Molecular Biology and Gene Expression: NMAT Biology Review

Introduction to Molecular Biology and Gene Expression

Molecular biology is a core topic in the NMAT Biology section and focuses on understanding how genetic information is stored, transmitted, and expressed at the molecular level. Gene expression explains how the information encoded in DNA is converted into functional products—primarily proteins—that determine cell structure, function, and behavior. A strong grasp of molecular biology concepts is essential for NMAT examinees because these principles form the foundation of genetics, biotechnology, medicine, and cellular physiology.

This review covers the structure and function of nucleic acids, the central dogma of molecular biology, DNA replication, transcription, translation, gene regulation, and post-translational modifications. Emphasis is placed on clarity, mechanisms, and key terms frequently tested in NMAT.

Nucleic Acids: DNA and RNA

Nucleic acids are macromolecules responsible for storing and transmitting genetic information. They are composed of repeating units called nucleotides.

Each nucleotide consists of:

• A pentose sugar (deoxyribose in DNA, ribose in RNA)

• A phosphate group

• A nitrogenous base

DNA Structure

DNA (deoxyribonucleic acid) is a double-stranded molecule arranged in a double helix. The two strands run in opposite directions (antiparallel) and are held together by hydrogen bonds between complementary bases:

• Adenine (A) pairs with Thymine (T)

• Guanine (G) pairs with Cytosine (C)

The backbone of DNA consists of alternating sugar and phosphate groups, linked by phosphodiester bonds. The sequence of nitrogenous bases encodes genetic information.

RNA Structure and Types

RNA (ribonucleic acid) is typically single-stranded and contains uracil (U) instead of thymine. Several types of RNA play roles in gene expression:

• Messenger RNA (mRNA): carries genetic instructions from DNA to ribosomes

• Transfer RNA (tRNA): transports amino acids during protein synthesis

• Ribosomal RNA (rRNA): forms the structural and functional core of ribosomes

• Regulatory RNAs (e.g., miRNA, siRNA): involved in gene regulation

The Central Dogma of Molecular Biology

The central dogma describes the flow of genetic information within a biological system:

DNA → RNA → Protein

This process involves two major steps:

• Transcription: synthesis of RNA from a DNA template

• Translation: synthesis of protein from an RNA template

While this model explains most gene expression pathways, exceptions exist, such as reverse transcription in retroviruses.

DNA Replication

DNA replication is the process by which a cell copies its DNA before cell division. It is semi-conservative, meaning each daughter DNA molecule contains one original strand and one newly synthesized strand.

Key Enzymes in DNA Replication

• DNA helicase: unwinds the double helix

• Single-strand binding proteins: stabilize separated strands

• DNA primase: synthesizes RNA primers

• DNA polymerase: adds nucleotides in the 5′ to 3′ direction

• DNA ligase: joins Okazaki fragments

Leading and Lagging Strands

Because DNA polymerase can only synthesize DNA in the 5′ to 3′ direction:

• The leading strand is synthesized continuously

• The lagging strand is synthesized discontinuously in short fragments called Okazaki fragments

DNA replication is highly accurate due to proofreading activity of DNA polymerase, which corrects mismatched bases.

Transcription: DNA to RNA

Transcription is the synthesis of RNA using DNA as a template. It occurs in the nucleus of eukaryotic cells and in the cytoplasm of prokaryotes.

Stages of Transcription

Initiation

RNA polymerase binds to a specific DNA sequence called the promoter. In eukaryotes, transcription factors assist RNA polymerase in promoter recognition.

Elongation

RNA polymerase moves along the DNA template, synthesizing a complementary RNA strand by adding ribonucleotides.

Termination

Transcription ends when RNA polymerase reaches a termination signal, releasing the newly formed RNA molecule.

RNA Processing in Eukaryotes

Before mRNA can be translated, it undergoes post-transcriptional modifications:

• 5′ cap: protects mRNA and aids ribosome binding

• Poly-A tail: increases stability and regulates nuclear export

• RNA splicing: removal of introns and joining of exons

Alternative splicing allows a single gene to produce multiple protein variants.

Genetic Code

The genetic code is the set of rules by which nucleotide sequences are translated into amino acid sequences. It is based on codons, which are three-nucleotide sequences in mRNA.

Key properties of the genetic code:

• Triplet code: three nucleotides per codon

• Degenerate: multiple codons can code for the same amino acid

• Non-overlapping and continuous

• Nearly universal across organisms

Start codon: AUG (codes for methionine)
Stop codons: UAA, UAG, UGA

Translation: RNA to Protein

Translation is the process of protein synthesis and occurs at ribosomes in the cytoplasm or on the rough endoplasmic reticulum.

Components of Translation

• mRNA: template containing codons

• tRNA: carries specific amino acids

• Ribosomes: composed of rRNA and proteins

• Amino acids: building blocks of proteins

Stages of Translation

Initiation

The ribosomal subunits assemble at the start codon of mRNA. The initiator tRNA binds to AUG.

Elongation

tRNA molecules bring amino acids to the ribosome. Peptide bonds form between adjacent amino acids, creating a growing polypeptide chain.

Termination

Translation stops when a stop codon is reached. The completed polypeptide is released.

Post-Translational Modifications

After translation, proteins often undergo modifications that affect their structure and function:

• Folding with the help of chaperone proteins

• Cleavage of signal peptides

• Phosphorylation

• Glycosylation

• Formation of disulfide bonds

These modifications are critical for protein activity, localization, and stability.

Regulation of Gene Expression

Gene expression is tightly regulated to ensure proteins are produced at the right time, place, and quantity.

Gene Regulation in Prokaryotes

Prokaryotic gene regulation often occurs at the transcriptional level and involves operons.

Operon Model

An operon consists of:

• Structural genes

• Promoter

• Operator

• Regulatory gene

Examples:

• Lac operon: inducible system activated in the presence of lactose

• Trp operon: repressible system inhibited by tryptophan

Gene Regulation in Eukaryotes

Eukaryotic gene regulation is more complex and occurs at multiple levels:

• Chromatin remodeling

• Transcriptional control

• Post-transcriptional regulation

• Translational control

• Post-translational modification

Epigenetic mechanisms such as DNA methylation and histone modification play a major role in regulating gene expression without altering DNA sequence.

Mutations and Their Effects

Mutations are changes in the DNA sequence and can affect gene expression and protein function.

Types of mutations:

• Point mutations (substitution)

• Insertions and deletions

• Frameshift mutations

• Silent, missense, and nonsense mutations

While some mutations are harmful, others may be neutral or beneficial and contribute to genetic diversity and evolution.

Recombinant DNA and Biotechnology (NMAT-Relevant Overview)

Molecular biology principles are applied in biotechnology and medicine.

Key concepts include:

• Restriction enzymes

• Plasmid vectors

• DNA ligase

• Polymerase chain reaction (PCR)

• Gel electrophoresis

These tools allow scientists to manipulate genes, diagnose diseases, and produce recombinant proteins such as insulin.

Importance of Molecular Biology in Medicine

Understanding gene expression is crucial in medical fields such as:

• Genetics and inherited diseases

• Cancer biology

• Pharmacogenomics

• Molecular diagnostics

• Gene therapy

Many NMAT questions test the application of molecular biology concepts to real-life medical scenarios.

Key NMAT Exam Tips

• Focus on understanding processes, not memorization alone

• Pay attention to enzyme functions and directionality (5′ to 3′)

• Be clear on differences between prokaryotic and eukaryotic gene expression

• Practice identifying steps in transcription and translation

• Review common experimental techniques and their purposes

Summary

Molecular biology and gene expression explain how genetic information flows from DNA to functional proteins. Mastery of nucleic acid structure, replication, transcription, translation, and gene regulation is essential for success in the NMAT Biology section. These concepts not only appear frequently in exams but also form the foundation of modern medicine and biotechnology. A strong conceptual understanding will help NMAT examinees analyze questions efficiently and accurately.

Molecular Biology and Gene Expression

Problem Sets (NMAT Biology)

Problem Set 1: DNA Structure and Replication

1. Which of the following best explains why DNA strands run antiparallel to each other?
A. To allow hydrogen bonding between bases
B. To maximize phosphate interactions
C. To ensure complementary base pairing
D. To facilitate enzyme binding

2. DNA replication is described as semi-conservative because:
A. Only one strand is copied
B. Each daughter molecule contains one parental strand
C. Replication occurs only at one end
D. Errors are conserved during replication

3. Which enzyme is responsible for removing RNA primers during DNA replication in eukaryotes?
A. DNA ligase
B. DNA polymerase α
C. RNase H
D. Helicase

4. The leading strand is synthesized:
A. Discontinuously away from the replication fork
B. Continuously toward the replication fork
C. Discontinuously toward the replication fork
D. Continuously away from the replication fork

5. Okazaki fragments are found on the:
A. Leading strand
B. Lagging strand
C. Parental strand
D. Template strand only

Problem Set 2: Transcription

6. Transcription begins when RNA polymerase binds to the:
A. Operator
B. Enhancer
C. Promoter
D. Terminator

7. In eukaryotes, which RNA polymerase transcribes mRNA?
A. RNA polymerase I
B. RNA polymerase II
C. RNA polymerase III
D. DNA polymerase

8. Which of the following is a post-transcriptional modification of eukaryotic mRNA?
A. Removal of introns
B. Addition of a methylated guanine cap
C. Polyadenylation
D. All of the above

9. The coding strand of DNA is identical to mRNA except that:
A. DNA contains uracil instead of thymine
B. mRNA contains thymine instead of uracil
C. DNA contains thymine instead of uracil
D. mRNA is antiparallel

10. Which structure signals the end of transcription in prokaryotes?
A. Promoter
B. Enhancer
C. Terminator sequence
D. Operator

Problem Set 3: Translation and Genetic Code

11. Translation occurs in the:
A. Nucleus
B. Mitochondria only
C. Ribosome
D. Golgi apparatus

12. Which RNA molecule carries amino acids to the ribosome?
A. mRNA
B. rRNA
C. tRNA
D. snRNA

13. The start codon for translation is:
A. UAA
B. AUG
C. UAG
D. UGA

14. A codon is composed of:
A. Two nucleotides
B. Three nucleotides
C. Four nucleotides
D. Five nucleotides

15. Which property of the genetic code ensures that multiple codons can code for the same amino acid?
A. Universal
B. Ambiguous
C. Degenerate
D. Continuous

Problem Set 4: Gene Regulation

16. The lac operon is an example of:
A. Positive gene regulation
B. Constitutive gene expression
C. Inducible operon
D. Repressible operon

17. In the lac operon, lactose functions as a(n):
A. Repressor
B. Inducer
C. Activator
D. Corepressor

18. Which molecule binds to the operator to inhibit transcription?
A. RNA polymerase
B. CAP protein
C. Repressor protein
D. Lactose

19. Enhancers in eukaryotic gene regulation:
A. Are located only upstream
B. Bind transcription factors
C. Inhibit transcription
D. Replace promoters

20. Epigenetic regulation commonly involves:
A. DNA sequence mutation
B. Histone modification
C. Codon reassignment
D. RNA translation

Answer Keys

Answer Key: Problem Set 1

1. A

2. B

3. C

4. B

5. B

Answer Key: Problem Set 2

6. C

7. B

8. D

9. C

10. C

Answer Key: Problem Set 3

11. C

12. C

13. B

14. B

15. C

Answer Key: Problem Set 4

16. C

17. B

18. C

19. B

20. B

NMAT Study Guide: Complete Preparation Guide for Medical School in the Philippines