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AU / Biochemistry / BCHE 3200 / What is an amino acid’s structure?

What is an amino acid’s structure?

What is an amino acid’s structure?


School: Auburn University
Department: Biochemistry
Course: Principles of Biochemistry
Professor: Werner bergen
Term: Spring 2018
Cost: 50
Name: BCHE 3200 Lecture Exam 1 Study Guide
Description: These are questions derived from the lecture and textbook material.
Uploaded: 02/16/2018
11 Pages 82 Views 3 Unlocks

Principles of Biochemistry (BCHE 3200) Lecture Exam 1 Study Guide Answers to questions are located at the end!

What is an amino acid’s structure?

Chapter 1

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.

What is the simplest form of a carbohydrate?

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

b. Nucleotides

c. Monosaccharides

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).

What is the most common monosaccharide?

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

Chapter 2

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.

Chapter 3

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?

Chapter 4

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?

Chapter 6

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?

Chapter 7

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.

Chapter 8

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)?


Chapter 1

1.) Central carbon atom that is bonded to a carboxyl group, an amino  group, a hydrogen, and a R group

2.) Carbohydrates


4.) Glucose

5.) Nucleotide

6.)Five-carbon sugar, a nitrogen-containing ring, and one or more  phosphate groups


8.)Functional Groups

9.) Adenosine Triphosphate (ATP)

10.) Monomers

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

16.) Enzymes

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

22.) Prokaryotes

23.) Eukaryotes

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

27.) Thermodynamics

28.) Spontaneous

29.) Energy

30.) Spontaneous exergonic

31.) Nonspontaneous endergonic

32.) Equilibrium (Not technically “possible”)

33.) Exergonic

34.) Endergonic

35.) Heat of a reaction at constant pressure

36.) First and Second Laws of Thermodynamics

Chapter 2

1.) Electronegativity

2.) Oxygen (Most) and Nitrogen

3.)The two atoms share electrons evenly

4.) Van der Waals forces

5.)London Dispersion Force

6.) Ka=[H+][A-]÷[HA]



9.) Equivalence point

Chapter 3

1.) Nonpolar


3.) Acidic

4.) Basic

5.) pI=pKa1+pKa2÷2

Chapter 4

1.)Primary Structure

2.)Secondary Structure

3.)Tertiary Structure

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

13.) Glycine

14.) Globular

15.) Noncovalent

16.) Myoglobin

17.) Heme

18.) Eight

19.) Protoporphyrin IX  

20.) Heat, large changes in pH, detergents, urea and guanidine  hydrochloride, and β-mercaptoethanol

21.) Yes

22.) 2; 2

23.) 4

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

29.) No

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.

33.) Spontaneous

34.) hsp70

35.) Protein-Folding Chaperones

Chapter 6


2.)Sum total

3.)Lock-and-key and induced fit

4.) Ordered, random, and ping-pong

5.)Peptide; ester


7.) Noncompetitive

8.)Suicide or trojan horse substrates

Chapter 7

1.)False (Quaternary structure)

2.)Feedback Inhibition

3.) Catalytic subunit (Six protein subunits organized into two trimers)  and regulatory subunit (Six protein subunits organized into three  dimers).

4.) Concerted



7.) Chymotrypsinogen

8.) 2

9.)Serine protease

10.) Serine 195; Histidine 57

11.) False

12.) Synthesized compound that mimics the form of the transition  state of an enzyme reaction

13.) Abzymes

14.) Coenzymes

15.) Vitamins and their derivatives

16.) NAD+ 

17.) NADH

18.) Pyridoxal, pyridoxamine, and pyridoxine and their  phosphorylated forms

19.) True

Chapter 8


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

4.)Fatty acids



7.)It indicates the number of carbon atoms and the number of double  bonds separated by a colon

8.) Glycerol


10.) Compound in which two fatty acids and phosphoric acid as  esterified to the three hydroxyl groups of glycerol

11.) Phosphoacylglycerols

12.) Sphingolipids

13.) Ceramides

14.) Steroids

15.) Cholesterol

16.) True

17.) Prokaryotes

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)

22.) True

23.) Β-carotene and retinol

24.) D3

25.) Rickets

26.) α-tocopherol

27.) Strong reducing agents, which are easily oxidized and thus  prevent the oxidation of other substances.

28.) Free radicals

29.) Vitamin K

30.) Prostaglandins

31.) Control blood pressure, smooth-muscle contraction,  inflammation, and prevention of blood clot formation 32.) Leukotrienes

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