AICE Biology Chapter 6

6.1 The Molecule of Life - Study Notes

Key Features of a Genetic Molecule

• Ability to store information: This means having instructions to control cell behavior.

• Ability to copy itself accurately: This ensures that exact copies are passed to daughter cells during cell division.

Historical Perspective

• Before the 1940s: Scientists believed proteins were the genetic material because they were complex enough to carry many instructions.

• 1940s to 1950s: New evidence proved that DNA, not protein, is the genetic material.

6.2 The Structure of DNA and RNA - Study Notes

DNA and RNA Overview

• DNA: Deoxyribonucleic acid

• RNA: Ribonucleic acid

  • Both are macromolecules (giant molecules) known as nucleic acids because they were first found in the nucleus.

  • Macromolecules are polymers, made of repeating smaller units called monomers.

  • The monomers of DNA and RNA are nucleotides, making them polynucleotides.

Nucleotides

• Made of three components:

  • Nitrogen-containing base

  • Pentose sugar (5-carbon sugar)

  • Phosphate group

Key Terms

• Nucleotide: A molecule with a nitrogen-containing base, a pentose sugar, and a phosphate group.

• Polynucleotide: A chain of nucleotides linked by phosphodiester bonds.

Nitrogen-Containing Bases

• DNA Bases: Adenine (A), Guanine (G), Thymine (T), Cytosine (C)

• RNA Bases: Adenine (A), Guanine (G), Uracil (U), Cytosine (C) (Uracil replaces Thymine)

• Purines (2 rings): Adenine (A) and Guanine (G)

• Pyrimidines (1 ring): Thymine (T), Cytosine (C), Uracil (U)

Pentose Sugar

• DNA contains deoxyribose (one less oxygen atom).

• RNA contains ribose.

Phosphate Group

• Gives nucleic acids their acidic properties.

Structure of ATP (Adenosine Triphosphate)

• ATP is a nucleotide, not part of DNA or RNA.

• Made of adenine, ribose, and three phosphate groups.

• Adenosine = adenine + ribose

• Forms: AMP (1 phosphate), ADP (2 phosphates), ATP (3 phosphates)

• Note: Adenine ≠ Adenosine (adenosine = adenine + sugar) and Thymine ≠ Thiamine (thiamine is a vitamin)

Dinucleotides and Polynucleotides

• Dinucleotide: Two nucleotides joined by a phosphodiester bond.

• Polynucleotide: Long chain of nucleotides linked by phosphodiester bonds, forming a sugar-phosphate backbone with bases sticking out sideways.

Structure of DNA

• Discovered by Watson and Crick in 1953, using data from Chargaff and Rosalind Franklin’s X-ray diffraction images.

• DNA is a double helix: two strands twisted around each other.

• Strands are antiparallel (run in opposite directions).

• Held together by hydrogen bonds between complementary bases.

Features of DNA

• Two polynucleotide chains

• Right-handed double helix

• Antiparallel strands (5’ to 3’ and 3’ to 5’)

• Sugar-phosphate backbone

• Bases project at right angles from the backbone

Complementary Base Pairing

• A pairs with T (2 hydrogen bonds)

• G pairs with C (3 hydrogen bonds)

• Purines always pair with pyrimidines (constant distance between strands)

• One complete turn of the helix = 10 base pairs

Complementary Base Pairing in Detail

• A-T (DNA) or A-U (RNA) = 2 hydrogen bonds

• G-C = 3 hydrogen bonds

DNA Replication

• DNA can “unzip” (breaking hydrogen bonds) and create two identical copies.

• Each strand acts as a template for a new complementary strand.

Structure of RNA

• Single-stranded polynucleotide

Types of RNA:

• mRNA (messenger RNA): Stays as a single strand

• tRNA (transfer RNA): Folds into complex shapes

• rRNA (ribosomal RNA): Forms part of ribosome structure.

6.3 DNA Replication - Study Notes

Overview of DNA Replication

• Discovered by Watson and Crick.

• Occurs during the S phase of the cell cycle.

• Controlled by enzymes.

Steps of DNA Replication

1. Unwinding of DNA

   • The two DNA strands are separated by breaking hydrogen bonds between bases.

   • This process is called “unzipping”.

2. Copying the DNA

   • The enzyme DNA polymerase attaches to each single strand.

   • It adds new nucleotides one at a time, matching them with complementary bases (A with T, C with G).

   • DNA polymerase works in the 5’ to 3’ direction only.

Leading and Lagging Strands

• Leading Strand:

  • Copied in the same direction as the DNA unwinds.

  • DNA polymerase moves smoothly, continuously adding nucleotides.

• Lagging Strand:

  • Copied in the opposite direction of the unwinding process.

  • DNA polymerase copies short fragments of DNA, called Okazaki fragments.

  • After copying one fragment, it moves back to copy the next piece.

Finishing the Process

• DNA ligase connects the new nucleotides with covalent phosphodiester bonds to form the sugar-phosphate backbone.

• It also joins Okazaki fragments to create a continuous strand.

Key Terms

• DNA polymerase: Enzyme that copies DNA by adding complementary nucleotides.

• Leading strand: The strand copied continuously in the 5’ to 3’ direction.

• Lagging strand: The strand copied in short fragments (Okazaki fragments) in the 5’ to 3’ direction.

• DNA ligase: Enzyme that joins nucleotides with phosphodiester bonds.

• Okazaki fragments: Short fragments of DNA formed on the lagging strand during replication.

Semi-Conservative Replication

• Each new DNA molecule contains:

  • One original (parent) strand

  • One newly synthesized strand

• This process is called semi-conservative replication because half of the original DNA is conserved in each new molecule.

Why Not Conservative Replication?

• In conservative replication, the original DNA would stay completely intact, and a completely new double-stranded molecule would be made.

• Semi-conservative replication was proven to be the correct method.

Additional Key Terms

• Semi-conservative replication: DNA replication method where each new molecule has one old strand and one new strand.

• Gene: A length of DNA that codes for a specific polypeptide or protein.

6.4 The Genetic Code - Study Notes

Overview of the Genetic Code

• After discovering the structure of DNA, scientists aimed to break the genetic code.

• Watson and Crick realized that the sequence of DNA bases is the genetic code.

• This sequence codes for the sequence of amino acids in proteins.

How the Genetic Code Works

1. Proteins control cell activities through enzymes.

2. Enzymes are proteins, made of unique amino acid sequences.

3. Amino acid sequences determine the structure and function of proteins.

4. Therefore, DNA controls the cell by coding for proteins.

5. The code for one polypeptide (protein) is called a gene.

Why a Triplet Code?

• There are 20 common amino acids and 4 DNA bases (A, T, C, G).

• 1 base per amino acid = only 4 possible codes (not enough).

• 2 bases per amino acid = 16 possible codes (still not enough).

• 3 bases per amino acid (triplet code) = 64 possible combinations (more than enough). This allows multiple codes for the same amino acid.

Features of the Genetic Code

• Triplet Code:

  • Each 3 bases (called a codon) code for 1 amino acid.

  • Example: TAC codes for methionine (Met).

• Universal Code:

  • The same codons code for the same amino acids in all living organisms.

• Start and Stop Signals (Punctuation):

  • Some codons are “start” codons (e.g., TAC for methionine) that signal the beginning of protein synthesis.

  • “Stop” codons signal the end of a gene during protein synthesis.

• Redundant/Degenerate Code:

  • More than one codon can code for the same amino acid.

  • Example: Cysteine is coded by both ACA and ACG.

Key Terms

• Gene: A section of DNA that codes for a specific polypeptide or protein.

• Triplet Code: Three DNA bases coding for one amino acid.

• Codon: A sequence of three bases in DNA or RNA that corresponds to a specific amino acid.

• Universal Code: The genetic code is the same across all organisms.

• Redundancy/Degeneracy: Some amino acids have more than one codon.

• Start Codon: Signals the start of protein synthesis (e.g., TAC).

• Stop Codon: Signals the end of protein synthesis.

6.5 Protein Synthesis - Study Notes

Overview of Protein Synthesis

• Summarized by the phrase: “DNA makes RNA and RNA makes protein.”

• Protein synthesis occurs in two stages:

  1. Transcription (DNA → mRNA)

  2. Translation (mRNA → Protein)

• DNA is found in the nucleus, but proteins are made at ribosomes in the cytoplasm.

• mRNA (messenger RNA) carries the genetic information from the DNA to the ribosomes.

Key Terms

• Transcription: The process of copying genetic information from DNA to a complementary mRNA strand.

• Translation: The process of converting the mRNA sequence into an amino acid chain (polypeptide) at the ribosome.

• mRNA (Messenger RNA): Carries the genetic code from the nucleus to the ribosome.

• tRNA (Transfer RNA): Transfers amino acids to the ribosome during translation.

• rRNA (Ribosomal RNA): Forms part of the ribosome structure.

• Codon: A sequence of three mRNA bases coding for one amino acid.

• Anticodon: A set of three bases on tRNA complementary to an mRNA codon.

1. Transcription (DNA → mRNA)

• Where? In the nucleus.

• Enzyme involved: RNA polymerase.

Steps:

1. Initiation:

   • RNA polymerase binds to the start of a gene.

   • DNA is unzipped (hydrogen bonds broken) to expose the template strand.

2. Elongation:

   • RNA polymerase reads the template strand (also called the transcribed strand).

   • Complementary RNA nucleotides pair with DNA bases:

     • A (DNA) → U (RNA)

     • T (DNA) → A (RNA)

     • C (DNA) → G (RNA)

     • G (DNA) → C (RNA)

   • Phosphodiester bonds form between nucleotides, creating the mRNA strand.

3. Termination:

   • RNA polymerase stops when it reaches a stop signal in the DNA.

   • The newly formed mRNA is released.

   • mRNA Processing (in Eukaryotes):

     • Primary transcript = unmodified mRNA.

     • RNA splicing: Removes non-coding regions called introns.

     • Remaining coding regions (exons) are joined together.

     • Alternative splicing allows one gene to code for multiple proteins.

     • After Transcription: mRNA leaves the nucleus through a nuclear pore to enter the cytoplasm.

2. Translation (mRNA → Protein)

• Where? At the ribosome in the cytoplasm.

Key Players:

• mRNA: Carries the codons (genetic code).

• tRNA: Brings amino acids to the ribosome.

• rRNA: Structural part of the ribosome.

tRNA Structure:

• Amino acid attachment site at one end.

• Anticodon at the other end (complementary to mRNA codon).

• Each tRNA carries a specific amino acid, matched by enzymes.

Steps:

1. Initiation:

   • mRNA binds to the ribosome (fits between the small and large subunits).

   • The first tRNA (with an anticodon matching the start codon, e.g., AUG for methionine) binds to the mRNA.

2. Elongation:

   • A second tRNA binds to the next codon on mRNA.

   • The two amino acids (carried by the tRNAs) form a peptide bond.

   • The ribosome moves (“clicks”) to the next codon.

   • The first tRNA leaves, and the process repeats with new tRNAs.

3. Termination:

   • Process continues until a stop codon is reached (e.g., UAA, UAG, UGA).

   • The completed polypeptide chain is released.

   • After Translation:

     • The polypeptide folds into its secondary and tertiary structures.

     • It may enter the endoplasmic reticulum (ER) for modification or transport.

Summary of Protein Synthesis

1. DNA → (Transcription) → mRNA (in the nucleus)

2. mRNA → (Translation) → Polypeptide (in the ribosome)

6.6 Gene Mutations - Study Notes

What is a Mutation?

• A mutation is a random change in the genetic material.

Types of Mutations:

1. Gene Mutation: Change in the base sequence of DNA.

2. Chromosome Mutation: Change in the structure or number of chromosomes.

Causes of Mutations:

• DNA replication errors (copying mistakes).

• Mutagens (factors causing mutations) such as:

  • Radiation (e.g., X-rays).

  • Carcinogens (cancer-causing chemicals).

Key Terms

• Codon: A sequence of three bases on mRNA that codes for an amino acid or stop signal.

• Anticodon: A sequence of three bases on tRNA that pairs with a codon on mRNA.

• Gene Mutation: A change in the DNA base sequence.

• Chromosome Mutation: A change in chromosome structure or number.

• Mutagen: An agent (like radiation) that causes mutations.

• Frame-Shift Mutation: A mutation caused by insertion or deletion, shifting the reading frame of codons.

Effects of Gene Mutations

• A change in the DNA base sequence may alter the amino acid sequence of a protein.

• This can change the protein’s structure and function, often causing harmful effects.

• Mutations in certain genes can lead to cancers.

Types of Gene Mutations

1. Substitution:

   • One base is replaced by another.

   • Effects:

     • May change the amino acid (missense mutation).

     • May have no effect if the new codon codes for the same amino acid (silent mutation).

   • Example of degeneracy in the genetic code:

     • TTT and TTC both code for lysine (no change in the protein).

   • Example:

     • Sickle Cell Anaemia (caused by a substitution in the gene for hemoglobin).

     • Normal sequence: Val–His–Leu–Thr–Pro–Glu–Glu–Lys

     • Mutated sequence: Val–His–Leu–Thr–Pro–Val–Glu–Lys

     • Result: Red blood cells become sickle-shaped, affecting oxygen transport.

2. Deletion:

   • A base is removed from the sequence.

   • Causes a frame-shift mutation, changing the reading frame of codons.

   • Result: Incorrect amino acids from the mutation point onward, leading to a non-functional protein.

3. Insertion:

   • An extra base is added to the sequence.

   • Also causes a frame-shift mutation, with similar effects to deletion.

Frame-Shift Mutations

• Occur due to insertion or deletion of bases.

• Shift the “reading frame,” altering every codon after the mutation.

• Consequences:

  • Major changes in the amino acid sequence.

  • Likely to produce non-functional proteins.

• Example:

  • Normal code:

    • TAG | TAG | TAG | TAG | TAG

  • Insertion: (added C):

    • TAG | TAG | TAG | TAG | CTA | GTA | GTA…

  • Deletion: (removed a base):

    • TAG | TAG | TAG | TAG | AGT | AGT | AGT…

• Key Point: Both insertion and deletion affect the entire sequence after the mutation, not just one codon.

Summary

• Mutations = Random changes in genetic material.

• Gene mutations: Affect DNA sequence → May change proteins.

• Chromosome mutations: Affect whole chromosomes.

• Types: Substitution (may be harmless), Insertion, and Deletion (usually harmful due to frame-shifts).

• Causes: Errors in replication, mutagens like radiation and chemicals.

Summary

• Structure:

  • Both DNA and RNA are polynucleotides made of nucleotides, each containing a pentose sugar, a phosphate group, and a nitrogenous base.

  • DNA: Has deoxyribose sugar, double-stranded (double helix), with bases adenine (A), thymine (T), guanine (G), and cytosine (C). A pairs with T, and G pairs with C.

  • RNA: Has ribose sugar, single-stranded (can fold back on itself, e.g., tRNA), with uracil (U) replacing thymine.

• Base Types:

  • Purines (double ring): Adenine, Guanine

  • Pyrimidines (single ring): Thymine, Cytosine, Uracil

• DNA Replication:

  • Occurs during the S phase of interphase via semi-conservative replication, producing two DNA molecules, each with one parent strand and one new strand.

• Protein Synthesis:

  • Transcription: DNA’s base sequence is copied into mRNA. In eukaryotes, the primary transcript undergoes splicing to remove introns (non-coding) and join exons (coding).

  • Translation: mRNA moves to a ribosome where tRNA delivers specific amino acids. Ribosomes read mRNA codons (sets of 3 bases), determining the amino acid sequence to form a polypeptide.

• Genes and Mutations:

  • A gene is a DNA segment coding for one polypeptide.

  • A gene mutation is a change in the DNA sequence, such as base substitution, insertion, or deletion.