Biology Notes Term 2 PDF

Biology Notes Term 2 ~10/01/2024~ Lock and Key, 1. The active site of an enzyme is a region (cleft or depression), to which another molecule/s can bind. This molecule is the substrate of the enzyme. 2. The shape of the active site allows the substrate of the enzyme to bind. 3. The...

Biology Notes Term 2 ~10/01/2024~ Lock and Key, 1. The active site of an enzyme is a region (cleft or depression), to which another molecule/s can bind. This molecule is the substrate of the enzyme. 2. The shape of the active site allows the substrate of the enzyme to bind. 3. The interaction of the substrate with the active site breaks the substrate apart. 4. Enzyme product complex is briefly formed, before the two product molecules leave the active site. Each type of enzyme will usually act on only one type of substrate molecule. This is because the shape of the active site will only allow one shape of molecule to fit. The modern hypothesis for enzyme action is known as the induced fit hypothesis. Enzymes and chemical reactions - Chemical reactions must occur continuously in living things - Examples: photosynthesis and breaking down food. - Can occur with the help of macromolecules called enzymes - Enzyme names usually end in -ASE - All enzymes are protein Function of enzyme: - Proteins that function as catalysts (help to speed up chemical reactions) - Will only catalyze one specific chemical reaction (1 substrate only 1 enzyme). Tons of enzymes at work at all times. - Enzymes won't change after a reaction occurs. 2 types of enzymes: 1. Endoenzymes (intracellular), act within cells in which they are produced - metabolic enzymes - plant enzymes 2. Exoenzymes (extracellular), liberated by living cells and act outside in its environment - act as digestive enzymes - microbial enzymes Lock and key hypothesis: 1. Molecules that bind to the enzyme are called substrates. The location where they bind is called the active site. 2. The substrate will bind into the active site 3. After the enzyme and substrate bind it is called an enzyme-substrate complex 4. The substrate may break apart or bond together to form a product Induced fit model (forced) - The active site is flexible, not rigid Factors affecting enzyme activity The activity of an enzyme describes how fast an enzyme catalyzes the reaction and is strongly affected by reaction conditions. Such as: - temperature - pH (per hydrogen)(Acid)(Hydrocide) - concentration of the enzyme and substrate Learning goals describe the effect of changes of temperature, pH, concentration of enzyme, and concentration of substrate on enzyme activity. Skin: collagen Fingernail and hair: keratin Enzymes, - are most active at an optimum temperature (usually 37*C in humans) - show little activity at low temperatures - lose activity at high temperatures as denaturation occurs Core chemistry skill identifying factors affecting enzyme activity Summary: - Enzymes catalyze (speed up) biological reactions - The substrate (the reactants) must bind to the enzyme at the active site - Enzymes are NOT reactants or products - Enzymes are NOT used up in a reaction - Enzymes may be used over and over again (so long as they have not been denatured) - Enzymes are specific to a particular substrate (or group of substrate) ~10/15/2024~ Building up (condensation) Breaking down (hydrolysis) Enzyme inhibition (prevent) - Cells must control enzyme activity to coordinate cellular activities - This can be done by: 1. Restricting the production of a particular enzyme (enzyme are proteins, so your body can control how much you make of them) 2. Inhibiting the action of an enzyme This may involve = a) competitive inhibition - these are molecules that are similar in shape to the substrate - they bind to the enzyme’s active site preventing the real substrate from binding - the molecule “competes” with the substrate for the active site - so now, the substrate cannot get into the active site because it is blocked by the Inhibitor. - this can be overcome by increasing the substrate concentration b) non-competitive inhibition - it will normally go into the allosteric site - the only problem is that the shape of the active site will change, which means that the substrate will no longer fit into the active site - adding more enzymes will help with the problem Allosteric regulation - activators - some enzymes have receptor sites away from the active site called allosteric sites. - (these enzymes are usually proteins made of several subunits each with an active site) - substance that bind to the allosteric sites may inhibit or stimulate (increase) the enzyme activity. - allosteric sites can hold only one substrate, either activator (positive) or non competitive inhibitor (bad) ~10/17/2024~ An immobilized enzyme is one whose movement in space has been restricted either completely or to a small limited region. Attachment to solid structure, incorporation in gels etc for use. Benefits: - Multiple or repetitive use of a single batch of enzyme - The ability to stop the reaction rapidly by removing the enzyme from the reaction solution - Enzymes are usually stabilized by binding - Product is not contaminated with the enzyme (especially useful in the food and pharmaceutical industries) - Easy separation of enzyme from the product - Allows development of an multienzyme reaction system - Reduces effluent disposal problems. Formative exam: 29 october (tuesday) ~10/22/2024~ DNA: makes up genes for all living things. Genes: blueprint for the human body. Genes are parts of DNA that code for particular traits or proteins. DNA stands for Deoxyribonucleic Acid Double helix shape DNA is made up of nucleotides Nucleotides are the basic units of DNA Recognize the similarities between the terms: - Nucleotide - Deoxyribonucleic acid - Nucleus Structure of a nucleotide, made out of 3 components: - A phosphate - Nitrogen base, adenine (A), thymine (T), cytosine (C), and guanine (G) - A sugar, Deoxyribose (5 carbon), base and phosphate is connected to the deoxyribose. The rule (Chargaff’s base-pair rule): Adenine (A) always pairs with Thymine (T) Cytosine (C) always pairs with Guanine (G) ~10/24/2024~ - James Watson and Francis Crick built the structure model of DNA. - Dna is antiparallel RNA, ribonucleic acid - Created from DNA replication - Single stranded What is RNA used for? Protein synthesis: to produce protein The function of protein: to build our structures Unlike DNA, RNA has several types: - Messenger RNA (mRNA) is used to send messages from DNA to be used elsewhere (ex: to create proteins for hormones, repair cells, help the immune system, etc.) - Transfer (tRNA) uses “ anticodons” to put amino acids in the correct order of mRNA codons Nucleotides contain: - Sugar (ribose) - A phosphate group, and a nitrogenous base The nitrogenous bases in, Rna are adenine (A), cytosine (C), guanine (G), and uracil (U). ~10/31/2024~ Pyrimidine: single ring (the square) - Cytosine - Thymine Purine: double ring (the rectangle) - Guanine - Adenine Bonded with hydrogen bond - Guanine and cytosine (triple bonded) - Adenine and thymine (double bonded) DNA replication Purpose: cells need to make a copy of DNA before dividing so each daughter cell has a complete copy of genetic information. - 3 proposed models on replication Correct model (proved by Meselson and Stahl experiment): Semiconservative guarantees that each daughter cell will receive 1 half of the original dna, reduces dramatic fatal mutations. Complementary pair for the dna that has been split in half Characteristic of DNA = 1. Replication of DNA - Base pairing allows each strand to serve as a template for a new strand - New strand is ½ parent template and ½ new dna  2. Antiparallel strand - Nucleotides in DNA backbone are bonded from phosphate to sugar between 3’ (3 prime) and 5’ (5 prime) carbons. - Dna molecule has “direction” - Complementary strand runs in opposite direction DNA replication = Step 1 = 1. Helicase enzyme: - unwind DNA using helicase enzyme - stabilized by single stranded binding proteins (the blue dots) 2. DNA gyrase - enzyme that prevents tangling upstream from the replication fork Step 2 = 1. RNA Primase: - adds a small section of RNA (RNA primer)to the 3’ end of template DNA. why? Because DNA polymerase 3 (enzyme that builds new DNA strand) can only add nucleotides to existing strands of DNA - primer is used to start up the process Step 3 = 1. Build daughter DNA strand - add new complementary bases - with the help of the enzyme DNA polymerase III Step 4 = 1. Replacement of RNA primer by DNA 2. Done by DNA polymerase I (review everything and remove RNA primer) ~10/31/2024~ Leading and Lagging strand 1. Limits of DNA polymerase III - can only build onto 3’ end of an existing DNA strand 2. Leading strand - continuous synthesis 3. Ligase - connects the okazaki fragments 4. Lagging strand, okazaki fragments - joined by ligase, “spot welder” enzyme ~11/07/2024~ Protein Synthesis Proteins have 2 main functions = 1. Structural: protein help make up all structures in living things - actin and myosin: muscle proteins - collagen: bones, teeth, cartilage, tendon, ligament, blood vessels, skin matrix - Keratin: nails, hair, horns, feathers. 2. Functional: other proteins help us to keep our bodies functioning properly and to digest our food. - enzymes: lower the energy of activation to digest our food and to assist in cellular metabolism. Protein structure is determined by the genetic code in your DNA. The section of DNA that codes for one protein is called a gene. A gene is a section of DNA that determines the 1 '0 sequence of amino acids in a protein. Therefore, the gene determines the shape and therefore, the function of the protein it codes for. 2 steps of protein synthesis: 1. Transcription, happens in nucleus 2. Translation, happens in cytoplasm If the process of protein synthesis were a play, these would be the roles of all of the people involved. The director is basically DNA (gene). The 3 assistant directors: mRNA, tRNA, rRNA. The cast are amino acids, and the stage is the ribosome. Stage crew: enzymes. Extra information: 1. Humans share most of the same protein families with worms, flies, and plants. 2. Hair grows by forming new cells at the base of the root. As they move upward through the skin, they are cut off from their nutrient supply and start to form a hard protein called keratin in a process called keratinization. As this occurs, the hair cells die. The dead cells and keratin form the shaft of the hair. 3. Fingernails grow about three or four times as quickly as toenails (toenails are thicker) 4. Each hair grows about ¼ inch/month and grows for up to 6 years. 5. The most expressive muscles are the facial muscles. We need 17 muscles to smile and 43 muscles to frown. 6. The most numerous are the skeletal muscles. When we walk for instance, we use 200 muscles. 7. There are 20 amino acids ~11/12/2024~ Act one: transcription The coded message of a gene on DNA has specific instructions on how to make each particular protein that our bodies need. - The instructions from a gene are copied from DNA to messenger RNA (mRNA) in the nucleus. - Then, the mRNA moves through the nuclear pores and into the cytoplasm where the proteins are made. - The process of making mRNA is called TRANSCRIPTION Steps in transcription = 1. Helicase unwinds the DNA (starting at the promoter) 2. Complementary RNA base pairs attach to form the mRNA strand 3. RNA polymerase forms the RNA sugar-phosphate backbone and checks for mistakes 4. The RNA detaches and leaves the nucleus, and the DNA winds back up Introns vs exons = Introns, 1. Non-coding sequences of a gene 2. Do not appear in mature mRNA molecules Exons, 1. Coding sequences of a gene 2. Collectively make the final RNA molecule Act two: translation - The mRNA code is made up of groups of three nucleotide bases known as codons. Each codon codes for a specific amino acid. Eg: AGC = serine, UGC = cysteine - The written code (codons) on mRNA is ‘translated’ into a specific amino acid sequence by ribosomes in the cytoplasm. - This is carried out with the help of relatively small transfer RNA (tRNA) molecules. - The tRNA also has a special sequence of 3 nucleotide bases known as an anticodon - There is at least one type of tRNA for each of the 20 amino acids. - As the correct amino acids are brought to the ribosome by the tRNAs, they are joined together via dehydration synthesis to form the protein that the original DNA coded for. mRNA codons: UCU GCC tRNA anticodons: AGA CGG ~11/19/2024~ Gene mutations: In biology, a mutation is an alteration of the nucleotide sequence of the genome of an organism. May occur in somatic cells (aren't passed to offsprings). May occur in gametes (eggs & sperms) and be passed to offsprings. Are mutations helpful or harmful? - Mutations happen regularly - Almost all mutations are neutral - Chemicals & UV radiation cause mutation - Many mutations are repaired by enzymes - Mutations can be bad, leading to cancer, aging, birth defects, self-aborted embryos - Mutations can also be good, making an organism survive better in its environment. Example = bacteria becoming antibiotic-resistance What causes mutations? There are two ways in which DNA can become mutated: 1. Mutations can be inherited 2. Mutations can be acquired - environmental damage - mistakes when DNA is copied - Change in the nucleotide sequence of a gene - May only involve a single nucleotide - May be due to copying errors, chemicals, viruses, etc. Starting codon (AUG) Stop codon (AUU, AGU, AUG) Types of gene mutations 1. Point mutations, a genetic mutation where a single nucleotide base is changed. - missense, a change in one DNA base pair that results in the substitution of one amino acid for another in the protein made by a gene (New amino acid). Example = sickle cell anemia. - nonsense, also a change in one DNA base pair. Instead of substituting one amino acid for another, altered DNA sequence prematurely signals the cell to stop building a protein (sudden appearance of stop codon (UAA, UGA, and UAG), therefore, the process will stop). This type of mutation results in a shortened protein that may function improperly or not at all. (premature ending of translation) Examples = duchenne muscular dystrophy and thalassemia. - silent, are mutations in DNA that don’t have an observable effect on the organism’s phenotype. Example = if the codon AAA is altered to become AAG, the same amino acid - lysine - will be incorporated into the peptide chain. 2. Frameshift - insertion, - deletions,