Biochem Textbook PDF

[Test \#1] (Chapter 1, 2, 3, 5 + 20) [ ] **Biology** is the science that studies living organisms and their interactions with other environments. The process of peer review helps to ensure that a scientists research is original, logical and thorough **The Study of Life** Inductive reasoning - p...

[Test \#1] (Chapter 1, 2, 3, 5 + 20) [ ] **Biology** is the science that studies living organisms and their interactions with other environments. The process of peer review helps to ensure that a scientists research is original, logical and thorough **The Study of Life** Inductive reasoning - poses possibility, takes a [general statement] and makes a [broad conclusion] - Ex. If you have tasted three cakes from the same bakery and they were all delicious, you might induce that all the cakes from this bakery are likely to be delicious. Deductive reasoning - takes a [broad statement] and makes a [general conclusion] - Ex. If you know that all cakes from a particular bakery are delicious, and you buy a cake from that bakery, you can deduce that the cake will be delicious. The Scientific Method - - - - - -  Basic (pure) Science - knowledge - - - Applied science - solving - - - **Properties of Life - 8** - Order - Sensitivity or Response to Stimuli - - Reproduction - - Adaptation - - - Growth and Development - Regulation/ Homeostasis - - - Metabolism - - - Evolution/Heredity - - - Levels of Organization of Living Things - - - - - - - - - - - - - - The Diversity of Life - - - - - - [Chapter 2 - The Chemical Foundation Of Life ] - - - The Structure of a Atom - - - Atomic Number + Mass - - - Isotopes - Chemical Reactions and Molecules - - - - - Ions and Ionic Bonds - - - - Covalent Bonds and Other Bonds and Interactions - Polar Covalent Bonds - - - - - Nonpolar Covalent Bonds - - Hydrogen Bonds + Van Der Waals Interactions - - - - - - Water - - - Water\'s Polarity - - Waters states: Gas, Liquid and Solid - - - pH, Buffers, Acids and Bases - - - - - - Carbon - - - Hydrocarbon - - Hydrocarbon Chains - - **Isomers** - - - - - - - -  Enantiomers **(mirror)** - Functional Group - - - [From my garde 12 class.. Not sure if have to know but is helpful ]  [Chapter 3 - Biological Macromolecules] **3.1 - Synthesis + Decomposition** Macromolecules are formed when 2 or more *monomers* are linked together to form *polymers* via *Dehydration Synthesis* (endothermic)*.* This process involves a hydrogen (H+) of one monomer interacting with a hydroxyl group (OH-) on a fellow monomer to produce a water molecule and a covalent bond between the 2 molecules.  *Hydrolysis* (exothermic) is the opposite of dehydration synthesis. Water is added to break the covalent bond between molecules. **3.2 - Carbohydrates C,H,O 1:2:1** Energy production and storage [Monosaccharides:] - - - - - [Disaccharides:] - - - [Polysaccharides:] Structural and Storage - - - - - **3.3 - Lipids C:H:O (carboxylic acid)** Storage of energy for long-term use, insulation, water repellant - - - - - **Saturated Fats** - - - **Unsaturated Fats** - - - - **Trans Fats** - - - **Steroids** - - - **Phospholipids** di*glycerol* - - - - **Phospholipid Bilayer** - - - **3.4 - Proteins C:H:O:N** **Functions of Proteins** - - - - - - - - Proteins are polymers, composed of the monomers, amino acid, held together by [peptide bonds] C-N Amino acids can be nonpolar, polar uncharged, polar charged, or special chemical groups Based on the amino side chain, they will determine the proteins function and shape **Primary Structure -** The specific amino acid sequence **Secondary Structure -** The initial folding of the amino acid chain by hydrogen bonding α-helix or β-pleated sheet. **Tertiary structure** - The final three-dimensional shape of the protein. **Quaternary structure** --The spatial arrangement of polypeptides in a multi-component protein  **3.5 - Nucleic Acids: DNA and RNA** **DNA** (double strand) - the blueprint for all proteins, genetic info storage - - **RNA** (single strand) - involved in converting these ''blueprints'' into proteins - - Nucleotide (monomers of nucleic acids) sequence determines the order of amino acids in a protein Nucleotides are composed of: a pentose sugar, nitrogenous base (A,T,C,G,U) and a phosphate group and form *phosphodiester* bonds **Pyrimidines**: [C]ytosine, [T]hymine, [U]racil **Purines**: [A]denine, [G]uanine **Types of RNA** **mRNA**: messenger RNA, messenger from DNA to cellular machinery with the code for protein synthesis **tRNA**: translational RNA, functions as a translate between mRNA and proteins **rRNA**: ribosomal RNA, most abundant, binds with proteins to form ribosomes **[Chapter 5: Structure and Function of Plasma Membranes]** **5.1 - Components and Structure** **Phospholipid Bilayer** - - - **The Fluid Mosaic Model** - - - **Glycoproteins** - sugars attached to proteins **Glycolipids** - sugars attached to lipids **Cholesterol -** helps membrane to maintain fluidity **Peripheral Proteins -** proteins associated with the surface of the membrane, can be on internal or external side **Integral Proteins -** proteins embedded in the membrane, interact with lipids' hydrocarbon chains, there are 2 kinds: *Protein channels -* allows substance to pass through the membrane through its hollow core *Protein carriers -* move substances across the membrane by changing shape  *Proteins and lipids drift across the membrane with proteins moving much slower* **5.2 - Passive Transport** **Movement Across the Membrane** Non-polar molecules pass easily through the membrane Polar molecules pass slower due to the interior of the membrane being hydrophobic and develop a *hydration shell* slowing them even further **Cell membranes have *Selective Permeability -*** Only allows certain substances passage **Passive Transport -** the movement of materials across the membrane from an area of high concentration to an area of lower concentration without the use of ATP **\ Concentration Gradient -** area of high concentration adjacent to an area of low concentration **Diffusion (simple):** the *passive* movement of low-molecular weight materials depending on their concentration gradient through the membrane *Facilitated Diffusion - passive* movement of materials across the membrane with the [help of integral ] [proteins] **Integral Proteins -** proteins embedded in the membrane, interact with lipids' hydrocarbon chains, there are 2 kinds: *Protein channels -* allows substance to pass through the membrane through its hollow core *Protein carriers -* move substances across the membrane by changing shape **Aquaporins -** since water molecules are polar they do not pass easily through the membrane as the interior is hydrophobic, aquaporins are carriers of water molecules, allowing billions to pass through the membrane within seconds. ***Osmosis*** - **Tonicity -** isotonic, hypotonic and hypertonic NOTE: water will [always] flow to the **hyper**tonic side - - - - - - - - **Osmoregulation** - - - - **Electrical Gradient -** a difference of charge across the membrane **Electrochemical Gradient -** combination of electrical and chemical forces that create a gradient. **3.3 Active Transport** **Active Transport** - - - - **Electrical Gradient -** a difference of charge across the membrane **Electrochemical Gradient -** combination of electrical and chemical forces that create a gradient. **Electrochem. Gradient** \[A rep. proteins\] **Sodium-pump 3 Na+ out and 2 K+ in** A form of primary active transport, it maintains the electrochemical gradient by which 3 Na+ ions are expelled from the cell and 2 K+ ions are inserted. This alters the charge of the membrane in certain areas and may be followed by secondary active transport. **5.4 - Bulk Transport** **Endocytosis -** the type of active transport that moves larger materials into the cell *[Phagocytosis] - "Cell eating" [clathrin] is a protein that coats and stabilizes the membrane in preparation for the membrane to extend and engulf the material* *[Pinocytosis] - ''cell-drinking'' process where smaller molecules are engulfed but the membrane folds in to form a pocket rather than form pseudopods like in phagocytosis* **Receptor-mediated Endocytosis -** variation of endocytosis that involves using specific binding proteins in the plasma membrane for specific molecules or particles, and clathrin-coated pits that become clathrin-coated vesicles **Exocytosis -** opposite process of endo. Where materials within a cell are held in a vesicle envelope, which then bonds to the membrane and opens to the exterior, releasing waste to the external environment of the cell.  [Chapter 20: Phylogenies and the History of Life] Phylogenetic Trees - - Classification levels - - - - Test \#2 [Test \#2 ] (Chapter 4, 14, 15, 16, 6, 7 +10) [Chapter 4: Cell Structure ] - - - **Microscopy** - - **Cell Theory 3 Parts:** - - - - All cells share 4 common components: 1. 2. 3. 4. Prokaryotic Cells - single-celled (unicellular) organism - - - - - - - - Cell size - - - **Eukaryotic Cells** - - - -  **The Endomembrane System:** Organelles that are continuously connected or connect through the use of vesicles, composed of: - - - - - - **The Plasma Membrane** - - - - - **The Cytoplasm** - - - - **The Nucleus** - -  [ ] - - The Nuclear Envelope - Chromatin and Chromosomes - - - - The Nucleolus - Ribosomes - - - - - Mitochondria - - - - - - - - Peroxisomes - - - Vesicles and Vacuoles - - Centrosome - - - Lysosomes - ''garbage disposal'' - **The Endomembrane System and Proteins** - The Endoplasmic Reticulum - - Rough ER - - - Smooth ER - - - Golgi Apparatus - - Lysosomes - - - **Cytoskeleton** - -  Microfilaments - - - - - Intermediate Filaments - - - - Microtubules - - - - Flagella and Cilia - - **Connections Between Cells and Cellular Activities** Extracellular Matrix of Animal Cells - - - - - Ex. Blood clotting - - - Intercellular Junctions - Tight Junctions - - - Desmosomes - Gap Junctions - [Chapter 14: DNA Structure and Functions] Frederick Meischer - Frederick Griffth - - - - - - - - - - Avery, Macleod and McCarty - - - - Hershey-Chase - - - - - - Chargaff - - - Watson and Crick - - Franklin - Meselson and Stahl - - - - **DNA Sequencing Techniques** Gel Electrophoresis - - - - - DNA packaging in Cells - - - - DNA Replication in Prokaryotes 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. Okazaki Fragment - DNA fragment that is synthesized in short stretches of the lagging strand DNA Replication in Eukaryotes - - - - - - - - - - - - - - - Mutations - - - - - - - - - - - - - - - - - - - Chromosomal Mutations - - - -  Cleavage furrow - only animals \*\* test question\*\* [Chapter 15 - Genes and Proteins ] **DNA** - **D**eoxyribo**N**ucleic **A**cid **RNA - R**ibo**N**ucleic **A**cid The Central Dogma: DNA→RNA→Protein - **Chromosome Theory of Inheritance**: genes are chromosomes passed from parents to their offspring Chromosomes are made of both DNA and proteins  **Genes**: a region of DNA of sequences that code for a specific RNA strand or protein Humans have **46 total**, 23 from each parent. Variants of genes are called ''alleles'' (eye color etc.) In humans and other eukaryotes, DNA is arranged into **chromatin** which is **DNA wrapped** around proteins called **histones** **chromosome- chromatid- chromatin** **Chargoff's Rule** A=T/U C=G **The Genetic Code:** - - - - [Each codon codes for either;] 1. or 2. 3 types of RNA are used during translation: mRNA messenger - reads the sequence of bases in DNA, produced by RNA polymerase tRNA transfer - brings amino acids to ribosomes to be made into polypeptide chain rRNA ribosomal - forms ribosomes  **Transcription: DNA → mRNA - Eukaryotes** **Steps** 1. - - codons to be read by the enzyme 2. 3. The 3 Eukaryotic RNA Polymerases - - - - - - - - - - - - - Prior to translation occurring, the following processes must happen to facilitate the export of mRNA to the cytoplasm - - - **mRNA Processing** - - - An anticodon is a three-nucleotide sequence in a tRNA that interacts with an mRNA codon through complementary base pairing  **Translation: RNA → Protein** 1. 2. - - - - 3. **Post Translational Modifications** Modifications are made to the protein enabling it to become functional. As well as transportation to the appropriate locations within the cell or to the membrane to be distributed. Protein Folding, modification and targeting - [Chapter 16: Gene Expression ] **Regulation of Gene Expression** - - Prokaryotic Vs Eukaryotic Gene Expression - - - - - - - - - **Prokaryotic Gene Regulation** - - - - - - The trp Operon: A repressible Operon  - - - - Catabolite Activator Protein (CAP): a transcriptional Activator - - - The lac Operon: An Inducible Operon - - - - - Eukaryotic Epigenetic Gene Regulation - - Epigenetic Control: Regulating Access to Genes within the Chromosome - - - - **Eukaryotic Transcription Gene Regulation** - The promoter and the Transcription Machinery - - - Enhancers and Transcription - - - Transcriptional Repressors - **Eukaryotic Post-Transcriptional Gene Regulation** RNA Splicing, The First Stage of Post- Transcriptional Control - - - - Control of RNA Stability - - - - - - - RNA Stability and microRNA - add more - - **Eukaryotic Translation and Post-Translational Gene Regulation** Initiation Complex and Translation Rate - add more - Chemical Modifications, Protein Activity and Longevity - - **Cancer and Gene Regulation** - Cancer: Disease of Altered Gene Expression - - Tumor Suppressor Genes, Oncogenes, and Cancer - - Cancer and Epigenetic Alterations - - - Could cause Cancer - - - [Chapter 6: Metabolism] **Energy and Metabolism** - - Carbohydrate Metabolism - - Metabolic Pathways - - - Anabolic Pathways - - - Catabolic Pathways - - **Potential, Kinetic, Free and Activation Energy** - Energy Types - - - - Free Energy - - - - **Endergonic Reactions and Exergonic Reactions** - - - - - Important concept in metabolism and energy is that of chemical equilibrium - -  Activation Energy - - - - - **Laws of Thermodynamics** Thermodynamics refer to the study of energy and energy transfer involving physical matter 1st Law - - - - 2nd Law - - - - **ATP: Adenosine Triphosphate** - - - - - - **Enzymes** - - - - - - Enzymes Active Site and Substrate Specificity - - - - - - Induced Fit and Enzyme Function - Metabolism Control Through Enzyme Regulation - Molecular Regulation of Enzymes - - - - - - - - - Enzyme Compartmentalization - - - Feedback Inhibition in Metabolic Pathways - - - - [Chapter 7: Cellular Respiration ] Energy in Living Systems - - - - - Electrons and Energy - - - Electron Carriers - - - - -  ATP in Living Systems - - - Energy From ATP - - - Phosphorylation - - - Substrate Phosphorylation - - Oxidative Phosphorylation - - Glycolysis - - - - - - - - Oxidation of Pyruvate - - - - - Citric Acid Cycle - - - - - - - - - - - - - Electron Transport Chain (ETC) - - - Overall - Chemiosmosis - - **Metabolism without Oxygen** - Lactic Acid Fermentation - - - - - Alcohol Fermentation - - - - **Connections of Carbohydrate, Protein and Lipid Metabolic Pathways** Connections of Other Sugars to Glucose Metabolism - - - Connections of Lipid and Glucose Metabolisms - - - **Regulation of Cellular Respiration** - - Regulatory Mechanisms - - - Control of Catabolic Pathways - [Chapter 10: Cell Reproduction] **Cell Division** Genomic DNA - - - - - Eukaryotic Chromosome Structure and Compaction - - - **The Cell Cycle** Control of the Cell Cycle - - Eukaryotic Cell division - - - - - - - - - - - - - - - - - - The **restriction point** is the point of no return  Meiosis - Meiosis 1 - Meiosis 2 - Meiosis 1 Prophase 1 - - - Metaphase 1 - Telophase 1 - Meiosis 2 - Prophase 2 - Metaphase 2 - Anaphase 2 - - Telophase 2 - Final Exam **[21, 42, 17, Cancer Lecture ]** **Chapter 21: Viruses** Viruses are small bundles of nucleic acids wrapped in proteins, considered to be non-living They **cannot** reproduce without a host and participate in parasitic relationships meaning the virus benefits, using the hosts mechanisms to produce more of itself and the host is harmed. They Vary in structure, methods of replication and the hosts they infect Different types of viruses will infect different kinds of cells but always enter animal cells via endocytosis and plant cells through tears in the cell wall. Once in the cell, the virus targets its genetic information to inject its own to rewire the cell to start producing more of the virus. Viral Morphology - - - Morphology - - - - - - - - [Case Study on Cervical Cancer aka Human Papilloma Virus (HPV)] HPV enters the host during sexual intercourse and is able to infect the basale layer of epithelial cells in the cervix through microtears where it then begins to replicate and spread. L1 and L2 are viral capsid genes and function in the viruses structure - - E6 and E7 are transforming genes and turn the cell into virus factories - - E1 and E2 participate in the viruses life cycle - - HPV Vaccine - variations all target some substrains of the disease - Discovery and Detection - - [Prions] - combination of ''proteinaceous'' and ''infectious'' named by Stanley Prusiner (1982) - - - Amyloids - accumulations of insoluble, fibrous proteins and they disrupt the normal structure of tissue Prions Transmission - [Bovine Spongiform Encephalopathy (BSE) and Humans] - - - - [History of HIV - Human Immunodeficiency Virus] - - - Transmission of HIV - - Infection - - - Post Infection - Types of Nucleic Acid - - - - - - - - **Baltimore Classification** Group 1- Viruses contain double stranded DNA as their genome. Their mRNA is produced and transcribed in much the same way as with cellular DNA, using the enzymes of the host cell. Group 2- Viruses have single stranded DNA as their genome. They convert their single-stranded genomes into a double stranded DNA intermediate **[Chapter 42: The Immune System ]** The human immune system can be broken into 2 categories 1. - 2. - **1st Line of Defenses** [The Mucous Membranes and Skin ] - - - [The Respiratory Tract] - - [The Digestive Tract] - - **Peritonitis - inflammation of the stomach lining, can be caused by bacteria entering the abdominal cavity by a hole in the digestive tract** Other types of defense include the preexisting bacteria present in our bodies actively fight off invaders **2nd Line of Defenses** - once an invader makes it past the walls, a more specific response is needed...at this stage the response is always the same  **Immune Proteins - complement system** - - - **Immune Proteins - Interferons (3 major proteins)** - - - - **[Cells who Kill Invaders]** - *3 major kinds for non-specific response* [Macrophages]: phagocytic cells - engulf foreign cells - - [Neutrophils]: non-specific killers - [Natural Killer Cells] - **The Lymphatic System** - complex of lymphatic vessels, lymph nodes and various organs [Functions:] absorption of excess fluid in the interstitial space and its return to the bloodstream, absorption of fat (in the villi of the small intestine) and immune system function. Lymph organs: spleen, thymus, bone marrow, tonsils, appendix. Lymph vessels are found throughout the body. White liquid circulating the lymph vessels is called [lymph fluid] and has bacteria and viruses filtered out via ducts and organs before returning to the bloodstream **Inflammation:** a standard response to an invader in the body but may also be caused by other factors (muscle injury) Indications of inflammation are: Pain, redness, swelling, heat [Steps of Inflammatory Response:] 1. 2. - 3. - [The Temperature Response] When macrophages attack they send a signal to the brain to increase the body temperature because, **Fever** **inhibits microbial growth** **However too high of a fever will denature cellular enzymes, and temps higher than 40℃ are often fatal** [**Specific Immunity**] - involves the action of leukocytes (2 wbc/100 body cells) major types are T and B cells Note: [all lymphocytes are white blood] cells but [not all white blood cells are lymphocytes] **Types of Lymphocytes:** **1. T cells** - originate in bone marrow but migrate and mature in **thymus** - - [There are 4 main types of T cells] - - - - **2. B cells** - originate and mature in **bone marrow** and when exposed to an antigen they become: - - **3. Natural Killer (NK) cells** (membrane penetrations) **The MHC:** A protein group called the [major histocompatibility complex (MHC)] enables lymphocytes to identify and differentiate the host from the invader (on nearly every body cells surface) - - - **Antigens:** most are proteins or polysaccharides that form a foreign complex which triggers the immune response - - - **[Triggering the Immune Response]** - - IL-1 then stimulates T helper cells (T~H~) to initiate 2 different responses: 1. 2. **T Cells - The Cellular Response** T~H~ cells secrete **interleukin-2,** This stimulates proliferation of **cytotoxic T cells (T~C~).** These recognize and destroy cells with the specific antigen found on the antigen-presenting cell. →T~C~ cells will also attack transplanted tissue and cause graft rejection. →The drug cyclosporine inactivates T~C~ cells. **B Cells - The Humoral Response** B cells recognize invaders but don't attack them directly, they instead mark the pathogen for destruction using non-specific immune defenses T helper cells identify the MHC complex on B cells and after complexing with B cells, they divide into either Plasma or Memory Cells **Antibodies (immunoglobulins) -** proteins which recognize and bind to antigens with very high **specificity** - - **Epitopes -** the part of an antigen that interacts with an antibody Each are recognized by a different antibody (high specificity) - **Antigens:** most are proteins or polysaccharides that form a foreign complex which triggers the immune response **Antibody Diversity** - (DNA segments that code for different parts of the receptor molecule are stitched together) - Most antibodies have at least 2 identical **valence (antigen binding sites)** **Antibody Structure** - - -  [Antibody Transfer ] Some pre-existing antibodies can be passed from mother to fetus through the placenta and breast milk [Producing Antibodies - Clonal Selection] **The Primary Immune Response:** The first encounter with a foreign antigen - - - Producing Antibodies: Clonal Selection **The Secondary Immune Response:** The second, third, fourth, fifth ect. encounter with an antigen - - **Thursday Lecture:** **Passive Immunity -** when antibodies aren't made by the person but transferred into them via placenta, breastmilk or antivenin and they eventually wear off **Active Immunity -** the process of the body forming memory cells from exposure to the antigen **Vaccination -** induces a primary immune response without an actual active infection, so that memory cells can be developed. ** The patient receives the immunological benefit without the pathological condition.** Causes memory B cells to be produced ∴ eliciting a faster and larger immune response in the secondary encounter **Variolation -** a method of inoculation used first used to immunize individuals with variola (smallpox) - - **Types of Vaccines:** 1. 2. 3. 4. **Herd Immunity:** when enough people in a group or area have achieved immunity (protection) against a virus or other infectious agent to make it very difficult for the infection to spread. **[Issues with Vaccinations]** - - - - - **Allergies -** A **hypersensitivity reaction** is an immune reaction, against a harmless substance, that results in tissue injury or death. **There are four types of reaction:** 1. 2. 3. 4. A **food sensitivity** is NOT a hypersensitivity reaction as there is not immune response involved, and are usually linked to a lack of a certain enzyme (e.g no *lactase* to break down *lactose)* **Transplants:** transfer of a partial or full organ from one location to another either from donor (living or deceased) to recipient or from one location in a patient to another locations in the same patient Used when no other therapies will be effective or if affected organ has lost function - - - - Problems with Organ Transplants Include: - - - - - - **Immunological Issues** Humans cannot accept organs from every other human; the new organ is recognized as "non-self"; it acts as an antigen and starts an immune response. - - **Hyperacute Rejection (24 hours):** form of rejection that manifests itself in the minutes to hours following transplantation. It is caused by the presence of pre-existing antibodies in the recipient that recognize antigens in the donor organ. Non specific, inflammation prevents organ from receiving adequate blood supply resulting in tissue death **Acute Rejection (first week):**Results from the immune system recognizing the new tissue as foreign. Has the blood vessels and tissues destroyed **Chronic Rejection (months-years):** Arteries in the graft tissue become blocked, leading to loss of blood flow and tissue death. **Acute Vascular Rejection:** occurs 4 to 8 days after **xenotransplantation** (different species) - **Immunosuppression:** drug or radiation therapy to stop the production of leukocytes, and therefore stop tissue rejection. - - **Domino Transplant:** involves multiple organs moving between multiple people **[Biotechnology Ch. 17]** **Recombinant DNA Technology** - the new term for ''genetic engineering'' and refers to the [intended manipulation of any organism\'s genome]. It generally involves the placement of a human gene into a bacteria for the mass production of a product, Also involves adding new genes to products, e.g. food (GM foods) **All gene experiments are composed of the same 4 stages:** 1. 2. 3. 4. **Plasmids -** extra piece of DNA found within many bacterial cells, it is physically separate from bacterial chromosome - - - Their role in DNA recombination is to accept the DNA of a different organism, transfer it to bacteria, which will transcribe and translate the new gene. The product can then be collected, purified, and sold commercially (e.g. insulin) **Restriction Enzymes (Endonucleases) -** bacterial proteins that cleave DNA at [restriction sites] - - **Polymerase Chain Reaction:** takes minute amounts of DNA (sequence of interest) and amplifies it to larger amounts **Electrophoresis:** a technique of DNA recombination using an electric field to separate the strands of DNA based on size - - **Transgenic Plants:** many crops or modified to sustain certain temperatures/conditions, increase nutrition/product and pesticide resistance **Short Tandem Repeats (Microsatellites):** sequences of nucleotides in DNA that are between 2 and 13 nucleotides long, and can be repeated hundreds of times in a row - - - **Steps in DNA Fingerprinting** 1. 2. 3. **Protein Therapy:** used when genes are non-functional and we replace the product of that gene Ex. insulin replacement for diabetes - - - **Gene Therapy:** a technique for introducing the genetic material of a gene in a patient that lacks that gene because of a mutation - - **Vectors:** is the method used to introduce the new gene into the patient's cells. - - **Why Viruses?** - - [True] or Fale, both healthy and unhealthy cells can be targeted. **Somatic Cell Gene Therapy:** replaces DNA with regular body cells without affecting the gametes and so inheritable mutations are not prevented. has not been very successful; there are major hurdles that must be surmounted. **Germline Cell Gene Therapy:** manipulates the zygote at a VERY early stage, so all cells would carry the modified DNA. It is not a major area of research in humans because of the major problems that could arise. **Embryonic Development:** all animal embryos develop in the same 3 stages 1. 2. 3. **Stem Cells** - are undifferentiated cells that renew themselves for long periods through cell division. Stem cells could be used to restore tissues lost or damaged due to accident or disease. Types of stem cells: - - - **Blastocyst:** forms 3-4 days after fertilization, it has an outer layer that will form the placenta and the inner layer will form the embryo and is composed of embryonic stem cells **Adult Stem cells can be derived from:** - - - - **CRISPR** Clustered, regularly interspaced short palindromic repeats: is a technique for directly "editing" the genome of an organism. Using this technique, you can target a specific gene in a specific location and remove it. Cell Communication and Cancer Biology (NO Ch.) Cells communicate through direct contact via their cell junctions allow passage of molecules from one cell to another through specialized channels Cell-cell recognition occurs through membrane-bound proteins Cells can also release compounds called ''messenger molecules'' to communicate with another cell. These signals can be local or long-distance - - **Three stages of cell signaling:** 1. - **Specificity and Coordination:** Different cells express different collections of proteins to respond to different signals - **Signal Termination** - - - **Apoptosis (**regulated cell death**)**: Cells release a coordinated signalling event that results in the cell destroying itself from the inside out. This protects the body from dysfunctional cells, maintains tissues and repairs them. **The Caspase Cascade:** the main proteases that carry through apoptosis. This response can be triggered by - - - Accumulation of genetic mutations in core areas of the genome that govern cell signalling pathways can cause cells to act without control mechanisms in place Dysregulation of core signalling pathways in a cell can lead to cancer **Cancer** - refers to a collection of different diseases characterized by a lack of cell cycle control. The cells can invade adjacent tissues, or move through the blood or lymphatic systems to invade tissues further away (metastasis). **Tumour -** abnormal mass of tissue that results from excessive cell division that is uncontrolled and progressive. - - **Benign Tumors:** is one that does not metastasize. Its danger to the body depends on location and anything secreted from the tumour. **Malignant Tumor:** is one that has the ability to invade other tissues through metastasis, leading to organ damage at both the original location and the metastatic location **[Nomenclature]** - - - - - **Prostate Specific Antigen (PSA):** a glycoprotein produced by the prostate gland. Its role in the body is to make semen more liquid so sperm can swim more easily An **incidentaloma** is a tumour found by coincidence when using imaging technology (CT, X-ray, MRI) **Cell Cycle Control:** 1. 2. 3.