A Tour of the Cell

Microscopy

- Microscopes invented in 1590 & further refined in 1600s

- Cells 1st seen by Robert Hooke in 1665: looked at dead cells from bark of oak tree
o Lenses of Antoni van Leeuwenhoek
- Important tools of cytology, study of cell structure
- Light microscope (LM):
o Visible light pass through specimen & then through glass lens. Lenses refract
(bend) light in such way image of specimen is magnified as it is projected into the
eye
o Magnification: about 1000 times actual size of specimen
o Resolution: 0.2μm or 200nm regardless of magnification
o Resolution barrier when studying organelles
- Parameters in microscopy:
o Magnification: ratio of an object’s image size to its real size
o Resolution: clarity of the image; minimum distance 2 points can be separated &
still be distinguished as separate points
o Contrast: diff in brightness between light & dark & light areas of an image
 Methods to enhance contrast: staining & labelling cell components to
stand out visually
- Electron microscope (EM):
o Focus beam of electrons through specimen/onto its surface
o Resolution is inversely related to wavelength of light/electrons a microscope
uses (electron beams have shorter wavelength than visible light)
o Resolution of about 0.002nm (but cannot resolve structures smaller than about
2nm)
- Scanning electron microscope (SEM):
o Detailed study of the topography of a specimen
o Electron beams scans the surface of the sample, usually coated with a thin film
of gold. The beams excites electrons on surface, these secondary electrons are
detected by a device that translates the pattern of electrons into an electronic
signal sent to a video screen.
o Result is an image of the specimen’s surface that appears 3D
- Transmission electron microscope (TEM):
o Used to study internal structure of cells
o Aims electron beam through a very thin section of the specimen (stained with
atoms of heavy metals which attach to certain cellular structures which enhance
the electron density of some parts of the cell more than others). The electrons
passing through the specimen are scattered more in the denser regions, so fewer
are transmitted. The mage displays the pattern of the transmitted electrons
 - TEM & SEM use electromagnets as lenses instead of glass to bend the paths of the
electrons, ultimately focusing the image into a monitor for viewing.
- LM can study living cells – for EM the method to prepare the specimen kills the cells
- Specimen preparation for any type of microscopy can introduce artifacts, structural
features seen in micrographs that do not exist in the living cell.

Cell Fractionation

- Technique for studying cell structure & function

- Takes cells apart & separates major organelles & other subcellular structures from one
another
- Centrifuge: equipment used for this task
o Spins test tubes holding mixtures of disrupted cells at a series of >ing speed
o At each speed, the resulting force causes a subset of cell components to settle to
the bottom of the tube, forming a pellet
- Helps prepare specific cell components in bulk & identify their functions

Types of cells

- Prokaryotic
o Bacteria
o Archaea
- Eukaryotic
o Fungi
o Animals
o Plants
o Protists: diverse group of mostly unicellular eukaryotes

Comparing Prokaryotic & Eukaryotic Cells

- All cells:
o Bounded by selective barrier: plasma membrane (aka cell membrane)
o Semifluid, jellylike substance inside cells: cytosol, in which substances are
suspended
o Contain chromosomes, which carry genes in form of DNA
o Ribosomes, tiny complexes that make proteins according to instructions from
the genes
- Comparing:
o In e cells, most DNA is in nucleus, which is bounded by a double membrane. In p
cells, DNA is concentrated in region that is not membrane-enclosed, called the
nucleoid
o In e cells , the cytoplasm refers only to the region between the nucleus & plasma
membrane. Within the cytoplasm, suspended in cytosol, are a variety of
organelles of specialised form & function. Almost all p cells don’t have
 membrane bounded structures but some contain regions surrounded by
proteins within which specific reactions take place
o E cells are generally larger. Size important for function (metabolism, produce
enzymes). A high
surface-to-volume ratio
facilitates the exchange of
materials
between a cell and its environment.
o Plasma membrane: selective barrier that allows passage of enough oxygen,
nutrients & wastes to service entire cell

The Nucleus: Information Central

- Nuclear envelope: encloses the nucleus, separating its contents from the cytoplasm
o Double membrane separated by narrow space
o Perforated by pore structures which regulate entry and exit of molecules
o Lined by nuclear lamina, a netlike array of protein filaments that maintains the
shape of the nucleus by mechanically supporting nuclear envelope
- Within nucleus are chromosomes, which appear as a mass of chromatin (DNA &
proteins) & 1 or more nucleoli, which function ribosome synthesis

Ribosomes: Protein Factories

- Complexes made of ribosomal RNAs & proteins
- Cellular components that carry protein synthesis
- Not membrane bounded & thus not considered organelles

Endomembrane System
- Regulates protein traffic & performs metabolic functions
- Many of the diff membrane-bounded organelle of the e cell are part of this system
- System includes:
o Nuclear envelope
o Endoplasmic reticulum
o Golgi apparatus
o Lysosomes
o Various kinds of vesicles & vacuoles
o Plasma membrane
- Carry out tasks in cell, incl. synthesis of protein, transport of proteins into membranes &
organelles or out of the cells, metabolism & movement of lipids & detoxification of
poisons
- Membranes in system are related either through direct physical continuity or by transfer
of membrane segments as tiny vesicles (sacs made of membrane)

The Endoplasmic Reticulum: Biosynthetic Factory

- ER: extensive network of membranes that accounts for more than half the total
membrane in many e cells
- Consists of a network of membranous tubules & sacs called cisternae
- Separates the internal compartment of the ER called the ER lumen (cavity) or cisternal
space from the cytosol
 - Is continuous with the nuclear envelop, the space between the 2 membranes of the
envelop is continuous with the lumen of the ER
- 2 distinct, though connected, regions of the ER:
o Smooth ER (outer surface lacks ribosomes)
o Rough ER (studded with ribosomes on outer layer)

The Golgi Apparatus: Shipping & receiving center

- After leaving ER, many transport vesicles travel to the GA
- Warehouse for receiving, sorting, shipping & some manufacturing
- Products of the ER, such as proteins are modified & stored & then sent to other
destinations
- Extensive in cells specialised for secretion
- Consists of group of associated, flattened membranous sacs – cisternae – looks like
stack of pita bread (a cell may have 00s of stacks)
- Er  cis Golgi  medial Golgi  trans Golgi  cell membrane/ lysosomes

Lysosomes: Digestive Compartments

- Membranous sac of hydrolytic enzymes that many e cells use to digest (hydrolyse)
macromolecules
- Lysosomal enzymes work best in acidic environ found in lysosomes
- If a lysosome breaks open/leaks its contents, the released enzymes are not very active
because cytosol has near-neutral pH
- Excessive leakage from a large no. of lysosomes can destroy a cell by self-digestion

Vacuoles: Diverse Maintenance Compartments

- Large vesicles derived from the ER & Golgi apparatus
- Integral part of a cell’s endomembrane system
- Vacuolar membrane is selective in transporting solutes: as a result, the solution inside
differs in composition from the cytosol
- Food vacuoles: formed by phagocytosis (engulf smaller organisms/food particles)
- Contractile vacuoles: found in many freshwater protists, pump excess water out of cells.
- Central vacuoles: found in many mature plant cells, hold organic compounds and water.

Mitochondria & chloroplasts change energy from 1 form to another

- Mitochondria: sites of cellular respiration, the metabolic process that uses oxygen to
drive the generation of ATP by extracting energy from sugars, fats & other fuels
- Chloroplasts: sites of photosynthesis. Process converts solar energy to chemical energy
by absorbing sunlight & using it to drive the synthesis of organic compounds such as
sugars from carbon dioxide & water

Cytoskeleton
- Network of fibres that organises structures & activities in cell
- Extends throughout the cytoplasm
 - Composed of three types of molecular structures: microtubules, microfilaments, and
intermediate filaments.
- Role:
o Give mechanical support to the cell & maintain its shape
o Stabilised by a balance between opposing forces exerted by its elements
o Provides anchorage for many organelles & even cytosolic enzyme molecules
o Can be quickly dismantled in 1 part of cell & reassembled in new location,
changing the shape of cell

Extracellular components & connections between cells

- Help coordinate cellular activites

Cells walls of Plants

- Distinguishes plant from animal cells
- Protects plant cell, maintain its shape & prevents excessive uptake of water
- The carbohydrates present in the cell wall vary depending on the cell type:
o Plant and protist cell walls – cellulose
o Fungal, cell walls - chitin
- Middle lamella hold cell walls of adjacent cells together

Extracellular Matrix (ECM) of Animal Cells

- Collagen forms strong fibers outside the cells
- Fibers are embedded in network woven out of proteoglycans
- Integrins: connects to cytoplasm
- Roles:
o Holds cells together in tissues
o Contributes to properties of bone, cartilage, skin, etc.
o Filters materials passing between different tissues
o Orients cell movements in development and tissue repair
o Plays a role in chemical signalling

Plasmodesmata in Plant cells

- Channels that perforate and connects cells
- Water & small solutes can pass freely from cell to cell

Tight junctions
- Barrier that prevents leakage of extracellular fluid across a layer of epithelial cells

Desmosomes
- Fasten cells together into strong sheets

Gap functions
- Provide cytoplasmic channels from 1 cell to an adjacent cells
 - Consists of membrane proteins that surround a pore through which ions, sugars, amino
acids & other small molecules may pass
- For communication between cells in many types of tissues

The Chemical Context of Life

Matter
- Organisms are composed of matter: anything that takes up space & has mass
- Exist in many forms
- E.g. rocks, metals, oils, gases, living organisms

Elements & Compounds

- Matter is made up of elements: substance than cannot be broken down to other
substances by chem reaction
o 92 naturally occurring elements
- Compound: substance consisting of 2 or more diff elements combined in fixed ratio
o E.g. table salt is NaCl (ratio 1:1), Water - H2O (ratio 2:1)
o Has diff characteristics from elements

The Elements of Life

- Of the 92 natural, about 20-25% are essential elements needed to live healthy life &
reproduce
o Humans need 25 elements, but plants need only 17.
- O, C, H & N - make up approximately 96% of living matter
o Other 4% - Ca, P, K, S & few other
- Trace elements: required by organism in only minute quantities
o E.g. Iron (Fe) is needed by all forms of life but others required only by certain
species
- Some naturally occurring are toxic to organisms
o Humans: arsenic linked to numerous diseases & can be lethal
o Arsenic can make its way into the groundwater. Using water from drilled wells in
southern Asia, means millions of people have been exposed to arsenic-laden
water
Element’s Properties
- Each element consists of a certain type of atom diff from atoms in other elements
- Atom: smallest unit of matter that still retains properties of an element
o Would take about 1m of them stretch across a full stop at end of sentence
o The symbol C stands for both the element carbon & a single C atom

Subatomic Particles
- Tiny bits of matter are composed of subatomic particles
- Protons: +ve charge
- Electrons: -ve charge
- Neutron: neutral charge
- Protons and neutrons are packed tightly in dense
core: atomic nucleus at center of atom (P gives
nucleus +ve charge)
o Rapidly moving electrons form a “cloud” of -
ve charge around the nucleus
o The attraction between op. charges keeps
the electrons in the vicinity of the nucleus
- Dalton: used to measure atoms & subatomic
particles (same unit as atomic mass unit)
- Protons & Neutrons have same mass: close to 1
Dalton
- Electrons has mass of about 1/2000 that of a N or P
Atomic Number & Atomic Mass
- Atomic number: number of protons unique to element
- Mass number: total number of protons and neutrons in nucleus

- Almost all of an atom’s mass is concentrated in its nucleus

- Atomic mass: total mass of an atom

Isotopes
- Are diff atomic forms od the same element
- Radioactive isotope: nucleus decays spontaneously, giving off particles & energy
o When it leads to change in no. of protons, it transforms the atom to an atom of a
diff element
o E.g. when an atom of carbon-14 (14C) decays, it loses a proton, becoming an
atom of nitrogen (14N)
Radioactive Tracers
- Radioactive isotopes often used as diagnostic tools in medicine
o Are incorporated into biologically active molecules which are then used as
tracers to track atoms during metabolism
- Certain kidney disorders are diagnosed by injecting small doses of radioactively labelled
substances into the blood, then analysing the tracer molecules excreted in the urine.
- Also used in combination with sophisticated imaging instruments, such as PET scanners
that can monitor growth and metabolism of cancers in the body
- Radiation from decaying isotopes is hazard to life by damaging cellular molecules
o Severity of this damage depends on the type & amount of radiation an organism
absorbs
o Doses used in medical diagnosis are safe

Radiometric Dating
- In fossils, radioactive decay is measured to date relics to past life
o Provide large body of evidence for evolution
o Diff between organisms from the past & present to give insight into species that
disappeared over time
- “Parent” isotope decays into its “daughter” isotope at fixed rate
o Half-life: time taken for 50% of the parent isotope to decay
 - Each radioactive isotope has characteristic half-life not affected by temp, pressure or
any other enviro variable
- Radioactive dating: measures ratio of diff isotopes & calculate how many half-lives (in
yrs) have passed since organism was fossilised
o Range from seconds to billion years
- Electrons are found in diff electron shells, each with a characteristic avg distance &
energy level
o Can move from shell to shell by absorbing/losing amount of energy = to diff in PE
between position in old & new shell
o Absorbs: farther out of nucleus
o Loses: falls back to shell closer to nucleus. Lose energy released to enviro as heat
- Closer the electrons is to the nucleus, the lower PE

The Energy Levels of Electrons

- If an atom was size of football stadium, nucleus = eraser & electrons= mosquitos
- Atoms are mostly empty space
- Only electrons are directly involved in chem reactions - nuclei not close enough to
interact
- Electrons vary in amount of energy
- Energy: capacity to cause change
- Potential energy: energy that matter possesses because of its location/structure
o E.g. water on hill because of altitude
- Matter has natural tendency to move to lowest possible state of potential energy
- Electrons have PE due to their distance from nucleus
- -ve charged electrons are attracted to +ve charged nucleus
Electron Distribution
- Determined chem behaviour of an atom
- Valence electrons/shell: thous on the outermost

Electron Orbitals
- Orbital: 3D space where electron is found 90% of the time
o Exact location of location never known
o Used to describe the space

The Formation & Function of Molecules

- Chemical bonds: attractions that hold atoms close together
- Covalent bonds & ionic bonds: strongest

Covalent Bonds
- Covalent bonds: sharing of a pair of valence electrons by 2 atoms
- Molecules: 2 or more atoms held together by covalent bonds
- Ways to represent electron sharing:
o Molecular form: H2
o Lewis dot structure: H:H
o Structural formula: H – H
 Line represents single bond: pair of shared electrons
o Space filling model:

- Double bond: sharing 2 pairs of valence electrons

o E.g. O=O
- Valence: bonding capacity & is usually = to the no. of unpaired electrons required to
complete valence shell

- Atoms in molecule attract shared bonding electrons to varying degrees, depends on

element
- Electronegativity: the attraction of a particular atom for the electrons of a covalent
bond
o More EN = more strongly atom pulls shared electrons towards itself
- Nonpolar covalent bond: electrons shared equally
o 2 atoms have same EN: tug-of-war at standoff
o E.g. H2 (single bond), O2 (double bond)
 - Polar covalent bond: electrons no shared equally
o electrons of 1 atom is bonded to more EN atom
o E.g. bonds between H & O atoms of water
- O is 1 of the most EN elements, attracting shared electrons more strongly than H
- In covalent bond between O & H:
o Electrons spend more time near O nucleus than H nucleus
o Because electrons are -ve charged & are pulled towards O in water molecule, the
O atom has 2 regions of partial -ve charge (δ-)
o Each H atom has δ+
- Individual bonds of methane (CH4) are less polar because the EN of C & H are similar

Ionic Bonds
- Ions: When the more EN atom takes an electron away from its partner. Result from op
charged atoms/molecules
- Cation: +ve charged ion
- Anion: -ve charged ion
- Because they are op. charged, they attract each other known as an ionic bond

- Compounds formed by ionic bonds are called ionic compounds or salts

- Unlike a covalent compound, an ionic compound does not consist of molecules

- ‘Ion’ refers to entire molecules that are electrically charged
 - Enviro affects strength of ionic bonds
o Dry salt crystal: bonds are strong (required hammer & chisel to break into 2)
o Wet salt crystal (dissolved in water): ionic bonds weaker (come apart)
o Most drugs are made as salts (stable when dry & can come apart when wet)

Weak Chem Interactions

- Holds functional form of many large biological molecules
- 2 molecules in the cell may adhere temporarily by weak interactions
- Reversibility: Two molecules can come together, affect one another in some way, and
then separate.

Hydrogen Bonds
- The attraction between a H (δ+) and an electronegative atom
- In living cells: partners usually O & N atoms

Van der Waals Interactions

- A molecule with nonpolar covalent bonds may have +ve & -ve charged regions
- Electrons not always evenly distributed: may accumulate at any instant by chance in 1
part of molecule
o Result: regions of +ve & -ve charge enabling all atoms to stick to each other
- VDW Interactions: individually weak & occur only when atoms & molecules are very
close tighter
o Interactions can be powerful when they occur simultaneously
- E.g. allow gecko lizard to walk straight up wall: interactions between foot molecules &
molecules of the wall are so number, they support its body weight
- Weak interactions may form in molecules & between parts on large molecules e.g.
proteins
- Cumulative effect of weak interactions reinforce 3D shape of molecule
Molecular Shape & Function
- Size & shape of molecule: key to its function in living cell
- Linear: molecule consisting of 2 atoms, e.g. H2 or O2
- Shapes determined by the positions of the atoms’ orbitals

- When atom forms covalent bonds, the orbitals in valence shell undergo rearrangement
- Molecular shape crucial:
o Determined how biological molecules recognise & respond to 1 another with
specificity
o Biological molecules only bind if shape are complementary
- E.g. opiates (drugs) relieve pain & alter mood by weakly binding to specific receptor
molecules on surfaces of the brain cells.
o Why would brain cells carry receptors for opiates, compounds not made by
body?
o Because they have similar shape to endorphin & mimic them by binding to
endorphin receptors in brain
Chemical reactions
- Chemical reactions: the making & breaking of chem bonds that lead to changes in
composition of matter
- Reactants: starting materials
- Products: resulting materials
- Reaction between H & O forming water:

- Summarise photosynthesis:

- Reverse reaction: H & N molecules can combine to form NH3 & can decompose to
regenerate H & N:

- Concentration of reactants: affects rate of reaction

o Greater concentration of reactant molecules = more frequently they collide with
1 another to have opportunity to react & form products
o Also, as products accumulate, collisions resulting in the reverse reaction become
more frequent
- Chemical equilibrium: point at which reactions offset one another
o forward & reverse reactions occur at same rate & concentrations stop changing
o Dynamic: reactions still going on in both directs but no effect on concentrations
o Concentrations have stabilised at particular ration & DOES NOT mean
concentrations of P & R are
 Water & Life

The Molecule That Supports All of Life

- ¾ of Earth’s surface consist of water
o Form: liquid (most), solid (ice), gas (water vapor)
o The only common substance to exist in natural enviro in all 3 states

Hydrogen Bonds
- Shape: wide V with 2 H atoms joined to O atom by single covalent bonds
o O is more electro-ve than H so electrons closer to O than H: polar covalent
bonds

- Polar molecules: unequal sharing of electrons (overall charge is unevenly distributed)

- O has 2 regions of partial -ve charge (δ-) & each H has a partial +ve charge (δ+)
- Properties of water arise from attractions between opposite charged atoms of diff water
molecules:
o Partially +ve H of 1 molecule is attracted to the partially -ve O of nearby
molecule
o The 2 molecules are held together by a hydrogen bond

- Liquid form: H bonds are very fragile

o About 1/20 as strong as a covalent bond
o H bonds form, break & re-form with great frequency
 o Each last a few trillionths of a second, but molecules are constantly forming new
H bonds with partners (most water molecules H bonded to neighbours)
- Conclusion: properties of water emerge from H bonding, organising water molecules
into higher level of structural order

Properties of water contributing to Earth’s suitability for life

1. Cohesive behaviour
2. Ability to moderate temp
3. Expansion upon freezing
4. Versatility as solvent

Cohesion of Water Molecules

- Result of H bonding – water molecules close to each other
- Arrangement of molecules in liquid water constantly changing, but at any given moment
many molecules are linked by multiple H bonds
o Linkages make water more structured than most other liquids
- Cohesion: H bonds hold substance together
o Transport water & dissolved nutrients against gravity in plants
a. Water from roots reaches leaves through network of water-conducting cells
b. As water evaporates from a leaf, H bonds cause water molecules leaving the
veins to tug on molecules farther down
c. Upward pull is transmitted through water-conduction cells all the way to
roots
- Adhesion: clinging of 1 substance to another
o Cling to cell walls help counter downward pull of gravity
 - Surface tension: measure of how difficult it is to stretch/break surface to liquid
(cohesion)
o At interface between water & air, an ordered arrangement of water molecules
are H bonded to 1 another & to water below, but not to air above
o Asymmetry gives water high ST (behaves as coated with invisible film)

Moderation of Temp by Water

- Absorbs heat from air that is warmer & releases stored heat to air that is cooler
- Effective heat bank: absorb/release large amount of heat with slight change in own
temp

Temperature & Heat

- Kinetic energy: anything that moves/energy of motion
o Atoms & molecules have KE – always moving, although not necessarily in any
particular direction
o The FASTER a molecule moves, the GREATER its KE
- Thermal energy: KE associated with random movement of atoms/molecules
o Related to temp, but NOT SAME thing
- Temperature: the avg KE of molecules in body of matter, regardless of volume
o While TE of a body of matter reflects total KE, thus reflects matter’s volume
- Example: water heated in coffeemaker
o Avg speed of molecules >es
o Thermometer records this as > in temp of liquid
o Total amount of TE >es
o ALTHOUGH, pot of coffee has higher temp than water in pool, pool contains
more TE because greater volume
- 2 objects of diff temp are bought together:
o TE passes from warmer to cooler object until the 2 are same temp
o Molecules in cooler speed up at expense of TE of warmer object
o Ice cube cools drink NOT by adding coldness, BUT by absorbing TE from liquid as
ice melts
o TE in transfer from 1 body to matter to another: Heat
- Calorie (cal): 1 unit of heat
o Amount of heat it takes to raise the temp of 1g of water by 1°C
o Also, amount of heat 1g of water releases when it cools by 1°C
- Kilocalorie (kcal): 1,000 cal
o Quantity of heat required to raise the temp of 1kg of water by 1°C
 o (‘Calories’ in food packages are actually kcal)
- 1 joules (J) = 0.239 cal, 1 cal = 4.184 J

Water’s High Specific Heat

- Ability of water to stabilise temp
- Specific heat: amount of heat that must be absorbed/lost for 1g of a substance to
change temp by 1°C
o Is 1 calorie per gram and per degree Celsius, abbreviated as 1 cal/(g ·°C)
- Example: ethyl alcohol (type in alcoholic beverages)
o SH of 0.6 cal/(g · °C), only 0.6 cal is required to raise the temp of 1g of ethyl
alcohol by 1°C
- Can also be defined as how well a substance resists changing its temp when it
absorbs/releases heat
o E.g. Iron pot hotter than water because same amount of heat will raise temp of
1g of iron faster than 1g of water
o Water resists changing its temp; when it does, it absorbs/loses large quantity of
heat for each degree of change
- Result of H bonding:
o Heat must be ABSORBED to BREAK H bonds
o Heat is RELEASED when H bonds FORM
o A cal of heat causes relatively small change in water temp because much of the
heat is used to disrupt H bonds before the water molecules can begin moving
faster
o When the water temp drops slightly, many additional H bonds form, releasing a
considerable amount of energy in the form of heat.
- Relevance to life on Earth
o Large body of water can absorb & store a huge amount of heat from the sun in
the daytime & during summer while warming up only a few degrees
o At night & during winter, the gradually cooling water can warm the air
o Helps moderate air temp in coastal areas
o Stabilize ocean temps, creating a favourable enviro for marine life
o Conclusion, keeps temp fluctuations on land & in water within limits that permit
life.
o Because organisms are made primarily of water - better able to resist changes in
their own temp than if they were made of a liquid with a lower SH

Evaporative Cooling
- Molecules of any liquid stay close together through attraction. Molecules moving fast
enough overcome attractions to depart liquid & enter air as gas (vapor)
- Vaporisation/evaporation: transformation from liquid to gas
- Even a low temps, the speediest molecules can escape into air (occurs at any temp)
o E.g. glass of water at room temp will eventually evaporate completely
- If a liquid is heated, the avg KE of molecules >es & the liquid evaporates more rapidly
 - Heat of vaporization: quantity of heat a liquid must absorb for 1g of it to be converted
from the liquid to the gaseous state
o To evaporate 1 g of water at 25°C, about 580 cal of heat is needed—nearly 2x
amount needed to vaporize a gram of alcohol or ammonia.
o For the same reason that water has a high SH, it also has a high heat of
vaporization relative to most other liquids
o Resulting from the strength of its H bonds, which must be broken before the
molecules can exit from the liquid in the form of water vapor
- Effects of high amount of energy required to vaporize water:
o Global scale: helps moderate Earth’s climate. Considerable amount of solar heat
absorbed by tropical seas is consumed during the evaporation of surface water.
As moist tropical air circulates poleward, it releases heat as it condenses &
forms rain
o Organismal level: accounts for the severity of steam burns, caused by the heat
energy released when steam condenses into liquid on the skin.
- As liquid evaporates, the surface of the liquid that remains behind cools down (its temp
<es)
o This evaporative cooling occurs because the “hottest” molecules, those with the
greatest KE, are most likely to leave as gas
o E.g. 100 fastest runners at a college transferred to another school, the avg speed
of the remaining students would decline
- Effects of evaporative cooling:
o Stability of temp in lakes & ponds
o Prevents terrestrial organisms from overheating
o Evaporation of water from the leaves of a plant helps keep the tissues in the
leaves from becoming too warm in sunlight
o Evaporation of sweat from human skin dissipates body heat & helps prevent
overheating on a hot day/when excess heat is generated by activity
o High humidity on a hot day >es discomfort - high concentration of water vapor in
the air prevents evaporation of sweat from the body

Floating of Ice on Liquid Water

- Less dense as solid than as liquid (i.e. ice floats on water)
- Water expands and become less dense when they solidify
o Result of H bonding
- Temps above 4°C, water:
o Expands as it warms and contracts as it cools
- As the temp falls from 4°C to 0°C, water:
o Begins to freeze because more of its molecules are moving too slowly to break H
bonds
o At 0°C, the molecules become locked into a crystalline lattice, each water
molecule H bonded to four partners. H bonds keep the molecules at “arm’s
length,” far enough apart to make ice about 10% less dense (10% fewer
molecules in the same volume) than liquid water at 4°C
- When ice absorbs enough heat for its temp to rise above 0°C, H bonds between
molecules are disrupted.
o As the crystal collapses, the ice melts & molecules have fewer H bonds, allowing
them to slip closer together
- Water reaches its GREATEST DENSITY at 4°C:
o Then begins to expand as the molecules move faster. Many connected by H
bonds, though only briefly: constantly breaking and re-forming.
- Ability of ice to float – important in suitability of the enviro for life
o If ice sank, then eventually all ponds, lakes, & even oceans would freeze solid,
making life impossible on Earth with only upper few inches of the ocean melting
in summer
o INSTEAD, when a deep body of water cools, the floating ice insulates the liquid
water below, preventing it from freezing and allowing life to exist under the
frozen surface
o Provides solid habitat for some animals, such as polar bears and seals
- Global warming - caused by CO2 & other “greenhouse” gases in the atmosphere
o In the Arctic, the avg air temp has risen 2.2°C since 1961
o Affected seasonal balance between Arctic sea ice & liquid water, causing ice to
form later in the year, melt earlier, & cover smaller area.
o Extreme challenge to animals that depend on ice for their survival
Water: The Solvent of Life
- Solution: liquid that is a completely homogeneous mixture of 2 or > substances
- Solvent: the dissolving agent solution
- Solute: Substance that is dissolved
- Aqueous solution: solute is dissolved in water (solvent)
- Example: salt in water (ionic compounds = NaCl)
o O regions (-ve charge) attracted to sodium cations
o H regions (+ve charge) attracted to chloride anions
o Hydration shell: sphere of water molecules around each dissolved ion

- Compounds do not need to be ionic to dissolve in water

- Some molecules dissolve when water molecules surround each solute molecule, forming
H bonds with them
- Large molecules (proteins) can dissolve in water if they have ionic & polar regions on
surface
- Polar compounds dissolving in water: biological fluids (blood), sap of plants & liquid
within cells
Hydrophilic & Hydrophobic Substances
- Hydrophilic: any substance that has an affinity for water
o Does not need to dissolve, e.g. some molecules in cells so large they don’t
dissolve
o Cotton consists of giant molecules of cellulose (numerous regions of +ve & -ve
charges that form H bonds). Water adheres to cellulose fibres (cotton towel
great at drying body yet does not dissolve in washing machine). Cellulose also in
walls of water-conducting cells in a plant
- Hydrophobic: substances that do not have affinity for water. Non-ionic & nonpolar
(can’t form H bonds) repel water
o E.g. vegetable oil, does not mix stably with water-based substances (vinegar)
o Results from prevalence of nonpolar covalent in boil between C & H which share
electrons almost equally
o In cell membranes

Solute Concentration in Aqueous Solutions

- Molecular mass: sum of the masses of all the atoms in a molecule
- Mole: called Avogadro’s number 6.02 x 1023
- Molarity: number of moles of solute per L of solution, a unit of concentration

Possible Evolution of Life on Other Planets

- More than 800 planets found outside solar system – few have presence of water vapor
- Mars:
o Has ice cap at both poles like Earth
o Ice present just under surface of Mars & has enough water vapor in atmosphere
for frost to form
o 2015: scientists found evidence of water flowing w/ other studies suggesting
conditions could have supported microorganismal life
Acidic & Basic Conditions on Living Organisms
- Occasionally, a H atom in a H bond between 2 water molecules shifts from 1 molecule to
another
o H atom leaves its electrons behind & what is transferred is a H ion (H+), a single
proton with a charge of 1+
o Water molecule that lost proton is now hydroxide ion (OH-), with 1- charge
o Proton binds to other water molecule making that molecule a hydronium ion
(H3O+)

- By convention, H+ (does not exist on its own in aq solution) is used to represent H3O+
- Double arrows = reversible reaction that reaches a state equilibrium when water
molecules dissociate at same rate that they are being reformed from H+ & OH-
o At equilibrium point, concentration of water molecules greatly exceeds concen.
of H+ & OH-
o In pure water 1 in every 554m is dissociated (rare)
o concentration of H+ and of OH- in pure water is therefore 10-7 M (at 25°C)
o Important: H+ & OH- are very reactive – changes in their concen. affect cell’s
proteins & other complex molecules
- In pure water:
o Concentration of H+ & OH- are equal
o Adding certain kinds of solutes, called acids & bases disrupts balance
- pH scale: describe how acidic or basis a solution is

Acids & Bases

- What causes aq solution to have imbalance in H+ & OH- concentrations?
o When acids dissolve in water, they donate additional H+ to solution
o Acid: substance that >es the H ion concentration of a solution

o Base: substance that <es the H ion concentration

 Direct: < H+ concentration by accepting H ions

 Indirect: dissociating to form hydroxide ions which combine with H ions &
form water
 - Basic solutions: solutions w/ higher concentration of OH- than H+
- Neutral: H+ & OH- concentrations are equal
- Weak acids: acids that reversibly release & accept back H ions

o Equilibrium favours reaction in left direction

o When carbonic acid is added to pure water, only 1% of the molecules are
dissociated at any particular time (enough to shift balance of H+ & OH- from
neutrality)

The pH Scale
- In aq solution at 25°C, the product of H+ & OH- concentrations is constant at 10-14

o Brackets: molar concentration

o In neutral solution at 25°C, (H+)=10-7 & (OH-)=10-7
o If acid is added to solution to > (H+) to 10-5 M, then (OH-) will decline by
equivalent factor to 10-9
- Acid adds H ions to a solution & removes OH ions (tendency for H+ to combine with OH-
to form water)
- Base >es OH- concentration & < H+ concentration by the formation of water. I.
- pH scale compresses range of H+ and OH- concentrations by employing logarithms.
 - pH of solution: the -ve logarithm (base 10) of H ion concentration:

- pH DECREASES as H+ concentration INCREASES

- Example: pH 10 (H concentration=10-10 M & OH concentration of 10-4M)
- Neutral aq solution at 25°C = pH 7
o pH value < than 7 = acidic solution; the lower the no. the more acidic the
solution.
o pH above 7 = basic solutions
o Most biological fluids, such as blood & saliva, are within the range of pH 6–8
o Gastric juice in human stomach: pH = 2
- Each pH unit represents a tenfold difference in H+ and OH- concentrations
o pH 3 is NOT 2x as acidic as a solution of pH 6, BUT 1,000 times (10 x 10 x 10)
more acidic
o Slight change in pH: concentrations of H+ & OH- change substantially

Buffers
- Slight change in pH harmful because chem processes of cell are sensitive to
concentrations of H & OH ions
- Example: blood – pH very close to 7.4, slightly basic
o Person cannot survive for more than few min if pH drops to 7 or rises to 7.8
o Chem system in blood maintains stable pH (buffers)
- 0.01 mol of strong acid added to 1L pure water
o pH drops from 7 to 2, BUT
o Same amount added to blood: pH from 7.4 to 7.3
- Buffers: substances that allow biological fluids to maintain relatively constant pH
despite addition of acids or bases
o Minimises changes in concentrations of H+ & OH- in solution
o Accepts H ions when solution are in excess & donates H ions if they have been
depleted
o Most contain weak acid & its corresponding base (combine reversibly with H
ions)
- Carbonic acid:
o Contributes to pH stability in blood & many other biological solutions

o Forms when CO2 reacts with water = H2CO3

 o Chemical equilibrium between carbonic acid and bicarbonate acts as pH
regulator
o If the H+ concentration in blood begins to fall (pH rises), the reaction proceeds to
the right & more carbonic acid dissociates, replenishing hydrogen ions
o When the H+ concentration in blood begins to rise (pH drops), the reaction
proceeds to the left, with HCO3- (base) removing the H ions from the solution &
forming H2CO3
o Thus, carbonic acid–bicarbonate buffering system consists of an acid & a base in
equilibrium with each other
o Most other buffers are also acid-base pairs.

Acidification: Treat to Oceans

- Increase in atmospheric CO2:
o Caused global warming & climate change
o About 25% of human-generated CO2 is absorbed by the oceans
- When CO2 dissolves in saltwater, it reacts with water to form carbonic acid (lowers
ocean pH)
o Ocean acidification: alters delicate balance of conditions for life in ocean
- pH of the oceans is 0.1 pH unit lower now than at any time in the past 420,000 years
o Recent studies predict that it will drop another 0.3–0.5 pH unit by end of century
- As seawater acidifies, the extra H ions combine with carbonate ions (CO32-) to form
bicarbonate ions (HCO3-), <ing carbonate ion concentration
o Predict that ocean acidification will cause the carbonate ion concentration to <by
40% by the year 2100
o Great concern: carbonate ions required for calcification, production of calcium
carbonate (CaCO3) by many marine organisms, incl. reef-building corals &
animals that build shells.
o Coral reefs are sensitive ecosystems that act as havens for a great diversity of
marine life. (loss of coral reef = loss of biological diversity)

Carbon & The Molecular Diversity of Life

Carbon: Backbone of Life

- Organisms such as plants are made up of chem based mostly on C
- C enters biosphere through producers (photosynthesis that use solar energy to
transform CO2 into C-based molecules of life, taken up by consumers)
- Able to form large, complex & varied molecules – diversity of organisms
- Proteins, DNA, carbohydrates, & other molecules that distinguish living matter from
inanimate material are all composed of C atoms bonded to 1 another and to atoms of
other elements.
Organic Chemistry
- Study of carbon compounds, regardless of origin
- Major elements of life—C, H, O, N, S, and P
- Uniform from 1 organism to another: common evolutionary origin of all life.

Carbon atoms
- C can form four bonds: great diversity
- Chem characteristic of an atom linked to electron configuration
o Determines kinds & no. of bonds an atom will form with other atoms

Formation of Bonds with C

- C: 6 electrons - 2 in 1st shell & 4 in 2nd thus has 4 valence electrons in a shell that can
hold up to 8 electrons
o Usually completes its valence shell by sharing its 4 electrons with other atoms so
7 electrons are present
- Usually forms single/double covalent bonds in organic molecules
- Each atom acts as an intersection point from which a molecule can branch off in as
many as 4 direction
o Enables carbon to form large, complex molecules
- When a carbon atom forms four single covalent bonds, the arrangement of its four
hybrid orbitals causes the bonds to angle toward the corners of an imaginary
tetrahedron
- Number of unpaired electrons in valence shell of atom is generally = to atom’s valence,
no. of covalent bonds it can form
 - In CO2, a single C atom is joined to 2 atoms of O by double covalent bonds
o O=C=O

o Because CO2 is simple & lacks H, it is often considered inorganic

Molecular Diversity Arising from Variation in Carbon Skeleton

- C chains form the skeletons of most organic molecules
- Vary in length & may be straight, branched, or arranged in closed rings
- Some have double bonds, which vary in no. & location
o Variation is important source of molecular complexity & diversity that
characterise living matter
- Atoms of other elements can be bonded to skeleton at available sites

Hydrocarbons
- Organic molecules consisting of only C & H
- Atoms of H are attached to C skeleton whenever electrons are available for covalent
bonding
- HC are major components of petroleum, called fossil fuel because it is composed of
decomposed remains of organisms that lived m of yrs ago
- Although HC are not prevalent in most living organism, many cell’s organic molecules
have regions consisting of only C & H
- E.g. molecules known as fats have long HC tails attached to a non-HC component
 - Neither petroleum nor fat dissolve in water: both are hydrophobic compounds because
bonds are non-polar C-to-H linkages
- HC undergo reactions that release large amount of energy

Isomers
- Compounds that have same molecular formula but diff structures
- Structural isomers: diff in covalent arrangements of their atoms

- Cis-trans isomers: differ in their spatial arrangements due to inflexibility of double

bonds
o Single bonds allow the atoms they join to rotate freely
o Double bonds: do not rotate freely
o Cis: same side
o Trans: opposite sides
o Subtle diff in shaper between isomers can have dramatic effect on biological
activites of molecules
 - Enantiomers: isomers that are mirror images of each other & that differ in shape due to
an asymmetric carbon, 1 that is attracted to 4 diff atoms or groups of atoms
o Levo (L): left
o Dextro (D): right
o Cannot be overlayed (right-hand won’t fit into the same space as left-hand)

o Important in pharmaceutical industry: 2 enantiomers of a drug may not be

equally effective
 Methamphetamine: 1 is addictive drug ‘crack’, other is ingredient in
vapor inhaler for nasal congestion
 Demonstrates that organisms are sensitive to even the subtlest variation
in structure

Chemical Groups
- Functional groups: chem groups that affect molecular shape, contributing to function
- E.g. Estradiol (type of estrogen) & Testosterone
o Both are female & male sex hormones
o Are steroids, organic molecules with common carbon skeleton in form of 4 fused
rings
o Differ only in chem groups attached to rings (in blue in figure), contributing to
function:
- 7 chem groups most important in biological processes:
o 1st 6 groups can be chemically reactive
o Of the 6, all except sulfhydryl are hydrophilic (soluble)
o Methyl group not reactive, but serves as recognisable tag on biological molecules
ATP: Source of Energy for Cellular Processes
- ATP (adenosine triphosphate): more complicated organic phosphate
- Consists of an organic molecule called adenosine attached to a string of 3 phosphate
groups:

- When 3 phosphates are present, as in ATP, 1 phosphate may be spilt off as result of
reaction with water
- Having lost 1 phosphate, ATP becomes adenosine diphosphate, or ADP
- ATP: sometimes said to store energy, but more accurate to think of it as storing the
potential to react with water
- Reaction releases energy that can be used by the cell.

o Pi = inorganic phosphate ion, HOPO32-

Carbon: Summary
- Versatility of C – great diversity (can form 4 bonds)
- Properties emerge from unique arrangement of its skeleton & chem groups attached
 The Structure and Function of Large Biological Molecules

The Molecules of Life

- Large molecules can be sorted in 4 main classes: carbohydrates, lipids, proteins &
nucleic acids
- All are huge except for lipids: macromolecules

Macromolecules
- Are polymers built from monomers
- Polymer is a long molecule consisting of many similar/identical building blocks linked by
covalent bonds
o E.g. large carbohydrates, proteins & nucleic acids
- Monomers: repeating units that serve as building blocks of polymers
o Form polymers
o Some have their own function
- Each class of polymer is made up of a diff type of monomer
o But chem mechanisms by which cells make & break down polymers are same

The Synthesis & Breakdown of Polymers

- Enzymes: specialised macromolecules that speed up chem reactions
- Dehydration reaction: 2 molecules are covalently bonded to each other with the loss of
a water molecule
o E.g. reaction connecting monomers
o When a bond forms between 2 monomers, each contribute part of water
molecule:
 1 monomer provides hydroxyl group (-OH)
 Other provides hydrogen (-H)
o Reaction is repeated as monomers are added to chain 1 by 1, making polymer
(polymerisation)
- Hydrolysis: water breakage; addition of water molecule
o E.g. polymers disassembled to monomers
o H attaches to 1 monomer
o OH attaches to other

- Digestion: example of hydrolysis in body

o Bulk of organic material in food is in form of polymers that are too large to enter
cells
o Within digestive tract, various enzymes attack the polymers, speeding up
hydrolysis
o Released monomers are absorbed into bloodstream for distribution to all body
cells which can use dehydration reactions to assemble monomers into new, diff
polymers that perform specific functions required by cell
 - Dehydration & hydrolysis can be involved in formation & breakdown of molecules that
are not polymers, such as some lipids

The Diversity of Polymers

- Inherited diff between close relatives/siblings reflect small variation in polymers,
particularly DNA & proteins
- Molecular diff between unrelated are more extensive (greater between species)
- Basis of diversity in polymers?
o Are constructed from only 40 to 50 common monomers (some occur rarely)
o Vast possibilities: like building words from 26 letter of the alphabet
o Key is arrangement – particular linear sequence that the units follow
- E.g. Proteins:
o Built from 20 kinds of amino acids arranged in chains typically 00s of amino acids
long
- Small molecules act as building blocks that are orders into unique macromolecules
- Despite immense diversity, can be ordered into 4 major classes: carbohydrates, lipids,
proteins & nucleic acids

Carbohydrates
- Serve as fuel & building materials
- Include sugars & polymers of sugars
- Simplest carbohy. are monosaccharides (simple sugars), and are monomers from which
more complex carbohydrates are built
- Disaccharides: double sugars consisting of 2 monosac. joined by a covalent bond
- Carbohy. macromolecules are polymers called polysaccharides, composed of many
sugar building blocks

Sugars
- Monosaccharides: have molecular formulas that are some multiple of the unit CH2O
o E.g. Glucose (C6H12O6)
- Trademarks of a sugar:
o 1 carbonyl group (C=O) & multiple hydroxyl groups (OH)
- Depending on location of carbonyl group, a sugar is either a:
o Aldose (aldehyde sugar): at end of C skeleton
o Ketose (ketone sugar): within C skeleton
o Glucose is an aldose but fructose (an isomer of glucose) is a ketose
- Criterion for classifying sugars:
o Most names end in -ose
o Size of the carbon skeleton ranges from 3 to 7 carbons long
 Hexoses: have 6 carbons e.g. glucose & fructose
 Trioses: 3 C sugars
 Pentoses: 5 C sugars

- Another source of diversity for simple sugars:

o The way their parts are arranged spatially around asymmetric C (a C attached to
4 diff atoms or groups of atoms)
o Glucose & galactose differ only in placement of parts around 1 asymmetric
carbon, small diff gives distinct shape & binding activities thus diff behaviours
- Drawing glucose with linear carbon skeleton is not completely accurate:
o In aq solutions, glucose molecules & most other 5 & 6 C sugars, form rings
because they are the most stable form of the sugars under physiological
conditions
 - Monosac. particularly glucose are major nutrients for cells/fuel for cellular work
o Cellular respiration: cells extract energy from glucose molecules by breaking
them down in a series of reactions
o C skeletons serve as raw material for synthesis of other types of small organic
molecules (amino & fatty acids)
o Others are incorporated as monomers into disacc. or polysac.
- Disaccharide: consist of 2 monosac. joined by a glycosidic linkage, covalent bond
formed by dehydration reaction
o E.g. maltose is a disacc. Formed by linking 2 molecules of glucose (used in
brewing beer)
o Most prevalent disacc. is sucrose (table sugar) with glucose & fructose as
monomers

o Plants transport carbohy. from leaves to roots & other non-photosynthetic

organs in form of sucrose
o Lactose, sugar in milk made from joined glucose & galactose
- Disacc. must be broken down into monosac. to be used for energy by organisms
- Lactose intolerance:
o Humans who lack lactase, enzyme that breaks down lactose
o Sugar is instead broken down by intestinal bacteria, causing formation of gas &
subsequent cramping
o Problem avoided: consuming dairy products treated with lactase to break down
lactose

Polysaccharides
- Macromolecules, polymers with a few 00 to 000 monosac. joined by glycosidic linkages
- Function:
o Storage material, hydrolysed to provide sugar for cells
o Building material for structures that protect the cell/whole organism
- Architecture & function are determined by its sugar monomers & by position of its
glycosidic linkages

Storage Polysaccharides
- The form that plants & animals store sugars for later use
- Plants store starch, a polymer of glucose monomers, as granules within cellular
structures known as plastids (which incl. chloroplasts)
o Synthesising starch enables plant to stockpile surplus glucose
o Glucose = major cellular fuel, starch = stored energy
o Sugar can later by withdrawn from its carbohy. ‘bank’ by hydrolysis breaking
bond between glucose monomers
- Most animals have enzymes that can hydrolyse plant starch, making glucose for nutrient
for cells
o Major sources of starch in diet: potato tubers & grains, fruits of wheat, corn, rice
o Most glucose in starch are joined by 1-4 linkages (no. 1 C to no. 4 C), like maltose
o Simplest form of starch, amylose, is unbranched
o Amylopectin, more complex starch, is branched polymer with 1-6 linkages at
branch points
- Animals store a polysac. called glycogen, a polymer of glucose that is more extensively
branched
o Vertebrates store mainly in liver & muscle cells
o Hydrolysis of glycogen in these cells releases glucose when demand for sugar
increases
o Stored fuel cannot sustain animal for long
o In humans, glycogen stores are depleted in about a day unless they are
replenished by eating
o Low carbohy. diets result in weakness & fatigue
Structural Polysaccharides
- Build strong materials
- Cellulose (polysac.) is major component in tough walls that enclose plant cells
o Plants produce 100b tons of cellulose per year
o Most abundant organic compound on Earth
o Like starch, has 1-4 glycosidic linkages, BUT linkages in these 2 polymers differ: 2
slightly diff ring structures for glucose
- When glucose forms a ring, the hydroxyl group attached to the no. 1 C is positioned
either below or above plane of ring
o 2 ring forms for glucose are called alpha (α) and beta (β)
o In starch, all glucose monomers are in α configuration
o In cellulose, glucose monomers are in β configuration, making every glucose
‘upside down’ with respect to its neighbours

- Differing glycosidic linkages give distinct 3D shapes

o Certain starch molecules are largely helical, fitting their function: efficient storing
glucose units
o Cellulose molecule is straight & never branched. Some hydroxyl groups on its
glucose monomers are free to H bond with hydroxyls of other cellulose
molecules lying parallel in it
- In plants, parallel cellulose molecules are grouped into units called microfibrils
o Are cable like & a strong building material for plants
o Important substance for humans because cellulose is major constituent of paper
& only component of cotton
- Unbranched structure of cellulose fits its function: imparting strength to parts of the
plant
- Enzymes that digest starch by hydrolysing its α link- ages are unable to hydrolyse the β
linkages of cellulose due to the diff shapes of these 2 molecules
- Almost all animals, incl. humans don’t digest cellulose (in food that passes through
digestive tract & is eliminated with faeces
o Along the way, the cellulose abrades the wall of the digestive tract & stimulates
the lining to secrete mucus, which aids in the smooth passage of food through
the tract
 o On food packages, “insoluble fibre” refers mainly to cellulose.
- Some microorganisms can digest cellulose, breaking it down into glucose monomers
o Cow has cellulose- digesting prokaryotes & protists in its gut which hydrolyse
the cellulose of hay & grass & convert the glucose to other compounds that
nourish the cow
o Termite has prokaryotes or protists living in its gut that can make a meal of
wood.
o Some fungi can also digest cellulose in soil & elsewhere, helping recycle
chemical elements within Earth’s ecosystems
- Chitin (a structural polysac.), is the carbohydrate used by arthropods (insects, spiders,
crustaceans etc.) to build their exoskeleton
- Exoskeleton: hard case that surrounds the soft parts of an animal
o Made of chitin embedded in a layer of proteins, the case is leathery & flexible at
1st but becomes hardened when proteins are chem linked to each other (insects)
or encrusted with calcium carbonate (crabs)
- Chitin also found in fungi – uses cellulose as building material for cell walls
- Chitin & cellulose have β linkages BUT the glucose monomer of chitin has a nitrogen-
containing attachment

Lipids
- A diverse group of hydrophobic molecules
- Are 1 class of large biological molecules that does not incl. true polymers
- Generally not big enough to be considered macromolecules
- Lipids are grouped with e/o because they share 1 important trait: mix poorly with water
- Hydrophobic behaviours are based on molecular structure
- Have some polar bonds associated with O, lipids consist mostly of HC regions
- Varied in form & function
- Incl. waxes & certain pigments
Fats
- Not polymers, BUT are large molecules assembled from smaller molecules by
dehydration reactions
- A fat is constructed from 2 kinds of smaller molecules: glycerol & fatty acids

- Glycerol: an alcohol with each of its 3 C bearing a hydroxyl group

- Fatty acid: has long C skeleton, usually 16 or 18 C atoms in length
o The C at 1 end of the skeleton is part of a carboxyl group, functional group that
gives molecules the name fatty acid
o Rest of the skeleton consists of a HC chain
- Reason fats are hydrophobic: the relatively non-polar C-H bonds in the HC chains of
fatty acids
o Fats separate from water because the water molecules H-bond to 1 another &
exclude the fats
- Making a fat:
o 3 fatty acid molecules are each joined to glycerol by an ester linkage, a bond
formed by dehydration reaction between hydroxyl & carboxyl group
o Resulting fat, called a triacylglycerol, thus consists of 3 fatty acids linked to 1
glycerol molecule
- Fatty acids in a fat can all be the same or can be 2 or 3 diff kinds
- Terms saturated & unsaturated fats are commonly used in context of nutrition
o Refer to structure of the HC chains of the fatty acids
- If there are no double bonds between C atoms composing a chain, then as many H
atoms as possible are bonded to the C skeleton. Such a structure is said to be saturated
with H, & the resulting fatty acid is therefore called a saturated fatty acid
- Unsaturated fatty acid has 1 or more double bonds, with one fewer H atom on each
double-bonded C
o Nearly every double bond in naturally occurring fatty acids is a cis double bond,
which creates a kink in the hydrocarbon chain
- Saturated fat: a fat made from saturated fatty acids
o Most animal fats are saturated: The HC chains of their fatty acids—the “tails” of
the fat molecules—lack double bonds, and their flexibility allows the fat
molecules to pack together tightly.
 o Solid at room temp
o Animals fats: lard & butter are
- Unsaturated fats: built of 1 or more types of unsaturated fatty acids
o Usually liquid at room temp
o Plants & fish fats: oils, olive oil & cod liver oil
o Kinks where cis bonds are located prevent molecules from packing close enough
to solidify at room temp

- “Hydrogenated vegetable oil”: unsaturated fats have been synthetically converted to

saturated fats by adding H, allowing them to solidify
o E.g. peanut butter, margarine are hydrogenated to prevent lipids from
separating out in liquid (oil) form
- Diet rich in saturated fats: 1 factor contributing to CVD known as atherosclerosis
o Deposits called plague develop within walls of blood vessels, causing inward
bulges that impede blood flow & reduce resilience of vessels
- Process of hydrogenating:
o Produces saturated fats & also unsaturated fats with trans double bonds
- Trans fats can contribute to coronary heart disease
o Espec. common in baked goods & processed foods
- Major Function of Fats:
o Energy storage
o HC chains of fats are similar to gasoline molecules & just as rich in energy
o 1g of fat stores more than twice as much energy as a gram of polysac. such as
starch
o Plants: are immobile, can function with bulky energy storage in form of starch
o Animals: carry energy stores with time, so there is advantage to having more
compact reservoir of fuel – fat
- Humans & other mammals stock long-term food reserves in adipose cells, which swell &
shrink as fat is deposited & withdrawn from storage
 o Adipose tissues cushions vital organs such as kidneys
o A layer of fat beneath the skin insulates the body (thick in marine animals)

Phospholipids
- Major constituents of cell membranes
- Is similar to a fat molecule BUT has only 2 fatty acids attached to a glycerol rather than 3
o The 3rd hydroxyl group of glycerol is joined to a phosphate group, which has a -ve
electrical charge in the cell
o Typically, an additional small charged/polar molecule is linked to the phosphate
group
- 2 ends of phospholipids show diff behaviours with respect to water
o The HC tails are hydrophobic & are excluded from water
o The phosphate group & its attachments form a hydrophilic head
- When phosphates are added to water, they self-assemble into a double-layered sheet
called a “bilayer” that shields their hydrophobic fatty acids tails from water
- At surface of a cell:
o Hydrophilic heads of the molecules are on outside of bilayer, in contact with
aqueous solutions inside & outside of the cell
o Hydrophilic tails point towards interior of bilayer, away from water
- Phospholipid bilayer forms boundary between cell & its external enviro & establishes
separate compartments within eukaryotic cells

Steroids
- Are lipids, characterised by a C skeleton consisting of 4 fused rings
- Chem groups attached to the rings distinguish them from others
- Cholesterol: a type of steroid and is a crucial molecule in animals
o Common component of animal cell membranes
o A precursor from with other steroids, such as sex hormones, are synthesised
 - In vertebrates, cholesterol is synthesised in the liver & is obtained from the diet
- High level of cholesterol in blood may contribute to atherosclerosis (CVD)

Membrane Structure & Function

Life at the Edge

- Plasma membrane: surrounds the cell & is boundary that separates a living cell from its
surroundings & controls all inbound & outbound traffic
o Selective permeability: allows some substances to cross it more easily than
others
- Ability of the cell to discriminate in its chem exchanges is fundamental to life

Cellular membrane
- Are fluid mosaics of lipids & proteins which are stable ingredients of the membrane
(carbohy. also important)
- Ability of phospholipids to form membranes is inherent in their molecular structure:
o Amphipathic molecule: has both hydrophilic & hydrophobic region
- A phospholipid bilayer can exist as a stable boundary between 2 aq compartments
because hydrophobic tails are sheltered from water while hydrophilic heads are
exposed to water
 - Most membrane proteins are amphipathic
o Reside in phospholipid bilayer with their hydrophilic regions protruding
o Maximises contact of hydrophilic regions of proteins with water in the cytosol &
extracellular fluid
o Provides hydrophobic parts with a non-aq enviro
- Fluid Mosaic Model: membrane is a mosaic of protein molecules bobbing in a fluid
bilayer of phospholipids
o Currently accepted model of arrangement of molecules in plasma membrane
o Proteins are not randomly distributed in membrane
o Groups of proteins often associated in long-lasting, specialised patches, where
they carry common functions. Called lipid rafts because specific lipids are found
in patches

The Fluidity of Membranes

- A membrane is held together mainly by hydrophobic interactions (weaker than covalent
bonds)
- Most lipids & some proteins can shift sideways – in the plane of membrane
o Rapid
- Rarely may flip-flop across membrane, switching from 1 phospholipid layer to the other
o Adjacent phospholipids switch positions about 107 times per sec
o Can travel about 2 μm—the length of many bacterial cells—in 1 sec
- Proteins are larger than lipids & move more slowly, BUT some membrane proteins do
drift
 o Some move in highly directed manner, perhaps driven along cytoskeletal fibers
in the cell by motor proteins connected to the membrane proteins’ cytoplasmic
region
o Other are held immobile by their attachment to the cytoskeleton or the
extracellular matrix

- Membrane remains fluid as temp <es until the phospholipids settle into a closely packed
arrangement & membrane solidifies (bacon grease turning into lard when cool)
- Temp at which membrane solidifies depends on types of lipids it is made of
o As temp <es, the membrane remains fluid to a lower temp if it is rich in
phospholipids with unsaturated HC tails
o Because of kinks in the tails where double bonds are located, unsaturated HC
tails cannot pack together as closely as saturated HC tails, making membrane
more fluid
- The steroid cholesterol, wedged between phospholipid molecules in plasma membranes
of animals cells, has diff effects on membrane fluidity at diff temps
o At high temps: e.g. 37 C, cholesterol makes the membrane less fluid by
restraining phospholipid movement
o Because it also hinders the close packing of phospholipids, it lowers the temp
required for the membrane to solidify.
o Thus, cholesterol can be thought of as a “fluidity buffer” for the membrane,
resisting changes in membrane fluidity that can be caused by changes in temp
o Compared to animals, plants have very low levels of cholesterol; steroid lipids
buffer membrane fluidity in plant cells.
-
 - Fluidity of a membrane affects both its permeability & the ability of membrane proteins
to move to where their function is needed
o When membrane solidifies, its permeability changes, & enzymatic proteins may
become inactive if their activity requires movement within the membrane
o Membranes that are too fluid cannot support protein function
- Extreme enviro are a challenge for life, resulting in evolutionary adaptations that include
diff in membrane lipid composition

Evolution Differences in Membrane Lipid Composition

- Fishes living in extreme cold have membranes with high proportion of unsaturated HC
carbons , enabling membranes to remain fluid
- Bacteria thrive at temps >er than 90C – their membranes incl. unusual lipids that may
prevent excessive fluidity
- Ability to change the lipid composition of cell membranes in response to changing temp
has evolved in organisms that live where temp vary
o Many plants that tolerate extreme cold: the % of unsaturated phospholipids > in
autumn, keeping the membranes from solidifying during winter
- Natural selection - favoured organisms whose mix of membrane lipids ensures
appropriate level of membrane fluidity for their environ
Membrane Proteins & Their Functions
- Membrane is collage of diff proteins, often clustered together in groups, embedded in
fluid matrix of lipid bilayer
- Plasma membrane of RBC:
o > than 50 kinds of proteins have been found so far
- Phospholipids form main fabric of membrane , BUT proteins determine most of
membrane’s function
- Diff types of cells contain diff sets of membrane proteins, & various membranes within a
cell each have unique collection of proteins
- Two major populations of membrane proteins:
o Integral proteins: penetrate the hydrophobic interior of the lipid bilayer.
 Majority are transmembrane proteins, which span the membrane; others
extend only part-way into the hydrophobic interior.

 The hydrophobic regions consist of 1 or more stretches of non-polar

amino acids, typically 20–30 amino acids in length, usually coiled into α
helices
 The hydrophilic parts are exposed to the aq solutions on either side of
the membrane.
 Some proteins also have 1 or more hydrophilic channels that allow
passage through the membrane of hydrophilic substances (even of water
itself
o Peripheral proteins are not embedded in the lipid bilayer at all
 Are loosely bound to surface of membrane, often to exposed parts of
integral proteins
- Cytoplasmic side of membrane: some proteins are held in place by attachment to
cytoplasm
- Extracellular side: certain membrane proteins may attach to materials outside cell
 o In animal cells, membrane proteins may be attached to fibers of the extracellular
matrix; integrins are 1 type of integral, transmembrane protein
o Attachments combine to give animal cells a stronger framework than plasma
membrane alone
- Cell-surface membrane proteins that carry out diff functions:
o Transport through cell membrane
o Enzymatic activity
o Attaching a cell to either its neighbouring cell or the extracellular matrix
o May carry functions by itself

- E.g. CD4 is a protein on the surface of immune cells: helps HIV infect these cells, leading
to AIDS
o Some don’t have AIDS & show no evidence of HIV infected cells
o Resistant people have an unusual form of a gene that codes for an immune cell-
surface protein called CCR5
o Although CD4 is the main HIV receptor, HIV must also bind to CCR5 as a “co-
receptor” to infect most cells
o An absence of CCR5 on the cells of resistant individuals, due to the gene
alteration, prevents the virus from entering the cells
o Interfering with CD4 causes dangerous side effects because of its many
important functions in cells
o Discovery of the CCR5 co-receptor provided a safer target for development of
drugs that mask the protein & block HIV entry
The Role of Membrane Carbohydrates in Cell-Cell Recognition
- Cell-cell recognition: cell’s ability to distinguish 1 type of neighbouring cell from another
(crucial to functioning of organism)
- Important for e.g.:
o Sorting of cell into tissues & organs in animal embryo
o Rejection of foreign cells by immune system
- Cell recognise other cells by binding to molecules, often containing carbohy., on the
extracellular surface of the membrane
- Membrane carbohy.:
o Usually short, branched chains of fewer than 15 sugar unites
o Some are covalently bonded to lipids, forming molecules called glycolipids
o Most are covalently bonded to proteins, called glycoproteins
- The carbohy. on the extracellular side vary from species to species, among individuals of
the same species, and even from one cell type to another in a single individual
- Diversity of the molecules & their location on the cell’s surface enable membrane
carbohy. to function as markers that distinguish 1 cell from another
o The four human blood types designated A, B, AB, and O reflect variation in the
carbohydrate part of glycoproteins on the surface of RBC

Synthesis & Sidedness of Membranes

- Membranes have distinct inside and outside faces
- The 2 lipid layers may differ in lipid composition & each protein has directional
orientation in the membrane
- How membrane sidedness arises:
o Asymmetrical arrangement of proteins, lipids, & their associated carbohy. in the
membrane is determined as the membrane is being built by the endoplasmic
reticulum (ER) & Golgi apparatus (components of the endomembrane system)