The Cell Cycle and DNA

The Cell Cycle

• Cells grow, duplicate genetic material, and divide during the cell cycle.
• Interphase and the mitotic (M) phase are the two main phases.
• Regulation is vital for growth, development, and genetic stability.

Phases of the Cell Cycle

• Interphase is the longest phase (90% of the cycle), preparing the cell for division.

G1 Phase (Gap/Growth 1)

• Cell size increases.
• Organelles replicate.
• Synthesis of proteins and enzymes needed for DNA replication takes place.
• The G1 checkpoint ensures the cell is large enough and has enough resources.

S Phase (Synthesis Phase)

• DNA replication occurs, creating sister chromatids for each chromosome.
• Centrioles replicate in animal cells

G2 Phase (Gap/Growth 2)

• Additional growth occurs.
• Organelles continue duplicating.
• The G2 checkpoint verifies correct DNA replication before mitosis.

M Phase (Mitosis and Cytokinesis)

• Mitosis involves nuclear division in prophase, metaphase, anaphase, and telophase.
• Cytokinesis is the division of the cytoplasm.

Mitosis: Nuclear Division

Prophase

• Chromatin condenses into visible chromosomes.
• The nuclear envelope breaks down.
• The mitotic spindle forms from microtubules.

Metaphase

• Chromosomes align at the metaphase plate.
• Spindle fibers attach to chromosome centromeres.
• The Metaphase Checkpoint ensures proper spindle fiber attachment.

Anaphase

• Sister chromatids separate and move to opposite poles via spindle fibers.
• Each chromatid becomes a separate chromosome.

Telophase

• Chromosomes decondense back into chromatin.
• New nuclear envelopes form around each chromosome set.
• The mitotic spindle breaks down.

Cytokinesis: Cytoplasm Division

• In animal cells, a cleavage furrow pinches the cell into two.
• In plant cells, a cell plate forms, becoming the cell wall.

Regulation of the Cell Cycle

• Checkpoints control the cell cycle.
• The G1 checkpoint ensures readiness for DNA replication.
• The G2 checkpoint verifies DNA replication accuracy.
• The M checkpoint ensures correct chromosome attachment before separation.
• Cell cycle progression is regulated by Cyclins and Cyclin-dependent kinases (CDKs).
• Damaged or unnecessary cells are eliminated through apoptosis.
• Cancer results from uncontrolled cell division due to mutations in regulatory genes.

Karyotyping

• Karyotyping is a lab technique to examine chromosomes and detect abnormalities linked to genetic disorders.

Steps in Karyotyping

• A sample is collected from blood, amniotic fluid, or bone marrow.
• Cells are grown and stimulated to divide in cell culture.
• Chromosome harvesting halts metaphase division for visibility.
• Chromosomes are stained (e.g., Giemsa) for banding patterns.
• Microscopy and analysis arrange chromosomes in a karyogram.

Chromosome Structure and Classification

• Humans have 46 chromosomes (23 pairs).

Types of Chromosomes

Autosomes

• 22 pairs of non-sex chromosomes.

Sex Chromosomes

• 1 pair determines biological sex (XX-females, XY-males).

Chromosome Abnormalities

Numerical Abnormalities

Aneuploidy

• Extra or missing chromosomes occur (e.g., Trisomy 21 - Down syndrome).

Monosomy

• One chromosome is missing from a pair (e.g., Turner syndrome - 45,X).

Structural Abnormalities

Deletions

• Part of a chromosome is missing.

Duplications

• Extra copies of a chromosome segment exist.

Inversions

• A chromosome segment is reversed.

Translocations

• A chromosome fragment attaches to a non-homologous chromosome.

Applications of Karyotyping

• Prenatal diagnosis detects fetal genetic disorders.
• Cancer diagnosis identifies chromosomal changes in cancer cells.
• Infertility studies determine chromosomal causes of reproductive issues.
• Evolutionary biology compares chromosome structures between species.

Limitations of Karyotyping

• Small mutations or single-gene disorders cannot be detected.
• Requires dividing cells, limiting use in some cases.
• Additional genetic testing may be needed for confirmation.

Conclusion

• Understanding the cell cycle is crucial for cell growth, division, and disease mechanisms like cancer.
• Karyotyping detects chromosomal abnormalities and diagnoses genetic conditions.
• Both topics are essential in genetics, medicine, and biotechnology.

Section 16.2: The Cell Cycle and Mitosis

• Mitosis includes prophase, metaphase, anaphase, and telophase.
• Mitosis in plant and animal cells differs in centrioles and cytokinesis.
• Each mitosis phase duration can be calculated.

Reproduction of Somatic Cells

• Each cell undergoing mitosis yields two identical daughter cells.

Functions of Mitosis and Cytokinesis

Growth

• It allows organism growth from a single zygote to multicellularity.

Maintenance

• It replaces worn-out or dead cells, ensuring tissue integrity.

Repair

• It regenerates damaged tissue or body parts in some organisms.

Key Processes for Successful Mitosis

• DNA must be replicated before mitosis.
• Replicated chromatin condenses into chromosomes.
• Each new nucleus gets a complete chromosome set.
• Cell cytoplasm divides, forming two functional daughter cells.

Phases of Mitosis

Prophase

• Chromatin condenses into visible chromosomes.
• The nuclear membrane breaks down.
• The nucleolus disappears.
• Centrioles migrate to opposite poles (animal cells).
• The spindle apparatus forms.

Metaphase

• Chromosomes align at the metaphase plate (cell equator).
• Spindle fibers attach to the centromeres of each chromosome.
• Sister chromatids connect to spindle fibers from opposite poles.

Anaphase

• Centromeres split, separating sister chromatids.
• Spindle fibers shorten, pulling chromatids toward opposite poles.
• Other microtubules lengthen, pushing the poles apart.

Telophase

• Chromatids (now chromosomes) reach opposite poles.
• Chromosomes uncoil into chromatin.
• Spindle fibers break down.
• The nuclear membrane and nucleolus reappear, forming two distinct nuclei.

Cytokinesis

• In animal cells, a cleavage furrow pinches off the cytoplasm.
• In plant cells, a cell plate forms a new cell wall.

Mitosis in Plant vs. Animal Cells

Similarities

• Both undergo the same mitosis phases.
• Both use a spindle apparatus to separate chromosomes.
• Both produce identical daughter cells.

Differences

• Animal cells have centrioles; plant cells do not.
• Animal cells use a cleavage furrow; plant cells use a cell plate for cytokinesis.
• Animal cells are rounded during division; plant cells are rectangular due to the cell wall.

Regulation of the Cell Cycle

• Regulatory proteins and external signals control cell division.

Internal Regulation

• Proteins control progression through checkpoints (G1, G2, M).

External Factors

• Growth factors, hormones, and nutrient availability influence cell division.

Cancer: A Failure of Cell Cycle Regulation

• Cancer involves uncontrolled, rapid cell division due to regulatory signal failure.
• Cancer cells do not undergo normal interphase.
• They divide continuously, forming tumors.

Application of Mitosis Research

• Studies in non-human organisms have informed human mitosis understanding.
• Genetic research has identified genes regulating cell division and contributing to cancer.
• Advances in microscopy and fluorescent tagging track proteins/chromosomes during division.

DNA Structure and Replication - Section 18.1

Key Discoveries in DNA Research

• Friedrich Miescher (1869): Discovered nucleic acid in white blood cells.
• Phoebus Levene (Early 1900s): Identified DNA and RNA nucleotides as nucleic acids.
• Frederick Griffith (1928): Discovered the "transforming principle" in pneumonia-causing bacteria.
• Avery, MacLeod, McCarty (1944): Identified DNA as the transforming agent.
• Hershey and Chase (1952): Confirmed DNA carries genetic information using radioactive labelling.
• Erwin Chargaff (1940s): Adenine pairs with thymine, cytosine with guanine, known as Chargaff's Rule.
• Rosalind Franklin (1950s): Showed DNA’s helical structure via X-ray diffraction.
• Watson and Crick (1953): Developed the double-helix model of DNA.

Structure of DNA

Components

• Nucleotides are made of a phosphate group, deoxyribose sugar, and a nitrogenous base.

Four Nitrogenous Bases

• Adenine (A), Thymine (T), Cytosine (C), Guanine (G).
• A-T (2 hydrogen bonds), C-G (3 hydrogen bonds).

Double Helix

• Two antiparallel strands (5’ to 3’ and 3’ to 5’).
• Sugar-phosphate backbone supports bases.

DNA Replication

Semi-Conservative Model

• Each new DNA has one original and one new strand.

Stages of Replication

Initiation

• Begins at a replication origin.
• Helicases unwind DNA, forming a replication bubble and forks.
• binding proteins prevent strands from rebonding.

Elongation

• DNA polymerase adds nucleotides in the 5’ to 3’ direction, using the parent strand.
• The leading strand is synthesized continuously.
• The lagging strand is synthesized in Okazaki fragments in the opposite direction.
• Primase lays down RNA primers for Okazaki fragment synthesis.
• DNA polymerase extends primers with complementary DNA nucleotides.
• DNA polymerase I removes RNA primers, replacing them with DNA.
• DNA ligase seals Okazaki fragment gaps.
• Proofreading by DNA polymerase ensures accuracy.

Termination

• Replication forks meet or reach termination sequences.
• Telomerase extends ends of eukaryotic chromosomes.
• The replication machine disassembles, and DNA rewinds.

RNA vs. DNA

Differences

• RNA has ribose sugar instead of deoxyribose.
• RNA uses uracil (U) instead of thymine (T).
• RNA is single-stranded, DNA is double-stranded.

Genes and the Genome

Gene

• A DNA unit directing protein production.

Genome

• The total DNA content in an organism.

Non-coding DNA

• It is now known to have regulatory functions.

Key Enzymes in DNA Replication

• Helicase unwinds the DNA helix; Single-Strand Binding Proteins (SSBs) stabilize the unwound strands
• Primase lays down RNA primers; DNA Polymerase III extends new DNA strands.
• DNA Polymerase I removes RNA primers; DNA Ligase seals Okazaki fragment gaps.
• Telomerase extends chromosome ends.

Protein Synthesis and Gene Expression - Section 18.2

Key Concepts

• Genetic information is encoded in DNA.
• Gene expression involves transcription and translation.
• Proteins are synthesized based on the genetic code.

Introduction to Protein Synthesis and Gene Expression

• 1953: Watson and Crick’s DNA structure publication.
• Frederick Sanger: Proteins are sequences of amino acids.
• Central Dogma: DNA → RNA → Protein.
• DNA sequence determines amino acid sequence.
• Transcription (DNA → mRNA), translation (mRNA → Protein).

The Genetic Code

• Triplet Code: Three nucleotides (codon) encode one amino acid.
• Redundant: Multiple codons can code for the same amino acid.
• Continuous: Read in a linear sequence.
• Universal: Nearly all living organisms use the same code.
• Stop Codons: UAA, UAG, UGA (end of translation).
• Start Codon: AUG (Methionine) – initiates translation.

Transcription (DNA to RNA)

Initiation

• RNA polymerase binds to the promoter.
• DNA unwinds, exposing the template strand.

Elongation

• RNA polymerase synthesizes mRNA (5’ to 3’).
• Uracil (U) replaces thymine (T) in RNA.

Termination

• RNA polymerase reaches a stop signal and detaches.
• mRNA is released, and DNA reanneals.

Translation (RNA to Protein)

Initiation

• mRNA binds to a ribosome.
• The first tRNA (methionine) binds to the start codon.

Elongation

• tRNA molecules bring amino acids.
• Peptide bonds form between amino acids.
• The ribosome moves along the mRNA.

Termination

• A stop codon is reached.
• The polypeptide is released.
• Ribosomal subunits detach.

RNA Types in Protein Synthesis

mRNA

• Carries instructions from DNA to ribosomes.

tRNA

• Transfers amino acids to the ribosome.

rRNA

• Forms ribosomes.

Gene Expression Regulation

• Genes are expressed only when needed.
• Regulation ensures proteins are made only when required.
• Prokaryotes: Transcription and translation occur simultaneously.
• Eukaryotes: Transcription occurs in the nucleus; translation in the cytoplasm.

Genomics and Proteomics

Genomics

• Study of complete DNA sequences, including gene interactions.

Proteomics

• Study of all proteins expressed by a genome.

Applications

• Identifying gene interactions.
• Studying disease-related proteins.
• Developing new medical treatments.

Section 18.3: Mutations and Genetic Recombination

Key Terms

• Mutation: A permanent change in genetic material.
• Somatic Cell Mutation: In body cells, not passed to offspring.
• Germ Line Mutation: In reproductive cells, can be inherited.
• Point Mutation: Affects a single nucleotide.
• Silent Mutation: Does not affect protein function.
• Mis-Sense Mutation: Alters but maintains functional protein.
• Nonsense Mutation: Results in a nonfunctional protein.
• Frameshift Mutation: Alters the reading frame.
• Mutagen: A factor causing mutations.
• Physical Mutagen: High-energy radiation (X-rays, UV light).
• Chemical Mutagen: Alters DNA.
• Carcinogenic: A substance that promotes cancer.
• Mitochondrial DNA (mtDNA): DNA found in mitochondria, inherited from the mother.
• Genetic Engineering: The manipulation of an organism’s DNA.
• Recombinant DNA: DNA that contains genetic material from different sources.
• Restriction Enzyme (Endonuclease): Enzymes that cut DNA at specific sequences.
• Restriction Fragment: DNA fragments created by restriction enzymes.
• Gel Electrophoresis: A technique used to separate DNA fragments based on size.
• DNA Fingerprint: A unique pattern of DNA fragments used for identification.

Mutations and Their Role in Genetic Variation

• DNA constantly changes due to environmental and cellular factors.
• Most changes are repaired; some persist as mutations.
• Germ line mutations (in gametes) can be passed on.
• Somatic cell mutations (in body cells) are not inherited but can cause cancer.

Types of Mutations

Point Mutations

• Types include silent, missense, and nonsense mutations.

Frameshift Mutations

• The reading frame is shifted, usually resulting in nonfunctional proteins.

Chromosomal Mutations

• Affect multiple genes by rearranging genetic material.
• It can result in loss or duplication of chromosome segments.
• It can result in alterations in regulatory sequences.

Causes of Mutations

Spontaneous Mutations

• Occur naturally during DNA replication.
• DNA polymerase errors can introduce mutations.

Induced Mutations

• Caused by exposure to mutagens.
• Physical Mutagens: High-energy radiation like X-rays and UV light.
• Chemical Mutagens: Alter DNA structure

Mutations and Genetic Variation

• Mutation accumulation leads to genetic diversity.
• Some mutations are harmful; others may be beneficial.
• Mitochondrial DNA (mtDNA) is inherited from the mother and used to trace ancestry.

Genetic Engineering and Recombinant DNA

• Scientists can manipulate DNA.
• Recombinant DNA contains genetic material from different species.

Restriction Endonucleases (Restriction Enzymes)

• Cuts DNA at specific sequences (restriction sites).
• It creates "sticky ends" that can bind to complementary DNA.

Creating Recombinant DNA

• Cut DNA with a restriction enzyme.
• Insert the desired gene into a plasmid (vector).
• Seal with DNA ligase.
• Insert recombinant DNA into the host cell.

Gel Electrophoresis (DNA Fingerprinting)

• Separates DNA fragments based on size and charge.

Applications

• Crime scene investigations, paternity tests, evolutionary studies.

Applications of DNA Technology

• Investigating Cancer Genes
• Lung cancer and smoking examples shown.
• Oncogenes are mutated genes that cause cancer.
• Tumor-suppressor genes regulate cell division; mutations lead to uncontrolled growth.
• Mutations in the P53 gene (a major tumor suppressor) increase cancer risk.

Using DNA Fingerprinting

• It determines genetic relationships.
• Solves forensic cases.
• Identifies evolutionary links.

Genetic Modification

• Creates genetically modified organisms (GMOs).
• Produces medications (e.g., human insulin).
• Raises ethical and environmental concerns.

Overview of Meiosis

• Meiosis reduces the chromosome number by half, yielding four genetically different haploid gametes.

Phases of Meiosis

Meiosis I

• Reductional division takes place.

Prophase I

• Chromosomes condense, and homologous chromosomes pair up (synapsis) to form tetrads.
• Crossing over occurs, increasing genetic variation.

Metaphase I

• Homologous chromosome pairs align at the metaphase plate.
• Independent assortment increases genetic variation.

Anaphase I

• Homologous chromosomes separate and are pulled to opposite poles.
• Sister chromatids remain attached at their centromeres.

Telophase I & Cytokinesis

• The cell splits into two haploid daughter cells.

Meiosis II

• Equational division takes place.

Prophase II

• Chromosomes condense again.

Metaphase II

• Chromosomes align along the metaphase plate.

Anaphase II

• Sister chromatids separate and move toward opposite poles.

Telophase II & Cytokinesis

• The cytoplasm divides, resulting in four genetically unique haploid cells.

Gamete Formation

Spermatogenesis

• Occurs in the testes.
• Produces four functional sperm cells.

Oogenesis

• Occurs in the ovaries.
• Produces one egg and three polar bodies.

Significance of Meiosis

Genetic Variation

• Crossing Over (Prophase I) recombines genetic material.
• Independent Assortment (Metaphase I) provides random chromosome assortment.
• Random fertilization increases genetic diversity.

Maintains Chromosome Number

• It prevents doubling of chromosome numbers.

Produces Gametes for Sexual Reproduction

• Spermatogenesis produces sperm cells.
• Oogenesis produces eggs.

Comparison: Meiosis vs. Mitosis

• Mitosis- 1 division, produces 2 daughter cells, Genetic variation - No, Role- Growth & repair
• Meiosis- 2 divisions, produces 4 daughter cells, Genetic variation - yes, Role- Sexual reproduction

Nondisjunction and Genetic Disorders

What is Nondisjunction?

• Chromosomes fail to separate properly during meiosis.
• It can occur in Meiosis I or Meiosis II.
• It results in monosomy (one missing chromosome) or trisomy (one extra chromosome).

Common Disorders Caused by Nondisjunction

• Down Syndrome (Trisomy 21) caused by an extra copy of chromosome 21.
• Turner Syndrome (Monosomy X) is a female missing one X chromosome.
• Klinefelter Syndrome (XXY Syndrome) is a male with an extra X chromosome.
• Patau Syndrome (Trisomy 13) caused by an extra chromosome 13.
• Edwards Syndrome (Trisomy 18) caused by an extra chromosome 18.

Twins and Genetic Variation

Fraternal (Dizygotic) Twins

• Occur when two separate eggs are fertilized.
• Genetically similar to normal siblings.

Identical (Monozygotic) Twins

• Form when one fertilized egg splits.
• Genetically identical.

Diagnosis and Treatment of Nondisjunction Disorders

Diagnostic Techniques

• Karyotyping visualizes chromosomes.
• Amniocentesis extracts fetal cells.
• Chorionic Villus Sampling (CVS) examines placental tissue.
• Non-Invasive Prenatal Testing (NIPT) is a fetal DNA blood test.

Treatment Options

• Treatments focus on managing symptoms.
• Therapies improve the quality of life.
• Hormone therapy and surgical management are options.