Essay: Exploring Cell Structure and Function: The Complexities of Life



PART –I- CELL AND MOLECULAR BIOLOGY

I.A ORIGIN OF LIFE

I.B CELL STRUCTURE

I.C ORGANELLE STRUCTURE AND FUNCTION

I.D CELLULAR PROCESSES

I.E THERMODYNAMICS

I.F CELL METABOLISM (INCLUDING PHOTOSYNTHESIS/ENZYMOLOGY)

I.G MITOSIS/MEIOSIS

I.H BIOMOLECULES

I.I EXPERIMENTAL CELL BIOLOGY

 

PART A CELLULAR AND MOLECULAR BIOLOGY

I.A ORIGIN OF LIFE

I.A.1 Cell Theory:

• All living things are composed of cells

• Cell is the Basic functional Unit of life

• Chemical reactions of life take place inside the cell

• Cells arise only from pre-existing cells

• Cells carry genetic information in the forms of DNA. This genetic material is passed fro parent cell to daughter cell.

Theory of endosymbiosis: eukaryotes emerged when mitochondria and chloroplasts; once free living prokaryotes, took up permanent residence inside other larger cells. ~1.5 bya

All Cells Prokaryotes (1-10um) Eukaryotes (10-100um)

• Enclosed by plasma membrane

• Contain cytosol

• Contain ribosomes & genetic material • No Internal membranes

• Circular, naked DNA

• Very small ribosomes

• Metabolism is anaerobic or aerobic

• Cytoskeleton absent

• Mainly Unicellular • Distinct membrane bound organelles

• DNA wrapped with histone proteins into chromosomes

• Large ribosomes

• Metabolism is aerobic only

• Cytoskeleton present

• Mainly multicellular with differentiation of cell types

I.B CELL STRUCTURE

I.C ORGANELLE STRUCTURE AND FUNCTION

Nucleus: surrounded by nuclear envelope, contains chromosomes

Nucleolus: Combines proteins imported from the cytoplasm with rRNA made in the nucleolus. Not membrane bound structures, but are actually a tangle of chromatin and unfinished ribosomal precursors.

Ribosome: “protein factories”, found free in cytoplasm or bound to ER (rough ER)

• Free Ribosomes : proteins for cells own use

• ER Ribosomes: proteins for export out of cell

Peroxisomes: contain catalase; converts hydrogen peroxide (H2O2) → into water + O2, also detoxifies alcohol in liver

Endomembrane system: regulates protein traffic and performs metabolic functions. Includes; Nuclear envelope, E.R., Golgi Apparatus, lysosomes, Vesicles, Vacoules, & plasma membrane.

Endoplasmic Reticulum:

• Rough ER: w/ ribosomes → proteins

• Smooth ER:

o Assists in the synthesis of steroid hormones + other lipids

o Stores Ca++ ions in muscle cells to facilitate normal muscle contraction

o Detoxifies drugs and poisons from the body

Golgi Apparatus: Process & Package substances produced in rough E.R.

Lysosomes: Sacs of hydrolytic (digestive) enzymes surrounded by a single membrane; principle site of intracellular digestion (autophagy). Apoptosis→ programmed cell death. (lysosomes are not generally found in plants).

Vesicles:

Vacuoles: “storage” large vesicle derived from the E.R. and Golgi

• Mature cells generally have a single large central vacuole

• Fresh water protists have contractile vacuoles to pump out water

• Food Vacuoles are formed by the phagocytosis of foreign material

Mitochondria: “site of Cellular Respiration” outer double membrane  & inner series of membranes called Cristae. Contain their own DNA

Chloroplasts: Contains Chlorophyll. Found in plants and algae. Have double outer membrane along with inner membrane system called thylakoids.

Cytoskeleton:

• Maintains cell shape

• Controls position of organelles within the cell

• Involved with flow of the cytoplasm, “Cytoplasmic Streaming”

• Anchors cell in place by interacting with extracellular elements

• Cytoskeleton includes microtubules & Microfilaments

Microtubules: hollow tubes made of protein tubulin that make up cilia, flagella, and spindle fibers.

Microfilaments: assembled from actin filaments and help support shape of the cell

Centrioles, Centrosomes: two centrioles oriented @90o to each other make up one Centrosome and consist of 9 triplets of Microtubules arranged in a circle. Plant cells lack centrosomes but have MTOC’s. In animal cells, the MTOC is synonymous with centrosome.

Microtubule Organizing Center (MTOC): non-membranous structures that lie outside the nuclear membrane. Organize spindle fibers and give rise to the spindle apparatus. REQUIRED FOR CELL DIVISION.

Plasma Membrane:

• Fluid Mosaic Model: (S.J. Singer 1972) – Selectively permeable membrane, constantly moving around, everything is not fixed

• Eukaryotic Cell: Phospholipid bilayer – amphipathic- hydrophobic/hydrophilic

• Integral Proteins: have nonpolar regions that span the hydrophobic interior

• Peripheral Proteins: loosely bound to the surface of the membrane

• Cholesterol Molecules: are embedded in the interior of the bilayer to stabilize the membrane.

• Average membrane: ~40% lipid & 60% proteins

• Some proteins are attached to cytoskeleton, while some drift.

• Glycolipids: (carbohydrate covalently bound to lipids) Glycoproteins ( carbohydrate covalently bound to proteins) → both may serve as signaling structures to distinguish cell type.

Cell Wall

• Plant & Algae: made of Cellulose

• Fungi: made of Chitin

• Middle Lamella: thin layer formed when a plant cell divides into two new cells.

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I.D CELLULAR PROCESSES

I.D.1 PASSIVE TRANSPORT

passive transport: movement of molecules down a concentration gradient from gradient of [High] → [Low] until an equilibrium is reached.

• Simple Diffusion: does not involve protein channels

• Facilitated Diffusion: involves protein channels, hydrophilic protein channel

• Counter Current Exchange: Special case of simple diffusion; the flow of adjacent fluids in opposite directions that maximize the rate of simple diffusion ( seen in fish gills) (Does this play in the loop of Henle?)

• Diffusion: random movement of molecules or other particles form a higher concentration to a lower concentration.

• Osmosis: Diffusion of water

Solvent: substance that does the dissolving

Solute: Substance that is dissolved

Hypertonic: greater concentration of Solute than another solution

Hypotonic: Lesser concentration of solute than another solution

Isotonic: two solutions containing equal concentrations of solutes

Plasmolysis: process by which a cell loses water in hypertonic solution

Cytolysis: Swelling of a cell in hypertonic solution

Osmotic Potential: tendency of water to move across a permeable membrane into a solution

Water Potential: results from two factors; solute concentration and pressure. Water potential of pure water =0; water potential inside a cell is negative. Water will move from a high water potential to a lower water potential.

Turgid: a cell that is ‘swelled’ (plant cell)

Turgor Pressure: keeps plants full with water “crisp” plays a role in regulation of stomata.

Aquaporins: special water channel proteins found in certain cells that facilitate the diffusion of massive amounts of water across a cell membrane.

I.D.2 ACTIVE TRANSPORT

movement of molecules against a gradient (requires energy)

• Sodium Potassium Pump: moves Na+ and K+ ions against a gradient, pumping two K+ ions for every three Na+ ions. (Na+ → outside; K+ ions inside of cell) (necessary for action potential)

• Electro Transport Chain: consists of proteins that pump protons across the cristae membrane (mitochnidria) (H+ → outside CHECK THIS)

• Contractile Vacoule: in fresh water Protista pumps excess water that has duffue inward because the cell lves in a hypertonic environment.

• Exocytosis: IN nerve cells occurs as vesicles release neurotransmitters into a synapse.

• Pinocytosis: “cell drinking”  uptake of large, dissolved particles

o plasma membrane invaginates around the particles and encloses them in a vesicle.

• Phagocytosis: “cell eating” engulfing of large particles or small cells by pseudopods. Cell membrane warps around the particle and encloses it in its vacuole.

• Receptor-mediated endocytosis: large quantity take-up of specific molecules. ( once ligand binds receptor, receptor migrate & cluster turning inward and becoming a coated vesicle that enters the cell. (ex: cells take in cholesterol this way)

• Bulk Flow: overall movement of a fluid in one direction in an organism. (GIVE EXAMPLE)

I.D.3 CELL COMMUNICATION

Quorum Sensing:  bacterial cells secrete molecules that enable them to respond to changes in their population density. (ex bioluminescence in the bacteria vibro fischer)

Gap Junctions: cytoplasm-cytoplasm of adjacent cells. (muscle tissue of heart)

Paracrine Signaling:  release of local signals, such as growth factors form one cell to near-by cells.

Synaptic Signaling: how a neuron releases neurotransmitters into a synapse

Long Distance Signaling:

• Characteristic of the endocrine system in which hormones released by endocrine gland circulate the blood to reach target organ,

• Helper T cells send out an alarm to the entire immune system (more specific)

I.D.4 RECEPTORS

Cell Surface Receptors:

• Hydrophilic signaling molecules cannot diffuse through cell membrane, so they bind to receptors on the cell surface, that change shape on the inside → once inside, the signal is carried by a second messenger. (first messenger (Ligand) enters the cell. (cyclic AMP: most common second messenger)

A) Ion Channel Receptors: an allosteric receptor that opens and shuts a gate in a membrane allowing an influx of ions, Na+, K+, Ca2+, Cl-, ions.  (example: acetylcholine receptor; located in the plasma membranes of the skeletal muscle cells. Binding allows Ca2+ to diffuse into the muscle cell → muscle contraction.)

B) G-protein Coupled Receptors (GPCR): span the entire cell membrane” – signaling molecule → extracellular domain of receptor → conformational change of cytoplasmic domain → → → cAMP

C) Receptor Tyrosine Kinases (RTK’s): characterized by having enzymatic activity

• Catalyzes the transfer of phosphate groups of ATP to the A.A. Tyrosine

• Before binding; receptors exist as individual units

• After binding; individual units aggregate and activate the tyrosine kinase region which bonds to ATP.

Cytoplasmic Receptors:

• Small non-polar ligands diffuse directly through plasma membrane and bind to intracellular. (EX: such hydrophobic chemical messengers include; steroids, thyroid hormones, and NO (Nitric oxide), a gas that readily diffuses across the plasma membrane and switches genes on or off.)

I.F CELL METABOLISM

I.F.1 CELLULAR RESPIRATION

C6H1206 + 6O2 → 6CO2 + 6H2O + ENERGY

There are two types of cellular respiration:

1) anaerobic respiration: (oxygen not present)

• glycolysis; followed by alcoholic fermentation or lactic acid fermentation

2) aerobic respiration: (oxygen present)

• Glycolysis folloed by citric acid cycle “krebs cycle”, then the Electron Transport Chain, and Oxidative phosphorylation.

Adenosine Triphospate – ATP

• Consists of adenosine (adenine + ribosome) plus 3 phosphates

• ATP is unstable b/c the three phopsphates repel each other

• ATP → ADP releases Energy

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I.F.2 GlYCOLYSIS

2 ATP + 1 GLUCOSE → 2 PYRUVATE + 4 ATP

Ten step process that breaks down one molecule of glucose (6 carbon) into two 3 carbon molecules called Pyruvate or pyruvic acid and releases 4 molecuels of ATP BUT; it uses 2 ATP) Net Gain = 2 ATP.  Note: pyruvate is the raw material for the krebs cycle

• The ATP produced in  glycolysis is produced at substrate level phosphorylation – direct enzymatic transfer of phosphate to ADP

• Phosphofructokinase (PFK): enzyme that catalyzes the 3rd step in glycolysis; PFK is an allosteric enzyme, which inhibits glycolysis when theres enough ATP in the cell (HIGH ATP → inhibition of PFL → Low Glycolysis)

Structure of the Mtichondria:

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I.F.3 NAD+ and FAD:

“carry protons & electrons from glycolysis and the citric acid cycle to the electron transportation”

• Nicotinamide adenine dinucleotide (NAD+)    both co-enzymes & vitamin derivatives

• Flavin adenine dinucleotide (FAD)  /

NAD+ & FAD: oxidized form

NADH & FADH2: reduced form

• NADH carries 1 proton and 2 electrons

I.F.4 The Electron Transport Chain:

I.F.5 SUMMARY OF ATP PRODUCTION

ATP is produced in two ways:

1. Substrate level phosphorylation: when an exyme, a kinase, transfers a phosphate from a substrate directly to ADP

2. Oxidative phosphorylation: occurs during chemiosmosis (90% of all ATP produced in respiration is produced this way)

I.F.6 ANAEROBIC RESPIRATION (FERMENTATION)

• Catabolic process that consists of glycolysis + alcohol or lactic acid fermentation

• There are two types of anaerobes:

1. Facultative Anaerobes: simply do not use oxygen

2. Obligate anaerobes: cannot live in an environment containing oxygen Fermentation consists of glycolysis plus the reactions to regenerate NAD+ (necessary for anaerobic ATP production)

There are two types of Fermentation:

1. Alcohol Fermentation: pyruvate → ethyl alcohol and carbon dioxide, and oxidizes NADH → NAD+

2. Lactic Acid Fermentation: pyruvate → lactic acid or lactate, and oxidizes NADH back to NAD+

NOTE: Fermentations sole purpose is to oxidize the electron carriers so that glycolysis can continue in the cell. This can happen in muscle cells in the body under extreme exertion ?????

I.F.7 PHOTOSYNTHESIS

6 CO2 + 12 H20 + LIGHT → C6H12O6 + 6O2

Two main parts:

1. Light dependent reactions: use light to produce ATP to power the light independent reactions

2. Light Independent reactions: consists of the Calvin cycle which produces sugar

Photosynthetic Pigments:

• Absorb light; two major groups; chlorophylls and carotenoids

Chlorophyll a & b: are green and absorb all wavelengths in the red, blue, and violet range

Carotenoids: are yellow, orange, and red, and absorb blue, green, violet range (xanthophyll is a caratanoid w/ slight different variation)

Phycobilins: pigments found in red algae, absorb blue-green range

Antenna pigments: non-chlorophyllic pigments which pass electrons onto chlorophyll A

Chlorophyll a Structure:

• Head: single Mg surrounded by a poryphyrin ring (alternating double bonds; conjugation)

• Tail: hydrocarbon tail

The Chloroplast:

• Grana: consists of layers of membranes called thylakoids “light-dependent”

• Stroma: where light independent reactions occir

Photostems: light harvesting complexes in the thylakoid membranes (contains rxn center: chlorphyll a + antenna pigments) two types

• PSII: “PS680” operates first

• PSI: “PS700” operates second

There are two possible routes for electron flow:

1. Non-cyclic flow

2. Cyclic phosphorylation

NON-CYCLIC PHOSPHORYLATION

Step 1: Photostem II –P680: Energy → electrons in double bonds of head INCREASE

Step 2: Photolysis: provides electrons to replace the ones in chlorophyll A tgat jumped up in energy

• Photolyisis: splits water: H2O → 2H+ + 2electrons + O2 (waste)

Step 3: Electron Transport Chain: electrons from P680 → move through several proteins cytochromes → to P700 (electron flow is exergonic) → used to produce ATP via chemiosmosis “photophosphorylation” – from late.

Step 4: Chemiosmosis: protons released from photolysis pumped from stroma → thylakoid space (lumen) as these H+ diffuse through the ATP synthesis channels → back to stroma (ATP produced here powers the calvin cycle)

Step 5: NADP becomes reduced as it picks up (H+) from water in P680 → NADPH carries H+ to Calvin Cycle

Step 6: Photostem I (P700): electrons from Chlorophyll A becomes energized and captured by a primary electron receptor

• Electrons are replaced with electrons from P680 (instead of H20 like in Photostem II)

• Produces NADPH, not ATP (electron transport chain)

OVERVIEW

LIGHT → P680 (O2 RELEASED) → ATP PRODUCED → P700 → NADPH PRODUCED (NADPH carries H+ to the Calvin Cycle)

CYCLIC PHOSPHORYLATION

• Sole Purpose is to produce ATP (NO NADPH is produced and NO O2 released

• When chloroplasts run low on ATP they carry out cyclic Photophosphorylation

• Electrons travel from P680 e- transport chain to P700, to a primary e- acceptor and then back to the cytochrome complex in P680

THE CALVIN CYCLE

The process that occurs is carbon fixation!!!

Step 1: CO2 enters Calvin Cycle & becomes attatched to a 5-Carbon sugar; Ribulase biphospate (RuBP) forming a 6 Carbon molecule

Step 2: 6 Carbon molecule breaks down into two 3 carbon molecules (3-PGA)

Final Product = the three carbon sugar, (PGAL) phosphaglycaroldyn ?

I.G MITOSIS/MEIOSIS

MTOC: Microtubule Organizing Center: a.k.a a centrosome; in animal cells each contain a pair of centrioles

Note: a centromere is the region on the chromosome that links sister chromatids together

A kinetochore: is a protein complex on the centromere, which is necessary for attachment of spindle fibers.

MITOSIS: Produces 2 Diploid (2N) clones

Prophase:

1. Nuclear Envelope disappears

2. Chromosomes Condense

3. Spindle apparatus forms

Metaphase: Chromosomes line up @ metaphase plate

Anaphase: Spindle fibers pull apart sister chromatids

Telophase:

1. Two new nuclear envelopes develop

2. Chromosomes spread out

3. Spindle breaks down

Cytokinesis: dividing of cytoplasm which usually starts in Anaphase

• Animal Cell: Actin & Myosin Pinch cytoplasm → Cleavage Furrow

• Plant Cell: Cell Plate forms during telophase (vesicle from golgi)

Interphase: (M: Mitosis, G0, G1, S, G2)

• G0: arrested development (M Checkpoint: was everything done successfully)

• G1: Intense growth + biochemical pathway (G1 Checkpoint)

• S-Phase: “synthesis” of replication of DNA

• G2: “checkpoint” Needs Sufficient Mitosis Promoting Factor (MPF) to proceed

MEOSIS: produces 4 haploid (1N) daughter cells. For Sexual reproduction

Prophase I:

• Nucleus Dissasembles:

• Nucleolus Dissapears

• Nuclear Envelope breakds down

• Chromatin Condenses

• Spindle Develops

• Crossing over

Syapses: homologyous chromosomes pair up. These paurs are known as tetrads (4 chromosomes)

Chiasmata : region where crossing over occurs of non-sister chromatids.

Synaptonemal complex: protein structure that temporarily forms between homologous chromosomes → giving rise to the tetrad w/ chiasmata & crossing over.

Metaphase I: homologous pairs spread across metaphase plate. MT attached to kinetochores of one member of ech homologous paurs. (MT from other side atatches to 2nd member)

Anaphase I: Homologoes within tetrads uncouple and are pulled to opposite sides (disjungtion)

Telophase I: Nuclear membrane Develops. Each pole forms new nucleus that has half number of chromosomes. (from homologous pair to each chromosome = sister chromatids)

Meiosis II:

Prophase II: Nuclear Envelope disappears & Spindle develops etc. No Chiasmata, No Crossing over

MetaphaseII: chromosomes align on plate like in mitosis bit now with half # of chromosomes

Anaphase II: each chromosome is pulled in to 2 separate chromatids & migrate to opposite poles

Telophase II: Nuclear Envelope reappears & cytokinesis occurs → haploid cells (each chromosome = 1 chromatid)

I.H BIOMOLECULES

I.I EXPERIMENTAL CELL BIOLOGY