HUMDEV week 1💪

Lecture Overview on Cells and Development

• Focus on fundamental concepts of cellular biology

• History of Cell Biology

• Understanding of cell theory and its components

• Importance of subcellular structures in developmental biology

• Discussion on the cytoskeleton and its role in cell function

History of Cell Biology

• Robert Hooke (Seventeenth Century)

  • Used early microscope to observe cork, discovering it's made of smaller units—cells.

  • Initially thought cells existed only in plants and fungi.

• Tjeeroulders and Schleiden (Nineteenth Century)

  • Matthias Schleiden concluded that all plants are comprised of cells.

  • Theodor Schwann extended this to animal tissues, highlighting inter-scientific communication in advancing scientific knowledge.

• Cell Theory (1859)

  • Proposed components:

  1. All organisms are composed of cells.

  2. The cell is the basic unit of life.

  3. Cells arise from pre-existing cells.

Modern Cell Theory

• Expanded components:

  1. Cells contain hereditary information (DNA).

  2. All cells share a similar chemical composition, varying in protein production.

  3. Cells conduct essential physiological processes independently.

  4. Cellular function relies on the activities of subcellular structures.

Fundamental Facts

• Humans consist of approximately 100,000,000,000,000 cells.

• Cells in the body:

  • About 300,000,000 cells die every minute.

  • Each cell houses around 10,000 times more molecules than the stars in the Milky Way.

Advantages of Cellular Composition

• Increased efficiency via greater surface area for gas and nutrient exchange, and waste disposal.

• Specialization: Different cell types perform distinct functions, similar to a society with diverse roles (e.g., teachers, farmers).

Cell Structure and Subcellular Compartmentalization

Major Components of Mammalian Cells

• Understand different compartments and their roles.

• Plasma Membrane

  • Separates living cells from nonliving surroundings and is selectively permeable.

  • Includes receptors for signals from the external environment, crucial for communication and response.

Cellular Signaling

• Cells receive external signals that direct them to survive, grow, or differentiate.

• Examples of signaling pathways include proliferation and apoptosis (programmed cell death).

• Specificity of receptor-signal interactions leads to cellular responses.

Cellular Appendages

• Cilia and Flagella

  • Cilia (singular: cilium): Motile structures aiding in moving substances across cell surfaces (e.g., respiratory tract).

  • Play roles in fertilization (e.g., moving eggs).

  • Flagella: Longer than cilia, few in number, important for motility (e.g., sperm movement).

  • Disorders related to cilia known as ciliopathies (e.g., OFD syndrome).

Cytoplasm and Organelles

• Cytoplasm: Hosts various organelles and metabolic pathways.

  • Key activities: Glycolysis, RNA processing, protein synthesis.

• Mitochondria

  • Known as the powerhouse of the cell; crucial for energy production via cellular metabolism (e.g., Krebs cycle).

  • Function includes directing cellular differentiation, cell cycle control.

  • Mitochondria inherited maternally, with DNA encoding part of its functions.

• High-energy cells (e.g., muscle, renal cells) have more mitochondria.

Endoplasmic Reticulum (ER)

• Rough ER

  • Site for RNA translation into proteins.

  • Produces and processes proteins.

• Smooth ER

  • Engaged in lipid synthesis, carbohydrate metabolism, and detoxification.

• Disorders in ER function linked to various diseases (e.g., Alzheimer's, multiple sclerosis).

Golgi Apparatus

• Discovered by Camillo Golgi; serves as a packaging and sorting center for cellular products.

• Responsible for processing proteins and distributing them within or outside the cell.

Additional Organelles

• Vacuoles: Storage of water and other substances.

• Lysosomes: Contain digestive enzymes; assist in cellular apoptosis.

• Peroxisomes: Handle toxin breakdown and fatty acid metabolism.

Nucleus

• Primary location for DNA within the cell, encapsulated by a nuclear envelope.

  • Contains nucleoplasm, nucleolus (site of ribosome assembly), and nuclear pores for transport.

• Chromatin Structure:

  • DNA wrapped around histones forms chromatin; tightly packed areas are transcriptionally inactive (heterochromatin).

• Different cell types activate specific genes relevant to their function, impacting development.

Cytoskeleton and Cell Mobility

• Three components: Microtubules, Microfilaments, Intermediate Filaments.

  • Each plays a crucial role in maintaining cell shape, stability, and movement.

• Microtubules:

  • Largest and strongest; comprised of alpha and beta tubulin; involved in cell division, flagella, cilia, and intracellular transport.

• Microfilaments (Actin Filaments):

  • Composed of G-actin and F-actin; key in muscle contractions and cellular movement.

• Intermediate Filaments:

  • Provide structural support specific to different cell types (e.g., keratins in epithelial cells).

Mechanism of Cell Migration

• Cells migrate based on external signals influencing their movement.

• Collective vs. single-cell migration in tissue development, maintenance, and potential disease contexts.

Developmental Context

• Neural crest cells and primordial germ cells exemplify migration during development.

• Fate Mapping: Used in model organisms (e.g., zebrafish) to visualize and track cell movement.

Mechanisms and Genetic Influences

• Mutations can disrupt normal migration patterns of germ cells, leading to developmental abnormalities.

• Importance of signal transduction pathways for proper cellular orientation during migration in developmental processes.

Conclusion

• The cytoskeleton is vital for maintaining cellular structure and mediating movement, both in developmental and physiological contexts.

• Questions to review and reinforce understanding of key concepts presented.

Here are A+ second-year university notes structured the way high-distinction students usually organise them: clear hierarchy, mechanisms, key terms, and exam-relevant links. These are condensed but conceptually deep, so they’re easier to revise before exams.

DEV2011 — Lecture 1 NotesDNA, Chromosomes & Gene Expression

1. DNA and Chromosome OrganisationStructure of DNA

DNA (deoxyribonucleic acid) is the molecule that stores genetic information in cells.

Key structural features

• DNA consists of two antiparallel strands forming a double helix.

• Each strand is a polymer of nucleotides.

Each nucleotide contains:

• Phosphate group

• Deoxyribose sugar

• Nitrogenous base

Four DNA bases

Complementary base pairing

DNA strands are held together by hydrogen bonds.

Base pairing rules:

A ↔ T
C ↔ G

This complementary pairing allows:

• accurate DNA replication

• faithful transmission of genetic information

DNA Sequence and Genetic Information

The order of nucleotides (DNA sequence) encodes biological information.

These sequences form:

• genes

• regulatory regions

Together they control:

• protein production

• cell identity

• development

Chromosomes and ChromatidsChromosome

A chromosome is a highly condensed structure containing a long DNA molecule and associated proteins.

Humans possess:

• 23 pairs of chromosomes (46 total)

These include:

Chromatid

A chromatid is one copy of a replicated chromosome.

Important concept:

One chromosome (after replication) = two sister chromatids connected at the centromere.

Each chromatid contains one continuous DNA molecule.

DNA Packaging and Chromatin Structure

Human DNA molecules are extremely long (~2 metres per cell), so they must be compactly packaged.

Histones

DNA is wrapped around histone proteins.

This forms a structure called a nucleosome.

Structure:

DNA → wrapped around histone core → nucleosome → chromatin fibre → chromosome

Functions of DNA packaging

1. Compacts DNA

2. Organises chromosomes

3. Regulates gene expression

The accessibility of DNA determines whether genes can be transcribed or silenced.

2. Gene Structure

Humans have approximately 23,000 genes.

Important concept:

Gene number does NOT correlate with organism complexity.

Examples:

Complexity arises from:

• gene regulation

• alternative splicing

• regulatory networks

What is a Gene?

A gene is a DNA sequence that produces a functional product, typically:

• a protein, or

• a functional RNA

Examples of non-protein coding RNAs:

• microRNA (miRNA)

• rRNA

• tRNA

• long non-coding RNA

Coding vs Non-coding DNA

Previously many DNA regions were called “junk DNA”, but this is inaccurate.

Non-coding DNA often contains:

• regulatory elements

• chromatin structural sequences

• DNA bending regions

These sequences are essential for gene regulation.

Components of a Gene1. Promoter

A promoter is a regulatory DNA region located at the 5′ end of a gene.

Function:

• recruits RNA polymerase

• binds transcription factors

• initiates transcription

Key promoter elements include:

Promoters determine:

• when transcription begins

• transcription efficiency

2. Coding Region

The coding region contains the sequences that will ultimately produce a protein.

It consists of exons.

3. Exons

Exons are DNA sequences that encode protein.

Features:

• remain in the final mRNA

• translated into amino acids

Genes vary greatly in exon number:

• some genes → 1 exon

• others → >100 exons

4. Introns

Introns are non-coding DNA sequences located between exons.

Features:

• removed during RNA splicing

• do not appear in mature mRNA

Functions:

• regulate gene expression

• contain regulatory sequences

5. Regulatory Regions (Cis-regulatory elements)

These are DNA sequences that regulate transcription.

They bind transcription factors.

They may be located:

• close to the gene

• far away (distal regulatory elements)

These regions control:

• when genes are expressed

• where genes are expressed

• how strongly genes are expressed

Enhancers and SilencersEnhancers

Enhancers are DNA sequences that increase gene transcription.

Mechanism:

1. Transcription factors bind enhancer

2. DNA loops to promoter

3. RNA polymerase activity increases

Enhancers are cell-type specific.

They are crucial for developmental gene regulation.

Silencers (Repressors)

Silencers reduce or inhibit gene transcription.

Mechanism:

• transcription factors bind silencer region

• transcription machinery is blocked or inhibited

Result:
gene expression decreases or stops.

3′ Untranslated Region (3′ UTR)

The 3′ UTR is a non-coding region at the end of the mRNA.

Functions:

• regulates mRNA stability

• controls translation efficiency

• signals termination of transcription

It also contains sites for microRNA binding.

3. Central Dogma of Molecular Biology

The central dogma describes the flow of genetic information:

DNA → RNA → Protein

Step 1 — Transcription

DNA is copied into RNA by RNA polymerase.

This occurs in the nucleus.

Product:
pre-mRNA (nuclear RNA)

RNA Processing

Before leaving the nucleus, RNA undergoes post-transcriptional modification.

Three major processes occur:

1. 5′ Cap addition

A modified guanine cap is added.

Functions:

• protects RNA from degradation

• helps ribosome recognition

2. Poly-A Tail Addition

A sequence of adenine nucleotides is added to the 3′ end.

Functions:

• stabilises mRNA

• regulates export from nucleus

• enhances translation

3. RNA Splicing

Introns are removed and exons are joined.

This produces mature mRNA.

Alternative Splicing

Different combinations of exons can be joined.

Result:
one gene → multiple protein variants

This greatly increases protein diversity.

mRNA Export

Once processed, mRNA exits the nucleus and enters the cytoplasm.

Translation occurs on ribosomes.

Translation

Ribosomes convert the mRNA nucleotide sequence into amino acids.

Key features:

• translation begins at start codon (AUG)

• ribosome reads mRNA from 5′ → 3′

Codons

A codon is a sequence of three nucleotides.

Each codon specifies one amino acid.

Example:

Translation Process

1. Ribosome binds 5′ cap

2. Ribosome scans for start codon

3. tRNA delivers amino acids

4. amino acids form polypeptide chain

5. translation stops at stop codon

The polypeptide then folds into a functional protein.

Antisense RNA

RNA molecules can bind complementary sequences.

This complementary sequence is called antisense.

Functions:

• block translation

• regulate gene expression

Antisense interactions are used in:

• natural gene regulation

• experimental gene knockdown

Protein Production from Genes

Important principles:

One gene → one mRNA

Each mRNA is transcribed from one gene.

One gene → multiple proteins

Occurs through:

Alternative splicing

Different exon combinations produce different proteins.

This is essential for:

• tissue-specific gene expression

• developmental regulation

Regulation of Gene Expression (Critical for DEV2011)

Gene expression must be precisely controlled during development.

Cells with identical DNA can become different cell types due to differential gene expression.

Levels of Gene Regulation

Gene expression can be regulated at multiple stages.

Chromatin Regulation

DNA accessibility is controlled by chromatin state.

Two major forms:

Histone modifications include:

• acetylation

• methylation

• phosphorylation

These influence transcription activity.

Transcription Factors

Transcription factors are proteins that bind specific DNA sequences.

Functions:

• activate transcription

• repress transcription

They control:

• spatial gene expression

• developmental timing

Regulatory Networks in Development

Genes rarely act alone.

They operate in gene regulatory networks (GRNs).

A GRN consists of:

• transcription factors

• regulatory DNA sequences

• signalling molecules

These networks control:

• cell fate

• tissue development

• body patterning

Feedback Regulation

Gene regulatory networks frequently use feedback loops.

Positive feedback

Product enhances its own expression.

Effect:

• stabilises cell identity

• creates irreversible developmental decisions

Example:
cell differentiation.

Negative feedback

Product inhibits its own expression.

Effect:

• maintains homeostasis

• prevents overexpression.

Importance for Developmental Biology (DEV2011)

Gene regulation determines:

• cell differentiation

• tissue patterning

• organ formation

• embryonic development

Small regulatory changes can produce major developmental effects.

Thus, understanding DNA structure, gene organisation, and gene regulation is fundamental for studying developmental processes.

If you want, I can also make a super condensed “exam cram sheet” version (1–2 pages) that lecturers usually base MCQs and short answers on in DEV2011.