Ch.5 - Biological MoleculesSee all chapters
All Chapters
Ch.1 - Introduction to Biology
Ch.2 - Chemistry
Ch.3 - Water
Ch.4 - Carbon
Ch.5 - Biological Molecules
Ch.6 - Cells
Ch.7 - The Membrane
Ch.8 - Energy and Metabolism
Ch.9 - Respiration
Ch.10 - Photosynthesis
Ch.11 - Cell Signaling
Ch.12 - Cell Division
Ch.13 - Meiosis
Ch.14 - Mendelian Genetics
Ch.15 - Chromosomal Theory of Inheritance
Ch.16 - DNA Synthesis
Ch.17 - Gene Expression
Ch.18 - Regulation of Expression
Ch.19 - Viruses
Ch.20 - Biotechnology
Ch.21 - Genomics
Ch.22 - Development
Ch.23 - Evolution by Natural Selection
Ch.24 - Evolution of Populations
Ch.25 - Speciation
Ch.26 - History of Life on Earth
Ch.27 - Phylogeny
Ch.28 - Prokaryotes
Ch.29 - Protists
Ch.30 - Plants
Ch.31 - Fungi
Ch.32 - Overview of Animals
Ch.33 - Invertebrates
Ch.34 - Vertebrates
Ch.35 - Plant Anatomy
Ch.36 - Vascular Plant Transport
Ch.37 - Soil
Ch.38 - Plant Reproduction
Ch.39 - Plant Sensation and Response
Ch.40 - Animal Form and Function
Ch.41 - Digestive System
Ch.42 - Circulatory System
Ch.43 - Immune System
Ch.44 - Osmoregulation and Excretion
Ch.45 - Endocrine System
Ch.46 - Animal Reproduction
Ch.47 - Nervous System
Ch.48 - Sensory Systems
Ch.49 - Muscle Systems
Ch.50 - Ecology
Ch.51 - Animal Behavior
Ch.52 - Population Ecology
Ch.53 - Community Ecology
Ch.54 - Ecosystems
Ch.55 - Conservation Biology
Nucleic Acids
Additional Practice
Cumulative Macromolecules

Concept #2: Primary and Secondary Structure

Concept #3: Tertiary and Quaternary Structure

Practice: Which of the following is not a function of proteins:

Practice: The bond that holds amino acids together is called a __________________________ bond.

Practice: Secondary structure results from:

Practice: All proteins have quaternary structure.

Practice: Proteins which lose their proper folded shape are ___________________________.

Additional Problems
A major limitation of the ribbon model of a protein is: a. It's hard to see how the backbone folds.b. It can't show the orientation of key side chains.c. It gives a false sense of open space in the protein.d. Both (a) and (c).e. (a), (b), and (c).
Relatively small organic molecules with a central carbon atom which is bonded to a carboxyl group, an amino group, a carbon containing group, and a hydrogen atom are called a. amino acids b. fatty acids c. enzymes d. peptides e. nucleotides
Functional groups found in amino acids include all of the following except a. -NH2 b. phosphate c. -COOH d. -OH e. alkyl (linked multiple carbons with hydrogens)
The specific amino acid sequence in a protein is its a. zero order structure b. primary structure c. secondary structure d. tertiary structure e. quaternary structure
Alpha helix and beta pleated sheets are examples of which level of protein structure? a. zero order b. primary c. secondary d. tertiary e. quaternary
Denaturation, a process in which a protein loses its native shape and function, is likely to be caused by all of the following except a. being transported from one cell to another in a living organism b. pH change c. temperature change d. ionic concentration change e. increase in hydrogen ion concentration
The primary building block (monomer) of proteins is:  a. A glucose molecule b. A fatty acid c. A nucleotide d. An amino acid e. Four interconnected rings
An amino acid contains:  a. Nitrogen b. Nitrogen and carbon c. Carbon d. Phosphorous e. Carbon and phosphorous
How are the monomers in proteins joined?  a. Phosphodiester bonds between amino acids b. Peptide bonds between amino acids c. Peptide bonds between nucleotides d. Phosphodiester bonds between nucleotides e. Peptide bonds between carbohydrates
If a protein is denatured, its structure has been changed enough to make the protein nonfunctional.  a. True b. False
Which of the following pertains to protein: a. CHON b. CH c. CHO d. CHONP e. None of these
There are 20 different amino acids in the proteins that make up living cells. The primary difference in the amino acids is in their: a. R groups b. number of R groups c. phosphate groups d. sequence of R groups e. more than one of the choices is correct
The shape of a folded protein is determined by: a. tertiary structure b. the sequence of amino acids c. whether peptide bonds have α or β glycosidic linkages d. the base pairing rules e. none of the choices is correct
Describe the secondary and tertiary structure of proteins.
A single 14-amino acid peptide chain is to be assigned from the following experimental information below. Your job is to provide the full triple letter code sequence (if possible), calculate its isoelectric point and show your logic behind your answer.Experimental information:(i) Amino acid analysis: Cx5, Dx1, Rx3, Nx1, Mx1, Wx1, Yx1, and Sx1(ii) Dinitrofluorobenzene (FDNB) analysis indicated the presence of C on reaction of the native peptide.(iii) Trypsin Digestion of the intact peptide produced 4 peptide fragments that were then exposed to Edman degradation analysis, they provided the following sequence information:Fragment 1: CYSRFragment 2: CCFragment 3: DWMRFragment 4: CNCR(iv) Cyanogen bromide digestion of the original intact peptide provided 2 peptide fragments, one 6 mer + homoserine lactone and one 7mer.(v) The resulting 7mer was HPLC isolated and subjected to Pepsin digestion followed by amino acid analysis. The Pepsin digested peptide fragments A and B, were assigned the following amino acid composition:Fragment A: S, Y, C, R       Fragment B: C and R
A single, 18-amino acid peptide chain is to be assigned from the following experimental information below, your job is to provide the full triple lettercode sequence (if possible) and show your logic behind your answer.(i) Amino acid analysis of the native peptide: Cx6, Rx2, Ex1, Yx1, Px1, Vx1, Ax1, Mx1, Wx1, Lx1, Kx1, and Tx1.(ii) Dinitrofluorobenzene (FDNB) analysis indicated the presence of C on reaction of the native peptide.(iii) The native peptide is subjected to DTT and Pepsin Digestion of the native peptide produced 4 peptide fragments that were then exposed to Edman degradation analysis, they provided the following sequence information:Fragment 1: YVPRMAC          Fragment 2: CC          Fragment 3: LCKETC          Fragment 4: WRC(iv) Following disulfide bond reduction, Cyanogen Bromide digestion of the original intact peptide provided 2 peptide, one 6mer + homoserine lactone and one 11mer.(v) The resultin 11mer was HPLC isolated and exposed to TCEP, this peptide was subjected to Trypsin digestion followed by amino acid analysis. The Trypsin digested peptide fragments: A, B, andC, were assigned the following amino acid composition:Fragment A: Cx2, Lx1, Kx1          Fragment B: Tx1, Ex1, Cx1          Fragment C: Cx1, Wx1, Ax1, Rx1
Match each definition and example to the level of protein structure.
If two proteins are said to be homologous, a) What does this mean?
Which of the followingsequences can form beta-sheet (beta-strand) structure?A. (Ala-Ser-Ala-Gly-Asn-Glu)B. (Ala-Tyr-Ala-Thr-Ser-Val)C. (Ala-Pro-Gly-Pro-Lys)D. all of the aboveE. only A and B
A newly isolated protein was found to contain 0.873% phenylalanine by weight upon amino acid analysis.a. What is the minimum molecular weight for the protein (assuming only one Phe residue per protein molecule)?b. Gel filtration of the protein gave an estimated molecular weight of 7.0 x 104 g/mol. How many Phe residues are in the protein? (Enter a whole number)
Which one of the tripeptides below:A. is most negatively charged at pH 7?B. contains sulfur?C. will have the greatest light absorbance at 280nm?D. contains the largest number of nonpolar R groups?
Amino acid analysis of an oligopeptide seven residures long gave the following amino acids:Asp  Leu  Lys  Met  Phe  TyrThe following facts were observed:a. Trypsin treatment had no apparent effect.b. The phenylthiohydantoin (PTH) derivative by Edman degradation was: (See th figure below)c. Chymotrypsin treatment resulted in 3 fragments, including a dipeptide and tetrapeptide. The tetrapeptide contained the amino acids Asp, Leu, Met, and Lys (in that order).d. Cyanogen bromide treatment yielded a dipeptide, tetrapeptide, and free Lys.What is the amino acid peptide sequence for this heptapeptide? Label N and C termini.
You are given a solution of "protein X". Protein X consists of 250 amino acid residues: 38% are valine, 24% are alanine, 20% are glycine, and 18% are isoleucine. What is the molecular weight of protein X? Describe how you determined this answer.
In the figure below, two amino acids are isomers of one another and they are:A. A and BB. B and CC. C and DD. B and D
The peptide KANYE has an N-terminal ________ residue and a C-terminal ________ residue.A. Glutamic Acid, LysineB. Glutamine, LysineC. Lysine, Glutamic AcidD. Serine, LysineE. Asparagine, Glutamic Acid
Given the following equilibrium, at what pH would the molecule most likely be in a zwitterionic form?H3N+-CH2-COOH ⇌ H3N+-CH2-COO- ⇌ H2N-CH2-COO-                          pKa1: 2.4                     pKa2: 9.6A. 1.2B. 2.4C. 6.7D. 10.5E. 13.7
If the environmental conditions interfere with the hydrogen bonding within a protein, what may happen? Mark all answers that apply. A. The shape of the protein may changeB. The secondary structure of the protein may be affected.C. The protein may not function the same (could be better or worse)D. The peptide bonds will break, affecting the primary structureE. The protein may become denatured.F. Changes in hydrogen bonds will not affect protein shape or functioning.
Match the amino acid on the left with the fact on the right.
Concerning the collagen triple helix:A. It is composed of three separate α-helices that coil around each other.B. The triple helix is stabilized by ionic bonds that occur between different strands of the helix.C. proline residues in a single strand keep the strand in a rigid conformationD. All of the aboveE. none of the above
In a random (amino acid sequence) polypeptide chain, rotation is severely restricted about the following bonds:A. Bond from backbone α-C to α-NH2 or to α-COOH groupsB. Peptide bondC. Backbone α-C to theside chain carbonsD. Terminal α-NH2 to α-COOH groupsE. None of the above
The toxin associated with the foodborne disease botulism is a protein. To avoid botulism, home canners are advised to heat preserved foods to boiling for at least 12 minutes. What doe the heat do?/ How does it help?
An α helix would be destabilized most by:A. interactions between neighboring Asp and Arg residuesB. the presence of an Arg residue near the carboxyl  terminus of the α helixC. the presence of two Lys residues near the amino terminus of the α helix
In which macromolecule would you find one of these amide bonds? Give its special name.
What is a lectin? Pick one lectin and describe its function.
As the temperature around an enzyme rises, what happens? Mark all correct answers.A. the reaction rate can get faster.B. the enzyme can bind more than one reactant at once.C. the hydrogen bonds in an enzyme can break.D. the protein can change shape.E. the protein can denature.F. temperature has no effect on enzymes.
Explain the different mechanisms that regulate protein function. 
Researchers have isolated a previously unstudied protein, identified its complete structure in detail, and determined that it catalyzes the breakdown of a large substrate. The protein has two binding sites: one of these is large, apparently the binding site for the large substrate; the other is small, possibly a binding site for a regulatory molecule.Which of the following inferences is most consisten with the data?A. It is an enzyme that is regulated through allosteric inhibition.B. It is a transport protein that allows molecules to cross the plasma membrane.C. It is an enzyme that is regulated through competitive inhibition.D. It is a structural protein that is involved in cell-to-cell adhesion.
Proteins are polymers made up of monomers called amino acids. How many different amino typically combine to form proteins?
Describe what makes up the primary structure of a protein. What part(s) of a protein/amino acid determine the next levels of structure (secondary structure, tertiary structure, etc.)?
List and define 3 major roles of proteins in the body.
At equilibrium, the ratio of trans to cis isomers for the X-Pro peptide bond is about 1:1, whereas the ratio is 1000:1 in favor of the trans isomer for the ordinary peptide bonds. How do you account for unusual stability of a cis X-Pro?
What is the charge of the tetrapeptide Lys-Lys-His-Glu at pH 7?A. +2B. 0C. -2D. +1E. -1
Which of the following best describes the side chains of the nonpolar amino acids (glycine is not included)?A. They are organic bases with a positive charge.B. They are organic bases with a negative charge.C. They are primarily neutral hydrocarbon structures.D. They are ring structures.E. They contain hydroxyl, carboxyl, or sulphydryl groups.
Consider a β−sheet consisting of 6 β−strands connected through β−turns. How many β−turns are required?
Describe the four levels of protein structure. Distinguish between the following pairs: pyrimidine and purine, ribose and deoxyribose, the 5' end and 3' end of a nucleotide.
List and define the four levels of structure in a functional protein.
What kinds of interactions lead to the secondary and tertiary structures of proteins? What types of interactions must be disrupted to fully denature a protein, and how can this be done?
A newly isolated protein was found to contain 0.533% tyrosine by weight upon amino acid analysis.(a) What is the minimum molecular weight for the protein (assuming only one Tyr residue per protein molecule)?(b) Gel filtration of the protein gae an estimated molecular weight of 9.0 x 104 g/mol. How many Tyr residues are in the protein?
Extreme temperatures can be used to break the hydrogen bonds with a protein molecule. Which of the following levels of protein structure will be preserved even when these bonds are broken?A. The sequence of amino acids within a polypeptide.B. Helical folds within a polypeptide.C. Pleated folds within a polypeptide.D. Bonding of multiple polypeptide chains together.
Give the name (3 letter and 1 letter) of the following peptides.
Trypsin digestion of the polypeptide Asp-Arg-Val-Tyr-Lys-His-Pro-Phe gives:A. Asp-Arg, Val-Tyr-Lys, His, Pro-PheB. Asp, Arg-Val-Tyr, Lys-His-Pro-PheC. Asp-Arg, Val-Tyr-Lys, His-Pro-PheD. Asp, Arg, Val-Tyr, Lys, His-Pro-Phe
Describe the process of protein degradation by ubiquitination.
The tertiary structure of a protein is determined by:A. The primary structure of a protein.B. where it is produced in the cell.C. the quaternary structure of the protein.D. the number of amino acids it contains.
Describe the structure of protein (e.g. primary, secondary, tertiary... structure etc.) with the driving force of maintaining the structure.
Briefly describe the four levels of protein structure.i.) Primaryii.) Secondaryiii.) Tertiaryiv.) Quaternary
Which of the following bonds or interactions is/are possible contributors to the stability of the tertiary structure of a globular protein?A. Peptide bonds between a metal ion cofactor and a histidine residueB. Hydrophobic interactions between histidine and tryptophan R groups.C. Covalent disulfide cross-links between 2 methionine residues.D. Hydrogen bonds between serine residues and the aqueous surroundings.E. All of the above contribute.
Describe basic protein architecture.
In the polypeptide attached, put a box around the peptide bonds and encircle the R-groups. How many amino acids are in the polypeptide?
Explain the process of protein folding, include the role of chaperone proteins.