Biology 161 Study Guide – Step-by-Step Guidance for Key Concepts and Example Questions

Study Guide - Smart Notes

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Q1. How do we distinguish the four classes of biomolecules on the basis of their functional groups?

Background

Topic: Biomolecule Classification and Functional Groups

This question tests your understanding of how proteins, carbohydrates, lipids, and nucleic acids can be identified and differentiated based on the functional groups present in their structures.

Key Terms and Concepts:

Functional group: A specific group of atoms within a molecule that is responsible for certain chemical reactions and properties.
Biomolecule classes: Proteins, carbohydrates, lipids, nucleic acids.
Examples of functional groups: amino (-NH2), carboxyl (-COOH), hydroxyl (-OH), phosphate (-PO4), methyl (-CH3), sulfhydryl (-SH).

Step-by-Step Guidance

List the four major classes of biomolecules: proteins, carbohydrates, lipids, and nucleic acids.
Recall the main functional groups associated with each class. For example, proteins contain amino and carboxyl groups, carbohydrates have multiple hydroxyl groups, nucleic acids contain phosphate and nitrogenous bases, and lipids often have long hydrocarbon chains and sometimes phosphate groups (in phospholipids).
Think about how the presence or absence of these functional groups can be used to distinguish each class. For instance, the presence of a phosphate group is a key feature of nucleic acids and phospholipids, while amino and carboxyl groups are characteristic of amino acids (proteins).
Consider drawing or visualizing the basic structure of each biomolecule to see where these functional groups are located.

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Q2. Which monomers form which polymers? Why are polymerization reactions called condensation or dehydration and why are depolymerization reactions called hydrolysis?

Background

Topic: Monomers, Polymers, and Chemical Reactions in Biology

This question tests your ability to associate monomers with their corresponding polymers and to understand the chemical processes that build and break down biological macromolecules.

Key Terms and Concepts:

Monomer: A small molecule that can join with others to form a polymer.
Polymer: A large molecule made up of repeating monomer units.
Dehydration (condensation) reaction: A chemical reaction that joins two molecules by removing a water molecule.
Hydrolysis reaction: A chemical reaction that breaks a bond by adding water.

Step-by-Step Guidance

List the main biological polymers (proteins, nucleic acids, polysaccharides, and some lipids) and their corresponding monomers (amino acids, nucleotides, monosaccharides, fatty acids/glycerol).
Recall that polymerization involves joining monomers together, typically by removing a water molecule (dehydration/condensation reaction).
Understand that depolymerization (breaking down polymers) involves adding water to break bonds (hydrolysis reaction).
Think about why water is involved in both making and breaking these bonds, and how this relates to the terms 'dehydration' and 'hydrolysis.'

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Q3. What is the relationship between pH, [H+], and whether a compound functions as an acid or base?

Background

Topic: Acid-Base Chemistry and pH

This question tests your understanding of how pH relates to hydrogen ion concentration and the definitions of acids and bases.

Key Terms and Formulas:

pH: A measure of the hydrogen ion concentration in a solution.
Acid: A substance that increases [H+] in solution.
Base: A substance that decreases [H+] in solution.

Key formula:

Step-by-Step Guidance

Recall that pH is the negative logarithm (base 10) of the hydrogen ion concentration.
Understand that as [H+] increases, pH decreases (more acidic), and as [H+] decreases, pH increases (more basic).
Remember that acids donate H+ ions to solution, while bases accept H+ or donate OH-.
Practice converting between [H+] and pH using the formula above.

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Q4. Why do we say that “primary structure dictates secondary and tertiary structure”? What is the difference between the secondary, tertiary, and quaternary structure of a protein?

Background

Topic: Protein Structure and Function

This question tests your understanding of the levels of protein structure and how the sequence of amino acids determines the overall shape and function of a protein.

Key Terms:

Primary structure: The sequence of amino acids in a polypeptide chain.
Secondary structure: Local folding patterns (e.g., alpha-helix, beta-sheet) stabilized by hydrogen bonds.
Tertiary structure: The overall 3D shape of a single polypeptide, stabilized by various interactions (hydrogen bonds, ionic bonds, hydrophobic interactions, disulfide bridges).
Quaternary structure: The arrangement of multiple polypeptide subunits in a protein.

Step-by-Step Guidance

Recall that the primary structure is the unique sequence of amino acids in a protein.
Understand that the sequence of amino acids determines how the chain will fold into secondary structures (alpha-helices and beta-sheets) due to hydrogen bonding patterns.
Recognize that the tertiary structure is the overall 3D shape, which depends on interactions among side chains (R groups) and the secondary structures.
Know that quaternary structure arises when multiple polypeptide chains (subunits) come together to form a functional protein complex.

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Q5. What nucleotide structural features distinguish DNA and RNA molecules?

Background

Topic: Nucleic Acid Structure

This question tests your ability to compare and contrast the structural differences between DNA and RNA at the nucleotide level.

Key Terms:

Nucleotide: The monomer of nucleic acids, consisting of a sugar, a phosphate group, and a nitrogenous base.
DNA: Deoxyribonucleic acid; contains deoxyribose sugar and the bases A, T, C, G.
RNA: Ribonucleic acid; contains ribose sugar and the bases A, U, C, G.

Step-by-Step Guidance

Identify the sugar component in DNA (deoxyribose) and RNA (ribose), and note the difference at the 2' carbon (DNA lacks an -OH group at this position).
List the nitrogenous bases found in each: DNA uses adenine, thymine, cytosine, and guanine; RNA uses adenine, uracil, cytosine, and guanine.
Consider the structural implications of these differences for the stability and function of DNA and RNA.

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Q6. What three structural features distinguish one monosaccharide from another?

Background

Topic: Carbohydrate Structure

This question tests your understanding of the structural diversity among monosaccharides (simple sugars).

Key Terms:

Monosaccharide: The simplest form of carbohydrate (e.g., glucose, fructose).
Isomer: Molecules with the same chemical formula but different structures.

Step-by-Step Guidance

Recall that monosaccharides can differ in the number of carbon atoms (e.g., triose, pentose, hexose).
Consider the position of the carbonyl group (aldose vs. ketose).
Think about the spatial arrangement of hydroxyl groups around asymmetric carbons (stereochemistry).

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Q7. Why are there different types of glycosidic bonds but just one type of phosphodiester bond and one type of peptide bond? Why does the type of glycosidic bond matter?

Background

Topic: Types of Bonds in Biomolecules

This question tests your understanding of the chemical linkages that join monomers in biological polymers and the functional consequences of bond types.

Key Terms:

Glycosidic bond: A covalent bond joining two monosaccharides in carbohydrates.
Phosphodiester bond: The bond joining nucleotides in nucleic acids.
Peptide bond: The bond joining amino acids in proteins.

Step-by-Step Guidance

Recall that glycosidic bonds can form between different carbons and with different stereochemistry (e.g., alpha or beta), leading to structural diversity in carbohydrates.
Understand that phosphodiester and peptide bonds have a consistent linkage pattern (3'-5' in nucleic acids, carboxyl to amino in proteins).
Consider how the type of glycosidic bond affects the properties and digestibility of polysaccharides (e.g., cellulose vs. starch).

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Q8. What is the difference structurally between storage and structural polysaccharides?

Background

Topic: Polysaccharide Structure and Function

This question tests your ability to compare the structural features of polysaccharides used for energy storage (e.g., starch, glycogen) versus those used for structure (e.g., cellulose, chitin).

Key Terms:

Polysaccharide: A polymer of many monosaccharide units.
Storage polysaccharide: Polysaccharides like starch and glycogen that store energy.
Structural polysaccharide: Polysaccharides like cellulose and chitin that provide structural support.

Step-by-Step Guidance

Identify the types of glycosidic bonds present in storage (usually alpha) and structural (usually beta) polysaccharides.
Consider the degree of branching in the polymer chains (e.g., glycogen is highly branched, cellulose is unbranched).
Think about how these structural differences affect the function and digestibility of the polysaccharides.

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Q9. Can you associate each class of polymer with their monomers and the name of the bond that holds the monomers together? Can you name an example of each polymer and identify its function too?

Background

Topic: Biomolecule Structure and Function

This question tests your ability to connect the classes of biological polymers with their building blocks, the bonds that link them, and their biological roles.

Key Terms:

Polymer: Large molecule made of repeating monomers.
Monomer: Building block of a polymer.
Bond types: Peptide (proteins), glycosidic (carbohydrates), phosphodiester (nucleic acids), ester (lipids).

Step-by-Step Guidance

List the four main classes of biological polymers: proteins, nucleic acids, polysaccharides, and lipids (some lipids are not true polymers but are assembled from smaller units).
For each class, identify the monomer (e.g., amino acid for proteins, nucleotide for nucleic acids, monosaccharide for polysaccharides, fatty acids/glycerol for lipids).
Recall the type of bond that links the monomers (e.g., peptide, glycosidic, phosphodiester, ester).
Think of a specific example and its function (e.g., hemoglobin as a protein, cellulose as a polysaccharide, DNA as a nucleic acid, triglyceride as a lipid).

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Example Multiple Choice Q1. Which one of the following elements is not found in a nucleic acid?

Background

Topic: Nucleic Acid Composition

This question tests your knowledge of the elements that make up nucleic acids (DNA and RNA).

Key Terms:

Nucleic acid: A polymer made of nucleotides, containing elements such as carbon, hydrogen, oxygen, nitrogen, and phosphorus.

Step-by-Step Guidance

Recall the basic structure of a nucleotide: a sugar, a phosphate group, and a nitrogenous base.
List the elements present in each component (e.g., phosphate group contains phosphorus and oxygen; sugar contains carbon, hydrogen, and oxygen; nitrogenous base contains carbon, hydrogen, nitrogen, and sometimes oxygen).
Compare the answer choices to the elements found in nucleic acids and identify which one is not present.

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Example Multiple Choice Q2. Beta-hemoglobin is:

Background

Topic: Protein Structure and Function

This question tests your ability to classify biomolecules based on their structure and function.

Key Terms:

Hemoglobin: A protein in red blood cells that carries oxygen.
Polypeptide: A chain of amino acids linked by peptide bonds.

Step-by-Step Guidance

Recall that hemoglobin is a protein made up of multiple polypeptide chains (including beta-hemoglobin).
Review the definitions of amino acid, polypeptide, carbohydrate, and nucleic acid to distinguish between them.
Identify which category beta-hemoglobin fits into based on its structure and function.

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Example Multiple Choice Q3. In sickle cell anemia, a single amino acid substitution leads to beta-hemoglobin that is less able to carry oxygen. The reason this occurs is best explained as:

Background

Topic: Protein Structure and Disease

This question tests your understanding of how changes in protein structure can affect function and lead to disease.

Key Terms:

Sickle cell anemia: A genetic disorder caused by a mutation in the beta-globin gene.
Hydrophobic region: A part of a molecule that repels water and tends to cluster with other hydrophobic regions.

Step-by-Step Guidance

Recall that sickle cell anemia is caused by a single amino acid change in the beta-hemoglobin protein.
Understand how this substitution can alter the protein's shape and properties, especially regarding hydrophobic interactions.
Review the answer choices and consider which explanation best fits the molecular consequences of the mutation.

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Example Fill-in-the-Blank Q1. When nucleic acids are polymerized, the second _ (monomer) is attached to the first one by the formation of a _ linkage, which is formed by the phosphate group of the second monomer attaching to the 3’ carbon of the first one. As a result, a sugar-phosphate is created with the _ off to the side. In DNA, two _ - _ DNA strands are used to form a double helix, in which ‘G pairs with C’ and ‘A with T’ in what is called _______ pairing.

Background

Topic: Nucleic Acid Structure and Polymerization

This question tests your knowledge of how nucleic acids are built from nucleotides and the terminology associated with their structure.

Key Terms:

Nucleotide: The monomer of nucleic acids.
Phosphodiester linkage: The bond that joins nucleotides together.
Sugar-phosphate backbone: The repeating structure in nucleic acids.
Nitrogenous base: The part of the nucleotide that is not part of the backbone.
Antiparallel: The orientation of the two DNA strands.
Complementary pairing: The specific pairing of bases (A-T, G-C).

Step-by-Step Guidance

Recall the structure of a nucleotide and how nucleotides are joined during nucleic acid synthesis.
Identify the type of bond formed between nucleotides and which atoms are involved in the linkage.
Remember the terminology for the backbone and the orientation of DNA strands.
Recall the base pairing rules for DNA.

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Example Short Answer Q1. Rank the following in order by size: atom, electron, biomolecule, functional group, monomer

Background

Topic: Biological Organization and Scale

This question tests your understanding of the relative sizes of different chemical and biological entities.

Key Terms:

Electron: A subatomic particle.
Atom: The basic unit of a chemical element.
Functional group: A group of atoms within a molecule that has a specific chemical behavior.
Monomer: A small molecule that can join with others to form a polymer.
Biomolecule: A large molecule found in living organisms (e.g., protein, nucleic acid).

Step-by-Step Guidance

Recall the hierarchy of size from smallest to largest: subatomic particles, atoms, groups of atoms, small molecules, large molecules.
Arrange the given terms in order, starting with the smallest (electron) and ending with the largest (biomolecule).
Think about where functional groups and monomers fit in this hierarchy.

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Example Short Answer Q2. Using boxes to represent monomers, draw how two monomers become linked, including any -H and -OH groups that are directly involved in the reaction. Also, is this a dehydration or a hydrolysis reaction?

Background

Topic: Polymerization and Chemical Reactions

This question tests your understanding of how monomers are joined to form polymers and the chemical changes that occur during the reaction.

Key Terms:

Dehydration (condensation) reaction: A reaction that joins two molecules by removing water.
Hydrolysis reaction: A reaction that breaks a bond by adding water.

Step-by-Step Guidance

Draw two boxes to represent monomers, each with an -H or -OH group at the ends where they will join.
Show the removal of an -H from one monomer and an -OH from the other, which combine to form water ().
Indicate the new bond formed between the monomers after water is removed.
Decide whether this is a dehydration (condensation) or hydrolysis reaction based on whether water is produced or consumed.