Basic Biology I: Cells

How organisms work

Outline

Chemistry (pp. 8-10): atoms, molecules and bond, polar bonds, water
Biochemistry (pp. 11-17): four basic macromolecules
Cells (pp. 20-29): membrane, osmotic pressure, organelles,
endosymbiosis, cell division, gene expression
Enzymes and energy generation (pp. 57-58 and 64-69)

Chemistry
Name the components of atoms and
their role in determining the atoms
identity and in forming chemical bonds.
Distinguish between the 3 main types of
chemical bond
Understand the relationship between
water, polar and non-polar, and
hydrophilic and hydrophobic

Chemistry
At the bottom, biology is nothing but applied chemistry
All matter is composed of atoms
Elements such as carbon and oxygen are a group of atoms of
the same type. For instance, a nail made of iron is just a large
group of iron atoms.
There are 92 naturally occurring elements, plus about 25
artificially-created elements.
Living things are mainly composed of the elements carbon,
hydrogen, oxygen, and nitrogen. Another dozen or so
elements are also used: phosphorus, iron, magnesium, sodium,
potassium, chlorine, to name a few.

Atoms

Atoms have 3 components: protons, neutrons, and

electrons
The type of element (carbon, iron, etc. ) is entirely
determined by how many protons are in the nucleus.

protons and neutrons are in the nucleus

Protons have a +1 charge
Neutrons have no charge

Electrons circle around the nucleus, in a series of

shells.
Electrons have a -1 charge
Chemical bonds are created by movements of the
electrons between atoms

The number of protons determines which

element the atom is.
Hydrogen: 1 proton, carbon = 6 protons, oxygen = 8
protons.
Biological and chemical processes never change the
number of protons in any atom.

Normally, the number of electrons is equal to the

number of protons, so the atom has no electrical
charge: it is neutral.

Chemical Bonds

Atoms can combine with each other to form molecules.

A molecule is a defined number of atoms grouped into a defined spatial

relationship. For example, water, H2O, is 2 hydrogen atoms connected to
an oxygen atom. The oxygen is in the middle, and the hydrogens are
attached at an angle to it.

A large group of the same molecule is called a compound (just as a large

group of the same atom is called an element).

Molecules are held together by chemical bonds. Chemical bonds are

formed by the movement of electrons.

Chemical bonds are the result of 2 forces:

1. The octet rule, which means that atoms want to have 8 electrons in
their outer shell (2 in the case of hydrogen).
2. The attraction between atoms of opposite electrical charge.

The three main types of chemical bond are; ionic bond, covalent bond,
and hydrogen bond.

Ionic Bonds

In an ionic bond, one atom gives an electron

to another atom. This makes both atoms
ions, and they are held together because their
opposite charges attract each other.

In sodium chloride (table salt), sodium starts

out with 1 electron in its outer shell. The
next shell down has 8 electrons, so by giving
1 electron away, the sodium atom gets a full
outer shell. It then has a +1 charge.

Chlorine starts out with 7 electrons in its

outer shell. By gaining one more electron, it
gets 8 in the outer shell, and a -1 charge.

The + charged sodium and the charged

chlorine attract each other, and they pack
together in salt crystals.

Covalent Bonds

Covalent bonds occur when 2 atoms

share a pair of electrons. The
electrons spend part of their time with
both atoms, so the octet rule is
satisfied sufficiently.

A molecule of hydrogen gas, H2, has

2 hydrogen atoms. Each atom
provides 1 electron, so in the bond
each atom shares 2, a complete shell
for hydrogen.

The bond is symbolized as a line

connecting the 2 Hs: H-H

In water (H2O), the oxygen has 6

electrons in its outer shell, and it
shares one with each of the 2
hydrogens, giving 8 shared electrons
for oxygen and 2 for each hydrogen.

Covalent bonds are the most common

type in biological molecules.

Polar Covalent Bonds

Sometimes the electrons in a covalent bond arent

shared equally, because one atom attracts electrons
more strongly than the other. When this happens, the
electrons spend more time with one atom, and that
atom becomes slightly negatively charged. The other
atom becomes slightly positively charged. This is a
polar covalent bond, because the atoms form positive
and negative poles.

Water is a polar compound, because the oxygen is

slightly negative and the hydrogens slightly positive.
Oxygen attracts electrons more than hydrogen

Note that the total charge on the molecule is balanced,

same number of electrons as protons, but within the
molecule the charges are slightly separated.

(Bonds where the electrons are shared equally are called

non-polar.)

Polar molecules attract each other: the opposite

charges attract.

Hydrogen Bonds

The slight + and charges in polar

bonds attract each other. In biological
molecules, it is common for the
partial + charge on a hydrogen to
attract the partial charge on a
nearby oxygen or nitrogen. This
attraction is called a hydrogen bond.
A hydrogen bond is the attraction
between a hydrogen atom and the
small negative charge on another
atom.

Hydrogen bonds are very weak

compared to covalent bonds, but large
numbers of them can add up to a
strong bond. The strands of DNA are
held together by hydrogen bonds.

Hydrogen bonds also form between

different parts of the same molecule,
and between water and other
molecules.

Water

All life occurs in water. Most

molecules are dissolved in water: an
aqueous solution.

Water, H2O, is a polar compound.

The 2 hydrogens are held at an
angle to each other, and so the
oxygen end of the molecule is
partially negative and the hydrogen
end is partially positive.
Water forms many hydrogen bonds
with other water molecules and with
other polar substances. This causes
water molecules to stick together
(causing surface tension) and stick
to other things (causing capillary
action, how water gets from the
roots to the top of trees).

Water

Polar substances dissolve in

water, because water forms
hydrogen bonds with the polar
molecules. Thus, polar
substances are called
hydrophilic, or water-loving.

Non-polar substances dont

dissolve in water because they
cant form hydrogen bonds, so
they are called hydrophobic, or
water-fearing. Oils and fats are
examples of non-polar
substances.

Cells are surrounded by a

hydrophobic membrane. Keeps
the cells contents separated from
the outside world.

Hydrophilic coating reduces friction by

trapping a thin layer of water next to the boats
hull.

Biochemistry
Name the 4 types of macromolecule,
their subunits, and their functions in the
cell.
Distinguish between different sub-types
of carbohydrate, lipid, and nucleic acid
in terms of their structure and role in the
cell.
Understand how protein folding is
related to enzyme activity.

Organic Compounds
It used to be thought that only living
things could synthesize the
complicated carbon compounds
found in cells
German chemists in the 1800s
learned how to do this in the lab,
showing that organic compounds
can be created by non-organic
means.
Raw materials: coal and oil

Today, organic compounds are those

that contain carbon. (with a few
exceptions such as carbon dioxide
and diamonds)

Four Basic Types of Macromolecule

Most organic molecules in the cell are long chains of similar subunits.
Because they are large, these molecules are called macromolecules.
Each macromolecule has a different type of subunit.

The four types of macromolecule are:

1.
2.
3.
4.

carbohydrates (sugars and starches), Subunit = simple sugar.

lipids (fats). Subunits = fatty acids and glycerol
proteins, Subunits = amino acids
nucleic acids (DNA and RNA). Subunits = nucleotides

The cell also contains water, inorganic salts and ions, and other small
organic molecules.

Plants often produce secondary metabolites: special compounds that

attract pollinators, inhibit microorganisms, deter grazing animals, etc.
We have found uses for many of these secondary metabolites as
medicines, spices, and drugs.

Carbohydrates
Sugars and starches: saccharides.
The name carbohydrate comes from
the approximate composition: a ratio of
1 carbon to 2 hydrogens to one oxygen
(CH2O). For instance the sugar glucose
is C6H12O6.
Carbohydrates are composed of rings of
5 or 6 carbons, with OH groups
attached. This makes most
carbohydrates water-soluble.
Carbohydrates are used for energy
production and storage (sugar and
starch), and for structure (cellulose).

Sugars

Monosaccharides, or simple sugars, like glucose

and fructose, are composed of a single ring.
Glucose is the primary food molecule used by
most living things: other molecules are converted
to glucose before being used to generate energy.
Glucose can also be assembled into starch and
cellulose.
Fructose is a another simple sugar found in plants,
It is sweeter than glucose and is used to sweeten
may food products.

Disaccharides are two simple sugars joined

together. Most of the sweet things we eat are
disaccharides: table sugar is sucrose, glucose
joined to fructose. Plants use photosynthesis to
make glucose, but convert it to sucrose for ease of
transport.
Maltose, malt sugar, consists of two glucoses
joined together. It is a breakdown product of
starch, which yeast converts to ethanol when beer
is brewed.

Complex Carbohydrates

= polysaccharides (many sugars linked

together).
Can be linear chains or branched.

Some polysaccharides are used for food

storage: starch.
Starch is a glucose polymer, we have
enzymes that easily digest starch.
Starch is a convenient way to store
glucose in both plants and animals.

Some polysaccharides are structural: the

cellulose of plant cell walls and fibers is
a polysaccharide composed of many
glucose molecules, but linked together
differently than starch.
We dont have enzymes that can digest
these polymers. Cows and termites
depend on bacteria in their guts to digest
cellulose, producing methane as a
byproduct.

Lipids

Lipids are the main non-polar component

(hydrophobic) of cells. Mostly hydrocarbons
carbon and hydrogen.
They are used primarily as energy storage and
cell membranes.
4 main types: fats (energy storage),
phospholipids (cell membranes), waxes
(waterproofing), and steroids (hormones).
Waxes: waterproof coating on plants and
animals. Composed of fatty acids attached to
long chain alcohols.
The ability of plant to coat themselves in waxes
was crucial to the ability to live on dry land.

Steroids have carbon atoms arranged in a set of

4 linked rings.
Cholesterol is steroid; it is an essential
component of cell membranes (along with the
phospholipids).
Many human hormones are steroids

Triglycerides and Phospholipids

Triglycerides are the main type of fat.
A triglyceride is composed of 3 fatty
acids attached to a molecule of
glycerol.
Fatty acids are long hydrocarbon
chains with an acid group at one end.

Fats store about twice as much energy

per weight as carbohydrates like
starch.
Phospholipids are the main
component of cell membranes.
they have a glycerol with 2 fatty acids
attached, plus a phosphate-containing
head group instead of a third fatty acid.

The head group is hydrophilic, while

the fatty acids are hydrophobic.
Cell membranes are 2 layers, with the
head groups facing out and the fatty
acids forming the interior of the
membrane.

Proteins

The most important type of

macromolecule. Roles:
Enzymes: all chemical reactions in the
cellsare catalyzed by enzymes, which are
proteins: building up, rearranging, and
breaking down of organic compounds,,
generating energy
Structure: collagen in skin, keratin in hair,
crystallin in eye. Also, movement of
materials inside the cell.
Transport: everything that goes in or out of a
cell (except water and a few gasses) is
carried by proteins.

All organisms contain protein, but

animals have much more protein than
plants: most of the animal body is
composed of protein, while most of the
plant body is carbohydrate.
Proteins are 1/3 nitrogen. Acquiring
this nitrogen and getting rid of
nitrogenous waste is a big problem
animals face.

Amino Acids

Amino Acids are the subunits of

proteins.
Each amino acid contains an amino
group (-NH2) and an acid group
(COOH). Proteins consist of long
chains of amino acids, with the acid
group of one bonded to the amino
group of the next.
There are 20 different kinds of amino
acids in proteins. Each one has a
functional group (the R group)
attached to it.
Different R groups give the 20 amino
acids different properties, such as
charged (+ or -), polar, hydrophobic,
etc.
The different properties of a protein
come from the arrangement of the
amino acids.

Protein Structure

A polypeptide is one linear chain of

amino acids. A protein consists of one or
more polypeptides, and they sometimes
contain small helper molecules such as
heme.
After the polypeptides are synthesized by
the cell, they spontaneously fold up into a
characteristic conformation which allows
them to be active. The proper shape is
essential for active proteins. For most
proteins, the amino acids sequence itself
is all that is needed to get proper folding.
The joining of polypeptide subunits into a
single protein also happens
spontaneously, for the same reasons.

Denaturation is the destruction of the 3dimensional shape of the protein. This

inactivates the protein, and makes it
easier to destroy. Heat is the easiest way
to denature proteins: this is the effect of
cooking foods.

Nucleic Acids

Nucleotides are the subunits of nucleic

acids.
Nucleic acids store and transmit genetic
information in the cell.
The two types of nucleic acid are RNA
(ribonucleic acid) and DNA
(deoxyribonucleic acid).
Each nucleotide has 3 parts: a sugar, a
phosphate, and a base.
The sugar, ribose in RNA and
deoxyribose in DNA, contain 5 carbons.
They differ only in that an OH group in
ribose is replaced by a H in DNA.
The main energy-carrying molecule in
the cell is ATP. ATP is an RNA
nucleotide with 3 phosphate groups
attached to it in a chain. The energy is
stored because the phosphates each have
a negative charge. These charges repel
each other, but they are forced to stay
together by the covalent bonds.

DNA and RNA

DNA uses 4 different bases: adenine

(A), guanine (G), thymine (T), and
cytosine (C). The order of these bases
in a chain of DNA determines the
genetic information.
DNA consists of 2 complementary
chains twisted into a double helix and
held together by hydrogen bonds.
DNA is a stable molecule which can
survive thousands of years under
proper conditions
The DNA bases pair with each other: A
with T, and G with C.

RNA consists of a single chain that also

uses 4 bases: however, the thymine in
DNA is replaced by uracil (U) in RNA.
RNA is much less stable than DNA: it
is used to convey information for
immediate use by the cell.

Cells
List the tenets of the cell theory.
Know the essential difference between prokaryotes and
eukaryotes, and which types of organism belong to which group.
Understand how the cell membrane allows only certain molecules
in and out of the cell.
Explain what osmotic pressure is, and describe the function of the
cell wall in resisting osmotic pressure.
Explain the endosymbiotic theory for the origin of mitochondria
and chloroplasts.
Know the functions of these organelles: nucleus, mitochondria,
chloroplast, endoplasmic reticulum, Golgi body, lysosome
Understand the relationship between chromosomes, DNA, and
genes.
Understand the purpose of mitosis (but not the steps involved).
List the steps of gene expression and the molecules involved in
each step.
Know the purpose of the genetic code and transfer RNA

The Cell Theory

Use of the microscope for 150 years or so led to these basic
beliefs about cells:
1. All living things are composed of cells.
2. The cell is the smallest unit of life.
3. All cells arise from pre-existing cells.

Basic Cell Organization

All cells contain:
1. cell membrane that keeps the
inside and outside separate.
2. DNA-containing region that
holds the instructions to run the
processes of life.
3. Cytoplasm: a semi-fluid region
containing the rest of the cells
machinery.

Prokaryotes: (bacteria): simple

cells with DNA loose in the
cytoplasm. No nucleus or other
internal membrane-bound
organelles.
Eukaryotes (plants, animals, fungi,
protists): complex cells with DNA
in a nucleus separated from the
cytoplasm by a membrane.

Cell Membrane
Composed of phospholipids, with a
polar (and therefore hydrophilic)
head group, and 2 non-polar
(hydrophobic) tails. A bilayer with
the polar heads on the outsides and
hydrophobic tails inside satisfies all
of the molecule. The membrane is a
phospholipid bilayer.
The membrane also contains
cholesterol and various proteins.
The proteins act as sensors,
attachment points, cell recognition,
or they transport small molecules
through the membrane.
Only water, a few gasses, and a few
other small non-polar molecules can
move freely through a pure
phospholipid membrane.
Everything else must be transported
into the cell by protein channels in
the membrane.

Transport Across the Cell Membrane

Each type of molecule that crosses the membrane needs its
own transporter protein: the transporters are very specific.
Basic rule: things spontaneously move from high
concentration to low concentration (downhill). This
process is called diffusion.
To get things to move from low to high (uphill), you need
to add energy. In the cell, energy is kept in the form of
ATP.
Three basic transport mechanisms: passive transport for
downhill, active transport for uphill, and bulk transport for
large amounts of material in either direction.
Also need to deal with excess water entering the cell.

Passive and Active Transport

Passive transport uses protein channels

through the membrane that allow a
particular molecule to go through it,
down the concentration gradient.
Glucose is a good example: since cells
burn glucose for energy, the
concentration inside is less than the
concentration outside.

Active transport uses proteins as

pumps to concentrate molecules
against the concentration gradient.
The pumps use ATP for energy. One
example is the calcium pump, which
keeps the level of calcium ions in the
cell 1000 times lower than outside, by
constantly pumping calcium ions out.
The balance of sodium and potassium
ions is maintained with potassium high
inside and sodium low inside, using a
pump. Up to 1/3 of all energy used by
the cell goes into maintaining the
sodium/potassium balance.

Water in the Cell

Water also moves down the concentration

gradient. Since the cell is full of other
molcules, water wants to moves into the cell
to dilute them. This process is called osmosis,
and it exerts a pressure that can cause cells to
swell up and burst.
We say that pure water is hypotonic relative to
the inside of a cell: pure water has fewer
particles in it, so the water moves into the cell.
A plant cell in pure water swells up against the
cell wall: a nice crisp vegetable, for example.
Conversely, if cells are put into a concentrated
salt solution, water will leave the cells, moving
to dilute the water outside. The concentrated
salt solution is hypertonic: has more particles
in it than the inside of the cell. The cell shrinks
away from the cell wall: the plant wilts.
Normal body fluids are isotonic, having the
same concentration of particles as the inside of
the cell.
The most important function of the plant cell
wall is to defend against osmotic pressure.

Mitochondria and Chloroplasts

The mitochondria are the site where most of the

cells ATP is generated, when organic
compounds are broken down to carbon dioxide
and water, using oxygen.
All eukaryotes have mitochondria. The number
in a cell depends on that cells energy needs.
Mitochondria have their own circular DNA, the
same kind found in bacteria. This and other
evidence has led to the theory of endosymbiosis:
that mitochondria were once free-living bacteria
that developed a mutually beneficial relationship
with a primitive eukaryotic cell.
Chloroplasts are the organelles where
photosynthesis occurs. They are also the result
of endosymbiosis: chloroplasts are descended
from free-living photosynthetic bacteria.
Several types of algae have had 2 rounds of
endosymbiosis: The first event got the
chloroplasts established in the cells (creating red
and green algae). The second endosymbiosis
event occurred when another single-celled
organism (a protist) swallowed one of these
algae to create brown algae.

Endosymbiont Hypothesis

Nucleus
The main components of the nucleus are
the chromosomes. A chromosome is
composed of a single very long DNA
molecule plus the proteins that support it
and control it.
The DNA carries the genes, which are
instructions needed to build and maintain
the cell, respond to changes in the
environment, and to divide into 2 cells.
Each gene is a short region of the
chromosomes DNA. There are several
thousand genes on each chromosome.
What genes do: the nucleotide sequence of
each gene codes for a single polypeptide,
the chain of amino acids that make up
proteins.
Most eukaryotes have a small number of
chromosomes: humans have 46
chromosomes, corn plants have 20. The
number is fixed within a species: all
humans have 46 chromosomes except for
some genetic oddities.

Cell Division and Genes

Cells divide to make more cells. The
chromosomes must be precisely
divided so that each daughter cell gets
exactly the same DNA.
All the other organelles are just
randomly separated into the daughter
cells,

Key points about genes:

All cells within an organism have the
same genes.
What makes cells different from each
other is that different genes are turned
on and turned off in different cells.

Before a cell can divide, it must

replicate its DNA, so there are 2
copies of each chromosome (=2 DNA
molecules), attached at the
centromere.
Once the DNA has been replicated,
the cell is ready to divide, using the
process of mitosis.

Summary of Mitosis

Mitosis is normal cell division, which goes on throughout

life in all parts of the body.
Meiosis is the special cell division that creates the sperm and
eggs, the gametes. We will discuss meiosis separately.

Prophase:

Chromosomes condense
Nuclear envelope disappears
centrosomes move to opposite sides of the cell
Spindle forms and attaches to centromeres on the chromosomes

Metaphase
Chromosomes lined up on equator of spindle
centrosomes at opposite ends of cell

Anaphase
Centromeres divide: each 2-chromatid chromosome becomes
two 1-chromatid chromosomes
Chromosomes pulled to opposite poles by the spindle

Telophase
Chromosomes de-condense
Nuclear envelope reappears
Cytokinesis: the cytoplasm is divided into 2 cells

Gene Expression

Each gene is a short section of a

chromosomes DNA that codes for a
polypeptide.
Different genes are active (expressed) in
different cells
Genes are expressed by first making an
RNA copy of the gene called messenger
RNA,(transcription) and then using the
information on the RNA copy to make a
protein (translation).
Transcription occurs in the nucleus, but
translation occurs in the cytoplasm. The
messenger RNA needs to be transported
out of the nucleus.

Transcription

Transcription is the process of making an

RNA copy of a single DNA gene.
The RNA copy is messenger RNA
The copying is done by an enzyme: RNA
polymerase.
The bases of RNA pair with the bases of
DNA: A with T (or U in RNA), and G with
C. The RNA copy of a gene is just a
complementary copy of the DNA strand.
RNA polymerase attaches to a signal at the
beginning of the gene, then it moves down
the gene, adding new bases to the RNA
copy, until it reaches a termination signal at
the end of the gene.

Genetic Code

There are only 4 bases in DNA and

RNA, but there are 20 different amino
acids that go into proteins. How can
DNA code for the amino acid
sequence of a protein?
Each amino acid is coded for by a
group of 3 bases, a codon. 3 bases of
DNA or RNA = 1 codon.
Since there are 4 bases and 3
positions in each codon, there are 4 x
4 x 4 = 64 possible codons.
This is far more than is necessary, so
most amino acids use more than 1
codon.
3 of the 64 codons are used as STOP
signals; they are found at the end of
every gene and mark the end of the
protein.
One codon (AUG) is used as a
START signal: it is at the start of
every protein.

Transfer RNA

Transfer RNA molecules act as adapters

between the codons on messenger RNA and the
amino acids. Transfer RNA is the physical
manifestation of the genetic code.
Each transfer RNA molecule is twisted into a
knot that has 2 ends.
At one end is the anticodon, 3 RNA bases
that matches the 3 bases of the codon. This is
the end that attaches to messenger RNA.
At the other end is an attachment site for the
proper amino acid.
A special group of enzymes pairs up the proper
transfer RNA molecules with their
corresponding amino acids.
Transfer RNA brings the amino acids to the
ribosomes, which are RNA/protein hybrids that
move along the messenger RNA, translating
the codons into the amino acid sequence of the
polypeptide.

Translation

First step: initiation. The messenger RNA binds to a

ribosome, and the transfer RNA corresponding to the
START codon binds to this complex
The ribosome has 2 sites for binding transfer RNA.
The first tRNA with its attached amino acid binds
to the first site, and then the transfer RNA
corresponding to the second codon bind to the
second site.
The ribosome then joins the two amino acids
together.
Step 2 is elongation: the ribosome moves down the
messenger RNA a distance of one codon.
The old, empty tRNA is removed.
A new transfer RNA, matching the new codon,
binds
The ribosome attaches the new amino acid to the
growing polypeptide
The process repeats: the ribosome moves down the
messenger RNA, adding new amino acids to the
growing polypeptide chain.
The final step in translation is termination. When the
ribosome reaches a STOP codon, there is no
corresponding transfer RNA. Instead, the whole
complex falls apart, releasing the new polypeptide.

Internal Membrane System

The internal membrane system is a
group of organelles that has 3 basic
functions:
1. to manufacture new lipids and
membranes,
2. to synthesize membrane-bound
proteins,
3. to package proteins for export out of
the cell.

Proteins that span the membrane are

very hydrophobic. They need to be
synthesized directly into the
membrane.
We will talk about 4 organelles as
part of this system: the endoplasmic
reticulum (ER), the Golgi bodies, the
lysosomes, and the peroxisomes.

Endoplasmic Reticulum

Reticulum means network; the ER

is a network of tubules in the
cytoplasm, composed of membranes
just like the cell membrane. It
provides a membrane channel from
the nucleus to the cell membrane.
Two types, connected together: rough
ER and smooth ER
Rough ER looks rough because it is
studded with ribosomes, the cellular
machines that synthesize proteins.
Ribosomes on the rough ER make the
proteins that are inserted into the
membrane, using the instructions
from messenger RNA. Other
ribosomes, not attached to the ER,
make the non-membrane-bound
proteins.
Smooth ER has no ribosomes. It is
used to synthesize the lipids of the
membrane.

Golgi Body and Secretion

Proteins that are going to be secreted

out of the cell are synthesized in the
rough ER. They get finished in the
Golgi body: sugar molecules are
attached to some of the amino acids.
The sugars help protect the exported
proteins from degradation.
Golgi looks like a series of stacked
plates.
Vesicles are small, membrane-bound
organelles. Vesicles carry proteins
from the ER to the Golgi, and then
from the Golgi body to the cell
membrane. Secretion to the outside
world occurs by exocytosis: the
vesicle fuses with the cell membrane,
releasing its contents.
Proteins synthesized into the
membrane of the ER end up in the cell
membrane by the same mechanism

Lysosomes and Peroxisomes

Lysosomes are intracellular stomachs: they

are full of digestive enzymes that operate at
low pH. You can think of them as little acid
vats. Vesicles transport materials to the
lysosomes, and the lysosomes digest them.

Peroxisomes are membrane-bound sacs

used to break down fatty acids and some
other molecules. They generate hydrogen
peroxide, a poisonous molecule, in the
process, which is the source of the name
peroxisome.

Enzymes and Energy

State the two laws of thermodynamics.
Understand how enzymes catalyze chemical
reactions.
Diagram the relationship between glucose,
carbon dioxide, electrons, oxygen, and water
in the generation of energy.
Distinguish between glycolysis, the Krebs
cycle, and electron transport: what the starting
and ending molecules are, where they occur,
under what conditions do they occur

Energy in the Cell

All life needs energy. Cells convert
the chemical bond energy in food
molecules to chemical bond energy
stored in ATP molecules.
ATP energy is then used to run
metabolism and all other bodily
processes.

Food molecules contain potential

energy in their chemical bonds. We
are going to examine how this energy
is transferred to ATP.
calories are a measure of energy.
We are ignoring the difference between
calorie and :Calorie

Some foods contain more energy per

gram than others, because their
chemical bonds store more energy.
For instance, carbohydrates and
proteins store 4 calories per gram,
while fats store 9 calories per gram.

Thermodynamics

First Law: the total mount of energy in the

Universe is constant. Energy is neither
created not destroyed, it just changes form.
When energy is expended, part of it goes to
do useful work, and the rest ends up as waste
heat. None of it is lost, but it changes forms.

Second Law: disorder (entropy) increases.

Energy goes from useful forms to useless
heat.
Every energy transformation step is
inefficient (as a consequence of the Second
Law), meaning that some of the energy is
converted to waste heat at every step, and the
amount of useful work decreases with every
step.

Life is very orderly compared to non-living

things. Living things are able to locally
reverse the overall direction of entropy by
using a lot of energy.
The energy of living cells comes from the
Sun, and it ends up as waste heat.
In general, only about 10% of the total
energy in food gets used to do something
useful. The other 90% is lost as heat.

ATP

In living cells, energy is carried in

molecules of ATP, adenosine
triphosphate.
When the energy is used, one of the
phosphates attached to ATP is
released, giving ADP, adenosine
diphosphate.
ATP is made by adding a phosphate
to ADP.
ATP is constantly being generated,
and it is used almost as soon as it is
made.

How energy is stored in the ATP

molecule: The 3 phosphates each
have a negative charge, and so they
repel each other. When the bond
holding them together is broken, the
phosphates fly apart, like a spring
being released.

Metabolic Reactions

A metabolic reaction is the

conversion of one chemical
compound into another one inside a
living cell. Each different reaction
is catalyzed by a different enzyme.
For every metabolic reaction, you
start with reactants and convert
them to products.
The basic rule: reactions run
downhill: more energetic reactants
are converted to less energetic
products.
If a reaction needs to run uphill,
creating products that contain more
energy than the reactants, energy in
the form of ATP must be added.
Reactants are also called substrates.

Enzymes

Enzymes are proteins that cause

specific chemical reactions to occur.
Enzymes act as catalysts: they help
the reaction occur, but they arent
used up in the reaction.
All reactions require an input of
energy to get them started: the
activation energy. Think of touching
a match to a piece of paper to start a
fire: the match is supplying the
activation energy.
Enzymes work by lowering the
activation energy for a reaction. The
reaction occurs thousands or millions
of times faster than without the
enzyme. The little bit of activation
energy needed is supplied by the
collision of the molecules involved.
Enzymes are very specific for their
substrates: they work on only a very
limited number of similar molecules.

Oxidation of Glucose

The basic food molecule is glucose, a simple sugar that has 6 carbon atoms.
Energy from chemical bonds is transferred in the form of electrons. Oxidation
means removing electrons. Its opposite is reduction, which is gaining electrons.
LEO = Lose Electrons Oxidation; GER = Gain Electrons Reduction.
Cells oxidize glucose to form carbon dioxide and water. The cell removes high
energy electrons from glucose (in a series of steps), which converts it to carbon
dioxide. The energy stored in the electrons is used to make ATP. The electrons
(now low energy) are given to oxygen molecules, converting them to water.
By passing the electrons through a series of steps before their final destination in
water, the cell can harvest the energy efficiently. In contrast, burning releases the
energy all at once, so it cant be captured easily.
Some common forms of oxidation: burning and rusting.

Respiration: Three Steps

Respiration is generating energy by breaking down food molecules,
converting the energy in their chemical bonds to ATP energy.
All cells respire, including plants.

1. Glycolysis: The anaerobic breakdown of glucose into the 3-carbon sugar

pyruvate.
Long ago, before oxygen was present in the atmosphere, all cells used
anaerobic respiration, which means generating energy in the absence of
oxygen.
Many bacteria only have anaerobic respiration.
Plants and animals perform glycolysis in the cytoplasm, not in any organelle.
When no oxygen is present, yeast converts the pyruvate into ethanol.

2. Krebs cycle: removes high energy electrons from pyruvate, converting it

into carbon dioxide.
Most eukaryotes also use aerobic respiration, generating energy with the use
of oxygen. We use anaerobic respiration to start the process, but finish it with
aerobic. Aerobic respiration is much more efficient than anaerobic.
The Krebs cycle occurs in the mitochondria.

3. The electron transport chain is considered separately from the Krebs

cycle, but it is also part of aerobic respiration. It uses the energy from the
high energy electrons generated in the Krebs cycle to make ATP.

Glycolysis

Occurs in the cytoplasm, not in mitochondria

Does not use oxygen.
Almost all living things use this pathway.
Basic process: add phosphates (from ATP) to
each end of the glucose, then split it in half,
using that chemical bond energy to generate 4
ATPs.
Final 3-carbon products = pyruvate.
Net yield: 2 ATPs per glucose

Glycolysis also releases 2 electrons. These

electrons can be converted to energy if oxygen
is present, but they cause problems if not.
What to do with excess electrons? Give them
back to pyruvate in some way:
In yeast, the pyruvate gets converted to ethanol
when the electrons are added back. Ethanol is
the alcohol in alcoholic beverages like beer,
wine, and vodka.
In humans and many bacteria, pyruvate gets
converted to lactic acid. Causes muscle pain
during intense exercise when not enough
oxygen gets to the muscle cells.

Krebs Cycle

Requires oxygen, occurs in the

mitochondria
Conversion of pyruvate (from
glycolysis) to carbon dioxide, with
generation of high energy electrons
and ATP.
Pyruvate and pyruvic acid are the
same thing.

Preliminary steps before starting

the Krebs cycle: 3 carbon pyruvate
to 2 carbon acetyl CoA; third
carbon lost as carbon dioxide.
Generates high energy electrons
carried by NADH and FADH2
Krebs cycle: add 2 carbon acetyl
CoA to 4 carbon sugar, producing
citric acid. Then remove the 2 extra
carbons one at a time as carbon
dioxide, generate several high
energy electrons (NADH in the
diagram) plus some ATP.

Electron Transport

The final stage in aerobic respiration

The Krebs cycle generates many high
energy electrons. Also some from
glycolysis. These need to be
converted to ATP so the cell can use
them.
Electron transport pumps H+ ions
from the inner compartment to the
outer compartment of the
mitochondria.
This is uphill pumping, against the
concentration gradient.
Uses energy from high energy
electrons to run the pumps.

The final protein pump adds the

electrons (plus hydrogen) to oxygen,
producing water.
The H+ level builds up between the
membranes. It flows back into the
inside through a special protein
channel called ATP synthase, which
uses the energy of their flow to
combine ADP and Pi into ATP. This
is the main way energy is generated
in the cell.