LECTURE 1- TOUR OF THE CELL
Discovery of Cells
1660 – microscopes! Robert Hooke coined the term “cells”
1670’s – Anton van Leeuwenhoek, Made many microscopes and looked at EVERYTHING!
• Schleiden and Schwann
All organisms composed of one or more cells.
The cell is the structural unit of life.
• added: Cells can only arise by division from a pre-existing cell
Two types of Cells:
No membrane-bound nucleus
No membrane-bound anything!
Compartmentalized, Protists, Fungi, Animals, Plants
A bit about sizes.
There are 1000 microns (µm) in 1 mm
Most eukaryotic cells are between10 and 100 microns (µm)
Most prokaryotic cells are about 5 microns (µm)
Eukaryotic Cells- Endomembrane System
Regulates protein traffic and performs metabolic functions in cell.
Genetic info = Chromatin
Chromatin = DNA + Protein
Have nuclear pores, stuff goes in and out.
facilitate movement, allows only certain things to enter.
DNA --> RNA --> PROTEINS
in nucleus in cytoplasm
Made of lamin proteins, give shape and stability. Fibres breakdown during mitosis.
Function: PROTEIN SYNTHESIS! • Large and small subunits
• rRNA and protein
Where are Ribosomes found in the Cell?
Free in cytosol, Attached to membranes (ER and nucleus). In Mitochondria and
Chloroplasts (different structurally)
Rough Endoplasmic Reticulum
“Rough” because ribosomes attached
Proteins to be exported out of cell
Proteins to be incorporated into membranes
Proteins to be imported into other organelles
Smooth Endoplasmic Reticulum
NO ribosomes! Stores calcium.
Two main functions:
• Acisternae comprises a flattened membrane disk that makes up the Golgi apparatus
-Manufacturing/modifying (add sugars)
• Shipping Cisternal Maturation Model
Cisternae is formed off th ER, vesicles bud off.
Lysosomes come from the Golgi, digestive compartments, work best in acidic environment.
1. Phagocytosis (“cell eating”)- cell eating, engulphs food.
2. Autophagy (“self eating”) - a damaged organelle becomes surrounded by a double
membrane and a lysosome fuses with outer membrane of vesicle, self eating.
Endomembrane system organelles
Mitochondria (Mitochondrion), Role in the cell is to make ATP!
Outer and Inner membranes
Matrix, Intermembrane Space, and Ribosomes
• Circular • All maternal!
Mitochondria used to be bacteria and the eukaryotic cells did not have them. The cell ate a
bacteria and storied it in a vacuole and did not eat it right away. Bacteria made atp so
eukaryotic cell didnt eat it and eventually this arrangement became permanent.
• Mechanical support
Microfilaments Made of actin and protein
Functions of Microfilaments (often working with motor protein myosin)
-Move (cilia back and forth motion, flagella snake like motion, anchored by a basal body,
structurally similar to centriole)
-Change cell shape
actin and myesin work together to do these things.
Microtubules (Hollow cylinders)
Tubulin, Very dynamic, grow out of centrosome.
Microtubules act as railway tracks for motility within the cell.
Kinesin: Move towards outside of cell, “+” end directed movement
Dynein: Move towards inside of cell, “-” end directed movement
-The centrosome is the microtubule organising center of the cell
Microtubules form cilia and flagella (attach to basal body at 9+0 pattern. )
dynein allows them to move. It reaches out and walks along the other. Causes bend and
makes them move.
Internal Structure of Cilia/ Flagella is called the Axoneme
Nine doublet microtubules+Two single microtubules in center
Cilia and Flagella attach to the cell at the Basal body “9+0” pattern
• Intermediate in size
• Stabilize cell structure • Very strong, resist tension
• No motility, no motor molecules
• Variety of different proteins
They are a major component of the cell's cytoskeleton, and provide support for normal axonal radial
growth (i.e. increases in axon's diameter). Neurofilaments are composed of polypeptidechains or
subunits that are related structurally to the intermediate filaments of other tissues such as keratin
The Extracellular Matrix is found on the OUTSIDE of the cell
The ECM is mainly composed of glycoproteins (proteins attached to long sugar chains)
Collagen is an example of a glycoprotein.
Proteoglycan--> small core protein with many carb chains covalently attached.
Extracellular Matrix Functions:
Cells are connected to other cells via Junctions
1. Tight Junctions
Two membranes almost fused
Fasten cells together, Connected to keratin
3. Gap Junctions
Small hole between cells so tiny signalling molecules can move between the two cells
Macromolecules- Chapter 5 Lecture 3
Polymers- make all different sorts of finalized products.
Monomers- small units, like lego pieces, slightly different colors/sizes, can be assembled
Many macromolecules are formed from condensation reactions. regardless of carbs, fat,
proteins they all assemble somewhat similarly. one hydrogen from monomer one forms with
one OH from monomer two making water and leaving you with polymers When you put them
condensation reaction/dehydration reaction, loss of water.
Condensation reactions are catalysed by enzymes.
Long Polymer Broken Down:
does not happen spontaneously. enzymes grab monomers and pull them together.
hydrolysis reaction- long polymer breaks down into shorter polymer or monomer
water is necessary for this reaction, water comes in and splits it.. one monomer and one
shorter polymer are the result. Lysosome Vesicles
- acidic pH
these are sugars also called saccharides. every carb is formed similarly (c, h, o)
when those atoms come together they do so in a predictable ratio. 1 carbon: 2 hydrogen: 1
oxygen. they end in ose
Two mono-saccharides linked = disaccharide Glucose
Glucose + Fructose Sucrose
Glucose + Galactose Lactose
Polysaccharides = hundreds or thousands
of mono-saccharides linked together
Example 1: Glycogen
Used to STORE carbohydrates
Example 2: Starch
good food source, filling, long term source of energy
Cellulose: not used for storage so much as it is used for structure. Polysaccharides.
alpha - OH on bottom
beta- OH on top
when cellulose is formed its using beta isomers, they switch, every second glucose is upside
down, we don't have an enzyme that can break up beta glucose monomers.
other eukaryotes eat cellulose, cows technically do not digest the grass, the bacteria in their
gut does it for them.
They are Hydrophobic
within the middle water molecule, there is a slight difference in charge, the oxygen is slightly
negative, hydrogen's are slightly positive. water is a polar molecule meaning one end of the
molecule has a different charge than the other end. things that are polar like other things that
are polar, causing an electrostatic attraction.
Hydrocarbon chains are NOT charged. Therefore they are non-polar, or hydrophobic. A hydrocarbon chain with a carboxy group on end is called a fatty acid.
fatty acids are monomers for storage fats, they are variable in their length.
13-20 carbons long
Hydrophobic and Hydrophillic molecules do not mix i.e salad dressing.
Storage Fats = 3 fatty acids + 1 glycerol
a condensation reaction occurs and a hydrocarbon tail attaches. They are called triglycerols
because there are three fatty acids that have attached.
How lipids are stored in cell...
human adipose cell (fat cell)
Saturated vs. Unsaturated Fats
Saturated = no double bonds
Unsaturated = double bonds
Refers to whether there are double bonds in the hydrocarbon chain or not.
No double bonds! Solid at room temp. I.E butter.
Food labels have to tell you if something is mostly saturated or not.
Most animal fats are saturated, steak, bacon, the hard white fat.
Liquid at room temp. fatty acids are in the molecules that have double bonds, double bond
kinks that fatty acid and makes a bend..they don't pack tightly because there is space in
between the bend. As a result these are liquid at room temp.
Can either be CIS or Trans..
CIS will form a bend, trans will not.
Plants and fish generally have cis unsaturated fats. (e.g. Olive oil)
adding hydrogen's artificially saturates the molecule. i.e margarine, shortening.
you could take oils, and do this process called hydrogenation to make them solid which was
convenient. trans fat survive for a really long time.
Phospholipids = Glycerol + 2 Fatty Acids + phosphate and another small molecule
almost the same as a storage lipid. instead of three fatty acids they only have two plus a
phosphate group and another group that is named "group" because it could be tons of things.
this forms membranes. They have a amphipathic region that is hydrophobic and hydrophillic
region. the fatty acid tails are hydrophobic and the top part (group) like water making them
hydrophillic. any molecule that has both sections on same molecule is ampthipathic.
they do not look anything like other fats. they are hydrophobic. example:cholesterol. They
make four carbon/hydrogen rings. OH group on one end and C and H on other end.
Testosterone and oestrogen are made from cholesterol.
Polymers of amino acids linked end-to-end in a specific sequence. I.E enzymes, hormones, structure, movement, storage, receptors. Etc.
the proteins are the work horses of the cell, many functions
monomer: amino acid
Amino acids link together from condensation reactions to form proteins.
every amino acid has a carbon in middle.
one bond to AMINO group, bottom bond to hydrogen, third bond to a carboxle group, fourth
bond is to side chain, identity to specific amino acid depends on what the side chain is.
Non polar side chains are HYDROPHOBIC. Polar side chains are HYDOPHILLIC.
Electrically charged side chains; hydrophillic
these are electrically charged side chains that are acidic or basic. fully charged, negatively
(acidic) or positively (basic).
when amino acids join together they do so in a condensation reaction resulting in a bond
between two amino acids which is a peptide bond.
Four Levels of Protein Structure....
Primary= Amino Acids in order
Secondary Structure = Hydrogen bonds between atoms of the polypeptide backbone.
3D shape that is in a small localized area. This little section coils up and between coils are
hydrogen bonds that hold it together. (alpha) OR...
the beta pleated sheet. small areas of the peptide line up so they are parallel with each other
and hydrogen bonds hold its shape.
Tertiary Structure = 3D shape
Due to interactions between side chains. the bigger 3d shape of entire protein
functionality is very dependent on 3d shape. van der waals (no charge) forces fold proteins
together in areas that are hydrophobic. this course is weak. ionic bonds. I.E R groups.
Fourth Level- interacts between different proteins. come together and form finished functional
protein. Collagen is in extracellular matrix, each individual protein is one of those fibres.
Comes together with two other collagen proteins and wrap themselves around each other and
1.Composition (physical structure and biological activity)
2. Selective Permeability (passive and active transport)
Lipids (phospholipids and cholesterol!)
cell membranes contain about a 50/50 ratio between lipids and proteins.
the lipid that makes up cell membrane is primarily a phospholipid. phospholipids are
amphipathic molecules (hyrophobic and hydrophillic). this is critical in how they are able to
form a membrane.
Phospholipids = Glycerol + 2 Fatty Acids + phosphate + another small molecule Phospholipid Bilayer
they turn and wiggle and move around to organize themselves into two rows so that the fatty
acid tail (hydrophobic) and the hydrophillic tale are on the outside interacting with water.
mostly water on inside of cell, also mostly water on outside of cell. because it is two layers it is
called a phospholipid Bilayer. also when we talk about these we will refer to two different
leaflets. top row is one leaflet bottom row is other leaflet. They will form spontaneously in
mitochondria have 4 rows of phospholipids
Unsaturated vs Saturated hyrdocarbon tails
unsaturated- increased fluidity
saturated- decreased fluidity
Different membranes have different proportions.
Cholesterol affects membrane fluidity.
hydrophobic molecules each one has a tiny OH group. these molecules are not even or
straight and this affects all the other molecules around. it disrupts them. cholesterol comes
from our diet also the smooth ER makes cholesterol along with making phospholipids for the
phospholipids move side to side rapidly but almost never flip-flop. they are constantly in
motion, if you could tag and follow one phospholipid you will see that it will zip around left and
right but on the other hand they can not go from top to bottom or flip. the hydrophillic head
does not want to go into the middle part so switching/flipping is not possible
there are times when a phospolipid has to flip because it may be needed on the other leaflet,
the enzymes help with this the enzyme is called flippase.
proteins are another important component of membranes. they can be either integral or
peripheral. these names refer to where abouts in the membrane that the protein is found.
integral proteins penetrate into the hydrophobic region of the bilayer. they are also called
trans-membrane proteins. The reason they are so stuck in the structure is because in the
middle area it has positioned itself so that the amino acids with hyrophobic side chains are all
in the middle area.
top and bottom have hydrophillic side chains
hydrophobic interact in the middle of bilayer.
Integral protiens have a lot of alpha helixes. most of these proteins are asymmetrical.
peripheral proteins- not embedded, on surface of membrane. these do not fit into membrane
instead they sit on the edge of membrane.
carbs attach to both proteins and lipids. when attached to lipids they are called glycolipids and
attached to protein they are called glycoproteins. carbs only live on the outside of the cell,
they act as flags for signalling
Fluid Mosaic Model
lipid-fluid bilayers -proteins
- intergral and peripheral
all of this together is the fluid mosaic model
Biological membranes are barriers to solute movement Selective permeability
passive transport happens on its own. when molecules are moving from a high concentration
to a low concentration. down gradient.
active transport needs energy, normally atp. low concentration to high concentration. up
passive: simple diffusion, facilitated diffusion
in both cases there is no energy and moving down concentration gradient.
molecules move right through bilayer in SIMPLE DIFFUSION.
molecule has to be tiny, big will not fit. no proteins involved. the molecules have to be
hydrophobic and non polar, has to be able to pass through. CO2 or O2
charged molecules will not go through bilayer, water will not diffuse through membrane
Aquaporin, integral membrane protein (goes all the way through). has an alpha helixes
second structure. its a channel or tunnel where water molecules can freely move from inside
to outside of cell. facilitated diffusion
in facilitated diffusion we rely on channel transport proteins and carrier transport proteins
channel proteins are just like tunnels. carrier proteins are a bit more difficult, they open at top,
take in molecule then open at other end.
passive, specific, saturable
usually uses ATP, transport may be against concentration gradient, transport proteins
involved, can be primary or secondary
in primary active transport the ATP is directly involved
sodium potassium pump is a protein and it is probably the best example of primary active
transport. its function is to maintain a high concentration of pottassium ions on inside of cell
and high conc of sodium ions outside cell.
Integral membrane glycoprotein
a conformational change is a fairly dramatic change. if another molecule comes and touches
it it has a "freak out". pumps job is to pump sodium out and potassium into cell. 3:2 ratio ATP is hydrolysed and the phosphate group attaches to the pump. that phosphate group is
the nudger, the pump now will have a "freak out". The binding of the phosphate causes a
conformational change in the protein, and the three Na+ are released to the outside of cell.
Two K+ are now able to bind on the exoplasmic side. The phosphate is released, causing
another conformational change. When K+ ions bind, yet another conformational change in
pump, so now open to cell side again. Cycle repeats.
Secondary Active Transport
ATP participates indirectly, Ion gradients Amino acids and sugars, Cotransport
Final way things get across the membrane…
Intracellular Digestion- Phagocytosis (engulphs)
Pinocytosis (cell drinking)
Ligand will bind to a receptor on the cell membrane.
metabolism is the sum total of all the chemical reactions happening in cell.
2000 chemical reactions all happening at once.
most reactions can be classified as being catabolic or anabolic.
catabolic break stuff down and release energy
anabolic reactions build up stuff and consume energy. condensation reaction is an example of
an anabolic reaction.
Gibb’s Free Energy (G)
if the gibbs free energy is negative that describes a reaction that is called exergonic, it
releases energy. they do not need energy.
a positive describes a reaction called endergonic, it needs energy absorbed
not energetically favourable
the cell will couple together the two types of reactions. one produces energy coupled with a
reaction that needs that energy.
Adenosine triphosphate (ATP) Currency for the cell
our cells use the hydrolysis of ATP as our