Biol 155Biol 155Human Human

PhysiologyPhysiologyInstructor: Dr. Robert HarrisInstructor: Dr. Robert Harris

Office: 1354 Biological Office: 1354 Biological SciencesSciences

Phone: 822-5709Phone: 822-5709

Email: Email: harris@zoology.ubc.caharris@zoology.ubc.ca

Course requirements:Course requirements: Texts:Texts: Fundamentals of Anatomy and Fundamentals of Anatomy and

Physiology 6Physiology 6thth ed. Frederic ed. Frederic H. MartiniH. Martini

Anatomy & Physiology Coloring Anatomy & Physiology Coloring Workbook, Workbook, 77thth ed. Elaine Marieb ed. Elaine Marieb

Read course synopsis!!!Read course synopsis!!! Failure to read it, or Failure to read it, or failure to listen to what I say does not constitute failure to listen to what I say does not constitute an excuse an excuse

Lecture Notes and synopsis are posted at: Lecture Notes and synopsis are posted at: http://www.science.ubc.ca/~biomania/biol153/lehttp://www.science.ubc.ca/~biomania/biol153/lecture/main01.htmcture/main01.htm

Mark BreakdownMark Breakdown

Biol 153:Biol 153: Lecture: Lecture: 60%60%

Lab:Lab: 40%40%

Course Total: 100%Course Total: 100%

The The lecture marklecture mark is based on: is based on: One mid-term exam in One mid-term exam in eacheach term: term: 20% 20% (10% (10%

each)each)

Winter exam:Winter exam: 20%20%

Final exam:Final exam: 20%20%

Total:Total: 60%60%

Mark Breakdown cont.Mark Breakdown cont.

Biol 155: Biol 155: marks will be based solely on the lecture marks will be based solely on the lecture

exams, which will be weighted as follows:exams, which will be weighted as follows: One mid-term exam in One mid-term exam in eacheach term: term: 30% 30%

(15% each)(15% each) Winter exam:Winter exam: 35% 35% Final exam:Final exam: 35% 35% Total:Total: 100% 100%

Atomic structure and Atomic structure and elementselements

An element is a substance that An element is a substance that retains its chemical and physical retains its chemical and physical characteristics even when it is characteristics even when it is broken down into its smallest units.broken down into its smallest units.

The smallest practical unit, for our The smallest practical unit, for our purposes is the atom.purposes is the atom.

The chemical The chemical characteristics are characteristics are

determined by the number determined by the number of protonsof protons

These are the These are the three forms of three forms of hydrogenhydrogen

All three have All three have one electronone electron

All three have All three have one protonone proton

Electron orbitsElectron orbits Number of Number of

electrons electrons generally equals generally equals number of protons.number of protons.

There are specific There are specific orbits (or shells), orbits (or shells), that contain a that contain a specific maximum specific maximum number of number of electronselectrons

Charged atomsCharged atoms

Atoms are most stable when Atoms are most stable when there are 8 electrons in the there are 8 electrons in the outermost shell.outermost shell. In order for the outermost In order for the outermost

shell to be filled, atoms will shell to be filled, atoms will either take in or give off either take in or give off electrons. When this happens electrons. When this happens there is a change in net there is a change in net charge.charge.

Charged atoms (ions) can be Charged atoms (ions) can be electrically attracted electrically attracted (opposite charges attract) (opposite charges attract) This is known as ionic bondingThis is known as ionic bonding Ionic bonds are fairly weakIonic bonds are fairly weak

Covalent bondsCovalent bonds Another way atoms can Another way atoms can

fill their outer shell is fill their outer shell is to share electrons with to share electrons with another atomanother atom

The electrons orbit The electrons orbit around BOTH nuclei around BOTH nuclei

This is known as a This is known as a covalent bondcovalent bond

Covalent bonds are Covalent bonds are much stronger than much stronger than ionic bondsionic bonds

Molecular dipolesMolecular dipoles

When covalent bonds When covalent bonds are formed, the are formed, the electrons may not be electrons may not be shared equally between shared equally between the atomsthe atoms

This unequal sharing This unequal sharing can result in an uneven can result in an uneven distribution of electrical distribution of electrical charges on the charges on the moleculemolecule This is known as a partial This is known as a partial

charge, or a dipolecharge, or a dipole

Hydrogen bondingHydrogen bonding Water molecules Water molecules

interact with each other interact with each other electricallyelectrically

The partial negative The partial negative charge around the charge around the oxygen is attracted to oxygen is attracted to the partial positive the partial positive charge around the charge around the hydrogenhydrogen

These very weak These very weak electrical attractions are electrical attractions are called hydrogen bondscalled hydrogen bonds

Ions in aqueous solutionIons in aqueous solution Water molecules can form hydrogen bonds with ionsWater molecules can form hydrogen bonds with ions Ions in solution have a layer of tightly bound water Ions in solution have a layer of tightly bound water

molecules around themmolecules around them This layer of water molecules is known as the This layer of water molecules is known as the

hydration spherehydration sphere Water can form hydrogen bonds with uncharged Water can form hydrogen bonds with uncharged

molecules as well (providing there is a partial molecules as well (providing there is a partial charge)charge)

pH is the negative log (the small p) of the pH is the negative log (the small p) of the hydrogen concentration (the large H)hydrogen concentration (the large H)

In pure water, some of the H2O molecules In pure water, some of the H2O molecules will dissociate into Hwill dissociate into H++ and OH and OH- -

The HThe H++ concentration in pure water is 0.1 concentration in pure water is 0.1 mM, or 1x10mM, or 1x10-7-7 moles/L (hence pH 7) moles/L (hence pH 7)

Molecular Molecular RepresentationsRepresentations

There are several There are several ways or ways or representing representing molecular molecular structuresstructures

Here are three Here are three representations of representations of glucoseglucose Linear modelLinear model Structural modelStructural model Space-filling modelSpace-filling model

Synthetic and Lytic Synthetic and Lytic ReactionsReactions Smaller organic Smaller organic

molecules can be molecules can be linked togetherlinked together Often this Often this

involves the involves the production of Hproduction of H22OO

Larger organic Larger organic molecules can be molecules can be broken down into broken down into subunitssubunits This often This often

consumes Hconsumes H22O, O, hence the term hence the term “Hydrolysis”“Hydrolysis”

Energetics of chemical Energetics of chemical reactionsreactions

In order for In order for chemicals to chemicals to react, they must react, they must first overcome an first overcome an energy barrierenergy barrier

This is known as This is known as the activation the activation energyenergy

Some bonds are Some bonds are easily easily reorganized, reorganized, resulting in a resulting in a lower activation lower activation energyenergy

Enzyme catalyzed Enzyme catalyzed reactionsreactions

Enzyme has binding Enzyme has binding sites for the sites for the reactantsreactants

The active region will The active region will attack the bonds in attack the bonds in the precursorsthe precursors

Once bonds have Once bonds have been reorganized, been reorganized, product is releasedproduct is released

Polymers in organic Polymers in organic systemssystems

A polymer is a chain made A polymer is a chain made up of repeating subunitsup of repeating subunits

Useful compounds are Useful compounds are often stored in the form of often stored in the form of a polymera polymer For example, glycogen is a For example, glycogen is a

branched polymer of branched polymer of glucoseglucose

Glycogen molecules can Glycogen molecules can have different numbers of have different numbers of glucose subunitsglucose subunits

Proteins are also polymersProteins are also polymers

Fatty acids and lipidsFatty acids and lipids

Phospholipids in aqueous Phospholipids in aqueous solutionssolutions

Phospholipids Phospholipids and glycolipids and glycolipids are amphipathicare amphipathic Meaning they Meaning they

have a have a hydrophillic hydrophillic region and a region and a hydrophobic hydrophobic regionregion

When they are When they are in solution, they in solution, they form micellesform micelles

Structure of Amino AcidsStructure of Amino Acids

All amino acids All amino acids have the same have the same basic structurebasic structure A carboxylic acid A carboxylic acid

sideside An amino group sideAn amino group side A side group on the A side group on the

central carboncentral carbon The side group is The side group is

referred to as the referred to as the R-groupR-group

Primary protein Primary protein structurestructure

Secondary protein Secondary protein structurestructure

The chain of amino acids can form folds The chain of amino acids can form folds and coils in different regions, depending and coils in different regions, depending on the amino acid sequenceon the amino acid sequence

Tertiary protein Tertiary protein structurestructure

The tertiary structure of The tertiary structure of a protein is the 3D shape a protein is the 3D shape of a single subunit.of a single subunit.

This is a combination of This is a combination of all the folds, coils and all the folds, coils and sheets.sheets.

This is usually dictated This is usually dictated by hydrophobic and by hydrophobic and hydrophilic interactions hydrophilic interactions with waterwith water

Tertiary and Quaternary Tertiary and Quaternary protein structureprotein structure

The quaternary The quaternary structure of a structure of a protein is the protein is the interactions interactions between the between the different subunitsdifferent subunits If a protein is only If a protein is only

composed of a composed of a single subunit, single subunit, there is no there is no quaternary quaternary structure structure

DNA and RNA structureDNA and RNA structure

Adenosine triphosphate Adenosine triphosphate (ATP)(ATP)

Adenosine Adenosine backbonebackbone

Three phosphate Three phosphate groups attached groups attached in a chainin a chain

Last two have Last two have high energy high energy bondsbonds

Characteristics of a lipid Characteristics of a lipid bilayer:bilayer:

At normal temperatures, a lipid bilayer is At normal temperatures, a lipid bilayer is liquid.liquid. This means that the phospho- and glycolipids This means that the phospho- and glycolipids

which make it up can move freely, within the which make it up can move freely, within the bilayer.bilayer.

Because of the hydrophobic layer in the Because of the hydrophobic layer in the centre, a bilayer is impermeable to water.centre, a bilayer is impermeable to water.

Because of the hydrophilic and hydrophobic Because of the hydrophilic and hydrophobic interactions, a bilayer is structurally quite interactions, a bilayer is structurally quite strong.strong.

Membrane fluidityMembrane fluidity

Membrane proteins:Membrane proteins:

DiffusionDiffusion

Effect of osmotic concentration on Effect of osmotic concentration on

cellscells

Cell membranes are semipermeable, and thus subject to Cell membranes are semipermeable, and thus subject to osmotic forces.osmotic forces.

Animal cell membranes are flexible, and allow for Animal cell membranes are flexible, and allow for inflation and deflation depending on the movement of inflation and deflation depending on the movement of waterwater

Transport of solutes Transport of solutes through cell membranesthrough cell membranes

Cell membranes are made up of Cell membranes are made up of phospholipids arranged in a bilayer.phospholipids arranged in a bilayer. The centre of the bilayer is hydrophobic, The centre of the bilayer is hydrophobic,

which means that hydrophilic molecules which means that hydrophilic molecules cant penetrate.cant penetrate.

Hydrophobic and lipid-soluble molecules can Hydrophobic and lipid-soluble molecules can penetrate cell membranes.penetrate cell membranes.

In order for hydrophilic molecules to be In order for hydrophilic molecules to be taken up, a transport mechanism is taken up, a transport mechanism is needed.needed. These transport mechanisms are integral These transport mechanisms are integral

membrane proteins.membrane proteins.

Ion channelsIon channels Ions are fairly small Ions are fairly small

molecules.molecules. Specialized proteins Specialized proteins

in the membrane form in the membrane form aqueous pores, which aqueous pores, which allow ions through.allow ions through.

The driving force is The driving force is the chemical gradientthe chemical gradient

These pores can be These pores can be quite selective.quite selective.

Most of these pores Most of these pores are regulatedare regulated

Example: CFTRExample: CFTR

Facilitated diffusionFacilitated diffusion

Molecules that are slightly larger need more Molecules that are slightly larger need more help in getting into or out of cells.help in getting into or out of cells.

Rather than a pore, molecules are actually bound Rather than a pore, molecules are actually bound to carrier protein, which translocates molecule.to carrier protein, which translocates molecule.

Driving force is still the chemical gradientDriving force is still the chemical gradient

Active transportActive transport

In order to move ions In order to move ions against a against a concentration concentration gradient, energy gradient, energy must be used.must be used.

Energy is supplied Energy is supplied by the hydrolysis of by the hydrolysis of the terminal high-the terminal high-energy bond of ATP.energy bond of ATP.

Example: Na-K-Example: Na-K-ATPaseATPase

Active secondary Active secondary transporttransport

ATPases only pump ions, nothing bigger.ATPases only pump ions, nothing bigger. Larger molecules are transported by coupling Larger molecules are transported by coupling

them to movement of an ion down its them to movement of an ion down its concentration gradient.concentration gradient.

Ions can also be transported in this way.Ions can also be transported in this way. Example: Na-coupled glucose uptake.Example: Na-coupled glucose uptake.

Membrane transport and Membrane transport and cyclingcycling

Molecules can bind to cell surface Molecules can bind to cell surface receptors and then be internalized.receptors and then be internalized.

This same mechanism can be used to This same mechanism can be used to recycle membrane.recycle membrane.

PhagocytosisPhagocytosis Phagocytosis also involves Phagocytosis also involves

membrane invagination.membrane invagination. This process does not involve This process does not involve

clathrin.clathrin. Pseudopods extend around a Pseudopods extend around a

particle, forming a phagosome.particle, forming a phagosome. Phagosome will fuse with a Phagosome will fuse with a

lysosome, containing digestive lysosome, containing digestive enzymes.enzymes.

There are smaller transport There are smaller transport mechanisms in the wall of the mechanisms in the wall of the secondary lysosome.secondary lysosome.

Cellular organellesCellular organelles

Most intracellular organelles are Most intracellular organelles are membrane-bound.membrane-bound.

Since membranes are barriers to Since membranes are barriers to diffusion of aqueous solutes, they allow diffusion of aqueous solutes, they allow for partitioning of cellular components for partitioning of cellular components

Such partitioning allows for the Such partitioning allows for the generation of gradients and/or the generation of gradients and/or the segregation of specific compounds segregation of specific compounds inside the cell, a process that is inside the cell, a process that is essential for life.essential for life.

Endoplasmic reticulumEndoplasmic reticulum

The endoplasmic reticulum consists of a The endoplasmic reticulum consists of a series of interconnected membrane-bound series of interconnected membrane-bound tubes and lamina that are all continuous.tubes and lamina that are all continuous.

It is essential in the production of It is essential in the production of membrane proteins.membrane proteins.

It also serves as a CaIt also serves as a Ca2+2+ storage organelle. storage organelle.

RibosomesRibosomes Ribosomes are Ribosomes are

enzymes made up enzymes made up of two subunits.of two subunits.

Ribosomes are the Ribosomes are the enzyme that enzyme that synthesize proteins, synthesize proteins, based on an mRNA based on an mRNA templatetemplate

Some ribosomes Some ribosomes are attached to the are attached to the ER and some a free ER and some a free in the cytoplasm.in the cytoplasm.

TranslationTranslation

Golgi apparatusGolgi apparatus

The Golgi apparatus is a contiguous system of The Golgi apparatus is a contiguous system of lamellae and cisternae.lamellae and cisternae.

It is responsible for post-translation It is responsible for post-translation modifications of proteins, formation of modifications of proteins, formation of secretory vesicles and membrane formation secretory vesicles and membrane formation and trafficking. and trafficking.

Membrane flowMembrane flow

Transport vesicles bud off the ER and are Transport vesicles bud off the ER and are transported to the forming face of the Golgi.transported to the forming face of the Golgi.

Membrane-bound proteins and secretory Membrane-bound proteins and secretory proteins then move through the Golgi, where proteins then move through the Golgi, where they are modified, usually by glycosylation.they are modified, usually by glycosylation.

The proteins and membranes are then packaged The proteins and membranes are then packaged into specific vesicles, which are targeted.into specific vesicles, which are targeted.

MitochondriaMitochondria

Mitochondria actually have two Mitochondria actually have two membranes, separated by a small space.membranes, separated by a small space.

Mitochondria also have their own DNA.Mitochondria also have their own DNA. Mitochondria are essential for oxidative Mitochondria are essential for oxidative

phosphorylation.phosphorylation.

NucleusNucleus

Nucleus also has two membranes.Nucleus also has two membranes. Nucleus protects the DNA and maintains Nucleus protects the DNA and maintains

a specific environment for the DNA.a specific environment for the DNA. Nuclear pores allow for transport into and Nuclear pores allow for transport into and

out of nucleus.out of nucleus.

Library tutorialLibrary tutorial

http://toby.library.ubc.ca/ereserve/er-coursepage

. cfm?id=1416

For the Biol 153 students: Lee Ann For the Biol 153 students: Lee Ann Bryant (from the library) will be here Bryant (from the library) will be here at the end of the lecture to give a at the end of the lecture to give a short talk about the library short talk about the library assignment.assignment.

Cell cycleCell cycle

DNA DNA condensationcondensation