Exam #3 Review PDF

**[Biotechnology]:** the use of technology to modify organisms, cells, and other molecules to achieve practical benefits - **Agriculture:** - Pest and disease resistant crops - Dramatically higher crop yields - Foods with enhanced nutrition - **Human health:** - Improved treatment...

**[Biotechnology]:** the use of technology to modify organisms, cells, and other molecules to achieve practical benefits - **Agriculture:** - Pest and disease resistant crops - Dramatically higher crop yields - Foods with enhanced nutrition - **Human health:** - Improved treatment of disease through more effective medicine - Improved diagnosis and screening for genetic diseases \*Tremendous potential, but limited success so far - **Forensic science:** - Improved capabilities of law enforcement - Important reforms to the criminal justice system **[Genetic engineering:]** the manipulation of a species' genetic material/genome by adding, deleting, or transplanting gene from one to another, in ways that do not normally occur in nature **[Bioengineering:]** mass production of hormones and other materials **[Tools of biotechnology:]** - **Chop** up DNA, with restriction enzymes, from a donor species that exhibits a trait of interest - **Amplify** small samples of DNA into more useful quantities - **Insert** pieces of DNA into bacterial cells or viruses - **Grow** separate colonies of bacteria or viruses, each containing some donor DNA \*Not all are always used, sometimes only one or a few are used **[Chop in detail:]** - Restriction enzymes 1. A gene of interest is located on a section of DNA from the donor species 2. Restriction introduces restriction enzymes that target a particular base-pair sequence on either side of the gene 3. Restriction enzymes bind to their target base-pair sequence and cut the strand of DNA The gene of interest has now been separated from the donors DNA **[Amplify in detail:]** - Polymerase chain reaction (PCR) 1. A solution containing an isolated segment of DNA is heated, separating the double-stranded DNA into two-single strands 2. The enzyme DNA polymerase is added along with primers and a large number of free nucleotides, and the solution containing the segments is cooled 3. DNA polymerase adds complementary bases to each single strand Two identical copies of the original segment of DNA \*This process can be repeated again and again until there are billions of identical copies of the target sequence **[DNA polymerase:]** fills in a missing sequence, which allows you to make a copy - Chain reaction when it splits over and over again into identical copies of the original segment of DNA **[Insert in detail:]** - Using plasmids to transfer DNA from one organism to another 1. Using the same restriction enzyme, a single cut is made in a bacterial plasmid 2. The two segments now share complementary bases at their ends and fit perfectly together 3. The plasmid, now including the gene of interest, is inserted back into the bacterial cell where it can be expressed and replicated Take the piece of interest and add it with a plasmid, put it in a bacterial cell, can be grown and replicated **[Grow in detail:]** - Creating a gene library 1. A large amount of DNA is chopped up using restriction enzymes 2. Each piece is inserted into a plasmid, and each type of plasmid is introduced into different bacterial cell 3. The bacteria are allowed to divide repeatedly, each producing a clone of the foreign DNA fragment it carries Gene library **[Gene library]**: all of the different bacterial cells that contain all the genes of the different fragments of the original DNA **[Transgenic:]** an organism that contains some DNA from another species in its cells **[Recombinant DNA:]** a new combination of DNA, from combining DNA nucleotide segments from different sources **[Animal cloning: ]** - Of a sheep: 1. Isolate an egg cell from one sheep and a mammary cell from another 2. Remove nucleus from each cell 3. Implant the nucleus from the mammary cell into the egg cell 4. Induce cell division to stimulate normal early development, and grow the dividing cells in culture until they reach the embryo stage 5. Transplant the embryo into the uterus of a surrogate mother sheep Surrogate mother gives birth to a cloned sheep - Success rate of 0.1% - 3% - Many have enlarged organs, increased kidney problems, brain malformations, and impaired immune systems May be due to DNA modifications of differentiation or from the telomere differences **[PCR-number of copies for X cycles:]** One cycle = 2 copies **[Primers:]** short, single-stranded nucleic acid sequence that acts as a starting point for DNA synthesis, essentially \"priming\" the process by providing a location for DNA polymerase to begin adding nucleotides to build a new DNA strand - Short stretches of DNA that target unique sequences and help identify a unique part of genome **[Plasmid:]** a small, circular DNA molecule found outside the main chromosome in bacteria, and can be replicated independently **[Restriction enzymes:]** an enzyme that recognizes and binds to a specific sequence of four to eight bases in DNA and cuts the DNA at that point - Permit the cutting of short lengths of DNA that can be inserted into other chromosomes of otherwise utilized - Isolates a specific piece of DNA - To produce DNA fragments with known sequences at each end **[CRISPR:]** Clustered Regularly Interspaced Short Palindromic Repeats - System that allows editing of DNA with a great deal of precision and efficiency - Enables researchers to modify almost any gene in any organism - Naturally occurs in almost half of all bacteria as a mechanism for recording encounters with viral DNA and using that information to protect against future infections - Chop out defective gene and insert DNA that you want - Allows specific targeting of gene to manipulate or replace the gene - Risks: - Legal issues surrounding who invented it and who can profit from it - Ethical issues - Difficult to predict the consequences of introducing altered genes into genomes of natural populations **[How CRISPR works:]** 1. After identifying a particular DNA sequence of interest, researchers synthesize an RNA "guide" molecule with a sequence that matches the target gene to be sliced 2. The sequences for the CRISPR RNA and Cas9 enzyme are introduced to target cells using a plasmid 3. Within the cell, the RNA leads to Cas9 enzyme to exactly the desired location on the DNA, and Cas9 cuts the DNA there 4. At the location where the DNA is cut, a sequence can be inserted that repairs or alters the host cell's DNA **[Golden rice:]** the addition of beta-carotene producing genes in white rice \*\*\*White rice + daffodil genes + bacterial gene golden rice - Daffodil + bacterial = beta-carotene - Increased vitamin A content - Done because over 250000 children go blind each year in Southeast Asia because of vitamin A deficiency **[Bt corn:]** corn engineered to contain spores of the bacterium *Bacillus thuringiensis* (Bt) to kill insect pests - Does not harm humans - Used for insect resistance---grows its own insecticide 1. Caterpillars destroy corn plants 2. Bacterial gene coding for Bt crystals, which are poisonous to caterpillars, are inserted directly into the corn plant's DNA Prevent insect predation, so pesticides are no longer needed **[Genetically modified crops:]** - Done for two common reasons: 1. Plants with insecticides engineered into them 2. Plants with herbicide-resistant genes engineered into them - Corn: 36% - Cotton and soybeans: 93% **[GMO:]** Genetically Modified Organism(s) - Done for: - Desirable traits - Insect resistance - Herbicide resistance - Better nutrients/nutritional value - Faster growth - Larger in size and quantity wise - Has led to loss of genetic diversity among crop plants **[Cloning:]** the production of genetically identical cells, organisms, or DNA molecules - To make an identical copy - Exactly the same genome as the donor individual **[Gene therapy:]** screening made for genetic disorders - Generally, focuses on three scenarios: 1. Is a given set of parents likely to produce a baby with a genetic disease? Ex. Tay-Sachs disease 2. Will a baby be born with a genetic disease? Ex. Cystic fibrosis, sickle-cell anemia, down syndrome, etc. 3. Is an individual likely to develop a genetic disease later in life? Ex. Cancer - Poor record of success: - Difficulty getting the working gene into the specific cells where it is needed - Difficulty getting the working gene into enough cells and at the right rate to have a physiological effect - Difficulty arising from the transferred gene getting into unintended cells - Difficulty regulating gene expression **[DNA fingerprinting:]** uses the unique nucleotide sequences of DNA to identify individuals or samples - DNA from all humans is almost completely identical, approximately 99.9% of the DNA sequences of two individuals are the same Even so, in comparing two individuals' genomes of three billion base pairs, a one-tenth of a percent difference still translates to about three million base-pair differences; these differences give each individual their own unique genome (exception is identical twins) **[STR's and determining DNA fingerprint:]** Short Tandem Repeats, short sequences (commonly 4-5 nucleotides long) that repeats over and over within a noncoding region of DNA - Number of repeats is what varies among individuals - Used for determining a person's genetic fingerprint - The real power of DNA fingerprinting comes from simultaneously determining the alleles an individual carries (the person genotype) at 13 different STR locations 1. **Amplify the STR region**: for each of the 13 STR regions used, the DNA fragment is amplified using PCR, resulting in huge numbers of those fragments - The fragments differ in size depending on how many times the repeating unit of that STR is repeated 2. **Sort the fragments by size:** amplified DNA fragments are poured into an electrophoresis gel and an electrical charge is applied - Because DNA is a negatively charger molecule, the fragments move toward the positively charged electrode; smaller pieces (having fewer repeats) move across to gel more quickly than larger pieces do 3. **Identify the genotype:** the number of repeats within an STR region (indicating an individual's genotype) is determined by comparing the fragments with DNA fragments known lengths **[Chromosome:]** one or more unique pieces of DNA, vary in length and can consist of hundreds of millions of base pairs - Prokaryotic cells: circular and smaller attached to cell membrane - Eukaryotic: linear and longer in the nucleus - 23 from each parent - Ours are always linear **[Telomeres:]** sections of noncoding, repetitive DNA that act as a protective cap on the tip of each chromosome - Short repeat that is repeated a few hundred times - Protect ends and control aging - Gets shorter every time a cell divides - Decide what cells will die - When too much DNA is lost the cell dies - Some cells rebuild them: - Single celled eukaryotes - Cells that produce gametes **[Centromere:]** The region of contact between sister chromatids, located near the center of two strands - Keep two identical strands/chromosomes tied together as they are replicated **[Binary fission:]** splitting of prokaryotic cell through replication - Exact copy of DNA is created---parent cell is divided to create two genetically identical daughter cells - Also called asexual reproduction 1. Cell elongates 2. Begins to pinch in two **[Cell cycle:]** - **Gap 1:** the cells primary growth phase; normal cellular functions take place, where we start - **G0:** some cells pause in G1 phase and enter this state, which is a 'resting" phase outside the cell cycle; cells may stay in the G0 phase for days or even years; just sitting around in there - **DNA synthesis / S phase:** the cell begins preparations for divison; every chromosome creates an exact duplicate of itself in a process called replication---makes new DNA through replications - **Gap 2:** second period of growth and preparation for cell division; sits there to rebuild itself **[Cell cycle checkpoints:]** regulate the cell cycle in eukaryotes---process is blocked until specific signals trigger continuation - **G1/S:** assessing DNA damage and cell growth - Enough nutrition and food? - **G2/M:** assessing DNA synthesis - Got all the DNA, and two copies of each chromosome? - **Spindle assembly:** assessing anaphase readiness during mitosis - Set up all the spindle fibers already/correctly? **[DNA replication:]** 1. Unwind and separate 2. Reconstruct and elongate **[DNA polymerase:]** takes DNA and puts together many pieces (-mers) on a template and uses the bases to add new ones, to make a polymer **[Helicase:]** undoes/pulls apart the helix **[DNA:]** double-stranded/helix with a sugar-phosphate backbone held together by covalent/hydrogen bonds and bases which pair with each other A-T and G-C through hydrogen bonds - Makes the plan, and what is done afterwards/when the plan has started - Not just functional - **Nucleotides:** A, T, C, G - **RNA:** uses U in place of T - New strands always grow 3' to 5' **[Apoptosis:]** programmed cell death---the killing of cells because it is best for the body, cell suicide **[Mitosis: ]** - Generates old cell replacements through growth and development - Nearly all somatic cells undergo - In animals, the rate of mitosis varies for different types of cells 1. Chromosomes condense 2. Chromosomes line up in the middle of the cell 3. Each chromosome is pulled apart from its duplicate 4. New nuclear membrane form around each complete set of chromosomes 5. Cell divides Two daughter cells that are identical **[Cytokinesis:]** Moving the inside of the cell to split into two separate daughter cells, which then pinch into four haploid daughter cells (sexual) **[Homologue:]** The maternal and paternal copies of a chromosome **[Sister chromatid:]** The two identical copies/strands of replicated chromosome **[Cancer:]** telomere rebuilding and unrestrained cell growth/uncontrolled cell division that can damage adjacent features - When in lymph glands, it can grow and metastasis in the lymph glands easily spread to all else in the body - Disruption of the DNA interferes with a cell's ability to regulate cell division - Mutations in genes - Serious health issues - Second leading cause of death in US - 20% of all deaths - Not cured, but being greatly reduced - Different because: - No contact inhibition: - Cells divide indefinitely: grow crazily - Have reduced stickiness: don't attach to each other well, and can go to other places **[Immortal cells:]** cells that don't die off **[Metastasis:]** the movement of cancer cells to other parts in the body - Shed and spread - Dangerous - Uncontrollable growing - Squeeze cells out of the way and stops their normal function **[Contact inhibition:]** cancer cells continue to keep growing on top of each other and stick up **[Benign:]** tumors that are just masses of normal cells that do not spread and are not going to kill you **[Malignant:]** result of unrestrained growth of cancerous cells **[Chemotherapy:]** drugs that interfere with cell division in the goal of slowing down the growth of tumors - Kills growing cells, not just the unhealthy ones - Wipe on the big ones that are trying to kill you, hopefully kill all of them (the small ones) **[Meiosis: ]** - Reduce the amount of genetic material in gametes - Produces gametes that differ from one another with respect to the combinations of alleles they carry - Takes place in gonads - Reduces the genome by half **[Meiosis in depth:]** 1. **Interphase:** each chromosome in a homologous pair replicates to form two sister chromatids 2. **Meiosis 1:** homologue pairs separate 3. **Meiosis 2:** sister chromatids separate, creating four haploid cells containing a copy of each chromosome 4. **Interphase:** chromosomes replicate in preparation 5. **Prophase 1:** replicated chromosomes condense, spindle is formed, homologous pairs of sister chromatids come together and cross over, nuclear membrane disintegrates 6. **Metaphase 1:** homologues move toward the center of the cell and line up 7. **Anaphase 1:** homologues separate and are pulled to opposite poles, sister chromatids going to each side are a mix of maternal and paternal genetic material 8. **Telophase 1 and cytokinesis:** sister chromatids arrive at the cell poles and the nuclear membrane reassembles around them, cell pinches into two daughter cells and chromosomes may unwind slightly 9. **Prophase 2:** chromosomes in daughter cells condense, spindle forms 10. **Metaphase 2:** sister chromatid pairs line up at center of cell 11. **Anaphase 2:** sister chromatids are pulled apart by the spindle fibers toward opposite cell poles 12. **Telophase 2 and cytokinesis:** the nuclear membrane reassembles around the chromosomes, two daughter cells pinch four haploid daughter cells **[Reduction of chromosome number:]** process where the number of chromosome in a cell is halved, during meiosis, resulting in the production of haploid daughter cells **[Haploid:]** have one copy of each chromosome **[Diploid:]** two copies of each chromosome **[Male gametes:]** sperm cells **[Female gametes]:** ova or egg cells **[Crossing over:]** (genetic recombination) occurs when homologous chromosomes swap genetic information **[Sexual reproduction:]** produces offspring from the fusion of two reproductive cells (gametes) in fertilization - Meiosis - Variation adds the most to life - During fertilization, two haploid cells marge and create a new individual with the proper diploid human genome of 46 chromosomes **[Asexual reproduction:]** a single parent produces identical offspring---the offspring inherits their DNA - Fast **[Autosome]:** a non-sex chromosome, one of 22 numbered pairs of chromosomes in most human cells **[Nondisjunction:]** unequal distribution of chromosomes during cell division/meiosis \*\*\*Extra autosomes can cause disease like Down syndrome or death **[Extra sex chromosomes can be OK: ]** - Just can lead to syndromes - XXY: Klinefelter syndrome (male) - X: turner syndrome (female) - XYY: metamales - XXX: metafemales **[Effect of mother's age on down syndrome:]** - As you get older and older the more the eggs you have get damaged - Higher chance of giving birth to a child with down syndrome (presence of extra copy of chromosome \#21) **[Determination of sex:]** - **Humans:** determined by males giving X or Y - Males: XY - Females: XX - **Birds:** females determine sex of offspring - **Ants, bees, wasps:** determined by number of chromosomes sets an individual has - **Turtles:** environment determines sex of offspring - Warmer: female - Cooler: male - **Limpets:** landing on top makes them a male **[Proprioception:]** sense of where you are - Allows your tongue to know exactly where your teeth are going to be, so it does not get in the way **[Tongue:]** - Your tongue has to coexist with hard, sharp teeth - Nothing but muscle **[Trade off of speaking vs. possibly choking:]** - Trachea for breathing---goes to lungs - Esophagus for food and drinks---goes to stomach **[Evolution of brain size due to predation:]** - The decision to not eat is in the higher order brain - Predation greatly increased brain size, especially in prey---brains began registering lots of info to maintain energy balance - Trying to get away from being eaten - Trying to get food to eat - Systems to figure out what was going inside the body with the food, and to know when they were no longer hungry **[Norm of starvation for metabolism:]** starvation is part of the norm (50 years) for most people throughout history - Bodies are programmed to want excess - Especially want sweet and fat - Our body adapts to starvation - Metabolism slows down if you starve or overexercise yourself (extreme diets) **[Homeostasis:]** the hormones also regulate bone mass, immune function, body temperature, and activity levels - Is not the same in each person---dozens of parts very due to genetic and environmental differences **[Why is thin deal in our society?]** The idea of being able to compare yourself to everyone else is relatively new - We have evolved to see ourselves different then from what we actually look like - We want to look ideal, but opposite sex does not want the exact same thing **[Fibonacci numbers and golden ratio:]** A lot of natural looking things, structures, people, etc. that we find to be pretty contain the Fibonacci numbers **[Importance of symmetry:]** what makes you attractive - Guides parts to go into the right places---produce healthy and good offspring - Displaying a good quality of genes to potential mate **[Effect of ancestry on retention of calories:]** - Hunter gathers hold on to food more - Europeans more constant **[Ghrelin:]** makes you hungry when the stomach is empty---growling of stomach **[Leptin:]** stops hunger when energy reserves are good **[Pyy:]** stops hunger when blood sugar is good **[Peptide Y:]** makes you hungry when your mind thinks you should be hungry **[Obesity epidemic and effect on mortality:]** Mortality does not go up with obesity---overweight fit individuals have half the death rate of thin but sedentary **[BMI:]** Body Mass Index - Weight/height\^2 - Excess and low weight is bad - Lower cholesterol is a greater predictor of death than high cholesterol **[\ ]** **[Accuracy of BMI for health predictions:]** - Used the averaging of weight from the 60's to create BMI---when smoking was around, which drops your weight - People live longer when in the considered "above normal weight" - Better measures being found for BMI **[Fat vs fit:]** - Fit: what really matters, fit but fat live longer **[Effectiveness of dieting:]** - Not very effective - \>95% of people who lose weight return to their original weight within a year **[Fat = survival = power = attractiveness ]**