Fundamentals of Biochemistry Study Guide (2025/2026 Syllabus)
Part 1: The Foundations of Biochemistry
1. What are the four major classes of biological macromolecules?
ANSWER ✓ The four major classes are proteins, nucleic acids (DNA and RNA), lipids,
and carbohydrates.
2. What type of bond is central to the structure of most biological
macromolecules?
ANSWER ✓ The covalent bond is central, particularly in forming the polymer backbone
(e.g., peptide bonds in proteins, phosphodiester bonds in nucleic acids).
3. What are the key differences between prokaryotic and eukaryotic cells?
ANSWER ✓ Prokaryotic cells lack a membrane-bound nucleus and organelles, while
eukaryotic cells have a true nucleus and compartmentalized organelles.
4. What is the primary force driving the spontaneous folding of proteins and the
formation of lipid bilayers?
ANSWER ✓ The hydrophobic effect, which is the tendency of nonpolar substances to
aggregate in an aqueous solution to minimize the disruption of hydrogen-bonding
water molecules.
5. What does the first law of thermodynamics state in the context of biochemistry?
ANSWER ✓ Energy cannot be created or destroyed, only converted from one form to
another. The total energy of a system and its surroundings is constant.
6. What does the second law of thermodynamics state?
ANSWER ✓ The total entropy (degree of disorder) of a system plus its surroundings
always increases for a spontaneous process.
7. How is the change in free energy (ΔG) related to the spontaneity of a reaction?
ANSWER ✓ If ΔG is negative, the reaction is spontaneous (exergonic). If ΔG is positive,
the reaction is non-spontaneous (endergonic) and requires an input of energy.
8. What is the role of ATP in cellular energy coupling?
ANSWER ✓ ATP hydrolysis (ATP → ADP + Pᵢ) is a highly exergonic reaction (ΔG << 0).
This reaction is coupled to endergonic processes, driving them forward by making the
overall free energy change negative.
, 9. How do enzymes increase the rate of a biochemical reaction?
ANSWER ✓ Enzymes lower the activation energy (Eₐ) required for the reaction to
proceed. They do this by stabilizing the transition state of the reaction.
10. What is the difference between a cofactor and a coenzyme?
ANSWER ✓ A cofactor is a general term for a non-protein chemical compound required
for an enzyme's activity. A coenzyme is a specific type of organic cofactor, often derived
from vitamins (e.g., NADH, FADH₂).
Part 2: Amino Acids, Peptides, and Proteins
11. What is the general structure common to all 20 standard amino acids?
ANSWER ✓ A central alpha (α) carbon bonded to an amino group (-NH₂), a carboxyl
group (-COOH), a hydrogen atom, and a unique side chain (R group).
12. What property distinguishes the 20 amino acids from one another?
ANSWER ✓ The chemical nature of their side chains (R groups), which can be nonpolar,
polar uncharged, positively charged (basic), or negatively charged (acidic).
13. What is the pKa of a functional group?
ANSWER ✓ The pKa is the pH at which half of the molecules of that species are
deprotonated. It is a measure of the tendency of a group to lose a proton.
14. How do you calculate the net charge of an amino acid at a given pH?
ANSWER ✓ Compare the pH to the pKa of each ionizable group. If pH > pKa, the group
is deprotonated. If pH < pKa, the group is protonated. Sum the charges of all groups.
15. What is the isoelectric point (pI)?
ANSWER ✓ The pH at which an amino acid or protein has a net charge of zero.
16. What type of bond links amino acids together in a protein chain?
ANSWER ✓ A peptide bond (a type of amide bond) formed by a condensation
(dehydration) reaction between the amino group of one amino acid and the carboxyl
group of another.
17. What are the four levels of protein structure?
ANSWER ✓ Primary, secondary, tertiary, and quaternary structure.
18. What is the primary structure of a protein?
ANSWER ✓ The linear sequence of amino acids in a polypeptide chain, held together by
covalent peptide bonds.
Part 1: The Foundations of Biochemistry
1. What are the four major classes of biological macromolecules?
ANSWER ✓ The four major classes are proteins, nucleic acids (DNA and RNA), lipids,
and carbohydrates.
2. What type of bond is central to the structure of most biological
macromolecules?
ANSWER ✓ The covalent bond is central, particularly in forming the polymer backbone
(e.g., peptide bonds in proteins, phosphodiester bonds in nucleic acids).
3. What are the key differences between prokaryotic and eukaryotic cells?
ANSWER ✓ Prokaryotic cells lack a membrane-bound nucleus and organelles, while
eukaryotic cells have a true nucleus and compartmentalized organelles.
4. What is the primary force driving the spontaneous folding of proteins and the
formation of lipid bilayers?
ANSWER ✓ The hydrophobic effect, which is the tendency of nonpolar substances to
aggregate in an aqueous solution to minimize the disruption of hydrogen-bonding
water molecules.
5. What does the first law of thermodynamics state in the context of biochemistry?
ANSWER ✓ Energy cannot be created or destroyed, only converted from one form to
another. The total energy of a system and its surroundings is constant.
6. What does the second law of thermodynamics state?
ANSWER ✓ The total entropy (degree of disorder) of a system plus its surroundings
always increases for a spontaneous process.
7. How is the change in free energy (ΔG) related to the spontaneity of a reaction?
ANSWER ✓ If ΔG is negative, the reaction is spontaneous (exergonic). If ΔG is positive,
the reaction is non-spontaneous (endergonic) and requires an input of energy.
8. What is the role of ATP in cellular energy coupling?
ANSWER ✓ ATP hydrolysis (ATP → ADP + Pᵢ) is a highly exergonic reaction (ΔG << 0).
This reaction is coupled to endergonic processes, driving them forward by making the
overall free energy change negative.
, 9. How do enzymes increase the rate of a biochemical reaction?
ANSWER ✓ Enzymes lower the activation energy (Eₐ) required for the reaction to
proceed. They do this by stabilizing the transition state of the reaction.
10. What is the difference between a cofactor and a coenzyme?
ANSWER ✓ A cofactor is a general term for a non-protein chemical compound required
for an enzyme's activity. A coenzyme is a specific type of organic cofactor, often derived
from vitamins (e.g., NADH, FADH₂).
Part 2: Amino Acids, Peptides, and Proteins
11. What is the general structure common to all 20 standard amino acids?
ANSWER ✓ A central alpha (α) carbon bonded to an amino group (-NH₂), a carboxyl
group (-COOH), a hydrogen atom, and a unique side chain (R group).
12. What property distinguishes the 20 amino acids from one another?
ANSWER ✓ The chemical nature of their side chains (R groups), which can be nonpolar,
polar uncharged, positively charged (basic), or negatively charged (acidic).
13. What is the pKa of a functional group?
ANSWER ✓ The pKa is the pH at which half of the molecules of that species are
deprotonated. It is a measure of the tendency of a group to lose a proton.
14. How do you calculate the net charge of an amino acid at a given pH?
ANSWER ✓ Compare the pH to the pKa of each ionizable group. If pH > pKa, the group
is deprotonated. If pH < pKa, the group is protonated. Sum the charges of all groups.
15. What is the isoelectric point (pI)?
ANSWER ✓ The pH at which an amino acid or protein has a net charge of zero.
16. What type of bond links amino acids together in a protein chain?
ANSWER ✓ A peptide bond (a type of amide bond) formed by a condensation
(dehydration) reaction between the amino group of one amino acid and the carboxyl
group of another.
17. What are the four levels of protein structure?
ANSWER ✓ Primary, secondary, tertiary, and quaternary structure.
18. What is the primary structure of a protein?
ANSWER ✓ The linear sequence of amino acids in a polypeptide chain, held together by
covalent peptide bonds.
