4. Biomolecules

Proteins

All over the world, natural habitats are being fragmented into tiny islands by suburbs, ranches, farms, and roads. If asked to join a science panel to speak to Congress, could you explain how this fragmentation process could lead to extinction? How it could lead to speciation?

 Denaturation breaks the covalent bonds that hold the protein in its three-dimensional shape. Without the proper shape, the protein cannot function. 

 No. The covalent bonds that determine the protein's primary structure are not disrupted during denaturation, but these are not the bonds that hold the protein in its three-dimensional shape. 

 Denaturation destroys the primary structure of the protein, and the protein breaks down to monomers. 

 No. Primary protein structure is generally not affected during denaturation. 

 Different amino acids are substituted into the sequence, so the protein's properties change. 

 No. Denaturation does not involve substitution of amino acids. 

 The protein's pH changes, and the change causes the protein to lose its functionality. 

 No. Changes in pH may cause a protein to denature. Denaturation does not change the pH of the protein. 

 Denaturation breaks the intramolecular bonds, such as hydrogen bonds and van der Waals interactions, that hold the protein in its three-dimensional shape. Without the proper shape, the protein cannot function. 

Think of the bonds and interactions that influence the shape of a protein.

When a protein is denatured, why does it lose its functionality?

Neanderthals disappeared about 40,000 years ago when the modern human population increased. This is an example of what outcome(s) of secondary contact (see Table 24.4)? Predict one way this result might have come about. <IMAGE>

Post-Translational Modification of Proteins

 No. DNA is a polymer of nucleotides. What is the monomer used to form a protein? 

 No. Fatty acids are a component of triacylglycerols (fats) and phospholipids. 

 No. Purines and pyrimidines are nitrogenous bases present in nucleotides, the monomers of nucleic acids. 

Which polymers go with which monomers?

Protein molecules are polymers (chains) of __________.

 No. The double helix is the shape associated with the nucleic acid DNA. 

 No. The primary structure is the polypeptide's sequence of amino acids. 

 No. Although the secondary structure involves three-dimensional shapes, these shapes are confined to small regions of the polypeptide. 

 No. Quaternary structure is a feature of proteins that consist of two or more polypeptide chains, each with its own tertiary structure, combined to form a single functional protein. 

Review the levels of protein structure. .

The overall three-dimensional shape of a single polypeptide is called its __________.

A revolution in the study of human evolution is under way thanks to the invention of techniques that enable DNA sequencing of not only modern humans, but also ancient humans.

Modern humans (Homo sapiens) and archaic humans called Neanderthals (H. neanderthalensis) shared a common ancestor in Africa but diverged in different geographic areas. When modern humans migrated out of Africa and dispersed around the world starting about 100,000 years ago, they overlapped with Neanderthals in Europe. This scenario is best described as
a. species living in sympatry following allopatric speciation

b. species living in sympatry following sympatric speciation

c. species living in allopatry following allopatric speciation

d. species living in allopatry following sympatric speciation

Animation: Protein Functions

Post-translational Modifications and Chaperone Proteins

Structure and function of Biological Macromolecules

Which two functional groups are always found in amino acids?a) Carbonyl and amino groups.b) Carboxyl and amino groups.c) Amino and sulfhydryl groups.d) Hydroxyl and carboxyl groups.

What distinguishes a morphospecies?
a. It has distinctive characteristics, such as size, shape, or coloration.
b. It represents a distinct branch in a phylogeny of populations.
c. It is reproductively isolated from other species.
d. It is a fossil from a distinct time in Earth history.

Post Translation Modification

The specific amino acid sequence in a protein is its:a) Primary structure.b) Secondary structure.c) Tertiary structure.d) Quaternary structure.

Animation: Protein Structure

The primary building blocks (monomers) of proteins are:&nbsp;a) Glucose molecules.b) Lipids.c) Nucleotides.d) Amino acids.e) None of these.

Protein Structure

 a hydrogen bond joining amino acids together to form a polypeptide 

 No. Peptide bonds are not weak interactions, such as hydrogen bonds. 

 a covalent bond joining simple sugars together to form a polypeptide 

 No. Peptide bonds do not link simple sugars together. 

 a hydrogen bond joining nucleotides together to form a nucleic acid 

 No. A peptide bond is not a hydrogen bond, and it does not join nucleotides together. 

 a covalent bond joining nucleotides together to form a nucleic acid 

 No. Nucleotides are joined together by phosphodiester linkages, not peptide bonds. 

 a covalent bond joining amino acids together to form a polypeptide 

Consider the specific types of bonds present in the four types of macromolecules present in living systems.

The peptide bond is __________.

The structural level of a protein least affected by a disruption in hydrogen bonding is the
a. primary level.
b. secondary level.
c. tertiary level.
d. quaternary level.

Short Video: Cotranslational Transport

Biomolecules: The Proteins

Different proteins are composed of different sequences of                   .
a. sugars;
b. lipids;
c. fats;
d. amino acids;
e. carbohydrates

Which of the following describes vicariance?

a. Small populations coalesce into one large population.
b. A population is fragmented into isolated subpopulations.
c. Individuals colonize a novel habitat.
d. Individuals disperse and found a new population.

Assist in dehydration synthesis reactions.

Assist in protein folding or re-naturing.

What is the role of a chaperone protein?a) Assist in RNA and DNA folding.b) Assist in membrane transport.c) Assist in protein denaturation.d) Assist in dehydration synthesis reactions.e) Assist in protein folding or re-naturing.

Amino Acids

BioFlix: Protein Modifications

Post Translational Modifications

True or false? Speciation is a slow process. Justify your answer.

 the &alpha; helix or &beta; pleated sheets 

 No. Both the &alpha; helix and &beta; pleated sheets are types of secondary structure. 

 interactions among the side chains or R groups of the amino acids 

 No. These contribute to the tertiary structure of a polypeptide. 

 coiling due to hydrogen bonding between amino acids 

 No. This contributes to the secondary structure of a polypeptide. 

 the weak aggregation of two or more polypeptide chains into one functional macromolecule 

 No. This refers to the quaternary structure of a protein. 

 the sequence of amino acids along a polypeptide chain 

Consider which of these is the simplest level of protein structure.

The "primary structure" of a protein refers to __________.

 Organic molecules linked by dehydration reactions 

 No. This is also true of some carbohydrates and lipids. 

 No. Amino acids in a polypeptide are linked by dehydration reactions, not hydrolysis (which would separate them). 

 Carbohydrates with a hydrogen bond holding them together 

 No. Polypeptides are proteins, not carbohydrates. 

 None of the listed responses is correct. 

Consider the meaning of the prefix poly- and the suffix -peptide.

Which of the following represents a specific description of a polypeptide?

Three-spine sticklebacks are small fish that originated in the ocean and continue to exist there, but then some took up residence in hundreds of streams and freshwater lakes in the Northern Hemisphere. Predict whether you would expect to find different species in lakes today.

 No. The primary structure is the sequence of amino acids. 

 No. The tertiary structure is the overall three-dimensional shape of a polypeptide resulting from interactions between the R groups (side chains) of the various amino acids (hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bridges). 

 No. The quaternary structure is the aggregation of two or more polypeptide chains into one functional protein macromolecule. 

 No. There is no such thing as a pentiary structure in a protein. 

Consider size and the proximity of amino acids involved of these structures relative to the whole protein.

The &#945; helix and &#946; pleated sheet represent which level of protein structure?

5 Protein-Related Terms

Properties of Biological Macromolecules | AP Biology 1.4

Peptide bonds join the amine group on one amino acid with the R group of another amino acid.

Secondary protein structures are caused by hydrogen bonding between atoms of the peptide backbone.

Tertiary protein structure emerges when there is more than one polypeptide in a protein.

Which of the following is true of protein structure?a) Peptide bonds are formed by hydrolysis.b) Peptide bonds join the amine group on one amino acid with the R group of another amino acid.c) Secondary protein structures are caused by hydrogen bonding between atoms of the peptide backbone.d) Tertiary protein structure emerges when there is more than one polypeptide in a protein.

 No. A denatured protein is one whose shape has changed to the point that it cannot be catalytic, but there is a better answer. 

 No. Salt concentration and pH changes may indeed change the shape and, therefore, the catalytic function of an enzyme, but there is a better answer. 

 No. Heating the protein may indeed change the shape and, therefore, the catalytic function of an enzyme, but there is a better answer. 

 Treating the protein with a chemical that breaks hydrogen bonds 

 No. Breaking hydrogen bonds would alter the shape of an enzyme and might therefore change its catalytic function, but there is a better answer. 

 All of the listed responses are correct. 

Consider what factors are responsible for the shape of a polypeptide or protein.

Enzyme molecules require a specific shape to perform their catalytic function. Which of the following might alter the shape of an enzymatic protein?

 No. Sucrose is a disaccharide, and glucose is a monosaccharide. 

 No. Water has only three atoms; it must be at the beginning of this ranking. 

 No. Proteins are typically assembled from many amino acids. Expect to see protein at the end of the ranking. 

Keep your monomers and polymers straight. and

Which of the following lists ranks these molecules in the correct order by size from smallest to largest?

Proteins | Biological Molecules Simplified #2

Animation: Proteins

Denatured Proteins & Chaperones

Svante Pääbo and colleagues were the first to sequence the Neanderthal genome from fossils and compare the sequences to modern humans. According to the data shown here, did the two species interbreed when they overlapped in Europe? Explain. <IMAGE>

Protein Structure and Folding

What term is used for an amino acid chain that has greater than 50 covalently linked amino acids?a) Protein.b) Peptide.c) Amino acid.d) Polypeptide.

Major Elements in Biological Molecules: Proteins

Post Translational Modifications Of Proteins

Proteins may function as                   .
a. genetic material;
b. cholesterol molecules;
c. fat reserves;
d. enzymes;
e. all of the above

 All cause the misfolding of nucleic acids. 

 No. All of these are associated with another category of macromolecules. 

 All are associated with plaque buildup in arteries (atherosclerosis). 

 No. A high level of cholesterol in the blood is thought to contribute to atherosclerosis. 

 All are caused by the buildup of misfolded proteins in cells. 

 No. It is not known for certain that the buildup of misfolded proteins in the brain causes each of the three diseases. 

 All are associated with the buildup of lipids in brain cells due to faulty lysosome activity. 

 No. It is not the buildup of lipids that associates these diseases. 

 All are associated with the buildup of misfolded proteins in cells. 

Consider the cause more than the symptoms.

What do Alzheimer's, Parkinson's, and mad cow disease have in common?

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