BSC2010, week 3 Notes
BSC2010, week 3 Notes BSC2010
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This 10 page Class Notes was uploaded by Valerie Notetaker on Wednesday January 20, 2016. The Class Notes belongs to BSC2010 at University of Florida taught by Gillooly,James FMiyamoto,Michael MasaoOppenheimer,David G in Fall 2015. Since its upload, it has received 90 views. For similar materials see Integrated Principles of Biology 1 in Biology at University of Florida.
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Date Created: 01/20/16
BSC 2010 Notes 2 Chapter 3: Nucleic Acids, Proteins, and Enzymes January 20, 2016 Concept 3.3 some proteins act as enzymes to speed up biochemical reactants - Top hat question: o Which amino acid substitution for valine would least likely affect the three- dimensional shape of the resulting protein? Answer: Isoleucine - - How do enzymes catalyze a reaction? - Inducing strain o Bonds in the substrate are stretched, putting it in an unstable translation state. - Substrate Orientation o Substrates are bought together so that bonds can form. - Adding chemical groups o R groups may be directly involved in the reactions. - - Binding of substrate to enzyme is like a baseball in a catcher’s mitt. The enzyme changes shape to make the binding tight – “induced fit.” - - Shape changes upon Ca^2+ binding to CaM - Proteins are dynamic - Enzymes are really flexible - - Some enzymes require ions or other molecules in order to function: o Metal ions: Copper, Zinc, Iron o Coenzymes: Small organic molecules (NAD, FAD, ATP), add or remove chemical groups from the substrate. They can participate in many different reactions. o Prosthetic groups: Organic molecules permanently bound to their enzymes (heme, Flavin, retinal) - - Rates of catalyzed reactions: o There is usually less enzyme than substrate present, so reaction rate levels off when the enzyme becomes saturated. o Saturated All enzymes molecules are bound to substrate molecules. - Maximum rate is used to calculate enzyme efficiency – substrate molecules converted to products per unit time (turnover). - It ranges from 1 to 40 million molecules per second! Concept 3.4 Regulation of metabolism occurs by regulation of Enzymes - Enzyme- catalyzed reactions are part of metabolic pathways – the product of one reaction is a substrate for the next. - - Homeostasis o The maintenance of stable internal conditions. - Cells can regulate metabolism by controlling the amount of an enzyme – turn synthesis of enzymes off or on. - Cells can maintain stable internal conditions by regulating the activity of an enzyme. - Chemical inhibitors can bind to enzymes and slow down reaction rates- natural inhibitors regulate metabolism; artificial inhibitors are used to trait diseases, kill pests, and study enzymes function. o Example : drugs - - Irreversible inhibition – o Inhibitor covalently binds to a side chain in the active site. The enzyme is permanently inactivated. Example: Insecticide Malathion derived from DIPF. Example: Aspirin – can prevent from blood to clog. - Reversible inhibition (more common in cells): o A competitive inhibitor Competes with natural substrates for active site. Binds to the active site and preventing substrate from binding. o A noncompetitive inhibitor Binds at a site distinct from the active site, causing change in shape and function. Binds at a site other than the active site - - Allosteric regulation -- Non-substrate molecules binds a site other than the active site (the Allosteric site)- (non- competitive inhibitor will bind to this or are related to this.) o The enzyme changes shape, which alters the chemical attraction (affinity) of the active site for the substrate. o Allosteric regulation can activate or inactivate enzymes. - - Protein kinases regulate responses to the environment: o Many Enzymes are subject to allosteric regulation. o The active form regulates the activity of other enzymes, by phosphorylating allosteric or active sites on the other enzymes. - - Metabolic pathways: o The first reaction is the commitment step --- other reactions then happen in sequence. o Feedback inhibition (end – product inhibition) – the final product acts as a noncompetitive inhibitor of the first enzyme, which shuts down the pathway. - - pH affects enzyme activity: o Acidic side chains generate H+ and become anions. o Basic side chains attract H+ and become cations. o Example: Glutamic acid – COOH < -- > glutamic acid – COO + H - + o The law of mass action + The higher the H concentration, the more reaction is driven to the left to the less hydrophilic from. This can affect enzyme shape and function. o Protein tertiary structure (and thus function) is very sensitive to the concentration of H^+ (pH) in the environment. o All enzymes have an optimal pH for activity. - Temperature affects activity: o Warming increases rates of the chemical reactions, but if temperature is too high, non – covalent bonds can break and inactivate enzymes. High temp = denaturation. To keep cells alive you need a very cold temp Example: sperm and egg banks o All enzymes have an optimal temperature for activity. o Isozymes Catalyze the same reaction but have different composition and physical properties. o Isozymes may have different optimal temperature of pH, allowing an organism to adapt to changes in its environment. Reviews for chapters 2 & 3 - Macromolecules (polymer) formation always involve Covalent bonds - Hydrogen bonds are responsible for maintaining structures in nucleic acids (Complementary base paring) and proteins. - All five chemical bonds and interactions contribute to further structural maintenance. Hydrophilic vs. Hydrophobic - Polar and charged molecules are hydrophilic. - Nonpolar and uncharged molecules are hydrophobic. - Functional groups give hydrophilic property to molecules. - Three amino acids groups: nonpolar, polar, and electrically charged ones. Macromolecules - Carbohydrates - Lipids - Nucleic Acid - Proteins Protein: Structure and Function - Primary - Secondary - Tertiary - Quaternary Regulation of metabolisms through regulation of enzymes - Control the amount of an enzyme - Regulate the activity of enzymes o Inhibitors (competitive and noncompetitive) o Allosteric regulation - Feedback inhibition. 1/22/2016 Chapter 4: Cells: The Working Units of Life Concept 4.1 Cells Provide Compartments for Biochemical Reaction - Cell theory was the First unifying theory of biology. Cell theory states that: o Cells are the fundamental units of life o All organisms are composed of cells o All cells come from preexisting cells. o o Important implications of cell theory: Studying cell biology is the same as studying life. Life is continuous. Major key for chapter 4: - Prokaryotes vs. Eukaryotes - Plant cell s. Animal cell - Structure and Function of each organelle - - Most cells are tiny. o This is because diffusion is a key force that moves most molecules around the cell and allows them to interact. o Diffusion can move molecules over short distances rapidly, but it takes too long to move them long distances. When you have smaller cells surface area increase, and small cells want to have good and faster reactivity (this is why cells are small). - - The volume o of a cell determines the amount of metabolic activity it carries out per unit time. - The surface area o of a cell determines the number of substances that can enter or leave the cell - As the volume of a cell increases, the surface area does not increase as much. - Cells compensate by changing the shape of their shape to increase the surface area (by being flat instead of Spherical, or by having many invaginations.) Cells can be studied structurally and chemically - To visualize small cells, there are two types and microscopes: o Light microscopes -- use glass lenses and light Resolution = 2.0 o Electron microscopes – electromagnets focus an electron beam Resolution = 0.1 nm. - Chemical analysis of cells - Involves breaking them open to make a cell – free extract - The composition and chemical reactions of the extract can be examined. - The properties of the cell – free extract are similar to those inside the cell. The plasma membrane: - Is a selectively permeable barrier that allows cells to maintain a constant internal environment - Is important in communication and receiving signals - Often had protein for binding and adhering to adjacent cells - Chapter 5: cell membranes and signaling Two types of cells: Prokaryotic and eukaryotic o Prokaryotes are without membrane – enclosed compartments. o Eukaryotes have membrane – enclosed compartments called organelles, such as the nucleus. Concept 4.2 Prokaryotic Cells do not Have a Nucleus - Prokaryotic Cells: o Are enclosed by a plasma membrane o Do not have Nucleus o Have DNA located in the Nucleoid o The rest of the cytoplasm consist of: Cytosol (water, dissolved material) and suspended particles Ribosomes – sites of protein synthesis. o Most Prokaryotes have a rigid cell wall outside plasma membrane. o Some have an additional outer membrane that is very permeable. o Others have a slimy layer of polysaccharides, called the capsule. o Some prokaryotes swim by means of flagella, made of the protein flagellin. Example: Bacteria. o A motor protein anchored to the plasma or outer membrane spins each flagellum and drives the cell. o Some rod – shaped bacteria have a network of actin- like protein structures to help maintain their shape. Concept 4.3 Eukaryotic Cells have A Nucleus and other membrane – bound compartments - Eukaryotic cells o Have a plasma membrane, cytoplasm, and ribosomes – and also membrane – enclosed compartments called organelles. o Each organelle plays a specific role in cell functioning. Ex: like the different departments at an University. o – animal and plant cell figures were shown o KNOW THE ORGANELLES AND THERE FUNTIONS. o Plant cells: o Animal Cells: - Ribosomes are sites of protein synthesis: o They occur in both prokaryotic and eukaryotic cells and have similar structure – one larger and one smaller subunit. o Each subunit consists of ribosomal RNA (tRNA) bound to smaller Protein molecules. o Ribosomes are not membrane – bound organelles – in eukaryotes, they are free in the cytoplasm, attached to the endoplasmic reticulum, or inside mitochondria and chloroplasts. o In Prokaryotic cells, ribosomes float freely in the cytoplasm. - The nucleus is usually the largest organelle. o Site of DNA and DNA replication, DNA transcription to RNA. o It contains the nucleolus, where ribosomes begin to be assembled from RNA and proteins. o The nucleus is surrounded by two membranes that form the nuclear envelope. o Nuclear pores in the envelope control movement of molecules between nucleus and cytoplasm. o In the nucleus, DNA combines with proteins to form chromatin in long, thin threads called chromosomes. - The endomembrane system: o The endomembrane system includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, and lysosomes. o Tiny, membrane – surrounded vesicles shuttle substances between the various components, as well as to the plasma membrane. - Endoplasmic Reticulum (ER) – network of interconnected membranes in the cytoplasm, with large surface area. - Two types of ER: o Rough endoplasmic reticulum (RER) o Smooth endoplasmic reticulum (SER) - Rough endoplasmic reticulum (RER) HAS RIBOSOMES attached to being protein synthesis. o Newly made proteins enter the (RER) LUMEN o Once inside, proteins are chemically modified and tagged for delivery. o The RER participants in the transport of proteins to other organelles. o All secreted proteins and most membrane proteins, including glycoproteins, which are important for recognition, pass through the RER. - Smooth endoplasmic reticulum (SER) – MORE TUBLUR, no ribosomes. o It chemically modifies small molecules such as drugs and pesticides. o It is the site of glycogen Degradation in animal site o It is the site of synthesis of lipids and steroids. o It stores Calcium ions required from muscle contraction - The Golgi apparatus is composed of flattened sacs (cistemae) And small membrane – endorsed vesicles. o Receives proteins from the RER – can future modify them o Concentrates, packages, and sorts, proteins. o Adds carbohydrates to proteins o Site of polysaccharide synthesis in plant cells. - The Golgi apparatus has three regions: o The cis region receives vesicles containing protein from the ER. o At the trans region, vesicles bud off from the Golgi apparatus and travel to the plasma membrane or to lysosomes. o The medial region lies in between the trans and cis regions. - Primary lysosomes originate from the Golgi apparatus. o Membrane bound organelle. o They contain digestive enzymes, and are the site where macromolecules are hydrolyzed into monomers. o Lysosomes are connected to many of the disease. Like Parkinson’s. o o Macromolecules may enter the cell by phagocytosis – part of the plasma membrane encloses the material and a phagosomes is formed. o Phagosomes then fuse with primary lysosomes to form secondary lysosomes. o Enzymes in the secondary lysosomes hydrolyze the food molecules. - - Phagocytes are cells that take materials into the cells and break them down. - Autophagy is the programmed destruction of cell components and lysosomes are where it occurs. - Lysosomal storage diseases occur when lysosomes fail to digest the components. - Energy transforming organelles: o In eukaryotes, molecules are first broken down in the cytosol. o The partially digested molecules enter the mitochondria chemical energy is converted to energy – rich ATP. o Cells that require a lot of energy often have more mitochondria. - Mitochondria have two membranes: o Outer membrane – quite porous o Inner membrane – extensive folds called cristae, to increase surface area o The fluid – filled matrix inside the inner membrane contains enzymes, DNA, and ribosomes. That means it can make protein when they have their own DNA, and ribosomes. Answer: D Answer is : a Answer: d Answer: e
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