Exam Highlighted Topics - Biochemistry & Biology PDF

Unit 1 BioChem ​ Cell membrane: understand the cell membrane’s structure and how it allows it to perform its functions. – Forces of attraction and permeability. Fluid Mosaic model, membrane is not static. Function: Protection, support,, maintain shape, transport in/out of cell. Lipids:...

Unit 1 BioChem ​ Cell membrane: understand the cell membrane’s structure and how it allows it to perform its functions. – Forces of attraction and permeability. Fluid Mosaic model, membrane is not static. Function: Protection, support,, maintain shape, transport in/out of cell. Lipids:  -​ Made of phospholipid bilayer -​ Double layer (polar hydrophilic heads and non polar hydrophobic tails Cholesterol: Embedded into the phospholipid bilayer to increase the rigidity Proteins:  Integral proteins: Transmembrane proteins inside membrane Peripheral proteins: Attached to surface Membrane proteins functions: Structural support (anchor), communication (receptors) enzyme transportation channels. Carbohydrates Glycolipid: Lipid with carb chain attached to help the cell recognize other body cells. Glycoprotein: Protein with a carbohydrate tail to help with cell communication and transport Cholesterol: embedded into phospholipid bilayer, helps keep fluidity of membrane constant. Forces of attraction and permeability: What can cross membrane? Fats and other lipids (cholestorol). Small non polar molecules Small uncharged polar molecules (as in not ions). Water Glycerol Ethanol Other substances cross through protein channels. Why are protein channels used? -​ Hydrophobic -​ (anchors protein into membrane). Outer surface of membrane. -​ Hydrophilic -​ Extend into extracellular fluid and cytosol. -​ Hydrophobic interactions: hydrophobic tails interact with ercachother minimizing water exposure to form stable bilayer permeable to water soluble substances. -​ Permeability (size, charge, polarity): controls what goes in/out (small non polar pass [O2, CO2). Larger charged molecules like glucose need a transporter to pass. -​ Membrane proteins: transport proteins help larger or charged molecules cross (facilitated diffusion or active transport). -​ Fats and other lipids (cholesterol) can cross the membrane directly. -​ Protein Channels (doors; become semipermeable) allow certain substances in/out. -​ Why proteins are used for channels: -Within membrane: hydrophobic anchors protein into membrane -Outer surface: Hydrophilic, extend into extracellular fluid and cytosol -2 types of movement across membrane: Passive transport and active transport. ​ Types of transport: similarities and differences between osmosis, exocytosis, endocytosis, diffusion...and what types of substances use these different methods to enter/exit cells. Passive transport -​ Simple Diffusion, Facilitated, Osmosis Simple Diffusion: Movement of small substances directly across a membrane from high to low concentration -​ No energy needed (O2, CO2, Lipids, small polar molecules) Facilitated: Diffusion through protein channels from High to low concentration -​ No energy needed (Like a slide or a door). Osmosis: Diffusion of water from high to low concentration. Across semipermeable membrane Active transport Movement of molecules against concentration gradient Protein pump: Transports solutes “uphill” Costs energy=ATP For large molecules Endocytosis: Cellular eating Pinocytosis= Cellular drinking ​ Cell engulfs large molecules via vesicles that fuse with cell membrane Exocytosis- move out ​ Enzymes: structure: understand the general structure of an enzyme and different ways it can become inhibited. – How does it speed up a reaction? -​ Induced fit -​ Lowers Ea Unit 2: Metabolic Processes Be able to write the chemical equation for cellular respiration and photosynthesis and explain how they are complementary procedures and respect the laws of thermodynamics. Cellular respiration: Net Equation: O2 + C6H12O6 → CO2 + H2O and + ATP Occurs in cytoplasm and mitochondria. Stage 1: Glycolysis: in cytoplasm, anaerobic Investment: 1 Glucose 2 ATP, 2 NAD+ Net Product: 2 ATP 2 NADH, 2 pyruvate Stage 2: Pyruvate Oxidation/Krebs -​ In matrix -​ Aerobic. Reactants: 2 Pyruvate: 2NAD+ +2CoA + 2 Acetyl-CoA + 2NADH + 2 H+ + 2CO2 +​ 2 Coenzyme A Products:2 CO2, 3 NADH, 1 FADH2, 1 GTP (converted to ATP) CoA (recycled for further use). Total energy made per glucose: 2 ATP 8 NADH 2 FADH2 ETC: Fueled by proton motive force: NADH (krebs): 8x3= 24 FADH2 (krebs):2x2= 4 NADH(glyc)= 2x3= 6 ATP(Krebs)= 2 ATP (Glyc)= 2 = 38 ATP TOT ​ Be able to explain how ATP is made at the electron transport chain: -​ By way of chemiosmosis ATP synthase catalyzes the production of ATP by combining ADP and Pi. -​ Driving force→ Electron carrier molecules and oxidative phosphorylation. Electron carrier molecules are oxidized and protein molecules are reduced. -​ Chain consists of 4 protein complexes I, II, III, IV with increasing electronegativity along the chain. Electron flow from one complex to another is facilitated by two mobile shuttles. Oxygen is highly electronegative and is the driving force in the electron transport chain. It takes two electrons from cytochrom c (cyt c causing a chain reaction with electrons being passed from molecules that are more electronegative to molecules that are less electronegative. Proton motive force establishes an electrochemical gradient. Cells use this force to do work. Chemiosmosis→ Process in which ATP is synthesized using the energy of an electrochemical gradient and ATP synthase enzyme. Also used to pump substances across membranes and to drive the rotation of flagella in prokaryotes. Anaerobic Respiration know how the cells continue to create ATP in absence of oxygen and why ETC cant continue. Two ways: Anaerobic Respiration- Uses inorganic substances other than oxygen as the final oxidizing agent to produce ATP Fermentation- Uses an organic compound as 2 types: alcohol, and lactate the final oxidizing agent to produce ATP Alcohol: glucose from food is converted to CO2 ethanol, and ATP Ex. Breadmaking, brewing beer, wine. Lactate Fermentation: Glucose from food is converted into lactate and ATP. Ex. Yogurt, cheeses strenuous exercise. Describe why a runner will often cramp up after working out strenuously This is because as the runner expends tremendous energy, they are not getting adequate oxygen intake. Since oxygen is the driving force of the ETC, this causes the ETC to not function. Without adequate oxygen, the increasing EN along the ETC will not drive the proton motive force and protons will eventually accumulate on both sides of the membrane. As a compromise in order to continue to make ATP and eliminate pyruvate molecules the body converts this into lactic acid. Because of Lactic acid’s structure and it changing the pH, this becomes very uncomfortable. As lactate accumulates the discomfort increases eventually making it impossible to keep going. Be able to explain non cyclic electron flow of the light reactions of photosynthesis. Photosynthesis: 6CO2 + 12H2O—> C6H12O6 + 6O2 + 6H2O Photosynthesis occurs in two stages Light reactions: Thylakoid of Chloroplasts Calvin Cycle: -​ Stroma of chloroplast 3 Steps for light reactions: 1: Pigments embedded in thylakoid membrane absorb energy from sunlight and give up electrons to membrane proteins. 2. Movement of electrons and H+ ions leads to production of NADPH and ATP. 3. Electrons released by pigments are replaced by splitting of H2O (Insert Steps from Ppt if Harkish says its necessary). Why are photosynthetic carbon fixation reactions referred to as “Dark Reactions”? -​ Dont require light to occur, takes place in the chloroplasts, stroma and use ATP and NADH produced during light reactions to fix CO2 into glucose. -​ While they do not directly rely on light, the electron carriers that the Calvin cycle depends on do. Compare and contrast cellular respiration and photosynthesis. 1.​ Proton Motive Force (PMF): Both processes generate a proton gradient across a membrane (thylakoid in photosynthesis, inner mitochondrial membrane in cellular respiration) by using the energy from electrons moving through an electron transport chain (ETC). 2.​ ATP Production via Chemiosmosis: In both photosynthesis and cellular respiration, the proton gradient drives ATP synthesis through ATP synthase via a process called chemiosmosis. 3.​ Electron Transport Chains: Both processes use an electron transport chain to transfer electrons and create a proton gradient. In photosynthesis, the ETC is located in the thylakoid membrane, and in cellular respiration, it’s in the inner mitochondrial membrane. 4.​ Use of NAD(P)H: Both processes involve the use of electron carriers (NADH or NADPH) to carry electrons through the ETC, leading to ATP production. Differences to Keep in Mind: ​ Source of Electrons: In photosynthesis, electrons come from water molecules (H₂O), splitting them into oxygen, electrons, and protons. In cellular respiration, electrons come from glucose (C₆H₁₂O₆) that is oxidized during glycolysis and the Krebs cycle. ​ Final Electron Acceptors: The final electron acceptor in photosynthesis is NADP⁺, which becomes NADPH, while in cellular respiration, the final electron acceptor is oxygen (O₂), which combines with electrons and protons to form water. Genetics DNA Nucleotide Pyrimidines: Tymine cytosine Purines: Adenine, Guanine Steps of DNA Replicaition 1.​ As DNA uncoils and unwinds topoisomerases relieve tension on molecule. 2.​ DNA helicase breaks H bonds that hold two strands together produces a replication fork.  3.​ SSBP attach to each strand prevents H bonds from forming. 4.​ RNA primase attaches RNA primers to 3’ end of each strand 5.​ Starting at primers DNA polymerase III adds complementary DNA nucleotides to each strand.Lead Towards Rep fork, Lagging away. 6.​ DNA polymerase I replaces RNA primers with DNA, DNA ligase joins okazaki fragments. ​ DNA polymerase I and II proofread new strands and correct errors. ***DNA polymerase III constructs new strand in 5’-3’ direction only!!!! Lac operon Function 1.​ Three genes that code for β galactosidase -​ Promoter region which RNA polymerase must bind to before transcription can occur. -​ Operator region which overlaps with promoter region. -​ Lac1 protein can bind with operator and represses transcription by preventing RNA polymerase from binding with promoter. Lactose binds with lac1, causes it to chance shape and detach from operator. Allows RNA polymerase to bind to promoter and transcription to occur. When all the lactose has been broken down, the Lac1 protein returns to its original shape. Once again, RNA polymerase is returns to its original shape. prevented from binding to the promoter, and transcription stops. Review Quizzes Unit 4 1.​ Define Homeostasis: Maintenance of steady internal state. Homeostasis -/+ Feedback, example draw include monitors/sensors, coordinator, effector. Negative Feedback Stimulus Sensor Coordinator Effector Increase in Thermoreceptors Hypothalamus Blood vessels dilate  temperature integrator to increase surface area, sweat glands activate. Positive Feedback Stimulus Sensor Coordinator Effector Dust/irratant in nasal Mechano receptor Medulla oblongata in diaphragm/intercostal cavity brain muscles, throat and face expelling contents of nasal cavity to “reset”. Action potential and neurons, interpreting graphs Example: Pricking finger Step 1: Stimulus causes Na channel to open, delpolarization, sodium rushes in Step 2: K+ Channels open and potassium ions rush out cause repolarization Step 3: Undershoot causes hyperpolarization Step 4: Sodium and potassium pump restore membrane to resting potential (-70mmV) Be able to describe a reflex arc, how a nerve signal is sent across a neuron and how signals are sent across a synapse 1. Stimulus 2. Sensory 3. Inter neuron, Motor sends Effector Neuron transfers signal message to motor Pin applies Action potential Sends message Muscle pressure travels to muscle contracts. Chemical synapse: How does this work?: To transfer signals between neurons Synapse: Microscopic gap that separates neurons. Vesicles of axon terminal are filled with neurotransmitters. Neurotransmitters: Chemical messengers that diffuse across synapse to excite or inhibit post synaptic neuron. ​ ​ Membrane of post synaptic neuron contain receptors that react to neurotransmitters (ex. glutamate). Action potential will only be generated if threshold stimulus is reached. Define Homeostasis Homeostasis: Maintenance of steady internal state. Neuron -​ Label U4 R a) A: Dedrites :Highly branched projection of cytosol that carry signals toward cell body. B: Cell body: contains nucleus, and is the site of the metabolic reactions. C) Axon: Long thin extension of cytosol that conducts signals away from nerve cell body. Can be bundled together to form nerve fibres. D) Axon terminal: Small swelling at the end of axon, communicates with other neurons, muscles or glands by releasing chemicals into synapse. E) Nucleus b) If this were a motor neuron, it would relay signal from the brain and spinal cord to the muscles and glands. c) dendrites receive the signal. Action Potential Graph Interpret Excitatory vs. inhibitory Diabetes -​ Know types -​ Interpret Graph Functions of the Brain -​ Main things each lobe of the brain control Frontal Lobe Motor Areas control voluntary muscle movement. Association: Intelligence and personality. Parietal Lobe Sensory, Touch and temperature awareness Association areas: Emotions and interpreting speech. Temporal Lobe Sensory Areas related to vision and hearing. Association areas interpret memory and sensory information. Occipital Sensory related to vision. ​ Association: interpreting visual information.  -​ -​ Ie Lobe Control Hypothetical question: Pg. 536 ​ Loss of coordination and balance. ​ Unsteady or jerky movements. ​ Difficulty performing precise or complex motor skills, such as skating or controlling a hockey stick. The damage was most likely done to the frontal lobe which is responsible for speech production and coordinating modor areas that are responsible for speaking. The temporal lobe is responsible for interpreting text so that area and other parts of the brain involved in interpreting text were still in tact. 3. If person suffers trauma to side of the head, Identify lobe and consequences: ​ Temporal lobe. Consequences: Trouble interpreting memory and sensory information. I.E registration of visual queues and objects. Diabetes: Types, graphs (see worksheet) Types of Diabetes: Type 1: Inability for pancreas to produce insulin Treatments: Supplementary insulin after meals. Type 2: Inability for insulin to bind to receptors. Cells are insulin resistant. SEE PG 574 Q74 Thinking question Brights disease: Condition of the kidneys relating to the processing of proteins. a)​ Sample B is from the patient with diabetes mellitus. This is because there is a high concentration of glucose excreted into the urine. This is a sign that it was not able to be absorbed into the cells, or stored as glycogen b)​ Sample D: This urine is very dilute c)​ Excess protein is brights disease. Sample C. Because the kidneys are inflamed, they can not function to filter protein out of fluids properly.