The Cell - PSY1630

The cell is the basic unit of life.

Taxonomy of living organisms:

Kingdom animalia

kingdom plantae

kingdom fungi

Kingdom Protista

Similarities between all cells:

1. an outer cell membrane - enclosing and isolating the intracellular from the extracellular space. Substances can move in and out with a specific mechanism.

2. DNA - contains genetic informations and all the molecules that copy/read these instructions.

3. Cytoplasm: everything between plasma membrane and dna, consists of cytosol and various components organelles and protein structures.

two basic types of cells : prokaryotic and eukaryotic

Prokaryotic cells - do not have defined nucleus separating Dna from the cytoplasm

Eukaryotic cells - have a well defined nucleus and other membrane systems like organelles that characterise these cells and represent different compartments of the cytoplasm.

small cells have a larger surface to area ratio allowing for more nutrients to pass into the cell and wastes to exit more efficiently; there is a limit to how large a cell can be and be an efficient and metabolically active cell.

A Eukaryotic cell/ typical animal cell includes 4 major parts:

• Cell membrane outer boundary of cell

• Cytoplasm holds the cellular organelles

• Cell organelles perform specific functions of the cell

• Nucleus control centre of the cell

Cellular Organelles

• Isolate and physically organise chemical reactions in cells

• Nearly all organelles have an outer membrane which separates the inside of the organelle from the cytosol and the rest of the cytoplasm

• Provide separate locations for activities to occur in steps.

Organelles with membranes

Nucleus - protecting and controlling access to DNA

Endoplasmic reticulum - Routing, modifying new polypeptide chains, synthesising lipids; other tasks

Golgi Body - Modifying nre polypeptide chains; sorting, shipping proteins and lipids

Vesicles - Transporting, storing, or breaking down substances in cell; other functions

Mitochondrion - Makes ATP; powerhouse of the cell

Lysosomes - Breaking down unwanted substances

Peroxisome - Inactivating toxins

Organelles without membranes

Ribosomes: Assembling polypeptide chains

Centriole - anchor for cytoskeleton.

The animal cell:

• nucleus

  • keeps Dna Away from potentially damaging reactions in Cytoplasm

• ribosomes

  • Attach to rough ER and free in cytoplasm; site of protein synthesis

• rough ER

  • Modifies new polypeptide chains

• Smooth ER

  • Makes lipids, degrades fats, inactivates toxins

• Golgi body

  • modifies, sorts, ships proteins and lipids for export or for insertion into cell membranes

• Lysosomes

  • Digests, recycled materials

• Plasma Membranes

  • controls all kinds and amounts of substances moving in and out of the cell.

• Centrioles

  • Special Centers that produce and organise microtubules

• Mitochondrion

  • Powerhouse of the cell: produces ATP through cellular respiration

• Cytoskeleton: Microtubules, microfilaments, Intermediate filaments.

  • structurally supports, and gives shape to the cell; moves cell and its parts.

Plasma membrane

• Chemically composed of phospholipids and glycolipids organised in the lipids bilayer.

• often referred to Fluid Mosaic: it is not solid because molecules within the cell membrane are dynamic rather than static and can move around

• Receives information that permits the cell to sense and respond to environmental changes: Hormones, growth factors, neurotransmitters

• communication with other cells and the organism as a whole. Surface proteins allow cells to recognise each other, adhere, and exchange materials.

Fluid mosaic model

• Phospholipid Bilayer: hydrophobic tails face inward; hydrophilic heads face water.

• Mosaic of proteins : proteins float in the phospholipid bilayer

• Cholesterol: maintains proper membrane fluidity

  • unsaturated hydrocarbon tails increase membrane fluidity

  • phospholipids move rapidly; proteins drift very slowly

  • Cholesterol: Alters fluidity

  • fluidity is increased at lower temp and decreased at warmer temperatures.

• the outer and inner membrane surfaces are different

Membranes contain two types of proteins:

1. Integral membrane proteins:

   1. inserted into the membrane

   2. hydrophobic region is adjacent to hydrocarbon tails

2. Peripheral membrane proteins

   1. attached to either the inner or outer membrane surface

Functions of membrane proteins

• transport of materials across membranes

• enzymes

• receptors of chemical messengers

• identification: cell-cell recognition

• Attachment: membrane to cytoskeleton, intercellular junctions.

Membrane carbohydrates

• found on the outside surface of the membrane

• used for cell-cell recognition

• includes: Glycolipids, Glycoproteins, Major histocompatibility proteins

• vary greatly among species

• organ transplant require matching cell markers/immune suppression.

Cell Membrane is selectively permeable

1. Non-polar hydrophobic molecules

   1. dissole into the membrane and cross with ease

   2. the smaller the molecule, the easier it can cross

   3. O2, hydrocarbons, steroids

2. Polar Hydrophilic molecules

   1. small polar uncharged molecules can pass easily such as h2o CO2

   2. Large polar uncharged molecules pass with difficulty such as glucose

3. Ionic hydrophilic molecules

   1. charged ions or particles cannot get through example: Na+, K+, Cl+

Passive transport:

Diffusion

Osmosis

Facilitated Transport

Active transport:

Endocytosis and Exocytosis

Active transport

Diffusion

Movement of a substance from an area of high concentration to an area of low concentration. Concentration gradient. Does not require energy.

Osmosis

the diffusion of water molecules across a semi-permeable membrane. From an area of high water concentration to an area of low water concentration. Solutes cant move across the semipermeable membrane.

1. Hypertonic solutions - higher osmotic pressure due to the higher solute concentration than cell or lower water concentration than cell

2. Hypotonic solution - Lower osmotic pressure than cell due to lower solute concentration than cell or higher water concentration than cell.

3. Isotonic solution: Same osmotic pressure than cell.

Facilitated Diffusion

some substances cant pass due to size/charge. Membrane proteins facilitate the transport of solutes down their concentration gradient. no cell energy is required. Transport proteins - specific only transport very specific molecules (binding site)

Active Transport

Proteins use energy from ATP to actively pump solutes across the membrane. Solutes move against the concentration gradient and therefore energy is required^{.; requires protein carrier.}

Endocytosis

Transports molecules or cells into the cell via invagination of the plasma membrane to form a vesicle. Requires cell energy.

• Pinocytosis - cell drinking, small droplets of liquid are taken into the cell through tiny vesicles. Not a specific process as all solutes in droplets are taken in.

• Phagocytosis - “cell eating” Large solid particles are taken in by cell.

  • example: Amoebas take in their food particles by surrounding them with cytoplasmic extensions called pseudopods, particles are surrounded by a vacuole, which later fuses with the lysosomes and contents are digested

• Receptors mediated endocytosis: highly specific, materials moved into cell must bind to specific receptors first.

Exocytosis

used to export materials out of the cell. Materials in vescilces fuse with the cel membrane and are released to outside

• example: Tear glands export salty solution, pancreas uses exocytosis to secrete insuin

• neurotransmitter release from neurons.

All animal nd plant cells show a resting membrane potential difference;

• cells are not permeable to only one ion, but they show different permeabilities to any of them and they can change over time

• The resting membrane potential difference results from the different ions involved and the membrane permeability to each of them

• In real life, to calculate the equilibrium potential we use an equation related to the nernst equation, called the goldman-hodgkin-katz equation

Resting Membrane Potential in summary

• Electrical membrane potential exists across the plasma membrane; negative inside, positive outside.

• the RMP depends on an unequal distribution of Na+ K+, Cl- ions across the membrane.

• The unequal distribution is the result of an equilibrium between an electrical gradient and a chemical gradient, Electrochemical gradient.

• this equilibrium depends on the permeability of the membrane to the different ions

• At equilibrium, there is a constant flow of ions in/out of the cells with no net changes in the electric charge across the membrane

• This equilibrium is maintained over time through the activity of the sodium/potassium pump.

• At equilibrium, the ions with the highest permeability set the membrane potential.

Endoplasmic reticulum

• network within the cell

• extensive maze of membranes that branches throughout the cytoplasm

• ER is continuous with the plasma membrane and outer nucleus membrane

Rough endoplasmic reticulum

• Flat, interconnected, rough membrane sacs - ribosomes

• synthesis and modification of proteins

• packing, storage and transport of proteins that are secreted from the cell, example: antibodies

Smooth endoplasmic reticulum

• network of interconnected tubular smooth membranes

• Synthesis of phospholipids, fatty acids, and steroids

• breakdown toxic compounds

• helps develop tolerance to drugs and alcohol

• regulates level of sugar released from liver into the blood.

• calcium storage for cell and muscle contraction.

Golgi apparatus

• stacks of flattened membrane sacs that may be distended in certain regions. sacs are not interconnected.

• Works closely with the ER to secrete proteins.

• Receives proteins in transport vesicles from ER

• Modifies proteins into final shape, sorts, and labels proteins for proper transport.

• Shipping side packages and sends proteins to cell membrane for export or to other parts of the cell.

• Packages digestive enzymes in lysosomes.

Lysosomes

• small vesicles released from golgi containing at least 40 different digestive enzymes, which can break down carbs, proteins, lipids, and nucleic acids

• Optimal pH of 5

• Found mainly in animal cells

• Molecular garbage dump and recycler of macromolecules like proteins

• Destruction of foreign material, bacteria, viruses, and old/damaged cell components

• Digestion of food particles taken in by cell

• Lysosomal membrane breaks down causing rapid self-destruction.

Lysosomes, aging, and disease

• as we get older our lysosomes become leaky, releasing enxymes which cause tissue damage and inflammation: arthritis

• Steroids or cortisone-like anti inflammatory agents stabilise lysosomal membranes, but have other undesirable functions

• Diseases from mutant lysosomal enzymes are usually fatal:

• Pompe’s disease: defective glycogen breakdown in liver. Tay-Sachs disease: Defective lipid breakdown in brain. Common Genetic disorder amongst jewish people.

Nucleus

• double nuclear membrane

• large nuclear pores

• DNA is combined with histones and exists in two forms: chromatin, chromosomes

• Nucleolus: Dense region where ribosomes are made

• Houses and protects cell’s genetic info

• Ribosome synthesis

Nucleotides consist of Nitrogenous base & Sugar & Phosphates

Nitrogenous base : purine is made up of adenine & guanine. Pyrimidine is made up cytosine, thymine, & uracil.

Sugar: ribose or Deoxyribose.

Guanine - cytosine

Adenine - Thymine

Mitochondria

site of cellular respiration

Kreb’s cycle - Food (sugar) + O2 ——→ CO2 + h20 + ATP

Changes chemical energy of moleculres into the useable energy of the ATP molecule.

Oval/sausage shaped

contains their own DNA , ribsosmes, and make some proteins.

Can divide to form daughter mitochondria

Structure:

• inner and outer membrane

• intermembrane space

• cristae - inner membrane extensions

• Matrix - inner liquid.

Where do eukaryotic cells come from

1. cell gains a nucleus by the plasma membrane invaginating and surrounding Dna with a double membrane

2. Cell gains endomembrane system by proliferation of membrane

3. Cell gains proto mitochondria

4. Cell gains proto chloroplasts.

Eukaryotic cells include protist, fungi, plant & animal cells

Nucleus: protects and houses dna

Membrane bound organelles: Internal structures with specific functions:

• separate and store compounds

• store energy

• work surfaces

• maintain concentration gradients

Mitochondria ENDOSYMBIOTIC THEORY

Euchromatin

• lightly packed form of chromatin

• enriches in genes

• often under active transcription

• most active portion of the genome within the cell nucleus

Heterochromatin

• tightly packed form of DNA

• multiple varieties

• lie on a continuum between two extremes of constitutive and facultative heterochromatin.

Both play a role in the expression of genes

all cells of a given species package the same regions of DNA in constitutive heterochromatin, and thus in all cells any genes contained within the cinstutive heterochromatin, will be poorly expressed.

In most organisms , constitutiive heterochromatin occurs around the chromosome centromere and near telomeres.

The reagions of DNA packaged in faculatitive heterochromatin will not be consistent between the cell types within a species, this a sequence in one cell that is packaged in facutative heterchromatin may be packaged in euchromatin in another cell.

However, the formation of facultative heterochromatin is regulated and is often assosiated with morphogenesis or differentiation.

Example:

X chromosome inactivation in female mammals: one X chromosome is packaged as a facultative heterochromatin and silences, while the other X chromosome is pacaged as euchromatin and is expressed.

Why DNa has to replicate

• replication takes place during the S phase

• DNA needs to be unpacked, generally the genetical material is contained as chromatin, DNA+PROTEIN (histones), threadlike fibers that condense further during the cell dividion to form chromosomes.

1. parent DNA molecule, two complementary strands of base paired nucleutides

2. Replication begins; two stranf unwind and seperate from eachother at the specific sites along the lenght of the DNA molecule

3. Each ‘old’ strand serves as a structural pattern for the addition of bases according to the base-pairing rule

4. Bases positioned on each old strand are joined together into a new stranf. Each half-olf, half-new DNA molecule is just like the parent molecule.

Summary of DNA REPLICATION

1. Helicases unwind the parental double helix

2. single-strang binding proteins stabilise the unwound parental dna

3. the leading strand is synthesised continously in the 5—→ 3 direction by DNA polymerase.

4. The lagging strand is synthesised discontinously. Primase synthesizes a short RNA primer, which is extended by DNA polymerase to form an Okazaki fragment

5. After the RNA primser is replaced by DNA, DNA ligase joins the ozaki fragment to the growning strand.

RNA

Dna contains genetic information of the cell and determines its structure and controls its functions through the synthesis of proteins (1 gene = 1 protein). Dna is like a commander in the army; it doesnt exert its influence directly: its work is carried out by RNA

RNA VS. DNA

ribose vs. deoxyribose

Uracil vs Thymine

Shorter strands and single strands in RNA

Different types of RNA

mRNA: messenger, used as a template to make proteins

rRNA: ribosomal, makes up ribosomes

tRNA: transfer, matches amino acids to mRNA to help make proteins

Ribosome

• Simple molecular machine

• site of biological protein synthesis

• They link amino acids together in the order specified mRNA molecules.

• the small ribosomal subunit: which reads the RNA

• the large subunit, which joins amino acids to form a polypeptide chain.

• each subunit is composed of one or more rRna molecules and a variety of ribosomal proteins

Transcription: mRNA synthesis

1. Initiation: RNA polymerase binds to DNA, the section which contains gene unwinds

2. Elongation: Rna bases bind to DNA creating a single strand of mRNA

3. Termination: mRNA and the RNA polymerase detach from the DNA, and the mRNA goes to the cytoplasm.

mRNA processing: splicing (?)

Translation: the genetic code

mRNA is transcribed from DNA, then subjected to processing. Processed mRNA leaves the nucleus and associates with ribosomes to begin the process of translation to synthesize a protein molecule.

Each tRNA molecule attached at one end to a specific amino acid. The anticodon of the tRNA molecule pairs with the appropriate codon on the mRNA, alloqing amino acids to be linked in the order specified by the mRNA code.