Principles of Biochemistry (BCHE 3200) Lecture Exam 1 Study Guide Answers to questions are located at the end!
1.)What is an amino acid’s structure?
2.)What are compounds made up of carbon, hydrogen, and oxygen? 3.)What is the simplest form of a carbohydrate?
4.)What is the most common monosaccharide?
5.)What is the basic unit of the hereditary materials RNA and DNA? 6.)What is the structure of a nucleotide?
7.) _____ are poorly soluble in water because they are composed of long chains of hydrocarbons (Example: Palmitic Acid).
8.) _____ _____ are groups of atoms that give rise to characteristic reactions of organic compounds.
9.)What is the energy currency of the cell that contains ester and anhydride linkages that involve phosphoric acid?
10.) _____ are small molecules that may bond to many others to form a polymer.
We also discuss several other topics like What is the relationship between attention and eye movements?
11.) What are the polymers of the following?
a. Amino Acids
d. Glycerol and 3 fatty acids
12.) How do amino acids build proteins?
13.) How are polysaccharides built? If you want to learn more check out What are the 3 main branches of cultural anthropology?
14.) How are Nucleic Acids built?
15.) The three previous polymerization reactions are accompanied by the elimination of ____.
16.) ___ are a class of proteins that display catalytic activity. 17.) What is catalytic activity?
18.) What is catalytic effectiveness dependent on?
19.) ___ has the ability to catalyze its own processing and is considered to have been the original coding material (And still serves this function in some viruses).
20.) What is the RNA-World Theory?
21.) What is the Double-Origin Theory?
22.) What are microorganisms that lack a distinct nucleus and membrane-enclosed organelles (Include bacteria and cyanobacteria)? 23.) What are organisms whose cells have a well-defined nucleus and membrane-enclosed organelles?
24.) What is mutualism?
25.) What is parasitic symbiosis?
26.) What is hereditary symbiosis?
27.) What is the study of transformations and transfer of energy?
28.) If the change in free energy is negative (Free energy decreases), the reaction is _____ (Ball rolling down hill analogy).
29.) If the change is positive (Free energy increases), the reaction will not occur unless ___ is supplied from an external source. 30.) What does ∆G < 0 mean? We also discuss several other topics like Why do we study chordate?
31.) What does ∆G > 0 mean?
32.) What is signified by ∆G = 0?
33.) If a reaction is energy-releasing, it is ____.
34.) If a reaction is energy absorbing, it is ____.
35.) What is enthalpy?
36.) What does this equation signify? ∆G=∆H-T∆S
1.) ____ is the measure of the force of an atom’s attraction for electrons it shares in a chemical bond with another atom.
2.)What two elements are more electronegative than carbon and hydrogen?
3.)What does it mean for a bond to be nonpolar?
4.)What are noncovalent associations based on weak attractions of transient dipoles for one another?
5.)What is an attraction between transient induced dipoles? 6.)What is the formula for the acid dissociation constant (Ka)? 7.) Great the Ka, the ____ the acid.
8.)When concentrations of a weak acid and its conjugate base are equal, the pH of the solution equals the pKa of the ___ acid Don't forget about the age old question of What is a conformational isomer in organic chemistry?
9.)The ___ ___ is a point in an acid-base titration at which enough base has been added to neutralize the acid.
1.)What are amino acids that have nonpolar side chains? 2.)What are amino acids that have polar side chains that are electrically neutral at neutral pH?
3.)These acids have carboxyl groups in their side chains in addition to the one present in all amino acids
4.)These amino acids have basic side chains.
5.)What is the formula for the isoelectric point?
1.)What is the order in which amino acids are covalently linked together? 2.)What is the ordered 3-D arrangement in space of the backbone atoms in a polypeptide chain?
3.)What is the 3-D arrangement of all atoms in a protein, including those in side chains and in prosthetic groups?
4.)What is the arrangement of subunits with respect to one another? 5.)What are two Ramachandran angles?
6.)What are the two types/arrangements of the secondary structure? 7.)What are some features of the α-helix arrangement? 8.)What cause bending of the polypeptide backbone in α-helix structures?
9.)What are some features of β-pleated sheets?
10.) What are the different bulges in β-pleated sheets? 11.) What are reverse turns?
12.) What are some supersecondary structures?
13.) Every third positions of a collagen triple helix must be occupied by ____. Don't forget about the age old question of What kind of communication always has a mediator between the sender and receiver?
We also discuss several other topics like What is the meaning of ology?
14.) Proteins in which the backbone folds on itself to produce a more or less spherical shape.
15.) Tertiary structures depend on ____ interactions. 16.) ____ consists of a single polypeptide chain of 153 amino acid residues and a prosthetic group, heme, in a hydrophobic pocket. 17.) ___ is an iron-containing cyclic compound.
18.) Heme carries ____ α-helical regions, which are stabilized by hydrogen bonding in the polypeptide backbone.
19.) What is the organic part of the heme group?
20.) What causes denaturation?
21.) Can native conformation be recovered by removing mercaptoethanol and urea?
22.) Hemoglobin is a tetramer with _ α-chains and _ β-chains. 23.) Hemoglobin can bind up to _ molecules of O2.
24.) _____ _____ means that when one O2 is bound, it becomes easier for the next O2 to bind.
25.) What is the function of myoglobin?
26.) What is the saturation of myoglobin?
27.) What is the function of hemoglobin?
28.) What is the saturation of hemoglobin?
29.) Are the structures of oxygenated and deoxygenated hemoglobin the same?
30.) What is the effect of H+ on hemoglobin conformation called? 31.) BPG (Biphosphoglycerate) plays a role in the supply of O2 to the _____ ____.
32.) What are liposomes?
33.) Hydrophobic interactions are ____ processes.
34.) What was the first chaperone protein to be discovered? 35.) What aid in the correct and timely folding of many proteins?
1.)In the plot of the energies for a spontaneous reaction, the transition state lies at the ____ of the curve connecting the reactants and products.
2.)The overall order of a reaction is the ___ _____ of all the exponents.
3.)What are the two enzyme-substrate binding models? 4.) Chymotrypsin catalyzes the hydrolysis of ___ bonds and ____ bonds 5.)T/F : Inhibitors can be reversible or non-reversible.
6.)Which inhibition method involved two distinct binding sites? 7.)What are the substrates used in irreversible inhibition known as?
1.)T/F : ATCase and hemoglobin exhibit cooperative effects caused by subtle changes in secondary structure.
2.) ____ ___ is the process by which the final product of a series of reactions inhibits the first reaction in the series.
3.)What makes up the organization of ATCase?
4.)Proposed in 1965 by Monod, Wyman, and Changeux, what model describes allosteric activity in which conformations of all subunits change simultaneously and that the protein has two conformations?
5.)This model has a unique feature known as negative cooperativity. Also states the binding of a substrates induces a conformational change from the T form to the R form.
6.)What is an inactive protein that can be activated by specific hydrolysis of peptide bonds?
7.)What is synthesized and stored in the pancreas?
8.)P-nitrophenyl acetate is hydrolyzed by chymotrypsin in ___ stage(s). 9.)What is a class of proteolytic enzymes in which a serine hydroxyl plays an essential role in catalysis?
10.) ____ __ and ___ __are required for activation of chymotrypsin. 11.) T/F : Rate of reaction in a SN2 reaction follows first-order kinetics.
12.) What is a transition-state analog?
13.) _____ are antibodies that are produced against a transition-state analog and that have catalytic activity similar to that of a naturally occurring enzyme.
14.) What are nonprotein substances that take part in enzymatic reactions and are regenerated at the end of the reaction? 15.) What are organic coenzymes?
16.) What coenzyme is made up of a nicotinamide ring, an adenine ring, and two sugar-phosphate groups?
17.) What is NAD+ reduced to?
18.) What are the B6 vitamins?
19.) T/F : Pyridoxal and pyridoxamine phosphates are involved in the transfer of amino groups in a reaction called transamination.
1.)What is a heterogenous class of naturally occurring organic compounds classified together on the basis of common solubility properties?
2.)What does it mean for something to be amphipathic in nature? 3.)What are the two classifications of lipids?
4.)What are unbranched chains of carboxylic acids that are derived from the hydrolysis of animal fats, vegetable oil, or phosphodiacylglycerols of biological membranes?
5.)T/F : Unsaturated fatty acids contain only single bonds. 6.)T/F: The cis isomer is rare in unsaturated fatty acids. 7.)What is the purpose of fatty acid notation?
8.)Lipids formed by the esterification of three fatty acids to ____. 9.) Ester linkages are hydrolyzed by ____ when fatty acids are used by organisms.
10.) What is phosphaditic acid?
11.) What are phosphatidyl esters classed as?
12.) These contain sphingosine, are found in plants and animals, and are abundant in the nervous system.
13.) What are the parent compounds for glycolipids? 14.) Lipids with a characteristic fused-ring structure (Three six membered rings and one five-membered ring); include sex hormones and cholesterol.
15.) The presence of what can enhance the order and rigidity of the biological membrane?
16.) T/F : Animal membranes are less fluid and more rigid than plant membranes.
17.) Membranes of ___ are the most fluid.
18.) What are the two types of membrane proteins? 19.) What is the Fluid-Mosaic Model?
20.) What are the two options of microscopy for those wanting to view membranes?
21.) What is the principal carrier of cholesterol in the bloodstream? Consists of various lipids and a protein.
22.) T/F : Lipid soluble vitamins are hydrophobic.
23.) What are the two forms of Vitamin A?
24.) What is the most abundant form of Vitamin D in the body? 25.) What does Vitamin D deficiency lead to?
26.) What is the most active form of Vitamin E?
27.) What is an antioxidant?
28.) What does Vitamin E trap?
29.) What plays an important role in the blood-clotting process? 30.) These are derived from fatty acids and are first detected in seminal fluid.
31.) What is the function of prostaglandins?
32.) What are compounds derived from arachidonic acid that are found in WBCs (Leukocytes)?
1.) Central carbon atom that is bonded to a carboxyl group, an amino group, a hydrogen, and a R group
6.)Five-carbon sugar, a nitrogen-containing ring, and one or more phosphate groups
9.) Adenosine Triphosphate (ATP)
11.) a.) Proteins b.) Nucleic Acids c.) Polysaccharides d.) Lipids 12.) They connect the carboxyl group of one amino acid with the amino group of the next amino acid; thus, they has a sense of “directionality”
13.) By linking the first carbon of one sugar with the fourth carbon of the next sugar (They also have “directionality”)
14.) The 3’-OH of the ribose ring of one nucleotide forms a bond to the 5’-OH of the ribose ring of a neighboring nucleotide 15.) Water
17.) Ability to increase the rate of a chemical reaction 18.) Amino Acid Sequence
19.) Ribonucleic Acid (RNA)
20.) Appearance of a form of RNA capable of coding for its own replication was the pivotal point in the origin of life
21.) Development of catalysis and the development of a coding system came about separately
24.) Relationship that benefits both species
25.) One species gains at the other’s expense
26.) Larger host cell contains a genetically determined number of smaller organisms
30.) Spontaneous exergonic
31.) Nonspontaneous endergonic
32.) Equilibrium (Not technically “possible”)
35.) Heat of a reaction at constant pressure
36.) First and Second Laws of Thermodynamics
2.) Oxygen (Most) and Nitrogen
3.)The two atoms share electrons evenly
4.) Van der Waals forces
5.)London Dispersion Force
9.) Equivalence point
4.) Quaternary Structure
5.)Phi and psi
6.)α-helix and β-pleated sheet
7.) Helical conformation, each peptide bond is s-trains and planar, C=O of each peptide bond is hydrogen bonded to the N-H of the fourth amino acid residue, all R groups point outwards from the helix 8.)Proline
9.)Zigzag structure, chains lie adjacent to one another (Parallel to antiparallel directionality), R groups alternate above and below the plane, each peptide bond is s-trans and planar
10.) Classic, G-1, and Wide
11.) Parts of proteins where the polypeptide chain folds back on itself that are caused because of spatial (Steric) reasons (Contain glycine).
12.) βαβ, αα, β-meander, Greek Key
19.) Protoporphyrin IX
20.) Heat, large changes in pH, detergents, urea and guanidine hydrochloride, and β-mercaptoethanol
22.) 2; 2
24.) Positive Cooperativity
25.) Oxygen storage
26.) 50% at 1 torr partial pressure of O2
27.) Oxygen transport
28.) 100% when O2 pressure is 100 torr
30.) Bohr Effect
31.) Growing fetus
32.) Spherical aggregates of lipids arranged so that the polar head groups are in contact with water and the nonpolar tails are separated from water.
35.) Protein-Folding Chaperones
3.)Lock-and-key and induced fit
4.) Ordered, random, and ping-pong
8.)Suicide or trojan horse substrates
1.)False (Quaternary structure)
3.) Catalytic subunit (Six protein subunits organized into two trimers) and regulatory subunit (Six protein subunits organized into three dimers).
10.) Serine 195; Histidine 57
12.) Synthesized compound that mimics the form of the transition state of an enzyme reaction
15.) Vitamins and their derivatives
18.) Pyridoxal, pyridoxamine, and pyridoxine and their phosphorylated forms
2.)The molecule has one end with a polar, water-soluble group and one end with a nonpolar, hydrocarbon group that is insoluble in water 3.) Open-chain and fused-ring
7.)It indicates the number of carbon atoms and the number of double bonds separated by a colon
10.) Compound in which two fatty acids and phosphoric acid as esterified to the three hydroxyl groups of glycerol
18.) Intergral and Peripheral
19.) Model in which proteins and a lipid bilayer exist side by side without covalent bonds between them.
20.) Electron and atomic force
21.) Low-Density Lipoprotein (LDL)
23.) Β-carotene and retinol
27.) Strong reducing agents, which are easily oxidized and thus prevent the oxidation of other substances.
28.) Free radicals
29.) Vitamin K
31.) Control blood pressure, smooth-muscle contraction, inflammation, and prevention of blood clot formation 32.) Leukotrienes