Week 1: Cellular Biology and Genetics, University Notes

Cells: Basic Unit of Life

Cells: Basic unit of living organism, aqueous, enclosed by membrane and can self replicate

Diversity of Cells

Diversity of Cells comes from:

• Size
• Shape
• Chemical requirements

This diversity reflects function:

• Factories for production of hormones, scratch, fat, latex or pigments
• Burn fuel for mechanical work
• Generate electrical current

Living Things Characteristics

Living Things:

• Are organized
• Maintain homeostasis
• Reproduce
• Grow from simple
• Transform energy from the environment
• Respond to stimuli
• Adapt to environment

Sexual Reproduction- Fusion of two cells of same species pooling DNA Evolution- Gradual change in organisms over generations

• Believed that all cells stem from same ancestral cell

Major Divisions of Life

3 Major divisions of living things were found by comparing the genomes (Sequences) of various organisms.

• Bacteria
• Archaea
• Eukaryotes

Bacteria

Bacteria-

• Dominant and most diverse
• Most commonly single celled organisms, can join together to form multicellular structures
• Extremely small
• Cell wall surrounding plasma membrane containing cytoplasm and DNA
• Reproduce extremely quickly
• Group together in chains or clusters
• Shapes are spherical, rodlike or corkscrew

2 um spherical cells, e.g., Streptococcus rod-shaped cells, e.g., Escherichia coli, Salmonella spiral cells, e.g., Treponema pallidum

Aerobic- Use oxygen to oxidize food molecules Anaerobic- Do not use oxygen

• Carbon in any form is most common source of food
• Photosynthesis is a common example
• Mitochondria have evolved from bacteria

Archaea

Archaea-

• Found in hostile environments
• High temps, pH, low oxygen ect ..
• Resemble bacteria in outward appearance, more similar to eukaryotes in genome sequences
• Asgard cells were used to see resemblance

Eukaryotes

Eukaryotes Eukaryotes- Organisms whose cells contain distinct nucleus and cytoplasm

• Much larger
• Includes animals, plants and fungi- Along with a nucleus there are additional organelles (With membranes) present in eukaryotes.

Prokaryotes- Absences of a nucleus (archaea and bacteria) Yeast- Simple free living eukaryotes, use budding (asymmetrical dividing) to reproduce.

Organelle Functions

Functions of organelles were found by spinning the contents of a cell in a centrifuge to divide out organelles and tested what chemicals they released and their size/density.

Organelle/Part Function Nucleus Contains DNA of organism Nuclear Envelope Two spherical membranes containing nucleus

Chromosomes

Chromosomes

• Long threadlike structure composed of DNA and proteins that carry genetic information.
• Becomes visible during cell division

Mitochondria

Mitochondria

• Membrane enclosed
• Performs oxidative phosphorylation and produces most of the ATP in the cell (Chemical energy)
• Oxidize food molecules into ATP (Consumes oxygen Releases CO2) called Cellular Respiration
• Inner membrane which creates folds within the structure
• Contain own DNA and reproduce by dividing (Proves relation to aerobic bacterium engulfed by an anaerobic ancestor of present day eukaryotic cells)
• Symbiotic relationship with eukaryotic cell, provides both with metabolic support allowing for survival and reproduction
• Suggested that an asgard archaeon was the original capturer of the mitochondria

Chloroplasts

Chloroplasts

• Large, green only found in plants and algae
• Two membranes (Inner and outer)
• Internal stacks of membranes containing green pigment Chlorophyll
• Capture sunlight energy
• Carry out Photosynthesis (use of sun, carbon dioxide and water to form organic molecules - sugars and release oxygen byproduct)
• Produce the food and oxygen for the mitochondria to generate chemical energy (ATP)
• Evolved from photosynthetic bacteria engulfed by eukaryotic already containing mitochondria (Evolved after)chlorophyll- containing membranes inner membrane outer membrane

Endoplasmic Reticulum

Endoplasmic reticulum

• Irregular maze enclosed by a membrane
• Components and materials that are being exported out of the cell are made here
• Secrete large amounts of protein

Rough ER:

• Contain ribosomes used to translate RNA into protein

Smooth ER:

• No ribosomes

Golgi Apparatus

Golgi Apparatus

• Membrane enclosed
• Stacks of flattened sacs
• Modifies and package molecules made in the ER

05 O (A)

Lysosomes

Lysosomes

• Small, irregularly shaped
• Intracellular digestion occurs
• Releases nutrients from ingested food particles into cytosol
• Break down unwanted particle for recycling or removal from cell

Peroxisomes

Peroxisomes

• Small, membrane enclose
• vesicles that provide an isolated environment for reactions in which hydrogen peroxide is used to inactivate toxic materials

Transport Vesicles

Transport Vesicles

• membrane formed

Cytosol

Cytosol

• Everything left over after the membrane contained organelles have been removed
• Fraction of cytoplasm
• Water based gel solution containing variety of molecules
• Site of many chemical reactions
• In constant motion due to random thermal motion (molecules collide)

Cytoskeleton

Cytoskeleton

• Crisscrossing long fine fragments within the cytosol
• Anchor one end of the plasma membrane
• Give cell shape and capacity for directed movements
• Filaments assemble and disappear when needed

Three Filament types:

• Actin filaments: small, central part of machinery for muscle contraction (large amount in muscle cells)
• Microtubules: Largest, hollow tubes in dividing cells that help pull apart duplicate chromosomes
• Intermediate filaments: intermediate in thickness, strengthen animal cells

duplicated chromosomes (A) (B) (C)

Cell Wall

Cell Wall

• Only in plant cells
• Provide additional structure and support

Evolution of Mitochondria and Chloroplasts

How Mitochondria and chloroplasts evolved:

nonphotosynthetic bacteria photosynthetic bacteria plants animals fungi archaea chloroplasts single-celled eukaryote - TIME - mitochondria bacteria archaea ancestral prokaryote

Membrane Transport

Endocytosis and Exocytosis across plasma membrane:

IMPORT BY ENDOCYTOSIS endosome plasma membrane Golgi apparatus EXPORT BY EXOCYTOSIS

• Continual exchange of materials occur between ER, golgi apparatus, lysosomes, plasma membrane and outside of cell
• Transport vesicles mediate. They pinch off the membrane of one organelle and fuse to another
• Endocytosis- Carry in external materials
• Exocytosis- release of internal components to external

Motor Proteins- use energy stored in ATP to move through cytoplasm microtubules 20 μm

Cell Types

ANIMAL CELL centrosome with pair of centrioles microtubule chromatin (DNA) extracellular matrix nuclear pore vesicles 0 0 lysosome mitochondrion 5 um nucleolus endoplasmic reticulum nucleus plasma membrane ribosomes in cytosol Golgi apparatus intermediate filaments Golgi apparatus nucleolus mitochondrion chromatin (DNA) nuclear pore cell wall microtubule C vacuole (fluid-filled) peroxisome chloroplast ribosomes in cytosol PLANT CELL actin filaments lysosome 1 μm Three cell types are drawn here in a more realistic manner than in the schematic drawing in Figure 1-25. The animal cell drawing is based on a fibroblast, a cell that inhabits connective tissue and deposits extracellular matrix. A micrograph of a living fibroblast is shown in Figure 1-7A. The plant cell drawing is typical of a young leaf cell. The bacterium shown is rod-shaped and has a single flagellum for motility. A comparison of the scale bars reveals the bacterium's relatively small size. - flagellum ribosomes in cytosal outer membrane DNA plasma membrane cell wall BACTERIAL CELL . actin filaments peroxisome 5 um

Protozoans

Protozoans- A free living, nonphotosynthetic, single celled, mobile, eukaryote that lives in solitary

• Do not range in environments but range in behaviour and appearances
• Photosynthetic or carniverous
• Vary versitile in shaps and sizes
• Ex. Didinium- large, fast, carnivourus, paralyses prey and devours

Model Organisms for Study

Model Organisms- Living things selected to be studied as representatives of larger groups

Escherichia Coli

Escherichia Coli- Representative of Bacteria

• Small, rod shaped cell
• Lives in guts of humans and vertebrate
• Revealed how cells regulate gene expression and replicate and decode DNA to make protiens
• Used to produce large quantities of proteins such as insulin

Saccharomyces Cerevisiae

Saccharomyces cerevisiae- Model Eukaryote

• Also called Brewer's Yeast
• It is difficult to model and study eukaryotes directly, yeast is an easier representative
• Very closely related
• Small single celled fungi more closely related to animals then plants
• Cell wall, immobile and many organelles
• Understanding mechanism of cell division

Arabidopsis Thaliana

Arabidopsis Thaliana- Model Plant

• Understanding of mechanisms that enable palnts to grow towards sunlight and cycle of seasons

Other Model Animals

Other Model Animals

• Nematode worm (Caenorhabditis elegans)
• Extremely precise organisms (exactly 959 cells)
• View cell prescision with strict rules

Fruit Fly (Drosophila melangaster)

• Study of animal genetics (genes carry chromosomes)
• Genetic instructions in DNA lead to development of zygote to adult
• Extremely similar to humans
• Zebrafish
• Insight to developmental process (heart and blood vessels)
• Transperant fir first 2 weeks of life
• Mice
• Can be delibratly mutatated
• Understand how specific genes work in humans

• Scientists worked backwards by isolating organisms that are defective in cells to discover which protiens control cell cycle
• Successful in yeast (Reproduce rapidly)
• S. Pombe is where cdc and cdc2 genes for division were isolated (rod shaped divides by elongation)
• Placed mutant S. Pombe (Could not divide in warm temp) DNA in S. Cerevisiaeand it was able to regain function
• Even when using human DNA the results were the same proving the protien for cell division is the same in yeast and humans and all eukaryotes
• Indicates that the mechanisms for reading coded DNA are also the same

Human Models

Human Models- In vitro- in glass (cells get cultured) In vivo- in living (cells get cultured) Not always possible

• When harvested some cells will continue to perform same functions outside organism (Ex. Beating / Forming connections)
• Organoids- Some embryo cells can be coaxed into differentiating into various cell types
• Humans can also be studied in clinics

Bonding in Water

Bonding H2O

• Two extremely polar H-O bonds due to O high attractiveness
• Positive charge due to two H (+) and one O (-)
• Liquid at room temp, high boiling point and surface tension

Hydrogen Bonding

Hydrogen Bonding- Weak Non covalent interation between positive H and negative O, N, or F of another molecule.

• Key to water molecule structure
• Easily broken by random thermal motions
• Can create a network of continually breaking and reforming bonds (water)
• Can occur in single parts of a large molecule

Hydrophilic- water loving, rapidly forms hydrogen bonds with water Hydrophobic- water fearing, unchanged portion of molecule and does not form hydrogen bonds

Non-Covalent Bonds

Non covalent bond- Chemical association that does not involve shared electrons, singly weak, network is strong Electrostatic attraction- force that draws together oppositely charged atoms (Ex. ionic bonds; Non covalent), When + positive parts + + and negative + - + parts of a large + molecule meet, + + - electrostatic + + interactions draw them together (proteins)

• Van der Waals attraction- Weak non covalent due to fluctuating electrical charges that come into play between two atoms located very close to each other (London Dispersion)

Length: Covalent < Noncovalent: Ionic < Noncovalent: Hydrogen bond < Noncovalent: Van der waals attraction Strength: Covalent > Noncovalent: Ionic > Noncovalent: Hydrogen bond > Noncovalent: Van der waals attraction