HAP_2e_Lecture_Ch03

Basic Processes of Cells

• Basic processes common to all cell types:
  • Cell metabolism
  • Transport of substances
  • Communication
  • Cell reproduction

Cell Metabolism

• Cell metabolism – sum of all chemical reactions that cell carries out to maintain life:
  • Anabolic reactions – building reactions; small molecules bonded together to form macromolecules
  • Catabolic reactions – break down macromolecules into smaller molecules
  • Oxidation-reduction reactions convert energy in chemical bonds of nutrients into a form of energy (ATP) cell can use to fuel its processes

Cell Transport and Communication

• Transport – substances cell has produced or ingested to variety of destinations
• Communication – between cell and itself, its surrounding environment, and other cells; chemical and electrical signals

Cell Reproduction

• Cell reproduction – by cell division; process necessary for
  • Growth and development
  • Replacement of old, damaged cells

Animal Cell Components

• Animal cell components:
  • Plasma membrane
  • Cytoplasm
  • Nucleus

Plasma Membrane

• Plasma membrane – surrounds each cell, isolating internal structures and processes from external environment:
  • Provides structural support, means of communication with its surroundings and other cells, and cell identification
  • Defines intracellular space (contains intracellular fluid (ICF) or cytosol); separates it from extracellular space (contains extracellular fluid (ECF))

Cytoplasm

• Cytoplasm consists of
  • Cytosol – intracellular fluid; mostly water with dissolved solutes, inclusions (storage molecules), and proteins; site of many important chemical reactions
  • Organelles – cellular machines with very specific functions; suspended in cytosol; separate potentially damaging chemical reactions from surrounding cell structures (compartmentalization)
  • Cytoskeleton – network of protein filaments; creates and maintains shape; holds organelles in place; provides transportation for substances within cell

Nucleus

• Most cells contain nucleus; single roughly spherical organelle:
  • Enclosed in phospholipid bilayer similar to plasma membrane (nuclear envelope)
  • Contains most of cell’s DNA; primary location for making most RNA
  • DNA and RNA control organelle functions by coding for and synthesizing proteins

Cell Size and Diversity

• Cell Size and Diversity:
  • Cells vary widely in size and structure; enable performance of specialized functions
  • Example of Structure-Function Core Principle

Phospholipid Bilayer

• For plasma membrane to form effective barrier between ECF and cytosol, phospholipid bilayer must have parts that
  • interact with water in both fluid compartments without falling apart
  • repel water, keeping ECF and cytosol separated

Phospholipids

• Phospholipids are amphiphilic:
  • Phosphate group (hydrophilic polar head) – face each fluid compartment
  • Two fatty acids (hydrophobic tails) – face one another

Fluid Mosaic Model - Plasma Membrane

• Fluid Mosaic Model – plasma membrane is dynamic fluid structure with multiple components; some have ability to move within bilayer as phospholipids move themselves

Membrane Proteins

• Membrane proteins – main component of plasma membranes; two basic types:
  • Integral proteins – span entire membrane; “transmembrane” proteins
  • Peripheral proteins – found only on one side of membrane or other

Functions of Membrane Proteins

• Functions of membrane proteins:
  • Channels – transmembrane proteins allow certain substances to cross membrane and pass into or out of cell
  • Carrier proteins – integral proteins bind, change shape, and directly transport substances into and out of cell – more regulated
  • Receptors – bind to chemical messengers (ligands); trigger sequence of events within cell; example of Cell-to-Cell Communication Core Principle
  • Enzymes – speed up chemical reactions; vital to maintaining homeostasis
  • Structural support – when bound to cytoskeleton
    • Give cells shape
    • Help maintain structural integrity
  • Link adjacent cells to one another:
    • Anchor cells within tissue
    • Allow cell-to-cell communication

Other Membrane Components

• Other membrane components – lipids, carbohydrates, glycolipids, and glycoproteins:
  • Cholesterol – lipid; stabilizes plasma membrane’s fluid structure during temperature changes
  • Glycolipids and glycoproteins – carbohydrate bound to either lipid or protein respectively; identify cell as part of body (cell recognition)

Drugs and Membrane Receptors

• Many drugs are designed to resemble membrane receptor ligands:
  • Agonists – mimic ligand’s actions; stimulate receptor (example: narcotic pain killers such as morphine mimic actions of endorphins)
  • Antagonists – inhibit ligand’s actions by blocking receptor (example: antihistamines block receptors for histamine)

Selective Permeability of Phospholipid bilayer

• Phospholipid bilayer is selectively permeable; allows certain molecules to cross; prohibits passage of other molecules; critical to survival of cell
  • Substance may cross plasma membrane in several ways:
    • Some do not require expenditure of energy (passive transport mechanisms)
    • Others do require energy (active transport processes)

Variables and passive/active transport

• Three variables determine how substance is able to move across plasma membrane by passive or active transport:
  • Type of substance
  • Plasma membrane permeability to substance
  • Concentration of substance in cytosol and ECF

Passive Transport

• Passive transport includes:
  • Diffusion – movement of molecules from area of high concentration to area of low concentration – no energy needed (e.g. breathing AKA Gas exchange of O2 and CO2 in lungs)
    • Diffusion has multiple types
      • Simple- solutes moved along a concentration gradient from hi to low
      • Facilitated diffusion- same as simple but through protein channels.
  • Osmosis

Concentration Gradient

• Concentration gradient – force that drives many types of passive transport
  • More dye molecules in fluid on bottom of beaker than top; difference is concentration gradient; form of potential energy
  • All molecules have kinetic energy as long as thermal energy (heat) is present; causes dye molecules to move
  • Continues until dye is uniform throughout container (equilibrium)

Diffusion

• Diffusion – movement of solute molecules from high to low concentration; move down (with) concentration gradient until equilibrium (no net movement) reached

Simple Diffusion

• Simple diffusion – mostly nonpolar solutes (oxygen, carbon dioxide, lipids, and hydrocarbons); pass through phospholipid bilayer without membrane protein

Facilitated Diffusion

• Facilitated diffusion – charged or polar solutes (ions and glucose); cross phospholipid bilayer with help of membrane protein (carrier or channel)

Osmosis

• Osmosis – passive process; solvent (usually water) moves across membrane
  • Water moves from area with lower concentration of solute (more water molecules) across membrane to area with higher concentration of solute (less water molecules)

Water Movement

• Water moves across plasma membranes by two methods:
  • Water passes through channel proteins (aquaporins); primary route for osmosis of water
  • Small amounts of water can pass through phospholipid bilayer directly

Water Concentration

• A – more concentrated glucose solution (right); B – less concentrated (left)
• During osmosis, water moves from solution with lower solute concentration to one with higher concentration (B to A)

Equilibrium of Water Movement

• At equilibrium, concentration of water molecules on either side of membrane is equal; gradient is gone
• Results in change in volume of fluid on each side; water molecules leave A (volume decreases); water molecules move into B (volume increases)
• Volume changes have important consequences for cells; discussed next

Osmotic and Hydrostatic Pressure

• Osmotic pressure – pressure applied to solution to prevent water from moving into it by osmosis
  * E.g. Pressure in kidneys to allow for some water loos but not all
• Hydrostatic pressure – force water exerts on walls of its container

Pressures in Osmosis

• How do osmotic pressure and hydrostatic pressure work in osmosis?
  • Part 1 – hydrostatic pressures in A and B are equal (both sides are equal volume)
  • Part 2 – as water level rises, hydrostatic pressure in B gradually increases; if A were pure water, water molecules would flow into B until hydrostatic pressure of B were equal to its osmotic pressure; net osmosis would stop

Osmotic Gradient

• Both sides have solute, so both sides have osmotic pressure
• Difference between osmotic pressures in sides A and B is osmotic gradient
• Osmosis will stop when hydrostatic pressure in B reaches value of osmotic gradient; if osmotic gradient is 10 mmHg, net osmosis will stop when hydrostatic pressure difference between A and B is equal to 10 mmHg

Water Movement in Osmosis

• Appears that water molecules are moving from higher water concentration to lower water concentration; can be a useful way to imagine osmosis

Osmosis vs Diffusion

• Osmosis and diffusion are two fundamentally different forces for three reasons:
  • Osmosis requires presence of membrane; diffusion does not
  • Osmosis is reversible; diffusion is not
  • Solute movement in diffusion can be predicted by Fick’s diffusion law; solvent movement in osmosis cannot

Tonicity

• Tonicity – way to compare osmotic pressure gradients between two solutions: cytosol and ECF
  • Normally ECF is isotonic to cytosol; both fluids have approximately same concentration of solute; no net movement of water across plasma membrane; no volume changes in either fluid compartment

Hypertonic ECF

• Hypertonic ECF – solute concentration of ECF is higher than inside cell; more water molecules inside cell than outside; osmotic pressure gradient pulls water out of cell; cell shrinks (crenates)

Hypotonic ECF

• Hypotonic ECF – solute concentration of ECF is lower than inside cell; more water molecules in ECF than inside cell; osmotic pressure gradient pulls water into cell; cell swells and possibly ruptures (lysis)

Exercise, Sports Drinks, and Water

• Strenuous exercise results in water and electrolyte loss (sweating); ECF becomes hypertonic; draws water out of cells by osmosis
  • Sports drinks (mixtures of water, electrolytes, and carbohydrates) are hypotonic; replenish lost water, making ECF mildly hypotonic to cells; water moves back into cells; restore normal cytosol concentration
  • Plain water rehydrates just as well; care must be taken in severe dehydration; can rehydrate cells too quickly or overhydrate (hypotonic ECF); results in cellular swelling and possibly water poisoning

Diffusion vs Osmosis

• Diffusion – movement of solute across plasma membrane from higher solute concentration to lower solute concentration (with concentration gradient)
• Osmosis – movement of solvent across plasma membrane from area of lower solute concentration to area of higher solute concentration
• Isotonic ECF has same ability to cause osmosis as cytosol; no net water movement happens when cell is in isotonic ECF

ECF ability

• Hypertonic ECF has greater ability to cause osmosis than cytosol; cell in hypertonic ECF loses water by osmosis
• Hypotonic ECF has lesser ability to cause osmosis than cytosol; cell placed in hypotonic ECF will gain water; cytosol has greater ability to cause osmosis

Active Transport

• Active transport processes require energy (ATP) to proceed as solutes move against concentration gradients (low to high concentration)
• Both primary and secondary active transport processes use plasma membrane carrier proteins (pumps)

Types of Pumps

• Three types of pumps in plasma membrane:
  • Uniport – transport single substance through membrane in one direction (into or out of cell)
  • Symport – transport two or more substances through membrane in same direction (into or out of cell)
  • Antiport – transport two or more substances in opposite directions through membrane

Primary Active Transport

• Primary active transport
  • Sodium-potassium pump (Na^+ / K^ +) pump or (Na^+ / K^+) ATPase) – most vital for maintenance of Na^+ and K^+ concentration gradient homeostasis
  • Na^+ concentration is ten times greater in ECF than cytosol; K^+ concentration is ten times greater in cytosol than ECF
  • Pump maintains steep concentration gradients by transporting 3Na^+ out and 2K^+ into cell (against concentration gradients) for every ATP molecule hydrolyzed

Secondary Active Transport

• Secondary active transport – uses ATP indirectly to fuel transport pump
  • ATP is used to create and maintain concentration gradient of one substance
• Secondary active transport (continued):
  • Moving this substance across plasma membrane down concentration gradient provides energy to move another substance against its gradient

Electrophysiology

• Introduction to Electrophysiology
  • Charge separation exists across plasma membrane
  • Thin layer of positive charges lines outside of membrane; thin layer of negative charges lines inside of membrane
• Introduction to Electrophysiology (continued):
  • Separation of charges creates electrical gradient; provides energy for work
  • Membrane potential – electrical potential across plasma membrane; lectrophysiology – study of these potentials
  • Resting membrane potential – membrane potential when cell is at rest; measured in millivolts (mV); value is negative, meaning inside of cell is more negative than surrounding ECF

Active Transport via Vesicles

• Active transport using carrier proteins and channels is effective but has limitations; large polar macromolecules are too big to fit:
  • Vesicles – small sacs filled with large molecules too big to transport by other means
  • Enclosed in phospholipid bilayer; allows fusion with or formation from plasma membrane or other membrane-bound organelles
  • Active transport process; requires energy from ATP

Endocytosis

• Endocytosis – fluid, molecules (even cells) taken into cell; two basic types:
  • Phagocytosis (“cell eating”) –cells ingest large particles like bacteria or dead or damaged cells or parts of cell

Pinocytosis

• Pinocytosis (fluid-phase endocytosis or “cell drinking”) – cells engulf fluid droplets from ECF

Receptor-mediated endocytosis

• Receptor-mediated endocytosis – special form of pinocytosis; receptors fill vesicles with specific molecule (cholesterol, hormones, iron)

Exocytosis and Transcytosis

• Exocytosis – large molecules exit cell (secretion); vesicles fuse with plasma membrane, opening into ECF
• Transcytosis – molecules brought into cell by endocytosis, transported across cell to opposite side, and secreted by exocytosis

Organelles

• Organelles – cellular machinery with specific functions vital to maintaining homeostasis; some separated from cytosol by membrane (compartmentalization); others not enclosed in membrane
  • Membrane-bound: mitochondria, peroxisomes, endoplasmic reticulum, Golgi apparatus, and lysosomes; functions could be destructive to rest of cell
  • Organelles not enclosed in membrane: ribosomes and centrosomes

Mitochondria

• Mitochondria; “power plant” of cell; membrane-bound organelles; provide majority of ATP:
  • Each has own DNA, enzymes, and ribosomes
  • Membrane is double bilayer; smooth outer membrane; inner membrane highly folded into cristae

Enzymes and Proteins

• Each membrane has own unique enzymes and proteins:
  • Outer – large channels allow molecules from cytosol to enter inner membrane space (between two phospholipid bilayers)
  • Inner – more selective; transports only necessary solutes into matrix (innermost space) using specific transport proteins
• Matrix contains mitochondrial DNA, proteins, and enzymes specific for breakdown of organic fuels by oxidative catabolism (produces ATP)

Peroxisomes

• Peroxisomes – membrane- bound organelles; use oxygen to oxidize organic molecules; produce hydrogen peroxide (H2O2) to
  • Oxidize toxins (like alcohol) in liver and kidney to less toxic compounds; eliminated from body before causing damage
  • Break down fatty acids into smaller molecules; used for ATP production or other anabolic reactions
• Peroxisomes (continued):
  • Synthesize certain phospholipids; critical to plasma membranes of specific cells of nervous system

Ribosomes

• Ribosomes; tiny granular nonmembrane-bound organelles; site of protein synthesis
  • Composed of large and small subunits; each made of ribosomal proteins and ribosomal RNA (rRNA)
  • Free in cytosol; usually make proteins needed within cell itself
  • Bound to membranes of other cellular structures; produce proteins destined for export outside cell, for export to lysosomes, or for insertion into membrane

Endomembrane System

• Endomembrane System:
  • Form vesicles that exchange proteins and other molecules; synthesize, modify, and package molecules produced within cell
• Endomembrane System (continued):
  • Components of system:
    • Plasma membrane
    • Nuclear envelope
    • Endoplasmic reticulum (ER)
    • Golgi apparatus
    • Lysosomes

Endoplasmic Reticulum (ER)

• Endoplasmic reticulum (ER) – large folded phospholipid bilayer continuous with nuclear envelope; two forms:
  • Rough ER (RER) – ribosomes attached to membrane
  • Smooth ER (SER) – no ribosomes

Rough ER

• Rough endoplasmic reticulum
  • Products enter RER lumen; incorrectly folded polypeptide chains detected; sent to cytosol for recycling
  • Most proteins entering RER are for transport out of cell
  • Packages secretory proteins into transport vesicles made of phospholipid bilayer; sent to Golgi apparatus for further processing
  • Produces membrane components for membrane-bound organelles and plasma membrane, including integral and peripheral proteins

Smooth ER

• Smooth endoplasmic reticulum (SER) – no role in protein synthesis
  • Stores calcium ions – pumped out of cytosol; for future use
  • Detoxification reactions – limits damage caused by certain substances
  • Lipid synthesis – manufacture majority of plasma membrane phospholipids and cholesterol; also number of lipoproteins and steroid hormones

Golgi apparatus

• Golgi apparatus – between RER and plasma membrane; group of flattened membranous sacs filled with enzymes and other molecules
  • Proteins and lipids made by ER are further modified, sorted, and packaged for export in Golgi
  • Products packaged in Golgi can be:
    • Secreted from cell (exocytosis)
    • Become part of plasma membrane
    • Sent to lysosome

Cystic Fibrosis

• Cystic fibrosis – some cells are missing protein component of chloride ion channel
  • Causes deficient chloride ion transport in lungs, digestive and integumentary systems; results in abnormally thick mucus; blocks airways, causes digestive enzyme deficiencies, and very salty sweat
  • Mutation causes chloride channel protein to misfold slightly in RER; protein therefore destroyed even though it would be functional if inserted into membrane
  • Disease is caused by “overprotective” RER

Lysosomes

• Lysosomes – organelles responsible for digestion of worn out cells or cellular components:
  • Contain digestive enzymes (acid hydrolases)
  • Macromolecules broken down into smaller subunits; released to cytosol for disposal or reused to manufacture new macromolecules

Endomembrane system events

• Summary of endomembrane system events:
  • (1a) SER makes lipids and (1b) RER makes proteins and (2) each product is packaged into vesicles for transport to Golgi
  • (3) Golgi sorts and further modifies both lipids and proteins; packs into vesicles; may take three pathways once exiting Golgi:
    • (4a) Sent to lysosomes to undergo catabolic reactions
    • (4b) Incorporated into plasma membrane or membrane of another organelle in cell
    • (4c) Sent to plasma membrane where secreted (exocytosis)

Lysosomal Storage Diseases

• Group of diseases resulting from deficiency of one or more acid hydrolases of lysosomes:
  • Gaucher’s disease – deficiency causes accumulation of glycolipids in blood, spleen, liver, lungs, bone, and sometimes brain; most severe form is fatal in infancy or early childhood
  • Tay-Sachs disease – glycolipids accumulate in brain lysosomes; leads to progressive neural dysfunction and death by age 4–5
  • Hurler syndrome – large polysaccharides accumulate in many cells (heart, liver, brain); death can result in childhood from organ damage
  • Niemann-Pick disease – lipids accumulate in lysosomes of spleen, liver, brain, lungs, and bone marrow; severe form causes organ damage and neural dysfunction

Cytoskeleton

• Cytoskeleton – dynamic structure; changes function based on needs of cell:
  • Gives cell its characteristic shape and size; creates internal framework
  • Provides strength, structural integrity; anchoring sites’ support plasma and nuclear membranes and organelles
  • Allows for cellular movement where protein filaments are associated with motor proteins
  • Performs specialized functions in different cell types; for example, phagocytosis by macrophages, or contraction by muscle cells

Types of Filaments

• Cytoskeleton contains three types of long protein filaments; each composed of smaller protein subunits; allow for rapid disassembly and reassembly
  • Actin filaments
  • Intermediate filaments
  • Microtubules

Actin filaments

• Actin filaments (microfilaments) – thinnest filament; composed of two intertwining strands of actin subunits
  • Provide structural support, bear tension, and maintain cell’s shape
  • Involved in cellular motion when combined with motor protein myosin

Intermediate filaments

• Intermediate filaments – ropelike; made of different fibrous proteins including keratin; strong, more permanent structures
  • Form much of framework of cell; anchor organelles in place
  • Help organelles and nucleus maintain both shape and size
  • Help cells and tissues withstand mechanical stresses

Microtubules

• Microtubules – largest filaments; hollow rods or tubes composed of tubulin; can be rapidly added or removed; allow for size and shape changes within cell
  • Maintain internal architecture of cell; keep organelles in alignment
  • Motor proteins dynein and kinesin allow transport of vesicles along microtubule network

Centrosome

• Microtubules extend out from centrosome (gel matrix containing tubulin subunits)
  • When cell is not dividing, centrosome is microtubule-organization center located close to nucleus
  • Pair of centrioles (ring of nine groups of three modified microtubules) is critical for cellular division
  • Basal bodies – modified microtubules on internal surface of plasma membrane where flagella and cilia originate

Cellular Extensions

• Cellular extensions are formed by inner framework of cytoskeleton:
  • Microvilli
  • Cilia
  • Flagella

Microvilli

• Microvilli – Finger-like extensions of plasma membrane with actin filament core; help maintain shape;
  • Increase surface area of cells in organs specialized for absorption

Cilia

• Cilia – Hair-like projections composed of microtubules and motor proteins
  • Move in unison to propel substances past cells
  • Found in great numbers on each cell

Flagella

• Flagella – Solitary; longer than cilia
  • Found only on sperm cells
  • Beat in whiplike fashion; propel entire cell
• Flagella and cilia are structurally similar to centrioles except they contain two central microtubules not found in centrioles

Primary Ciliary Dyskinesia

• Rare genetic disorder; defect in one or more protein components of cilia and flagella
  • Affects many types of cells: respiratory passage linings, middle ear, uterine tubes (females), sperm (males)
    • Leads to buildup of mucus in lungs; increases risk of infection; progressive damage due to repeated infections and mucus plugs
    • Repeated ear infections may lead to hearing loss
    • Males may be infertile due to lack of sperm motility

Nucleus

• Nucleus – governing body that directs activities of other cellular components; largely determines type of proteins and production rate:
  • DNA housed in nucleus contains code (plans) for nearly every protein in body
  • Plans (genes) within DNA are executed by several different types of RNA to build wide variety of proteins

Nucleus Structures

• Nucleus consists of three main structures:
  • Nuclear envelope – membrane that surrounds nucleoplasm (cytosol-like gel containing many components – water, free nucleotides, enzymes, other proteins, DNA, and RNA)
  • DNA and associated proteins in nucleoplasm are loose structural arrangement (chromatin)
  • One or more nucleoli are suspended in nucleoplasm

Nuclear Envelope

• Nuclear Envelope: double phospholipid bilayer similar to that of mitochondria:
  • Outer membrane – studded with ribosomes; continuous with endoplasmic reticulum
  • Inner membrane – lines interior of nucleus; supported by network of intermediate filaments (nuclear lamina)
  • Nuclear pores – large protein complexes; connect nucleoplasm with cytoplasm; allows substances to move between two locations

Chromatin

• Chromatin – one extremely long DNA molecule and associated proteins; organize and fold molecule to conserve space:
  • Nucleosome – strand of DNA coiled around group of histone proteins; like beads on string
  • Reduces length of strand by about one- third
• During cell division, chromatin threads coil tightly and condense into chromosomes:
  • Human cells contain two sets of 23 chromosomes; one maternal and one paternal set (46 total)
  • Sister chromatids – identical copies of each chromosome; made in preparation for cell division; connected to one another at centromere
• Nucleoli: (singular – nucleolus) nuclear region responsible for synthesis of ribosomal RNA and assembly of ribosomes

Protein Synthesis

• Protein synthesis – manufacturing proteins from DNA blueprint using RNA
  • Gene expression – production of protein from specific gene; includes two processes :
    • Transcription – gene for specific protein is copied; creates messenger RNA (mRNA); exits through nuclear pore
    • Translation – occurs in cytosol; mRNA binds with ribosome, initiating synthesis of polypeptide (specific sequence of amino acids)
  • DNA®Transcription®mRNA®Translation®Protein

Genes and Genetic Code

• Gene – long chain of nucleotides; determines sequence of amino acids in specific protein
  • Four different nucleotides in DNA (A,T, G, C); each set of three nucleotides (triplet) represents different amino acid; each amino acid may be represented by more than one triplet
  • During transcription each DNA triplet is transcribed into complementary RNA copy; each 3-nucleotide sequence of mRNA copy is codon
• During translation at ribosome, each codon is paired with complementary tRNA (anticodon) with its specific amino acid attached; amino acid will be added to growing peptide chain
• Genetic code – list of which amino acid is specified by each DNA triplet

Mutations

• Mutations – changes in DNA due to mistakes in copying DNA or induced by agents (mutagens)
  • Common mutagens include ultraviolet light and other forms of radiation, chemicals (benzene), and infection with certain viruses
  • DNA mutations are basis for many diseases (cancer)

Amanita phalloides - The Death Cap Mushroom

• Amanita phalloides (and other Amanita) – responsible for 95% of mushroom-related fatalities worldwide
  • Tasty and resembles many nontoxic mushrooms; main toxin inhibits RNA polymerase; prevents formation of new strands of mRNA
  • Stops protein synthesis; disrupts many cell functions, leading to cell death
  • No antidote exists, although some have shown promise
  • Liver suffers most damage; patients who survive generally require liver transplant

Transcription

• Transcription – process of making mRNA copy of DNA (transcript); exits nucleus through nuclear pore into cytoplasm to ribosomes
  • RNA polymerase – enzyme builds transcript; binds to gene; brings in complementary nucleotides, linking them together to form mRNA
  • Proceeds in three general stages:
    • Initiation
    • Elongation
    • Termination

Transcription - Initiation

• Initiation – beginning of transcription; protein transcription factors bind to promoter region near gene on template strand of DNA; RNA polymerase also binds to promoter; DNA unwinds with aid of enzyme helicase

Transcription - Elongation

• Elongation – RNA polymerase covalently bonds complementary (to DNA template) nucleotides to growing mRNA molecule

Transcription - Termination

• Termination – when last triplet of gene is reached and newly formed pre-mRNA molecule is ready for modification

Transcription - pre-mRNA modifications

• After transcription, transcript (pre-mRNA) isn’t ready; must first be modified in several ways
  • Noncoding sections of gene do not specify amino acid sequence (introns); sections that do specify amino acid sequence are exons

pre-mRNA modifications - steps

• 1st thing to do is add poly-A-tail (helps in exporting, maintaining and protecting mRNA) and G-Cap (protects the transcript from being broken down)
• 2nd - RNA processing – introns in pre- mRNA must be removed and exons spliced together
• When complete, mRNA exits nucleus through nuclear pore; enters cytosol, ready for translation into protein

Translation

• Translation – Occurs at ribosome; nucleotide sequence of mRNA is translated into amino acid sequence with transfer RNA (tRNA) - RNA that carries amino acid
  • tRNA – made in nucleus; picks up specific amino acids and transfers to ribosome

Anticodon

• Anticodon – on one end of tRNA; sequence of three nucleotides complementary to codon of mRNA
• Other end of tRNA carries specific amino acid molecule (which amino acid is determined by anticodon)

tRNA binding sites for Ribosomes

• Each ribosome has three binding sites for tRNA:
  • A site (aminoacyl site) – binds to incoming tRNA carrying amino acid - adds another anticodon with amino acid on top next to methionine
  • P site (peptidyl site) – amino acid is removed from its tRNA; added to growing peptide chain - forms peptide bond through condensation
  • Empty tRNA then exits ribosome from E site (exit site); free to pick up another amino acid

Translation - steps

• Translation is organized into three stages (like transcription):
  • Initiation – initiator tRNA binds to mRNA start codon in ribosome’s P site
• Translation (continued):
  • Elongation – next tRNA binds to open A site; allows two amino acids to be linked by peptide bond; first tRNA exits from E site; second tRNA moves into P site; A site is open for next tRNA to bind
• Translation (continued):
  • Termination – end of translation; when ribosome reaches stop codon on mRNA and new peptide is released (UAA, UAG, UGA = stop codons)

Polypeptides

• Newly formed polypeptides must be modified, folded properly; sometimes combined with other polypeptides to become fully functional proteins; called posttranslational modification
  • Polypeptides destined for cytosol – synthesized on free ribosomes; fold either on their own or with help of other proteins
  • Polypeptides destined for secretion or insertion into an organelle or membrane – many require modification in RER; synthesized on bound ribosomes; sent to Golgi apparatus for final processing, sorting, and packaging

Connecting a DNA Triplet to a Particular Amino Acid

• tRNA anticodon nucleotides are same as those in DNA triplet, except that nucleotide T in DNA is replaced by U in tRNA

Cell Cycle

• Cell theory – cells cannot spontaneously appear; must come from division of cells that already exist; all forms of life result from repeated rounds of cell growth and division
• Almost all cells go through cell cycle; ordered series of events from formation of cell to its reproduction by cell division
• Cell division is required for growth and development as well as for tissue repair and renewal

Main Phases of Cell Cycle

• Cell cycle main phases: interphase and M phase (cell division)
• Interphase – period of growth and preparation for cell division; 3 subphases:
  • G1 phase (1st gap) – cell performs normal daily metabolic activities (production of new organelles, cytoskeleton, and other proteins); prepares cell for next phase
  • S phase (synthesis) – DNA synthesis (replication) occurs; vital for cell to proceed to next phase
  • G2 phase (2nd gap) – cellular growth; proteins required for cell division are rapidly produced and centrioles are duplicated

DNA synthesis or replication

• DNA synthesis or replication occurs in S phase; chromatin unwinds; each base pair is duplicated using existing DNA strand as template to build new strand:
  • DNA strands separated by enzyme helicase - breaks H bonds - moves 5' to 3' end (will use strand that starts at 3')
  • Strand used is the leading strand – helicase attaches roto this strand
  • Enzyme primase builds RNA primer on exposed DNA strands
    • RNA primase takes tiny pieces of RNA (RNA primer) and puts on lagging strand (15-16 long), spaces in between (pieces called okazaki fragments)
    • RNA polymerase I changes RNA primers to DNA primers (changes uracil to thyamine) and fills in the gaps by adding missing neucloties betweek okazaki fragments = still fragments, not attached
    • DNA ligase – joins pieces together on lagging strand

DNA replication

• DNA replication (continued):
  • DNA polymerase – (enzyme) adds nucleotides to RNA primer; necessary as enzyme can only add to existing chain of nucleotides
  • Enzyme proceeds in opposite directions along each strand as helicase separates them; RNA primers eventually removed and replaced with DNA nucleotides

End result of DNA replication

• DNA replication (continued):
  • End result is two identical double helices each with one old and one new strand; semiconservative replication; cell then proceeds into G2 phase

M Phase - Cell Division

• M phase (cell division) – two overlapping processes: mitosis and cytokinesis:
  • Mitosis = division of the nucleus
  • Cytokinesis = cell’s proteins, organelles, and cytosol are divided between two daughter cells AKA division of cytoplasm

Mitosis

• Mitosis – newly replicated genetic material is divided between two daughter cells
  • Makes all cells except gametes
  • En up with 2 daughter cells (copy of mother cell)
    • If cells not identical = mutation = can lead to cancer (unregulater cell divition)
• Interphase
  • Nuclear envelope encloses nucleus
  • Centriole pairs duplicated
  • Nucleus and nucleolus are clearly visible; individual chromosomes not distinguishable

4 stages of Mitosis

• Mitosis – division of genetic material; four stages:
  • Prophase
  • Met