Cellular & Molecular Principles of Life Study Notes

Cellular & Molecular Principles of Life

Lecture Overview

  • Overview of the module's key topics:

    • What is life?

    • Molecular building blocks of life

    • Introduction to cells

    • Introduction to genes

    • Origins of life

  • Instructor: Professor Phil Dash (p.r.dash@reading.ac.uk)

Module Introduction

  • The Cellular & Molecular Principles of Life module covers the fundamental components of life that are common across all organisms.

  • All known life forms are composed of cells, which are the basic units of life.

  • Cells are made from molecular building blocks, including:

    • Proteins

    • Lipids

    • Carbohydrates

  • These components are regulated and governed by genes.

Module Introduction - Lectures Breakdown

  • Week 1: Building blocks of life (molecules, genes, & cells) - Phil Dash

  • Week 2: Genome organisation & DNA replication - Susanna Cogo

  • Week 3: Gene expression control - Susanna Cogo

  • Week 4: Protein synthesis - Susanna Cogo

  • Week 5: Transport and trafficking in cells - Phil Dash

  • Week 6: Cytoskeleton - Phil Dash

  • Week 7: Energy production - Phil Dash & Renee Lee

  • Week 8: Cell death and the cell cycle - Phil Dash

  • Week 9: Cell communication and cell differentiation - Phil Dash

  • Week 10: Connecting cells in tissues - Phil Dash

  • Week 11: Robustness and adaptation - Phil Dash

Module Introduction - Practicals

  • Practical classes will allow students to:

    • Work in a laboratory environment

    • Learn fundamental scientific techniques.

  • Classes are compulsory and linked to module assessments.

  • Practical handouts available for download on Blackboard prior to classes.

Module Introduction - Assessment

  • Assessments include:

    • A scientific report

    • An exam:

    • Weighting: 40% Scientific report, 60% MCQ exam

    • Total of 50 questions covering all lectures and practicals.

    • Scheduled for assessment period post-Christmas.

    • Individual report on practical class due later in the semester.

All Life is Made of Cells

  • Types of cells:

    • Single cells: Prokaryotes and Eukaryotes

    • Multicellular: Includes invertebrates, vertebrates, plants, and humans.

Disease and Treatment

  • Treatments and diseases are linked to cellular function.

  • diseases can be traced back to something going wrong in our cells, and most treatments work with cells to help them work normally again.

  • Example medications:

    • Paracetamol: 500 mg tablets

    • Penicillin: 5,000,000 IU

    • Atenolol: 50 mg tablets

    • Salbutamol: various formulations

    • Herceptin: 150 mg powder for infusion

Are Viruses Alive?

  • Viruses are fundamentally different from cells:

    • They require host cells to replicate and cannot function independently.

    • they are tiny

    • Viruses have proteins on the outside to attach to cells and proteins inside to help organise the genome.

    • Viruses can’t metabolise and need a host to replicate

  • Example: The SARS-CoV-2 virus replication process involves:

    1. Binding of spike protein to ACE2 receptor on host cells.

    2. RNA release and translation to proteins using host ribosomes.

    3. Formation of new virions in the Golgi and subsequent release from the cell.

Defining Life

  • Common Criteria for Life:

    • Growth

    • Reproduction

    • Response to stimuli

    • Adaptation to the environment

    • Self-assembly

    • Evolution

  • Life is categorized by:

    • Evolution through natural selection

    • Separation from the environment by membranes

    • Metabolic activity. - generative energy

Molecular Building Blocks of Life

  • Four main groups comprise the molecular building blocks:

    1. Nucleic acids

    2. Proteins

    3. Lipids

    4. Carbohydrates

  • Each group exhibits considerable diversity, e.g., proteins consist of combinations of up to 20 amino acids.

  • there are 68 molecules that contrubure to the 4 major groups 

Nucleic Acids – DNA and RNA

  • Function: Encode information necessary for cell function.

  • Structure:

    • DNA and RNA are polymers consisting of a sugar-phosphate backbone; encoded information is found in the base sequence.

    • DNA located in the nucleus

    • DNA base pairing: Adenine (A) with Thymine (T) and Cytosine (C) with Guanine (G).

    • universial, degenerate and triplet

  • DNA Structure:

    • Double-helix with antiparallel strands, read from 5' to 3' end.

    • RNA is single-stranded.

    • base pairing allows for replication 

Amino Acids

  • Amino acids serve as the building blocks of proteins:

    • Common structure includes:

    • Carboxyl group

    • Amino group

    • Variability comes from differing R groups.

  • Nearly 500 types exist, yet only 20 amino acids are integrated into proteins through genetic coding (DNA).

Amino Acids Chart

  • Key Types Essential, Non-essential.

  • Essential: need from food 

  • Non Essential: we can make

  • Some examples include:

    • Alanine (A) - Codons: GCT, GCC, GCA, GCG

    • Phenylalanine (F) - Codons: TTT, TTC

    • Arginine (R) - Codons: CGT, CGC, CGA, CGG, AGA, AGG

Genetic Code

  • Links DNA sequence to protein structure:

    • Comprised of codons (triplets of nucleotides) specifying each amino acid.

    • With four nucleotides, there are 64 possible codons for 20 amino acids.

  • During translation, mRNA codons are read by ribosomes, and tRNA delivers corresponding amino acids.

Proteins

  • Integral functions in cells including:

    • Catalyzing reactions

    • Transport functions

    • Structural support

    • Repair mechanisms

  • Proteins consist of polypeptide chains that fold into specific three-dimensional structures essential for their function.

Lipids

  • Essential roles, including:

    • Membrane formation (cell boundaries)

    • Energy storage

    • Cell communication

  • Structure: Generally hydrophobic, some amphiphilic, e.g., phospholipids forming lipid bilayers in water.

Sugars

  • Main energy source for cells (e.g., glucose).

  • Structural roles in cells, often in complex carbohydrates.

Introduction to Cells

  • Cells are created when molecular building blocks combine correctly.

  • Lipid assembly results in vesicles or membranes that facilitate enzymatic reactions encoded by DNA.

Types of Cells

  • Prokaryotic Cells:

    • Simplest form, lack nucleus, includes bacteria and archaea.

    • no nucleas, mitrchondria.

    • capable of moving in search of food.

  • Eukaryotic Cells:

    • More complex, contain organelles, include plants and animal cells.

    • DNA in the nucleus

Common Features of Cells

  • All cells have:

    • Cell membranes are made of lipids

    • Ability to sense and respond to their environment (temp, pH and light) 

    • DNA for protein coding 

    • Shared building blocks (proteins, lipids, carbohydrates, nucleic acids).

  • Cells are dynamic, highly organised, and often highly specialised.

Sizes of Cells and Biological Molecules

  • Comparison of sizes ( volume) :

    • Prokaryotic cells: ~1 mm³

    • Eukaryote cells: ~1000 mm³

    • Viruses: Much smaller than both; require host cells.

  • Small molecules can diffuse substance quickly and so there is no need for organisation. 

  • In bigger cells diffusion slows down as there is a lot more organelles in the cell. So eukaryotic cells break themselves up into different compartments. 

  • Compartmentalisation in eukaryotic cells enhances efficiency and productivity.

  • Compartmentalisation is the formation of organelles 

  • from here, cells can change the number and type of organelles they produce in orfer to allow the cell to take on different functions to allow cells to specialise. 

  • specialised cells can be brought together to enable diversity of life ont he planet.

  • specialised cells: 

  • red blood cell, which is responsible for the transport of (haemoglobin) in the blood and so has lots of heamoglobin and no nucleus. 

  • skin cells, which act as a barrier between us and the environment. Cells are flat and overlap each other through their cytoskeleton.

  • Cilia line the upper respiratory tract which traps the mucus. so they focus on creating mucus 

Introduction to Genes

  • Genes are sequences of DNA that is transcribed into RNA. They tell the cell which proteins to make, how to use them, where to put them etc

  • genome is organised into chromosomes.

  • Definitions and functions of various RNA types:

    • mRNA (messenger RNA): translated into proteins.

    • tRNA (transfer RNA) and rRNA (ribosomal RNA): functions in protein synthesis.

    • miRNA (micro RNA): regulates gene expression.

Gene Information

  • Only about 2% of human DNA encodes genes; the rest includes non-coding DNA, which has essential functions. Examples include:

    • Regulatory sequences

    • Introns

    • Telomeres

  • Human genome has roughly 22,000 genes; statistics for other organisms vary.

  • a lot of the non-coding DNA is about control, the genes are the instructions for making proteins and the non-coding regions are importnat in telling cells how much of a protein to make, or when to turn it on or off. 

this allows DNA to be more responsive to their enviroment. 

The Origins of Life

  • Life’s beginnings span billions of years:

    • Major events include:

    • Formation of Earth’s crust

    • Presence of liquid water

    • Notable biological changes recorded in geological history.

  • Key terms: LUCA (Last Universal Common Ancestor), endosymbiosis theory explaining the origin of cells.

  • 1st: A planet collided with another planet. Nothing was living

  • 2nd: the 1st cells formed, all life originated from Luca, including bacteria, fungi and archea. which used methane

  • 3rd: the great oxidation period due to cells being metabolically active. these were prokaryotic cells

  • 4th: eukaryotic cells emerged which then formed more complex molecules

The mycoplasma is the smallest cell with the smallest genome. with 475 genes.

Endosymbiotic Theory

  • Mitochondria are the same size as bacteria. This is helpful because of compartamentalilsation, which allows things to occur faster. They used to be bacteria. (same for chloroplast)

  • Proposes that certain organelles (mitochondria, chloroplasts) originated from independent prokaryotic organisms.

  • First endosymbiosis likely involved the engulfing of aerobic bacteria by a proto-eukaryotic cell.

  • Subsequent endosymbiosis involved the incorporation of photosynthetic bacteria for chloroplast formation.

Eukaryotic Cell Structure

  • Eukaryotic cells consist of:

    • Nucleus

    • Golgi apparatus

    • Lysosomes

    • Cytoskeleton

  • The precise origin of the first eukaryotic cell remains undetermined.

Asgard Archaea

  • Discovered as potential ancestors to eukaryotes, possessing genes for proteins vital for eukaryotic functions, including cytoskeletal elements and nuclear transport proteins.

Conclusion and Further Reading

  • Suggested readings for deeper understanding:

    • Chapter 1: Life - Chemical, Cellular and Evolutionary Foundations

    • Chapter 6: A Tour of the Cell

    • Chapter 1: Cells, Genomes, and the Diversity of Life