BIOL 1501: Cell Biology
Dr. Ireland – Winter 2014
Two Types of Microscopy
• Fluorescence microscopy, scanning electron microscopy
• Gene delivery
• Marrow stroma
• Tendon and ligament
• Cardiac muscle
• A lot of controversy whether or not viruses are considered as living species.
• A bacterial cell is composed of…
o 70% water
o 30 % chemicals
4% ions, small molecules
Molecules in Cells • Water is the most common compound in cells.
• Cellular chemistry based on the carbon atom.
• Biomolecules are mostly comprised of chemical units called functional groups.
• Lipids, sugars, amino acids, and nucleic acids are the most common biomolecules in cells.
• Weak chemical bonds, e.g. ionic and hydrogen bonds, and very important in biomolecules.
o They govern the shape of large molecules, and help molecules adhere to each other.
• Water is held together with hydrogen bonds.
Polarity of Water Molecules- Hydrogen Bonding
• Water molecules are polar- the opposite ends have opposite charges.
• Polarity allows water molecules to form hydrogen bonds with each other.Hydrogen Bonds
• Hydrogen bonds are found between a hydrogen atom covalently bonded to one electronegative
atom and another electronegative atom.
• In cells, the electronegative atoms are usually oxygen or nitrogen atoms.
• The properties of water dictate most cellular processes.
• Hydrophilic things: compatible with water…
o Other polar molecules o A hydrophilic substance has an affinity for water.
• Hydrophobic things: incompatible with water…
o Non-charged, non-polar molecules.
o A hydrophobic substance does not have an affinity for water.
Important Functional Groups
• Functional groups: components of organic molecules involved in chemical reactions and
• The number and distribution of functional groups give each molecule its specific properties.
• The most important in the chemistry of life:
o Carboxyl: carboxylic acids, or organic acids; has acidic properties because the covalent
bond between oxygen and hydrogen is so polar. Found in cells in the ionized form with a
charge of 1- and called a carboxylate ion. Example: acetic acid.
o Amino: amines; acts as a base; can pick up an H from the surrounding solution (water, in
living organisms). Ionizes with a change of 1+, under cellular conditions. Example:
o Phosphate: organic phosphates; contributes negative charge to the molecule of which it
is a part (2- when at the end of a molecule, 1- when located internally in a chain of
phosphates. Has the potential to react with water, releasing energy.
Carbon: Organic Molecules
• Cells are 70-95% water.
• The rest is mostly comprised of carbon compounds.
• Carbon can form a huge number of large, complex molecules, such as…
o RNA o DNA
• Four classes of large biological molecules:
o Nucleic Acids
• Small organic molecules are joined together to form these larger molecules.
• Sugars form polysaccharides, fatty acids form fats/lipids/membranes, amino acids form proteins,
and nucleotides form nucleic acids.
• Carbohydrates: sugars and polymers of sugars.
o Simplest carbohydrates are monosaccharides, or single sugars.
o Carbohydrate molecules are polysaccharides, which are polymers composed of many
sugar building blocks.
• Starch, a storage polysaccharide of plants, is made up of glucose monomers.
• Plants store starch as granules inside chloroplasts and other plastids.
• Glycogen is a storage polysaccharide in animals, made up of glucose monomers.
• Humans and other vertebrates store glycogen mainly in liver and muscle cells.
• Lipids are the one class of large biological molecules that do not form polymers.
• Lipids are hydrophobic
o They consist mostly of hydrocarbons, which form non-polar covalent bonds.
• Most biologically important lipids are fats, phospholipids, and steroids.
• Fats are lipids: fats are constructed from two types of smaller molecules- glycerol and fatty acids. • Glycerol is a three carbon alcohol with a hydroxyl group attached to each carbon.
• A fatty acid consists of a carboxyl ground attached to a long carbon skeleton.
• Fatty acids are composed of a hydrophilic carboxylic acid head and a hydrophobic hydrocarbon
• At least 50% of the dry mass of most cells are proteins.
• Protein functions include:
o Structural support
o Defense against foreign substances
• Polypeptides are polymers built from the same set of 20 amino acids.
• A protein consists of one or more polypeptides.
• Amino acids are organic molecules with carboxyl and amino groups.
• Amino acids differ in their properties due to differing side chains. Peptides
• Peptides are bonded by peptide bonds.
• There is an N terminus and C terminus of a polypeptide chain.
• Amino acids are linked by single bonds called peptide bonds, formed by the carboxylic acid group
of one amino acid and the amino group of a second amino acid.
Protein Structure and Function
• A functional protein consists of:
o One or more polypeptides
o Twisted, folded, and coiled into a unique shape.
• The sequence of amino acids determines a protein’s three-dimensional structure.
• A protein’s structure determines its function.
Levels of Protein Structure
• Primary Structure: unique sequence of amino acids.
• Secondary Structure: coils and folds in the polypeptide chain.
• Tertiary structure: arises from interactions among side chains.
• Quaternary structure: found in multimeric proteins.
• Polypeptide folds at secondary structure in an aqueous environment, with hydrophobic region at
the core containing non-polar side chains, and hydrogen bonds may then be formed to the polar
side chains on the outside of the molecule.
• Polypeptides may be proteins or protein subunits. • Types of secondary structure:
o Alpha Helix
o Parallel Beta Pleated Sheet
o Anti-parallel beta pleated sheet
• Five classes of bonds that stabilize protein structure:
o Disulfide bond
o Hydrogen bond
o Van der Waals and hydrophobic interactions
o Ionic bond
• Alpha helices are represented by coiled ribbons, strands of beta sheets are represented by
arrows pointed from N terminus to C terminus.
Sickle Cell Disease
• A slight change in primary structure can affect a protein’s structure and ability to function.
• Sickle Cell disease:
o Inherited blood disorder
o Results from a single amino acid substitution in the protein hemoglobin.
The Structure of Nucleic Acids
• Nucleic acids are polymers called polynucleotides or oligonucleotides.
• Each polynucleotide is made of monomers called nucleotides.
• Each nucleotide consists of a nitrogenous base, a pentose sugar, and a phosphate group.
• The portion of a nucleotide without the phosphate group is called nucleoside.
• Level one of DNA organization is a double stranded anti-parallel double helix held together by
hydrogen bonds between base pairs.
Cell Biology Techniques
o Light Microscopy o Electron Microscopy
• Biochemical Techniques
o Cell Fractionation
o Molecular Technique
• Molecular Techniques
• Microscopes are used to visualize cells too small to see with the naked eye.
• The microscope has much better resolution than the human eye.
• In a light microscope (LM) visible light passes through a specimen and then through glass lenses,
which magnify the image.
• The electron microscope (EM) uses a beam of electrons which is either passed through or
bounced off the surface of the specimen.
• We can manipulate the following to get a better image:
o Magnification: ratio of object’s image size to its real life.
o Resolution: the minimum distance between two distinguishable points = clarity.
o Contrast: visible difference between regions of the image.
• LM can magnify to about 1000x
o Can enhance contrast and emphasize specific cell components: staining and labeling
o Sub-cellular structures, e.g. organelles too small to be resolved by LM- need EM
• Techniques include:
o Brightfield unstained
o Brightfield stained
o Differential interference contrast
Microscope Resolution • Resolution in an optical system can be described mathematically by Abbe’s equation:
• d = 0.612 * l
n sin a
o d = resolution
o l = wavelength of radiation
o N = refractive index of medium between light source and lens
o a = refraction angle
o 0.612 = Abbe’s Constant
• Two types of electron microscope:
o Scanning electron microscope (SEM) focuses a beam of electrons onto the surface of a
specimen: provide images that look 3-D (surface)
o Transmission electron microscope (TEM) passes a beam of electrons through a
• Breaks cells apart and separates organelles from one another.
• Ultracentrifuges fractionate cells into their component parts- organelles, etc.
• Biochemistry and cytology help correlate cell function with structure.
Density Gradient Centrifugation
• Gradient of sucrose or some other medium.
• Separate organelles based on density.
• Separation of biomolecules on analytical or prep scale.
• Usually in column (glass, plastic, steel)
• Maintains biological properties • Can study molecules after separation
• Ion exchange chromatography: surface change
• Gel filtration chromatography: size
• Affinity chromatography: biological properties
• Separation of biomolecules on analytical scale
• Often in a gel slab
• May damage biological properties
• Can sometimes study molecules after separation
• Polyacrylamide Electrophoresis:
o Native protein electrophoresis: surface charge and size
o SDS protein electrophoresis: size
• Agarose Electrophoresis:
o Sub Gel Electrophoresis: size – DNA
• Lipid bilayer:
o Mixture of proteins and lipids
o Non-covalent bonds
o Continuous double layer
o 4-5 nm thick
o Various proteins wedged in between the lipids
o Relatively impermeable barrier to most hydrophilic molecules
o Proteins anchored in a sea of lipid
Various functions: enzymic, transport, structural, receptors.
• Fats • Oils
• Some vitamins
• Some hormones
• Membrane lipids are glycerides
• Two fatty acids and a phosphate group are attached to a glycerol
o Fatty acid tails are hydrophobic
o Phosphate group and its attachments form a hydrophilic head
• Amphipathic molecules
o Both hydrophilic and hydrophobic
• Add phospholipids to water
o Self assemble into a bilayer
o Hydrophobic tails point toward the interior
• Self repair when damaged
• Phospholipids are the major component of all cell membranes
o The most abundant lipid in the plasma membrane
• Lipids characterized by a carbon skeleton consisting of four fused rings
• Cholesterol, an important steroid, is a component in animal cell membranes
• The boundary that separates the living cell from its surroundings
• Fluid mosaic model
o A membrane is a fluid structure with a “mosaic” of various proteins embedded in it
• Exhibits selective permeability
o Allows some substances to cross it more easily that others • Freeze-fracture studies of the plasma membrane supported the fluid mosaic model
o A specialize preparation technique
o Splits a membrane layer along the middle of the phospholipid bilayer
o Electron microscope
The Fluidity of Membranes
• Phospholipids in the plasma membrane can move within the bilayer
• Most of the lipids, and some proteins, drift laterally
• Rarely does a molecule flip-flop transversely across the membrane
• Problems with membrane structure can lead to disease
• Hyaline membrane disease (surfactant deficiency disorder)
o Preterm infants
o Lungs not fully mature at birth
o Respiratory distress
o Poor O2/CO2exchange
• Alzheimer’s disease
o Accelerated membrane P-lipids turn over
o Abnormal membrane repair
o May contribute to amyloid deposition
o Ultimately results in synaptic loss
• Heart Disease
o Faulty membrane repair
o Emphasized by vigorous exercise/muscle weakness
• Membranes contain many different proteins embedded in the fluid lipid bilayer
• Proteins determine most of the membrane’s function • Peripheral proteins are attached to the surface of the membrane
• Integral proteins penetrate the hydrophobic core
• Integral proteins that go all the way across the membrane are called transmembrane proteins
• The hydrophobic regions of integral proteins consist of one or more regions of non-polar amino
acids, often coiled into alpha helices
• Fatty acids vary in length and number and locations of double bonds.
• Saturated fatty acids have the maximum number of hydrogen atoms possible and no double
• Unsaturated fatty acids have one of more double bonds
• Lipids made from saturated fatty acids are called fats- solid at room temperature
o Most animal fats are saturated
• Fats made from unsaturated fatty acids are called unsaturated fats or oils, and are liquid at room
• Membrane lipids have a mixture of the two.
• Integral proteins that go all the way across the membrane are called transmembrane proteins.
• The hydrophobic regions of the integral proteins consist
• Six major functions of membrane proteins:
o Enzymic activity
o Signal transduction
o Cell-cell recognition
o Intercellular attachment
o Attachment to the cytoskeleton and extracellular matrix (ECM).
Protein Movement in Membranes • Proteins can move around- not a random movement, and have restrictions of where they can
• Some proteins bind to other cells, allowing cells to form clusters.
• Some proteins bind to molecules in the extracellular space, permitting cells to attach and crawl on
Membrane Carbohydrates and Cell-Cell Recognition
• Cells recognize each other by binding to surface molecules.
o Usually carbohydrates, on the plasma membrane.
Synthesis and Sidedness of Membranes
• Carbohydrates on the external side of the plasma membrane vary among species, individuals,
and even cell types in an individual.
• Membranes have distinct inside and outside faces.
• Proteins, lipids, and associated carbohydrates are distributed asymmetrically in the membrane.
o Determined when the membrane is built by the ER and Golgi apparatus.
Membrane Selective Permeability
• A cell must exchange materials with its surroundings.
• This is controlled by the plasma membrane.
• Plasma membranes are selectively permeable
• While large charged molecules cannot penetrate
The Permeability of the Lipid Bilayer
Channel and Carrier Proteins
• Some transport proteins- channel proteins- have a hydrophilic channel through which some
molecules or ions can pass.
• Other transport proteins- carrier proteins- bind to molecules
• Diffusion: tendency for molecules to spread out evenly into the available space. • At dynamic equilibrium, as many molecules cross a membrane one way as cross in the other
• Substances diffuse down their concentration gradient.
o The difference in concentration of a substance from one area to another.
• No work needs to be done to move substances down the concentration gradient.
• Diffusion of a substance across a membrane
• Transport proteins speed the massive movement of molecules across the plasma membrane.
• Channel proteins provide tunnels that allow a specific molecule or ion to cross the membrane.
• Channel proteins include:
o Aquaporins: facilitated diffusion of water
o Ion channels: may open or close in response to a signal (gated channels)
• Facilitated diffusion is still passive because the solute moves down its concentration gradient.
• Some transport proteins, however, can move solutes against their concentration gradients.
• Active transport moves substances against their concentration gradient
o Na /K ATPase: Potassium is moved in; sodium is moved out via active transport.
Creates a voltage due to the charges. ATP is released during this process. The sodium
and potassium gradients can be used to be move other ions in an out.
• Extracellular ligand-gated
• Intracellular ligand-gated
• These are found in extracellular space.
Ion Pumps and Membrane Potential
• An electrogenic pump is a transport protein that generates voltage across a membrane.
• The sodium-potassium pump is the major electrogenic pump of animal cells. • The main electrogenic pump of plants, fungi, and bacteria is a proton pump.
• Occurs when active transport of a solute indirectly drives transport of another solute.
• Plants use the hydrogen ion gradient generated by proton pumps to drive.
• Two types of co-transport:
o Symport: 2 solutes/ions move in the same direction.
o Antiport: 2 solutes/ions move in different directions.
• Uniport: one solute/ion in one direction.
• Problems with membrane proteins can lead to disease.
• Cystic fibrosis:
o Defect in Cl channels
o Excess fluid production in lungs
o Pancreatic insufficiency
o Range of other defects
o Kidney disease
o Inherited, autosomal, recessive
o Inadequate re-absorption of cystine
o Excessive concentration of cystine in urine
o May crystallize
o Kidney stones
Movement of Large Molecules across Membranes- the Endomembrane System
Bulk Transport across the plasma membrane • Small molecules and water enter or leave the cell through the lipid bilayer by transport proteins.
• Large molecules, such as polysaccharides and proteins, 10 times bigger than Na ion
o Cannot go through the membrane
o Requires structural change in the membrane itself
o Cross the membrane in bulk via vesicles
o Exocytosis and endocytosis
Exocytosis and Endocytosis
• Import: Endocytosis
• Export: Exocytosis
The Endomembrane System