BIOL 4341 Exam 1 study guide Updated 2022-2023, Exams of Nursing

Download BIOL 4341 Exam 1 study guide Updated 2022-2023 and more Exams Nursing in PDF only on Docsity! BIOL4341 Exam 1 study guide What is a hypothesis and what is necessary for a scientific hypothesis? -A hypothesis is a proposed explanation for a phenomenon. For a scientific hypothesis it must be testable via the scientific method and be falsifiable. What is a model in biology and why is it useful? -Models are commonly visual representations of understanding of biological process, generally simplifications. They are useful to test hypothesis’ and make predictions that can be falsified. What do false positive and false negative mean? -false positives are when you get a positive result, but it isn’t true. A false negative result is when you think there is no difference, but, there is. What does it mean for an experiment to be blinded? -When the information about the experiment is not known by the participant or experimenter (double blind if both) to eliminate bias, after the study or experiment is finished. What is confirmation bias? -The tendency to interpret newly obtained evidence as a confirmation of your existing beliefs or theories. What is Occam’s razor? -Rule of thumb that urges us when faces with two hypotheses that explain the data equally well to choose the simpler. STRUCTURE (shape) dictates the FUNCTION of proteins What does the cell theory of life state? -All living organisms are composed of one or more cells, the cell is the most basic unit of life, all cells arise from pre-existing cells, energy flow occurs within cells, cells contain DNA, all cells have the same basic chemical composition but contain unique components. What are the major eukaryotic organelles and what do they do? And what is the cytosol? -Membrane-bound nucleus, membrane-bound organelles, nucleus, ER, compartmental segregation of energy-yielding and energy-consuming reactions helps cells maintain homeostasis and stay away from equilibrium. -Nucleus: where ribosome synthesis takes place, nuclear envelope contains nuclear pores to regulate the traffic of proteins and RNA between the nucleus and cytoplasm. Envelope attached to ER. -ER: Network of flattened sacs and tubules that extend throughout the cytoplasm. Rough ER is covered w ribosomes which are engaged in protein synthesis. Smooth ER is the site of a variety of biochemical processes such as lipid and carbohydrate synthesis, storage and transport. -Golgi: Series of flattened cup-shaped sacs. Where proteins and lipids that were made in the ER are further processed and exported to their final destination. -Mitochondria: site of cellular respiration, converting O2 and nutrients to ATP AKA Powerhouse of the cell. -Lysosomes: acidic organelles where waste is digested and recycled into simple molecules that are brought back to the cytoplasm. -Peroxisomes: help detoxify the cells, break down fatty acids, in some reactions H2O2 is produced and further transformed into H2O. -Cytosol: very crowded and highly viscous solution where many reactions take place, not held by organelles. What is the cytoskeleton? Is it static or dynamic? -provides cellular shape and division, intracellular organization, intracellular transport paths, cellular mobility and consists of microtubules, actin filaments, intermediate filaments. It is very dynamic. What are the four major classes of biomolecules? -proteins, carbohydrates, lipids, nucleic acids. What does a negative vs positive delta G tell us about a reaction? -If negative the reaction is spontaneous, if positive it is not. What does a catalyst do? -increases the rate of a chemical reaction and lower activation free energy but does not alter delta G. Enzymatic catalysis offer acceleration under mild conditions, high specificity and possible regulation. What is Le Chatelier’s principle? A+B <-> C+D Change in concentration can affect the equilibrium of a system. What does the RNA world hypothesis state? -RNA can act both as the information carrier and biocatalyst. What is the central dogma of biochemistry (or molecular biology)? -DNA->RNA->Protein How does biology increase the rate of chemical reactions? -evolution and natural selection, natural selection favors some mutations. Describe the major types of intramolecular interactions. H-bonding Van der Waals, ionic and dipole -H-Bonding: Water can be an H donor and acceptor, h-bonding is cooperative, bonding between neighboring molecules are weak relative to H-O covalent bonds. Up to 4 H-bonds per H2O molecule gives water high boiling point, high melting point, unusually large surface tension. They are important Which amino acids are special, and what makes them special? What are alpha helices and beta sheets? - 𝛼 helix: Helical backbone is held together by H-bonds between the amides of an n and n+4 amino acids, right-handed helix with 3.6 residues (5.4 Å) per turn, Peptide bonds are aligned roughly parallel with the helical axis, Side chains point out. Peptide bond has a strong dipole moment (C=O (carbonyl) negative and N−H (amide) positive). All peptide bonds in the helix have the same orientation. -𝗉 sheet: stabilized by hydrogen bonds between adjacent segments that may not be nearby. Multi 𝗉- strand interactions are called 𝗉-sheets, Sheets are held together by the H-bonding of amide & carbonyl groups of peptide bonds from opposite strands. Describe primary, secondary, tertiary, and quaternary structure of proteins. -Primary: amino acid residues, 2D. -Secondary: Alpha helix and Beta sheets, local spatial arrangement of the polypeptide backbone. -Tertiary: Polypeptide chain, overall 3D spatial arrangement of atoms in a protein. There are two major classes fibrous and globular (water or lipid soluble). Stabilized by numerous weak interactions between amino acid side chains. -Quaternary: formed by the assembly of individual polypeptides into a larger functional cluster. Structure is as follows: Protein: Monomer – single subunit Dimer – formed by 2 monomers homodimer – 2 monomers are same protein heterodimer – 2 monomers are different proteins Trimer 3, tetramer 4, pentamer 5, hexamer 6, etc What does a chaperone do? -Prevent Misfolding and Aggregation of Unfolded Peptides Be able to calculate the pI of an amino acid. - average of the α- NH3 and α-COOH pKa values. If the side chain has an ionizable group then all three pKa values must be considered. What is the specific activity of an enzyme and how do you calculate it? -Describes the purity of the protein of interest. -specific activity = enzyme units / (vol. in µl x (protein conc. in mg per ml / 1000)) Determine the net charge of an amino acid at a particular pH given the pK values. Net charge, pK,, and pH Net charge, pKa, and pH A pH = pKa + log ([COO] / [COOH]) tis 0 = 2.34 + log ([COO}] / [COOH]) ~ 0.005 / 1 = [COO] / [COOH] pHO pHe 1/200 = [COO-]/[COOH] Predominant charged species: 0 4 ® Glycine At pH 5.97 BH = pKa + log ([COO'] / [COOH]) 5.97= 2.34 + log ([COO] / [COOH]) 4,266 / 1= [COO] / [COOH] i pl= 5.57 Net charge, pK,, and pH Net charge, pKa, and pH + NH, | pk, GH th COOH pka2.34 Coo- coo- HO pHe pHa cooH /coo- ° A a NH3+ / NH2 a “4 0 predominantly net charge “a 0 4 2 ‘lycine Px, =9.60 7 ou pl=5.97, Protein Structural Determination Methods: X-Ray Crystallography Steps needed * purify the protein * crystallize the protein * collect diffraction data * calculate electron density * fit known amino acid residues into density Pros * no size limits + well established Cons * difficult for membrane proteins * cannot resolve (see) hydrogens Xray diffraction pattern _., Column Chromatography f i | yd E sobs Protein sample (robe phase) (~~ sold porous matrix (etationary phase) Porous support ([Recorder—|Detector| ° Venue A Facto) == (li Column chromatography allows separation of a mixture of proteins over a solid phase (porous matrix) using a liquid phase to mobilize the proteins. Proteins with a lower affinity for the solid phase will wash off first Proteins with higher affinity will retain on the column longer and wash off later  SDS PAGE Separates Proteins by * Molecular Weight > < é¢ = F * SDS — sodium dodecyl sulfate — a detergent aaa = ¥ ¢ ° 97,400 -| Hs nat-0—$-0—(etauChy 22 66,200 -| ms BS 8 1 , 15:000-—y oo a, Sodium dodecylsulfate ° 5 ° ee = (sos) oe 31,000 -|eumy * SDS micelles bind to proteins and facilitate unfolding. * SDS gives all proteins a uniformly negative charge. 21.500- | ae * The native shape of proteins does not matter. 14400- * The rate of movement will primarily depend on size: small proteins will move faster. fs Common technique done utilizing SDS-PAGE - Western Blot Western Blotting Procedure Asgp.3 Load and separateprotein 2. Electrophoretically transfer 3. Block the membrane les on SDS-PAGE fractionated proteins onto PVDF with neutral protein Sy membi (BSA or milk casein) See 1 8 —* — > MEMBRANE GEL ® 6. Incubate the blot with 5. Incubate the membrane 4. Incubate the membrane chemiluminescent HRP with HRP-labeled secondary with primary antibody body specificto primary specificto target protein substrate and expose WESTERN BLOT ‘Oa 43 8 a 2 45 6 -Mass spectrometry (modern method): MALDI MS and ESI MS can precisely identify the mass of a peptide, and thus the amino acid sequence, can also be used to determine posttranslational modifications. BIOL4341 Exam 2 Study Guide – Ch 5 & 6 (&6 supplement) See lecture note/videos for CH5 and CH6. This guide is only meant to supplement your studying. Some terms to know and understand: Ligand: Molecule that binds to a protein Binding site: A region in the protein where the ligand binds Active site: The part of the enzyme where the substrate binds Substrate: surface on which other chemical reactions are performed Enzyme: proteins that act as biological catalysts. Catalysts accelerate chemical reactions. Apoenzyme: The protein part of an enzyme Holoenzyme: complete, functional enzyme, which is catalytically active. Holoenzyme consists of an apoenzyme together with its cofactors. Allosteric: Binding of an effector molecule (e.g., ligand) to one site affects the binding properties of a different site on the same enzyme (complex). Can be positive (increase) or negative Be able to determine inhibition types and their effects on kinetics (competitive inhibitors, uncompetitive, mixed). • Inhibitor’s area compound that decreases an enzyme’s activity. • Irreversible Inhibitors (inactivators or suicide inhibitors) o React w enzyme o One Inhibitor molecule can permanently shut off one enzyme molecule. o Often powerful toxins but also may be used in drugs. • Reversible Inhibitors bind to and can dissociate from an enzyme o Often structural analogs of substrates or products o Used as drugs to slow down a specific enzyme • Reversible inhibitors can bind to: o The free enzyme and prevent the binding of the substrate o The enzyme-substrate complex and prevent the reaction • Competitive Inhibitors: Resembles Natural Substrate and Competes with it for Binding to the Active Site • Uncompetitive Inhibitor: Inhibitor only binds to ES complex o does not affect substrate binding o inhibits catalytic function o Decrease in Vmax; apparent decrease in KM, No change in KM/Vmax • Mixed Inhibition: Inhibitor binds enzyme with or without substrate o binds to regulatory site o inhibits both substrate binding and catalysis o Decrease in Vmax; apparent change +/- in KM Interpret double reciprocal plots to identify inhibition type. Determine how Km and Vmax are altered by michaelis menton inhibitors. What is Kcat? • the Number of Product Molecules Made by Each Enzyme Molecule Per Time. • It is Also Known as the Turnover Number or Kcat and Does Not Vary with the Amount of Enzyme What is a measure of enzyme efficiency and how does each parameter effect it? • kcat / KM o Diffusion from the active site limits some enzymes o Can gain efficiency by having high velocity or high affinity for substrate: catalase vs. acetylcholinesterase What are the major classes of enzymes (EC classifications?) • EC 1, Oxidoreductases: oxidation/reduction reaction catalysis • EC 2, Transferases: transfer a functiona l group (e.g. a methyl or phosphate group) o Titin holds in place • Firing of motor neuron results in Ca2+ release from sarcoplasmic reticulum (muscle ER) • High Ca2+ binds to troponin, causes conformational change and movement which moves tropomyosin • Myosin binding sites are exposed on actin and myosin can bind and contract Myoglobin & hemoglobin - what do they do: Myoglobin (storage) and hemoglobin (transport) can bind oxygen via a protein-bound heme. How are they regulated? Cooperativity = positive homotropic regulation • Binding of a an effector molecule (e.g., ligand) to one site (commonly not the active site) affects the binding properties of a different site on the same protein (complex) • can be positive (increase affinity) or negative • homotropic o The normal ligand of the protein is the allosteric regulator. • Heterotropic o A different ligand affects binding of the normal ligand. How does substrate binding affect? • positive cooperativity o first binding event increases affinity at remaining sites o recognized by sigmoidal binding curves ▪ (S shaped curve) as seem with Hg transition state affinity curve o negative cooperativity ▪ first binding event reduces affinity at remaining sites ▪ Are any diseases associated with these proteins? • S i c k l e - c e l l a n e m i a d u e t o m u t a ti o n i n h e m o g l o b i n How does oxygen bind to hemoglobin and how does it affect binding affinity? • O2 binding triggers a T -> R conformational change. • Conformational change from the T state to the R state involves breaking ion pairs between the α1-�2 subunit interface. How can enzymes be regulated? • Transcription and Translation (Synthesis) • Degradation • Post-translational modifications • Localization / Compartmentalization o e.g., Lysosomal enzymes • Substrate availability • Activators and inhibitors o e.g., Allosteric modulators, Feedback inhibition How does protein phosphorylation work? Identify glycosylic bonds. • Two sugar molecules can be joined via a glycosidic bond between an anomeric carbon and a hydroxyl carbon Describe the linkage of disaccharides (e.g., beta 1->4) • The disaccharide formed upon condensation of two glucose molecules via a 1 alpha 4 bond is described as α-d- glucopyranosyl-(1alpha4)- d- glucopyranose. • The common name for this disaccharide is maltose. Be able to identify a reducing disaccharide. Be able to identify the fisher projection of D-glucose • Chiral carbohydrates are usually represented by Fischer projections . • Horizontal bonds are pointing toward you; vertical bonds are projecting away from you Be familiar with common monosaccharides, disaccharides, and polysaccharides covered in class and their functions. How can sugars be attached to other macromolecules what are these molecules important for? • Because sugars contain many hydroxyl groups, glycosidic bonds can join one monosaccharide to another. Oligosaccharides are built by the linkage of two or more monosaccharides by O-glycosidic bonds How does agarose gel electrophoresis work? What are the distinctions between different human blood groups that were covered in class? What is the extracellular matrix? • Material outside the cell • Strength, elasticity, and physical barrier in tissues • Main components: o proteoglycan aggregates o collagen fibers o elastin (a fibrous protein) • ECM is a barrier for tumor cells seeking to invade new tissues. o Some tumor cells secrete heparinase that degrades ECM What are the major types of lipids and ways to classify lipids? Be able to identify core components of lipids (head, backbone, tails). • Lipids that contain fatty acids (complex lipids) o subcategories: storage or membrane o Membrane lipids: Phospho-, Sphingo-, Glyco- • Lipids that do not contain fatty acids: o cholesterol, vitamins, pigments, etc. • Organic molecule head (polar and hydrophilic), phosphate backbone and fatty acid tails(hydrophobic) Be familiar with fatty acid delta and omega naming systems (e.g., 16:1 delta9). • delta numbering of carbon skeleton: 18:1Δ9 describes relative to the carbonyl carbon the first carbon of the alkene • omega numbering of carbon skeleton: 18:1ω9 describes location of the first • Play vital roles as signaling molecules between nearby cells What structures can lipids form in aqueous solutions? • Bilayers, vesicles and liposomes What function to membranes serve? • Compartmentalization (1) • separate energy-producing reactions from energy-consuming ones • keep proteolytic enzymes away from important cellular proteins • Scaffold (2) • Selectively permeable barrier (3) • Transport of solutes (4) • Response to external signals (5) • Intercellular interaction (6) • Energy transduction (7) • Store energy as a proton gradient • Support synthesis of ATP How can the composition of membranes vary across different leaflets, organelles, and species? Describe the major types of membrane proteins. • All membranes examined closely (plasma, nuclear or cytoplasmic) from plants, animals or microorganisms have the same ultrastructure Be able to determine what a hydropathy plot can tell you about a protein. How can lipids move in membranes? • Lipids move laterally • Hydrophobic is above 0 and hydrophilic is below 0 What is a lipid raft? • The plasma membranes of cells contain combinations of glycosphingolipids, cholesterol and protein receptors organized in glycolipoprotein lipid microdomains termed lipid rafts. Why do membranes fuse? What proteins can facilitate membrane fusion? Describe the types of membrane transporters. To seal openings What characteristics are important for determining whether a molecule will cross a membrane?