lead to organ and

tissue damage

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Elie Metchnikoff

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Had the original modern hypothesis of the

positive role played by certain bacteria; observed pops in rural europe that lived on fermented milk were long lived: milk fermented

with lactic acid producing bacteria

inhibits the growth of proteolytic

bacteria due to low pH produced by

fermentation of lactose

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Kary Mullis

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Developed PCR allowing amplification of millions of copies of DNA from SMALL starting samples

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dNTP

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deoxyribonucleotides bound to triphosphate groups!

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thermocyler machine

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used in PCR to take sample DNA/buffer thru various phases of heating/cooling to facilitate DNA replication process over various cycles