Flashcards in Final Exam Discussion Questions Deck (20):
Describe the four types of weak interactions and their contributions to protein folding and 3D structure
Hydrogen bonds - hydrogen bound to an electronegative atom, hydrogen bonds exist between carbonyl backbone and amine group
Van der Waals - transient dipole due to optimal distance
Electrostatic - opposite charges attract according to Coulomb's law
Hydrophobic effect - non polar molecules are driven together in an apparent attraction to minimize interactions with polar molecules and to exclude water in aqueous solutions
Individually these interactions are weak, but collectively they are strong. Responsible for creating proteins tertiary structure by interaction with amino acid residues and water within a single chain. 3D protein structure maintained by non polar covalent interactions of the peptide backbone
Describe the four levels of protein structure and use hemoglobin as an example
Primary - chain of amino acids held together by covalent bonds in peptide backbone; Hemoglobin has a heme attached to the polypeptide chain for oxygen binding.
Secondary - alpha helices and beta sheets, 3D structures maintained by noncovalent interactions of the peptide backbone. Hemoglobin has 8 alpha helices in each globin.
Tertiary - 3D fold of the protein formed by weak interactions (disulfide bonds), the heme helps twist the globes into shape by connecting to histidine residues on them.
Quaternary - interactions between multiple protein chains. In hemoglobin, two identical alpha chains and 2 identical beta chains.
Describe 3 types of chromatography and how they could be used to purify a target protein from a complex mixture of proteins
Size Exclusion - separates proteins by native size. Small proteins enter a column filled with porous beads and large molecules exit last.
Ion-Exchange - separates proteins by charg. Proteins with the same charge exit the column quickly, but proteins with opposite charge bind and travel slowly.
Affinity Chromatography - separates proteins that bind a specific molecule. Only allows proteins with affinity for the attached group to remain.
Compare and contrast the three types of membrane transport proteins
Secondary transporters - moves a molecule up or down a concentration gradient, must move 2 molecules across a membrane
Pumps - uses ATP hydrolysis to move a molecule up a concentration gradient, may move two molecules at a time
Channel - moves only one molecule down a concentration gradient
Compare and contrast the kinetics (as a function of substrate concentration) of a Michaelis-Menten enzyme and an allosteric enzyme. Include in your description the physical basis of each
Michaelis-Menten - hyperbolic curve for Vo vs. [SS], can have quaternary structure, one active site
Allosteric - sigmoidal curve for Vo vs. [SS], must have quaternary structure, multiple active sites
Both - have tertiary structures and lower the activation energy
What are the three principal ways metabolic processes are regulated? Give one detailed example of each of these from the metabolic pathways we discussed this semester.
Amount of enzymes - glycogen degradation vs. synthesis???
Enzyme activity - PK regulation in the liver: low blood glucose leads to phosphorylated PK and diminished activity, high blood glucose leads to dephosphorylated PK and a more active form
Access of Substrates - Fatty Acid Synthesis vs. Degradation: If acetyl CoA is available then it will be activated by acetyl-CoA carboxylase to form malonyl CoA and synthesize fatty acids. For degradation, carnitine or citrate must be available.
Compare and Contrast the citric acid cycle and the glyoxylate cycle
Both - occurs in plants, uses acetyl CoA as a substrate and citrate as an intermediate, uses oxaloacetate as an intermediate, forms amino acids from carbohydrates
CAC - occurs in animals
Glyoxylate - nets an extra molecule of succinate, allows cells to make carbs from fats
Describe the pathway of free glucose in the bloodstream through its complete oxidation to CO2 and water during cellular respiration, include relevant signaling molecules, metabolic pathways, key intermediates and locations of all metabolic steps.
Insulin shows that glucose is present, and a transporter brings it into the cell. Glucose is converted into pyruvate by glycolysis in the cellular membrane. Pyruvate is then turned into acetyl CoA by the PDH (activated by phosphatase, ADP, and pyruvate) and enters into the CAC (mitochondrial matrix) to release more CO2. After leaving the CAC, the NADH and FADH2 generated by the CAC now enter the ETC (inner mito membrane). The electrons pass through complexes 1-4 and the Q pool to generate CO2 and water.
During the semester, several diseases were discussed. Briefly describe the molecular basis of a disease example for each of the following.
a. A disease that is the direct result of a defect in protein structure or enzymatic activity
b. A disease resulting from a nutritional defect or toxin
c. A disease that is the result of a misregulation of enzyme activity
a. Sickle Cell Anemia - Sickle cell is the result of a hemoglobin mutation because of the substitution of valine for glutamine in position 6 of the beta chain. The valine is exposed in deoxyhemoglobin and interacts with other decoy HbS to aggregate and form mutated RBCs.
b. Scurvy - The molecular basis of scurvy is a lack of vitamin C. Vitamin C is needed for the enzyme hydroxyl prolate to convert proline into hydroxyproline, which is important for the stabilization of collagen.
c. Lactic Acidosis - Lactic acidosis is the buildup of lactate and acidic conditions that can damage tissues. Decreased phosphatase activity or enhanced kinase activity results in diminished PDH activity. The pyruvate is shuttled into the fermentation pathway instead of to acetyl-CoA.
Compare and contrast the reciprocal regulation strategies of glycolysis/gluconeogenesis vs. glycogen degradation/synthesis
Comparison - one thing controls opposing pathways
Glycolysis/Gluconeogenesis - F26BP is controlled by the bifunctional enzyme. Low blood glucose phosphorylates the enzyme, lowers the [F26BP], and stimulates gluconeogenesis. High blood glucose dephosphorylates the enzyme, increases the [F26BP], and stimulates glycolysis.
Glycogen Degradation/Synthesis - Phosphorylation of key enzymes in response to hormones stimulates degradation, and dephosphorylating stimulates synthesis. Glucagon causes glycogen degradation stimulation via kinases. Insulin causes glycogen synthesis stimulation via phosphatases
Describe the three stages of the carbon fixation reactions
1. Fixation of CO2 by ribulose 1,5-biphosphate (RuBP) to form 2 molecules of 3-phosphoglycerate through Rubisco
2. The reduction of 3-phosphoglycerate to hexose sugars: uses ATP and NADPH synthesized during the light reactions, very similar to the gluconeogenesis pathway.
3. The regeneration of ribulose 1,5-biphosphate
Compare and contrast the storage forms of fats and carbohydrates with respect to overall structure and fuel efficiency
Both - yield ATP
Fats - stored in triglycerols (glycerol backbone with three fatty acid chains), hydrophobic which causes them to be more space efficient, yield more ATP
Carbohydrates - stored in glycogen (alpha 1,4) linkages, made of glucose with OH groups so hydrophilic
Describe the molecular basis of ketosis experienced by diabetics
Ketosis occurs as a result of too much formation of ketone bodies. In diabetics, insulin function is impaired which prevents glucose uptake by the liver and adipose tissue. The liver degrades the fatty acids by beta-oxidation, but it cannot process the acetyl CoA because of a lack of glucose derived oxaloacetate. Excess ketone bodies are formed and released into the blood. Drop in pH = death
Describe the molecular details of acetyl-CoA carboxylase regulation with respect to hormonal signals
Carboxylase is inhibited when phosphorylated by AMP-dependent kinase (AMPK). Inhibition due to phosphorylation is reversed by protein phosphatase 2A. Insulin activates acetyl-CoA carboxylase, whereas glucagon and epinephrine inactivate acetyl-CoA carboxylase
Describe the molecular structure of DNA in all organisms. Contrast the differences in DNA structure between prokaryotes and eukaryotes.
All organisms - pyrimidine-purine base pairing, antiparallel strands, hydrogen bonds hold base pairs together, phosphodiester covalent bonds holding strands together, major and minor grooves
Prokaryotes - circular, supercoiled DNA
Eukaryotes - linear DNA organized into chromatic
Describe the mechanism by which DNA-binding proteins recognize specific DNA sequences
Specificity of replication is determined by correct H bonding between dNTP and DNA template and by the shape of the incoming base. dNTP binding makes a structural change that forms a pocket into which only the matching nucleotide fits. Helix has major and minor grooves for hydrogen bonding for AT or GC. Hydrogen bonding allows for sequence-specific interactions between DNA and the molecules it must interact with in the processes of replication and transcription.
Compare and Contrast DNA replication in prokaryotes and eukaryotes
Both - requires a template, primer, Mg, and helices; has a leading and lagging strand, requires multiple polymerases, has a ligase to seal backbone
Prokaryotes - uses telomerase, single origin of replication, occurs in the cytoplasm
Eukaryotes - multiple origins of replication, occurs in the nucleus
Describe how transcription is controlled in prokaryotes and eukaryotes
Prokaryotes - lac operon: responsible for lactose metabolism and should only be transcribed when lactose is present, the repressor binds to the operator site and prevents transcription; CAP protein; 1 polymerase
Eukaryotes - hormone acceptor, coactivators, remodeling, 3 polymerases
Compare and contrast protein biosynthesis in prokaryotes vs. eukaryotes
Both - have ribosomes, have mRNA, APE sites
Prokaryotes - initiation by fMet, 2 release factors
Eukaryotes - larger ribosome size, processes mRNA, initiation by methionine, 1 release factor