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Biochem 301-Exam 1 ACTUAL EXAM WITH QUESTIONS AND
100% CORRECT VERIFIED ANSWERS/ Biochem 301-Exam
LATEST 2025-2026 (BRAND NEW!!)
Ionic bond direct interaction between positive and negative ions covalent bond A chemical bond that involves sharing a pair of electrons between atoms in a molecule Electronegativity measure of how strongly atoms attract bonding electrons to themselves molecular weight ratio of the average mass of one molecule of an element or compound to one twelfth of the mass of an atom of carbon-12 (remember that this is a dimensionless quantity) macromolecule a molecule that contains a very large number of atoms. Examples would be proteins, nucleic acids, and carbohydrates. polymer
a macromolecule assembled with covalent linkages between smaller repeating units (Proteins, from amino acids, polysaccharides from carbohydrates, nucleic acids from nucleotides) hydrophobic
- Insolubility in water. - Water would rather interact with itself than with non-polar compounds.
- tendency of hydrophobic molecules to sequester themselves from water
- nonpolar and unable to form H bonds hydrophillic
- preferably interacts (dissolves) with water.
- compounds will be polar and will be able to interact with water through either hydrogen bonds or through ion-dipole or dipole-dipole interactions.
- They will contain electronegative and electropositive atoms. proton donor acid proton acceptor base hydronium ion
- form ATP
- composed of a 5 carbon sugar, N containing ring, and 1+ phosphate groups lipids
- insoluble in water but soluble in ethanol and ether
- poorly soluble in water bc they often include hydrophobic chains ether Amine RNH2, R2NH, R3N thiol R-SH Ketone ESTER
Amide sulfhydryl group do Co2 and H2O molecules have the same 3D shape? No because of the distribution of lone pairs of electrons and the hybridization of carbon and oxygen meaning of electronegativity chemical property that describes the tendency for an atom to attract a pair of electrons towards itself how does EN affect the distribution of electrons in a covalent bond between O and H? O = more EN than H
- means that in an O-H bond the electrons will be biased toward oxygen
- leaves a partial negative charge on O and partial positive charge on H
- makes bond polar draw two molecules of water that are hydrogen bonded. Label covalent and hydrogen bonds
Delta G equation delta G = delta H - T * delta S what does H stand for H = enthalpy (bonding energy); measured in heat units (joule or calories) what does a negative delta H mean? heat is released > exothermic what does a positive delta H mean? heat is consumed > endothermic process what does S stand for? entropy (randomness)
- units: J/K Meaning of negative delta G reaction is energetically favorable (exergonic)
meaning of positive delta G non-spontaneous endergonic (energy-absorbing) meaning of delta G = 0 equilibrium delta G must be (blank) for a reaction to proceed spontaneously negative what else factors into if a reaction will actually proceed (besides having a negative delta G) depends on kinetics and whether there is a pathway by which the reaction might proceed Calculate pH for [H+] = 0.05 M ph = log10 (0.05) = - 1. Calculate pH for [H+] = 0.0001 M
What is the numerical value of "physiological" pH?
Why is the physiological pH nearly constant from cell to cell? because of the biological buffers (phosphate for example) that serve to maintain that pH. what plays an important role in the buffering? why are they necessary proteins; necessary to maintain the max oxygen transfer to hemoglobin
- essential to maintain activity for most of the reactions that occur Write out the equations for the dissociation (ionization) of carbonic acid and the dissociation of HCl. H2CO3 ⇌ H+ + HCO3- HCl ⇌ H+ + Cl- Write out the equation for the neutralization of stomach acid (HCl) by Alka-Seltzer. H2CO3 + HCl ⇌ H+ + HCO3- HCl + HCO3- ⇌ H2CO3 + Cl- ⇌ H2O + CO Aspirin is an acid with a pKA = 3.5 for its carboxyl group. For it to be absorbed into the bloodstream, aspirin must pass through the hydrophobic membrane lining of the stomach or the small intestine. Since only electrically neutral or uncharged molecules can pass through membranes, predict whether more
aspirin is absorbed in the stomach where the pH of gastric juice is 1 or in the small intestine where the pH is about 6.
- Absorbed in the stomach since at pH 1 the aspirin will be protonated and hence neutral. 0 In the small intestine aspirin would be mostly in the conjugate base (negatively charged) and hence would not be readily absorbed. isoleucine structure Classify as: hydrophilic, hydrophobic, - /+ charged at pH 7
- neutral
- hydrophobic Histadine Structure Classify as: hydrophilic, hydrophobic, - /+ charged at pH 7
- neutral
- hydrophilic tyrosine structure Classify as: hydrophilic, hydrophobic, - /+ charged at pH 7
- neutral
- hydrophobic aspartate structure
adopts a wide range of random conformations and does not exhibit biological activity or function metalloprotein
- a protein with a metal ion coordinated by the side chains of the protein
- metal ion is a cofactor hemoprotein or heme protein
- subclass of metalloproteins and implies the presence of an iron atom coordinated by a heme prosthetic group (ring)
- the protein typically interacts with both the ring and iron atom alpha helix structure
- secondary structural element that forms hydrogen bonds between carbonyl oxygens and amide hydrogens on residue that are four apart describe the alpha helix structure
- Helix is right handed - 3.6 residues per turn - Side chains project away from the filament axis
- can be a few residues long (must be >4) to a thousand amino acid residues. beta sheet structure
- Formed between adjacent strands that can run parallel or antiparallel
- Satisfies the need to form hydrogen bonds between the amide hydrogens and carbonyl oxygens on opposite side of strands. beta sheet structure characteristics
- orientation of the hydrogen bonds alternates as one goes along the strands in a sheet
- side chains point alternatively above and below the sheet - less than 10 residues long. monomer: what is it and where does it exist protein derived from a single polypeptide chain and exists in solution as a monomer oligomer: characteristics Consists of an assembly of multiple chains that can be identical or different (quaternary structure) apoprotein The same protein (as a conjugated) without the cofactor or prosthetic group. a lot less stable than the holoprotein conjugated protein
- Contains a prosthetic group or cofactor that are normally required for function.
- The complete protein is sometimes called the holoprotein or holoenzyme if the protein is an enzyme
True of False? Because of the double bond nature of the peptide bond, the polypeptide backbone is free to rotate at random, providing flexibility to the protein. False; NOT free to rotate, REDUCED flexibility True of False? It is necessary to break peptide bonds in order to denature a protein False; it is NOT necessary True of False? Hydrophobic amino acid residues are usually found on the outside surface inside of globular proteins that is exposed to water molecules. False; found on the INSIDE True of False? Upon cooking, the change in color from clear to solid white is the result of irreversible denaturation of proteins, including albumin, in egg white. True True of False?
Because hydrogen bonds are so weak, but they contribute little to the secondary or tertiary structure of polypeptides. False; they contribute critically to the 2/3 degree structure because there are so many True of False? Many proteins that have a structural or protective role for an organism are insoluble in water and have a fibrous shape. True Botulinus toxin is one of the most poisonous substances known. It is sometimes produced by the bacterium Clostridium botulinum when food is improperly canned and can be fatal when consumed. However, contaminated food can be detoxified by boiling for 20 minutes or more. From this information, is the toxin an inorganic compound, a protein, or a nucleic acid?
- toxin is a protein that has a 3D structure
- neither an inorganic compound or a nucleic acid would be inactivated by heat Explain the mechanism of toxin inactivation by boiling.
- occurs because the toxin unfolds when heated and does not refold into its active form when the food is cooled down Explain the unusual features of collagen including both its amino acid composition and three- dimensional structure.
- unusual repeating motif in its sequence Gly-Pro-Hyp
- allows the protein to adopt an extended conformation in which three chains can come together to form a parallel right handed triple helix
primary structure of Protein the amino acid sequence of the polypeptide chain secondary structure of Protein alpha helix and beta pleated sheet alpha helix A spiral shape constituting one form of the secondary structure of proteins, arising from a specific hydrogen-bonding structure. beta pleated sheet One form of the secondary structure of proteins in which the polypeptide chain folds back and forth, or where two regions of the chain lie parallel to each other and are held together by hydrogen bonds. Tertiary structure of protein Defined by the hydrophilic and hydrophobic interactions between R groups of amino acid chains. Forms larger 3D shape quaternary protein structure association between two or more polypeptide chains within one protein
Bohr effect a decrease in the amount of oxygen associated with hemoglobin and other respiratory compounds in response to a lowered blood pH resulting from an increased concentration of carbon dioxide in the blood. write out the equation for the formation of bicarbonate ion from the reaction between water and CO that is catalyzed by carbonic anhydrase CO2 +H2O ⇌ H2CO3 ⇌ H+ + HCO3- General features of the Bohr Effect: metabolizing tissue vs. lungs
- in actively metabolizing tissue, hemoglobin released O and binds both CO2 and H+
- in the lungs, hemoglobin released both CO2 and H+ and binds O write out the equation for the interaction of hemoglobin, H+, and CO HbO2 + H+ + CO2 ⇌ O2 + Hb(CO2)(H)
- metabolizing tissue going right (muscle)
- Alveoli of lungs going left explain the effect of H+ and CO2 on the binding of oxygen by hemoglobin
- the lower pH of actively metabolizing tissue reduces the oxygen affinity of hemoglobin for oxygen
- change in conformation allows hemoglobin to become protonated on a histidine and at the N-terminus that are not available in oxygenated form
