HUMBIO3A Midterm Flashcards

• During glycolysis, glucose is broken down into two molecules of pyruvate.
• Cells are enclosed by a plasma membrane. Membranes provide a barrier, generate an organizational surface,

  and require a transport mechanism.
• Hydrophilic molecules dissolve in water due to charged atoms and polar groups. 


  Hydrophobic groups do not dissolve in water. Most of their atoms are uncharged and/or nonpolar.
• The lipid bilayer is made up of amphipathic phospholipids. Hydrophilic heads face out towards the water, and hydrophobic tails cluster in the center. 


  The lipid bilayer spontaneously seals to form a closed compartment. A planar phospholipid bilayer with edges exposed to water is unfavorable, while a sealed compartment is energetically favorable.
• Aquaporin is a hole in the plasma membrane so water can go through.
• Receptors are molecules that span the plasma membrane that receive information and interact with signals from the outside.
• The formation of a lipid bilayer is driven by water, pushing hydrophobic molecules out of the way.
• In situ hybridization of the mRNA is done by testing gene expression. you must transcribe using a strand complementary to the mRNA. This strand can be either DNA or RNA. Use fluorescent precursors, using labeled RNA as probes.
• Cells adhere and stick to each other tightly thanks to cadherins. We can test it out by using plasmid vectors, where you add DNA inserts and then cut with restriction nuclease. Then, you insert this protein into cadherin deficient cells.
• Kinases transfer phosphates from ATP substrates, in a process called phosphorylation. Once phosphorylated, a protein can bind to DNA or another partner protein. The same applies to activator proteins.
• Enhancers control gene expression from a distance.
• Proteins can be covalently modified by binding to a lipid. This way, they can go to the membrane.
• Cells must be able to move, divide, differentiate for specialized tasks, communicate, and digest nutrients to make energy.
• Food molecules go through catabolic pathways, in which you lose heat and you take energy from food and turn this energy into an oxidized food molecule. This is an energetically favorable process.
• After catabolism, cells go through the anabolic pathway, where they take the oxidized food molecule and turn it into the molecule the body needs. This is an energetically unfavorable process. Ultimately, the energy we use comes from the sun.
• ATP is the key energy currency of the cell. It hydrolyzes and becomes ADP and Pi. This reaction is very exergonic and spontaneous.
• Reaction coupling occurs when a favorable reaction drives an unfavorable one by using up its products. Another alternative is using the energy from ATP hydrolysis.
• Activation barriers inhibit spontaneous reactions from proceeding. A way to overcome this is through heating, but this triggers a lot of side reactions, that's why it is better to use a catalyst.
• Phospholipids are a type of lipid composed of two fatty acids, a glycerol, and a phosphate.
• The terminal bond in ATP is most prone to breaking because of the repulsion between the negatively charged phosphate groups.
• While the plasma membrane does form a boundary, it allows the entry and exit of biomolecules, such as through transport proteins in the membrane. Phospholipids are amphipathic, as a result, the plasma membrane will spontaneously reseal holes to maintain these hydrophobic/hydrophilic interactions. Finally, the plasma membrane uses channels and transport proteins to regulate certain ions' movement, allowing a charge separation.
• Enzymes can bring reactant molecules together and hold them just in the right position for a chemical attack to occur and they are specific for only certain substrates because of protein structure.
• Proteins and substrates are held together by non-covalent interactions like Van der Waals, electrostatic interactions, and hydrogen bonds.
• Enzymes are typically organized as neighbors in a complex so that each can hand off its product to be the substrate for the next enzyme down the line.
• Alcohol Dehydrogenase (ADH) detoxifies ethanol by converting it to acetaldehyde, but it can also convert methanol to formaldehyde.
• Competitive inhibition is when the active site is occupied by a different enzyme that resembles the substrate. Allosteric inhibition changes the shape of the protein. Feedback inhibition regulates the flow through biosynthetic pathways.
• Allosteric enzymes have an active site that binds substrates, and a regulatory site that causes conformational changes.
• The Lysozyme reaction mechanism consists of

  1. 6 sugars bound together by Oxygens
  2. Asp52 attacks one of the carbons and breaks one of the C-O bonds
  3. Glu35 protonates the Oxygen from the C-O bond
  4. Attacked Carbon gets attacked by an OH, kicking out Asp52
• The Stages of Metabolism:

  Stage 1: Breakdown of large macromolecules into simple subunits.

  Proteins -> amino acids

  Polysaccharides -> simple sugars

  Fats -> fatty acids

  starch -> glucose

  Stage 2: Breakdown of simple subunits into acetyl-CoA; accompanied by the production of limited amounts of ATP and NADH.

  Stage 3: Complete oxidation of acetyl-CoA to H2O and CO2; accompanied by the production of large amounts of ATP in the mitochondrion.
• The stepwise oxidation of sugar in cells ensures that at least 50% of the heat released can be stored as energy. These smaller activation barriers are overcome by body temperature.
• ATP carries phosphates. NADH, NADPH, and FADH2 carry electrons and Hydrogens. Acetyl-CoA carries acetyl groups.
• Glycolysis: In the first step, you must invest 2 ATP molecules and 1 glucose molecule, and you end up getting fructose 1,6-biphosphate. Then, this 6-2Carbon sugar is cleaved to make two 3-carbon molecules, glyceraldehyde 3-phosphate. Finally, you generate energy by releasing 2 NADH, 4 ATP, and two pyruvate.
• In step 6 of Glycolysis, glyceraldehyde 3-phosphate binds to an SH group from cysteine. The enzyme also binds noncovalently to NAD+. The sulfur then initiates a proton transfer from glyceraldehyde to NAD+, forming a very strong thioester bond. An inorganic phosphate then comes in and kicks out the S group to form 1,3-biphosphoglycerate.
• In step 7 of glycolysis, the high-energy phosphate group is added to ADP to form ATP, completing a substrate-level phosphorylation.
• The net result from glycolysis is 6 ATP molecules (you invest 2 at the beginning), 2 NADH, and 2 pyruvate.
• If there is no oxygen after glycolysis (anaerobic conditions), fermentation, trying to maintain electron balance, produces lactic acid. You must regenerate NAD+ for glycolysis to continue, and so you require lactate dehydrogenase for that. Since that is not present in yeast, you can form either two CO2 molecules or two ethanol molecules. This process requires 11 enzymes.
• Glycolysis alone produces 2 ATP; complete oxidation from glucose to water and carbon dioxide produces 30 ATP.
• In the mitochondrion, the citric acid cycle (CAC), generates NADH by oxidizing acetyl groups to CO2. In air, pyruvate is oxidized to give acetyl-CoA. Pyruvate Dehydrogenase is a multi-protein enzyme complex that catalyzes acetyl-CoA formation.
• The Citric Acid Cycle occurs in the mitochondrial matrix and it accounts for about 2/3 of the total oxidation of carbon compounds. Major end-products are CO2 and high-energy electrons in NADH. It does not directly use O2, but O2 is required to regenerate NAD+ at the end of the electron transport chain.
• After the enzyme removes a proton from the CH3 group on acetyl CoA, the negatively charged CH2 forms a bond with a carbonyl from oxaloacetate. Hydrolysis then kicks out S-CoA, which drives the reaction forward and forms citrate.