Molecular Biology 2025 Study Guide for Midterm
DNA REPLICATION
1. Know the steps in the “Central Dogma of Molecular Biology” (figure 5-1).
2. Know the structures and functions of the animal cell as per figure 1-13a.
3. Know the general structure of DNA nucleotides. Base - ribose - Phosphate, and how
they are connected.
4. DNA is a double helix, connected by H-bonds. How many for GC? How many for AT?
5. DNA replication has direction. Which way does it replicate?
6. Be able to explain how DNA replicates at the level of figure 5-11.
7. What are the functions of the following molecules: Helicase, RPA (replication protein A,
PCNA (proliferating cell nuclear antigen), RFC (replication factor C) and all three DNA
polymerases (figure 5-12).
8. There are three types of DNA repair systems: Base excision repair, Nonhomologous
end joining and homologous recombination. Know the basic differences between these
mechanisms.
9. Know how dimerization of thymines can occur, what it is and what is inhibited by this
dimerization?
Central Dogma of Molecular Biology (Fig. 5-1)
• DNA → RNA → Protein
• DNA is transcribed into mRNA, which is translated into a protein.
Structures & Functions of the Animal Cell (Fig. 1-13a)
• Key organelles:
o Nucleus: Stores DNA, site of transcription.
o Ribosomes: Protein synthesis.
o Endoplasmic Reticulum (Rough & Smooth): Protein & lipid synthesis.
o Golgi Apparatus: Modifies & ships proteins.
o Mitochondria: ATP production.
o Lysosomes: Digestive enzymes.
General Structure of DNA Nucleotides
• Composed of:
o Base: Purines (A, G) or Pyrimidines (C, T).
o Ribose Sugar: Deoxyribose in DNA (lacking 2’ hydroxyl).
o Phosphate Group: Forms phosphodiester bonds between nucleotides.
Hydrogen Bonds in Base Pairing
• Guanine-Cytosine (G-C): 3 hydrogen bonds.
• Adenine-Thymine (A-T): 2 hydrogen bonds.
Direction of DNA Replication
• DNA polymerase adds nucleotides 5’ → 3’.
, • Reads template 3’ → 5’.
Mechanism of DNA Replication (Fig. 5-11)
• Initiation: Helicase unwinds DNA, primase adds RNA primers.
• Elongation: DNA polymerase synthesizes new strands. Leading strand = continuous,
lagging strand = Okazaki fragments.
• Termination: DNA ligase joins Okazaki fragments.
Functions of Key Molecules (Fig. 5-12)
• Helicase: Unwinds DNA at replication fork.
• RPA (Replication Protein A): Stabilizes single-stranded DNA.
• PCNA (Proliferating Cell Nuclear Antigen): Sliding clamp, increases DNA polymerase
efficiency.
• RFC (Replication Factor C): Loads PCNA onto DNA.
• DNA Polymerases:
o Pol α: Initiates replication with RNA primer.
o Pol δ: Synthesizes lagging strand.
o Pol ε: Synthesizes leading strand.
DNA Repair Mechanisms
• Base Excision Repair (BER): Fixes small, non-helix-distorting damage (e.g., deaminated
bases).
• Nonhomologous End Joining (NHEJ): Repairs double-strand breaks quickly but with
errors.
• Homologous Recombination (HR): Repairs double-strand breaks using a sister
chromatid (error-free).
Thymine Dimerization
• UV light can cause thymine dimers, where adjacent thymines covalently bond.
• This prevents proper base pairing, blocking replication and transcription.
• Fixed by nucleotide excision repair (NER).
RNA TRANSCRIPTION AND TRANSLATION - BASIC INFORMATION
1. Know the three general phases of RNA polymerization.
2. What is the purpose of the 7-methylguanylate cap?
3. What is the purpose of the poly A tail?
4. What is the advantage of intron splicing?
5. What are the different binding sites of tRNA? In other words, how does tRNA work?
6. What is a codon? And what is a wobble base?
7. How is an mRNA strand stabilized?
8. During translation the rRNAs have three important binding sites: A, P and E. What’s
happening at each site?
9. Can more than one rRNA complex binding to an mRNA strand for translation?
DNA REPLICATION
1. Know the steps in the “Central Dogma of Molecular Biology” (figure 5-1).
2. Know the structures and functions of the animal cell as per figure 1-13a.
3. Know the general structure of DNA nucleotides. Base - ribose - Phosphate, and how
they are connected.
4. DNA is a double helix, connected by H-bonds. How many for GC? How many for AT?
5. DNA replication has direction. Which way does it replicate?
6. Be able to explain how DNA replicates at the level of figure 5-11.
7. What are the functions of the following molecules: Helicase, RPA (replication protein A,
PCNA (proliferating cell nuclear antigen), RFC (replication factor C) and all three DNA
polymerases (figure 5-12).
8. There are three types of DNA repair systems: Base excision repair, Nonhomologous
end joining and homologous recombination. Know the basic differences between these
mechanisms.
9. Know how dimerization of thymines can occur, what it is and what is inhibited by this
dimerization?
Central Dogma of Molecular Biology (Fig. 5-1)
• DNA → RNA → Protein
• DNA is transcribed into mRNA, which is translated into a protein.
Structures & Functions of the Animal Cell (Fig. 1-13a)
• Key organelles:
o Nucleus: Stores DNA, site of transcription.
o Ribosomes: Protein synthesis.
o Endoplasmic Reticulum (Rough & Smooth): Protein & lipid synthesis.
o Golgi Apparatus: Modifies & ships proteins.
o Mitochondria: ATP production.
o Lysosomes: Digestive enzymes.
General Structure of DNA Nucleotides
• Composed of:
o Base: Purines (A, G) or Pyrimidines (C, T).
o Ribose Sugar: Deoxyribose in DNA (lacking 2’ hydroxyl).
o Phosphate Group: Forms phosphodiester bonds between nucleotides.
Hydrogen Bonds in Base Pairing
• Guanine-Cytosine (G-C): 3 hydrogen bonds.
• Adenine-Thymine (A-T): 2 hydrogen bonds.
Direction of DNA Replication
• DNA polymerase adds nucleotides 5’ → 3’.
, • Reads template 3’ → 5’.
Mechanism of DNA Replication (Fig. 5-11)
• Initiation: Helicase unwinds DNA, primase adds RNA primers.
• Elongation: DNA polymerase synthesizes new strands. Leading strand = continuous,
lagging strand = Okazaki fragments.
• Termination: DNA ligase joins Okazaki fragments.
Functions of Key Molecules (Fig. 5-12)
• Helicase: Unwinds DNA at replication fork.
• RPA (Replication Protein A): Stabilizes single-stranded DNA.
• PCNA (Proliferating Cell Nuclear Antigen): Sliding clamp, increases DNA polymerase
efficiency.
• RFC (Replication Factor C): Loads PCNA onto DNA.
• DNA Polymerases:
o Pol α: Initiates replication with RNA primer.
o Pol δ: Synthesizes lagging strand.
o Pol ε: Synthesizes leading strand.
DNA Repair Mechanisms
• Base Excision Repair (BER): Fixes small, non-helix-distorting damage (e.g., deaminated
bases).
• Nonhomologous End Joining (NHEJ): Repairs double-strand breaks quickly but with
errors.
• Homologous Recombination (HR): Repairs double-strand breaks using a sister
chromatid (error-free).
Thymine Dimerization
• UV light can cause thymine dimers, where adjacent thymines covalently bond.
• This prevents proper base pairing, blocking replication and transcription.
• Fixed by nucleotide excision repair (NER).
RNA TRANSCRIPTION AND TRANSLATION - BASIC INFORMATION
1. Know the three general phases of RNA polymerization.
2. What is the purpose of the 7-methylguanylate cap?
3. What is the purpose of the poly A tail?
4. What is the advantage of intron splicing?
5. What are the different binding sites of tRNA? In other words, how does tRNA work?
6. What is a codon? And what is a wobble base?
7. How is an mRNA strand stabilized?
8. During translation the rRNAs have three important binding sites: A, P and E. What’s
happening at each site?
9. Can more than one rRNA complex binding to an mRNA strand for translation?
