2401 Lecture Notes for Exam 1
Hansen
The exams come from the notes, objectives, and the stuff I put on the board!
This course is Human Anatomy and Physiology.
What does that mean?
Anatomy studies structure. Name it, describe how it looks, what it is connected to etc. etc.
Physiology describes how the anatomy works; it's function. How do these structures, chemicals
and whatever do to carry out their function?
The structure is there to carry out the function and the function is derived from the structure.
Huh?
Structure and function are interrelated.
Arteries can be described as strong, muscular, flexible tubes.
Veins have the same basic anatomy as arteries but are a lot weaker.
Arteries carry high-pressure blood, veins carry low pressure blood.
A study hint
This course serves two purposes.
1. it’s a language course that teaches you the language and vocabulary of biology.
2. It also teaches you some normal physiology to help you understand how the human body
works and why things go wrong.
The index has around 3600 words.
2401 covers around half of the book.
You will be exposed to around 1800-2000 new words in this semester. That works out to 450500 words each exam.
Before you begin to panic, most of these words are built up from smaller words.
Anatomy means apart/cut
Physiology means nature/study of
Corrugator supercilii, orchidectomy
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It will help if you pay attention to the meaning of these words. The front and the back
covers of the book have some of the roots that form these words.
Since we are dealing with living things;
What makes something alive?
Each book has a different list; this is to help you think.
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Maintaining boundaries: Somehow, you have a way of dividing inside vs. outside. Cells use a
cell membrane. There are some really nasty ways for you to die if cells can’t maintain a
concentration gradient.
Responsiveness: The ability to sense and respond to changes in the environment. This is also
known as irritability.
Do rocks go in when it's cold out?
Plants respond, it's just not as obvious
Growth: Individual cells get bigger; organisms get bigger by increasing the number of cells
Reproduction: Produce more organisms
Movement: Not only obvious things like walking, but internal movement like circulation and the
movement of cell organelles.
Metabolism: All of the chemical changes that go on inside of a cell/organism.
Levels of organization
PAGE 3
We are made up of tiny little parts that make up bigger parts, which make up bigger parts etc.....
Biology (and chemistry) study life on different levels.
My list is a little broader than the book
Atomic: atoms/elements/ions like C, H, N, K+
Molecular: molecules are made up of atoms like H2O, glucose, DNA and proteins
Organelles: literally means little organs, these are structures found in a cell that are made of
molecules; like mitochondria, endoplasmic reticulum, ribosomes
Cellular/cells: muscle cells, neurons, this is the simplest level that life can exist, often called the
basic unit of life.
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Tissues: a group of cells and their matrix that perform a common function. muscle tissue,
nervous tissue
Organ: a group of tissues with a common function. heart, kidney, brain, even a sweat gland or a
serous membrane
Organ system: a group of organs with a common function. digestive system, endocrine system
organism: you'all
Homeostasis
PAGE 8
homeo/stasis
same/still
Homeostasis is the maintenance of a stable internal environment, in response to a
changing external environment.
We must maintain our internal environment within a fairly narrow range, if we don't,
we're dead! (Good homeostasis: you are well, bad homeostasis: you are sick, no homeostasis:
you are dead)
examples:
98.6oF
120/80
pH 7.4
blood glucose between 70-120 mg/dl
Homeostasis is regulated by negative feedback. (Most of the time.)
Feedback: occurs in a circular system where information is fed back to a control center.
A thermostat sends feedback to a relay that controls the AC.
Stretch receptors send information to the brain about blood pressure.
If the feedback causes an opposite reaction to the stimulus, it is negative feedback.
The response counteracts the stimulus.
If the room heats up, the thermostat causes the AC to cool it down, an opposite reaction.
If the stretch receptors say blood pressure is going up, the heart is told to slow down to lower
blood pressure.
Positive feedback also occurs. The response enhances the stimulus.
An example of this would be lighting a pile of newspaper or wood.
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childbirth is a good example of positive feedback, heatstroke is a bad example
There are three, sometimes four, components of a feedback system that you need to focus on.
The stimulus: the change that initiates the response of the homeostatic mechanism
Receptor/sensor: What detects the change from a normal range
Control center: "decides" what to do. The control center is often with the receptor.
Chemical messengers or nerves: takes the instructions from the control center to the effectors
Effectors: these are what actually will bring the system back to normal.
Examples of homeostatic mechanisms
Body temperature (a naked human can maintain his body temp. anywhere between 50oF to
130oF in still air with some constraints on humidity.)
The following is oversimplified, you will actually start to respond before your body temperature
rises and your brain anticipates the effect.
NORMAL BODY TEMP 98.6oF--> IT'S A HOT DAY--> BODY TEMP. RISES-->DETECTED BY THE HYPOTHALAMUS-->TELLS SWEAT GLANDS SECRETE
-->SURFACE BLOOD VESSELS
DILATE (FLUSH)
-->BODY TEMP IS REDUCED
What is the stimulus?
What and where is the receptor?
What and where is the control center?
What are the effectors?
What is the negative feedback?
Do it in reverse. Effectors are shivering and constriction of surface blood vessels.
Blood glucose (not in book)
PAGE 12
BLOOD GLUCOSE GOES ABOVE 100mg/dlDETECTED BY THE PANCREAS
INSULIN IS PRODUCEDCELLS TAKE UP GLUCOSE
LIVER STORES GLUCOSE
BLOOD GLUCOSE DROPS
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Some of the rest of the chapter is covered in lab.
Chemistry o'boy!
Page 24
I'm not going to follow chapter 2 very closely; I want to cover certain specific topics.
Everything is made of
Matter: anything that has mass and occupies space
(stuff)
Associated with matter is energy, potential and kinetic.
Potential energy can change to kinetic energy and vice versa. Each change can never be 100%
efficient. You have to put in extra energy when going from kinetic to potential and some energy
is lost as heat when going from potential to kinetic.
Potential energy is energy that isn't available now, but has the potential to be available.
Think of a firecracker or a cocked mousetrap
Kinetic energy (from kinesis/move) is energy that is being produced right now. For our
purposes, we can think of kinetic energy as movement, either on a gross level, or on a
molecular level.
Would we all agree an explosion is matter moving really fast!
We will be dealing with the kinetic energy found in small particles. Particles can be any small
ion, atom or molecule. All particles above absolute zero move. They can vibrate, or really
scoot. How much they move is dependent on:
Page 38
Temperature...the hotter the faster, think of what a microwave does to water molecules.
Density... the lower the density the faster particles can move through the media. This is because
they can move farther before they hit another particle.
Think of NIOSA at 5:30 vs 9:00!
Particle size... little particles move faster than bigger particles (use example of flicking a marble
vs a golf ball)
use bottle of nitroglycerine example, ask:
What type of potential energy?
What type of kinetic energy?
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We are going to race a hydrogen atom with a helium atom, which will win? How could we stack
the deck?
Let’s start with the elements. These are substances made of one type of atom. There are 92
naturally occurring elements.
Atoms are abbreviated with one or two letters from their English or Latin names.
O- oxygen
H- hydrogen
K- potassium (kalium, alkali comes from it)
Na-Sodium (Natrium)
Fe- iron (ferrous)
Pb- lead (plumbum)
Living organisms are made up of mostly C, O, H, N, Ca, P, (98%) K, Na, and Cl.
CHONCAP covers 98%
(know the symbols and the names, especially Natrium and Kalium)
Atomic Structure
PAGE 27
Atoms consist of a:
nucleus made of:
a) positive protons
b) neutral neutrons
-andNegative particles orbiting around the nucleus called electrons. In a neutral atom the number
of electrons will equal the number of protons, however, the number of neutrons can and will
vary.
Ask about charges, why do the electrons stay around?
Look at the appendix A-8
Atomic number: The number of protons in the nucleus, which also tells you how many
electrons there are supposed to be.
So, what will happen if you add a proton to a carbon atom?
The number of protons defines the element.
Atomic mass: The number of protons and neutrons in the nucleus of a single atom. (Electrons
don't weigh much, so they aren't counted) This isn't seen in the chart, the atomic mass is shown
as a superscript to the left of the atom. 12C
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Atomic weight: the average of all the atomic masses of all the isotopes of that particular element
found in nature.
page 28
Isotopes: most elements will vary in their number of neutrons, (but not protons). Carbon has 12C
which has 6 protons and 6 neutrons, 13C, 14C.(How many neutrons?) These three carbons with
different numbers of neutrons are called isotopes. To turn it around, isotopes have the same
number of protons but different atomic masses.
Some isotopes are unstable, they will spontaneously change their nuclear makeup, and emit
radiation in the process and these are radioactive isotopes. Not all isotopes are radioactive.
What will happen to an atom if you add/subtract an
electron?
proton?
neutron?
Let's move up to the molecular level
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Molecule: A substance made of two or more atoms chemically bonded together; it can be the
same, or, different atoms.
O2 H2 CO2 H2O
Molecular weight: the sum of all the atomic weights of the individual atoms that make up a
molecule.
CO2 what’s it's molecular weight? How about H2O?
The number of protons serves to define an element, however it is the electrons that are
responsible for chemical reactions. Chemical reactions are the making and breaking of the
chemical bonds that make up molecules.
Electron Shells
Electrons can be found at various energy levels, called shells, around the nucleus.
Think of planets revolving around the sun.
Each shell must be filled before the next shell will hold electrons.
Capacities:
shell 1 2 electrons
shell 2 8 electrons
shell 3 8 electrons (can hold more in larger molecules)
(there are more shells, I just want to stop here)
Element
Symbol
Atomic
Protons
Neutrons
7
Atomic
Shell 1
Shell 2
Shell 3
Hydrogen
Helium
Carbon
Nitrogen
Oxygen
Sodium
Chlorine
H
He
C
N
O
Na
Cl
number
1
2
6
7
8
11
17
1
2
6
7
8
11
17
mass
1
4
12
14
16
23
35
0
2
6
7
8
12
18
1
2
2
2
2
2
2
4
5
6
8
8
1
7
Atoms try to have their outer shells either completely full or completely empty. They will
either lose or gain electrons to stabilize their outer shell.
Hydrogen could either gain or lose one electron.
How about carbon?
How about sodium?
How about oxygen?
Atoms that have gained or lost electrons and have not formed chemical bonds, will be
charged. Lose an electron and have a +1 charge. Gain an electron and get a -1 charge. These
charged atoms (and molecules) are called ions.
Chemical reactions
The breaking or joining of chemical bonds.
Chemical bonds
Covalent bonds
PAGE 33
These are bonds that form between atoms that share one or more pair of electrons.
If they share one pair of electrons, it's called a single bond, two pairs a double bond, and three
pairs is a triple bond.
These bonds are symbolized with dashes between the atoms.
Single bond: Share one pair, one dash,
C-C
Double bond: share two pairs, two dashes
C=C
Triple bond etc.
C C
How and why do atoms share pairs of electrons?
It helps to only draw the outermost shell.
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H
H
H H
O
O
Notice that by doing this that both hydrogen and oxygen now have stable outer shells.
Covalent bonds can be polar or non-polar,
Polar covalent bonds have partial charges, tend to be water soluble, and can form hydrogen
bonds.
Non-polar covalent bonds just sort of sit there with no charge. They tend to be soluble in nonpolar solvents.
Polar covalent bonds
page 35
This is a special type of covalent bond. If a covalent bond is formed between atoms of differing
electronegativity (how much pull they have), the electrons will tend to spend more time around
the electronegative atom. This can lead to a molecule having a partial charge, especially if the
molecule is asymmetrical. The electronegative atom will be partially negative, the atom that is
sharing those electrons will be partially positive.
The three electronegative atoms that we will commonly see are oxygen, nitrogen and
phosphorous. They will form polar covalent bonds with hydrogen. So anytime you see OH, NH2
or PO4, it’s usually polar. There are other examples; we will just see these over an over.
H
H we hydrogens are a little bit positive
O we oxygens are a little bit negative
Hydrogen bonds
PAGE 37
(think Velcro or magnets)
These are weak bonds that form between the partial positive and negative portions of polar
covalent molecules.
Molecules that contain polar covalent bonds between H and O, and H and N, will form weak
electrostatic bonds. These bonds result from the slightly positive H being attracted to the slightly
negative N or O, of the other molecule. These bonds are called hydrogen bonds.
Hydrogen bonds can occur between different molecules or different parts of large molecules.
These bonds are individually weak, about 1/20th of the strength of an ionic bond, but are very
important biologically. They are responsible for making proteins and DNA function correctly.
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They are also responsible for making water a liquid at room temperature. If it wasn't for H bonds
we would all explode.
H+ H+ H+ H+
OOH+ H+
O-
This is where all the little negatives and little positives come together,
hold hands and sing Kumbaya.
Ionic bonds
page 34
Look at Na, its outer shell would be empty if it lost one electron. Look at Cl, it could use that
electron to fill its outer shell.
And that's what happens in ionic bonding, one atom completely loses an electron or two, one
gains that electron. There is no sharing. The one that loses the electron becomes positively
charged, the one that gains it becomes negatively charged. The two atoms are attracted and form
an ionic bond. the bond is formed because of their opposite charges attracting each other.
examples
Na+ + Cl-
 NaCl
Ca++ + 2Cl-  CaCl2
Summary
Covalent bonds are formed when atoms share one or more pairs of electrons.
Polar covalent bonds are formed when these atoms share the pairs unequally, resulting in
partial charges.
Hydrogen bonds are much weaker that covalent or ionic bonds. They are formed between
molecules containing polar covalent bonds; the hydrogen from one molecule is attracted to the
O, N, or P of the other molecule, because of their partial opposite charges.
Ionic bonds are formed when one atom completely loses one or more electron and another
gains that electron, or electrons.
The atoms become oppositely charged, and this charge difference is responsible for the bonding.
Most biological molecules will be a combination of ionic, covalent, and hydrogen bonds.
Chemical Equations
10
When talking about a chemical reaction, the reaction can be represented symbolically. These
symbols are called chemical equations.
example 2H
+ O  H2O
Most of the reactions that occur in our body are aqueous reactions, meaning in water.
We use water for our reactions because of some of its unique characteristics.
Characteristics of water.
Page 40
1. Water can be a component in a reaction, hydrolysis and dehydration synthesis
2. High specific heat: Water can hold and transport a lot of heat.
3. Water is a good lubricant. It's like really slippery for sure!
4. Water is a great solvent. Almost everything is at least a little soluble in water, especially the
wicked witch of the north.
5. It cushions. Would you rather fall in a swimming pool full of water or a swimming pool full
of other than water?
When something is dissolved in water it has formed a mixture, which is a substance made of
two or more components that are well, mixed together. A key characteristic of a mixture is that
the components are relatively easy to separate out again, they are not chemically bonded. (H
bonds don't count).
A mixture is not a compound.
There are three categories of mixtures:
PAGE 29
1. solutions
2. colloids
3. suspensions.
In a mixture there is usually more of one component than the other. The one present in the
greatest amount is called the solvent the one in lesser amounts is the solute.
In biological systems the solvent is always water. The solute will be various atoms, molecules
and ions.
Solutions are usually transparent, and won't separate. The solute molecules are usually atoms or
small molecules, like sugar in water.
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Colloids are usually translucent, also won't separate, the solute is usually large molecules like
proteins, like Jell-O or homogenized milk.
Suspensions are usually opaque, will separate, and the "solute" is larger such as the whole cells
found in blood. Paint is a suspension
What do you think is the main factor that determines whether a mixture is a solution, colloid or
suspension?
Dissociation
not/associate
Ionic compounds will split into their component ions in water. Some will almost completely
dissociate, some will partially dissociate, and some will slightly dissociate.
The reason they dissociate is that the polar water molecules can get between the ions and shield
their charges from each other, by forming shells of hydration. (Book calls them hydration
spheres)
Compounds that dissociate can also be called electrolytes, because solutions of these will
conduct electricity.
Certain ionic compounds will release H+ or OH- when they dissociate. These compounds are
called acids and bases, and the relative concentration of H ions and hydroxyl ions can be
measured by:
pH
Listen, this is important and tricky.
page 39/40
pH measures the H ion concentration. [H+]
The number is how many H+ you have.
When you measure pH, you are determining whether a solution is acidic, meaning it has more H+
than OH- or basic, which is the reverse.
Acids and bases are a specific type of dissociation.
When acids dissociate, they release H ions.
Often called proton donors.
HCl H+ + Clin water
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When bases dissociate, they produce anions that react with H ions. They either soak them up and
leave an excess of hydroxyl ions, or they release hydroxyl ions directly.
Bases make OH- either directly or indirectly.
Often and confusingly called proton acceptors.
NaOH  Na+ + OHNaHCO3  Na+ + HCO3- this will remove H ions and leave an excess of hydroxyl ions.
Measuring pH
pH is read on a scale of 0-14
any value less than 7 is acidic, any value greater than 7 is basic, and 7 is neutral.
At a pH of 7, the [H+]=[OH-]
The actual pH number represents the negative log of the H+ concentration in moles per liter.
A pH of 7 represents a concentration of 0.0000001 moles/liter.
This can also be written as
or 1 X 10-7
1
10,000,000
The negative 7 exponent is the log of hydrogen ion concentration, the negative of that is 7, see!
At pH 7 the OH- concentration equals the H+ concentration, that's why 7 is neutral.
When the pH value decreases, it represents an increase in H ion conc., therefore the solution is
more acidic.
pH decreases::acidity increases::[H+] increases::[OH-] decreases
When the pH value increases it represents a decrease in the H+ concentration, which is matched
by an increase in the OH- concentration, which means the solution is more basic.
pH increases::alkalinity increases::[H+] decreases::[OH-] increases
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acid
base
0
7
14
-
neutral, OH =H
+
acidity increases, more acidic, H+ conc. is increasing
alkalinity increases, more basic, OH- conc increasing
An Important Point
Since pH is a logarithmic value, a change of one unit represents a ten fold change in
concentration. A ph of 10 has 100,000 times more OH-, and 100,000 times less H+, than a pH of
5.
What do you need to understand about pH
1. How would you define pH?
2. What happens to [H+] and [OH-] when you change the pH value?
3. What happens to [H+] if you change [OH-]?
4. Why is pH 7 neutral?
5. Relate the terms acid and base to the previous questions.
Why is pH important?
Our body maintains a narrow range of pH
Normal is 7.4 (acidic or basic?)
You are in acidosis below 7.2, alkalosis above 7.6
Go much farther either way and you are dead!
Out of the book
Our cells are constantly producing CO2, which is acidic in solution. There is a normal level of
CO2 in the blood. More puts you in acidosis, less in alkalosis.
Remember CO2 up brings pH down!
Respiratory acidosis is usually caused by respiratory insufficiency like COPD. The lungs aren’t
able to allow CO2 to leave the body.
Respiratory alkalosis can be caused by hyperventilation. Too much CO2 is lost.
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Metabolic acidosis can be caused by alcohol intoxication, diabetic ketosis, or even too much
anaerobic exercise!
These conditions occur when our buffer systems are overloaded.
Buffers
Strong and weak, acids and bases.
When measuring pH you are only measuring H+ concentration. (And indirectly OHconcentration.)
A strong acid dissociates more than a weak acid, the H only counts if it is an ion. The same is
true for strong vs weak bases, OH only counts if it is floating around as an OH-.
Most biochemical reactions in our body are very pH sensitive. They only work in a narrow pH
range.
All of our body fluids have buffer systems to prevent the pH of our body from changing.
Buffer: any substance that resists pH changes in a solution. Buffers are weak acids and bases.
Buffers work by reacting strong acids with weak bases (the buffer), this will change the strong
acid into a different weak acid. The opposite is also true, react a strong base with a weak acid(
another buffer) and get a weak base plus water.
HCl +
NaHCO3  H2CO3 + NaCl
strong acid + weak base  weak acid + salt
NaOH +
H2CO3 
NaHCO3 + H2O
strong base + weak acid  weak base + water
Remember these systems have limits, when you go past that limit is when trouble starts.
Organic Compounds
page 42
Generally, any compound containing carbon and hydrogen. There are a few exceptions in really
small molecules like H2CO3.
Synthesis of Biological Molecules
Most of our organic molecules are made of repeating sub-units. They are assembled like popbeads.
The sub-units are called monomers, and the finished molecule is called a polymer.
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These are general terms, each class of molecule will have it's own specific name for the
monomer and polymer.
monosaccharide --> polysaccharide
amino acids --> polypeptide (protein)
These polymers are assembled by dehydration synthesis, because a water molecule is removed
to join the monomers.
They are disassembled by hydrolysis, a water molecule is inserted when the molecules are taken
apart.
Four general Categories of Organic Compounds
The four main types of biological molecules are carbohydrates, lipids, proteins and nucleic acids.
Nucleic acids are covered on the second exam.
Carbohydrates
page 44
Function: fuel, structural materials
Empirical formula of (CH2O)N. Carbs follow this formula in general, there is lots of
variation, but they usually are near that formula.
The monomers of carbohydrates are called monosaccharides.
They are usually seen as a ring structure
Examples:
glucose fructose ribose
Two monosaccharides can be joined by dehydration synthesis to become a disaccharide.
Example: glucose + fructose to make sucrose
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Polysaccharide: a polymer composed of many monosaccharides joined by dehydration
synthesis.
Examples: cellulose, glycogen
Lipids
page 46
These compounds also contain mostly C, H, and O, but are higher in H, and lower in O than
carbohydrates. No real empirical formula
We will discuss three classes of lipids, there are others.
Triglycerides, (fat)
These are composed of a glycerol backbone, joined to three fatty acids by dehydration synthesis.
explain: saturated/unsaturated/polyunsaturated/hydrogenated
The more saturated the fat, the higher the melting point; the longer the fatty acid chains the
higher the melting point.
Canola corn oil crisco butter
Triglycerides function as:
1. Insulation
2. Shock absorbers
3. Energy storage
Phospholipids
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Consist of a glycerol backbone, two fatty acids and a phosphate group
Take a triglyceride and replace one of the fatty acids with a phosphate group.
Phospholipids like to have their heads in water, (the hydrophilic end; and their feet out of the
water, the hydrophobic end.
They spontaneously form bilayers.
Phospholipids are the main components of the cell membrane, and function in lipid transport.
Steroids
Steroids are lipids but they sure don't look like triglycerides.
Why is it a lipid?
Steroids can be found in the cell membrane, (cholesterol), to help stabilize it.
Some hormones are steroids.
Vitamin D
Bile
Proteins
page 48
Contain C, H, O, N, and S. Only proteins have sulfur
Proteins are real common and perform diverse functions. Here are some examples:
1.
2.
3.
4.
5.
6.
structural proteins
contractile proteins
disease protection
hormones
enzymes
carriers
collagen
actin\myosin
antibodies
insulin
salivary amylase
hemoglobin
and much much more!
All proteins are polymers made up of monomers called amino acids.
There are 20 types of amino acids.
General structure
18
Proteins are assembled by dehydration synthesis; the carboxyl of one AA is bonded to the amino
group of the next, etc, etc.
Two AA forms a dipeptide, Three a tripeptide, on up to a polypeptide, and it's called a protein
when it reaches a MW>25,000 about 100 amino acids long.
Levels of protein structure
page 51
Primary: The kinds of AA and their arrangement.
Secondary: This is formed by H bonding between the N-H group of one amino acid with the
C=O of the amino acid four amino acids away.
This regular pattern of bonds usually forms a helix or a pleat.
Tertiary: This structure is caused by the H bonding of the side groups of the amino acids.
Since the amino acid side groups vary, the tertiary structure is dependent on the order and
arrangement of the side groups.
Proteins that are made of one long chain of amino acids stop at this point.
Quaternary: Some large proteins are made up of more than one polypeptide chain, and these
individual chains are H bonded to each other, forming a quaternary structure.
hemoglobin
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Tertiary and quaternary structures are what give proteins their biological
activity/function.
Notice that H bonds form all of these levels, except the primary structure.
H bonds are easily affected by temperature, pH, and ionic concentrations etc., etc.
If you affect the H bonds the molecules will change shape, if they change shape they don't work
very well, and if you change their shape enough, you stop working because your enzymes have
stopped working.
Some of our homeostatic mechanisms are maintaining pH, body temp., ionic concentrations to
keep our proteins in the proper tertiary and quaternary structure.
Use H bond hands analogy, mention why fever makes us feel bad.
Denatured proteins
If the temperature (pH etc.) change is small, the protein will go back to it's normal shape, when
the environment returns to normal.
-howeverIf you really affect the tertiary or quaternary structure of a protein, it may not go back to its
original shape. It may form a new shape.
When a protein has it's H bonds broken by heat, pH, etc., and it doesn't go back to the original
shape, the protein is denatured.
use broken slinky analogy, mention scrambled eggs.
You may have noticed that some of your proteins are not as sensitive to the environment as your
enzymes. Sitting in a hot tub at 105oF doesn't make the proteins of your skin turn into broken
slinkys.
Structural proteins are much more resistant to denaturization than enzymes because
structural proteins stop at the secondary level of structure. Instead of forming internal
tertiary structures, they H bond to the next protein, like Velcro, and form protein cables. They
have a lot more hydrogen bonds.
This linear, uniform, H bonding is much stronger than the bonding found in enzymes, because of
the amount of the H-bonds.
It takes a much bigger temperature change to affect structural proteins.
jello
Enzymes
page 53
20
The power tools of the cell
Enzymes are biological catalysts made of protein.
Catalyst: a chemical substance that alters the rate of a reaction without being consumed in that
reaction.
Chemical reactions: the making and breaking of chemical bonds (for our purposes)
Enzymes are what assemble and disassemble all of the other molecules that we need.
Break a bond: lactase breaks lactose into its two monosaccharides
fresh pineapple juice and Jello
Make a bond: aminoacyl synthetase forms the peptide bonds when amino acids are assembled
into proteins.
Enzymes catalyze (speed up) these reactions by orienting the molecules, and lowering the
necessary activation energy.
How much do they speed them up, how about a million times faster!
Enzyme structure
Some enzymes are made of protein, some enzymes are made of protein plus a non-protein helper
molecule called a cofactor.
These helpers are either metals, such as copper or iron or magnesium, or organic molecules
(sometimes called coenzymes) that we are unable to synthesize.
You know these organic cofactors(coenzymes) as vitamins; the metal ones are a portion of the
minerals that you need.
You need vit. C to make collagen.mitohcondria need copper
Naming enzymes
Each biological reaction has it's own enzyme.
Lactose can only be broken by lactase and lactase will only break lactose.
Enzymes end in ase and are named after their substrate, or the type of reaction that they catalyze.
lactose is the substrate for lactase
a dehydrogenase removes hydrogens
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We'll come back later for the Nucleic acids
Chapter 3
THE CELL
page 63
What is a cell?
Cells come in all different sizes, shapes, and functions. The cell illustrated in the text book, is an
artificial "Mr. average”, sort of like Ward Cleaver. This is still helpful, when we start to study
real cells, their structures will be similar to Mr. average.
In general a cell is a bag of stuff inside another bag of stuff.
Nomenclature
Inner bag: nuclear envelope
Outer bag: cell membrane/plasma membrane
Contents: cytoplasm
Parts of a cell
Cell membrane
page 65
Basic Function:
Barrier: The phospholipids block the passage of all polar molecules.
Regulates passage of materials: See proteins below
Sensitivity: Mainly through receptors, see proteins again
Structural support: desmosomes and the like
The cell membrane consists of two major components, phospholipids and protein. It also
contains carbohydrates to a lesser extent.
Phospholipids
The hydrophobic and hydrophilic portions of the phospholipids line up with the head in the water
and the feet out of the water. This leads to a bi-layer structure without any energy input.
Cholesterol helps to stiffen the membrane.
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Since this bi-layer is primarily lipid, only lipid soluble molecules (like oxygen, carbon dioxide,
and steroids) can pass.
All other molecules need another way to cross the cell membrane. They go through the:
Proteins
page 67
They float like icebergs in a sea of phospholipids, some on the surface, some embedded, and
some on the inner surface.
Proteins are responsible for most of the functional characteristics of the cell membrane.
These proteins can function as:
1.
Anchors: like desmosomes
2.
ID's: Cells carry identification molecules like the MHC
3.
Enzymes: Think of the liver
4.
Receptors: for intercellular communication, such as insulin receptors
5.
Pumps and pores
Movement through cell membranes
page 68
Particles, any solute dissolved in a solvent. I will use the word particle to represent any
molecule, atom, or ion dissolved in water.
Kinetic energy: all particles above absolute zero possess kinetic energy. This energy causes
the particles to always be moving, like a 3-year-old. The hotter the particles the more the
movement. Gas particles can move farther before they hit each other than liquids. Solids just sort
of vibrate.
A good way to picture this is a pool table right after the first break, but the balls never stops
moving.
Over time each particle can move some distance.
This random motion is what drives osmosis diffusion, and facilitated diffusion. The particles
will always be going from an area of higher concentration to a lower concentration.
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Diffusion
You need:
A concentration gradient
more here  less here
Semipermeable membranes are optional.
This is the movement of particles from an area of higher concentration to an area of lower
concentration. THAT'S ALL.
sugar in a glass
perfume in a room
as long as there is a concentration gradient, diffusion will occur "down the gradient" once all
concentrations are equal, equilibrium is reached. The particles still move, but there is no net
change in their numbers.
In the human body, oxygen and carbon dioxide move through diffusion.
Facilitated diffusion
This is a special case of diffusion. You need:
A concentration gradient
A membrane
Carrier molecules/pores
You may have a situation where there are more particles on one side of a membrane than the
other, however, there are no pores large enough for the particles. In facilitated diffusion there
are carrier molecules in the membrane that allow the movement of these particles. Think of these
carriers acting like revolving doors.
This is still a passive process, the energy for the movement is provided by the concentration
gradient, the particles are still moving downhill, and they will stop moving when equilibrium is
reached.
Glucose often moves by facilitated diffusion. (G.I. tract)
Osmosis
page 70
Another special case of diffusion. You need:
A concentration gradient
A semipermeable membrane, that will let the solvent molecules through, but not the solute.
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The solvent molecules will always move to the side with the highest solute concentration, to try
to reach equilibrium.
Water follows the particles.
Osmotic pressure: the greater the concentration gradient, the greater the force behind the
solvent movement.
The more particles in a solution, the greater it's osmotic pressure.
Remember the higher a solutions osmotic pressure, the more water it will try to suck in.
Take a RBC, it has the same osmotic pressure as 0.9% NaCl (physiological saline).
Put it in various solutions.
0.9% NaCl
(isotonic)
distilled water
(hypotonic)
2% NaCl
(hypertonic)
Filtration (not in book)
This is the only passive process that does not relate directly to the random movement of
particles. You need:
A hydrostatic pressure gradient (like the water pressure in your pipes)
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A semipermeable membrane
Filtration is the movement of molecules through a semipermeable membrane due to hydrostatic
pressure.
The pressure forces the small particles and water through, while the membrane forces the larger
particles to stay behind.
Mr. Coffee
In the human, filtration is used by the kidneys, and by the capillaries.
Movement of materials across a cell membrane that require energy (ATP)
Active Transport
page 75/76
Active transport is the movement of particles from an area of lower concentration to an area of
higher concentration.
You need:
To be moving against a concentration gradient
A membrane with carrier molecules/pumps
ATP
The carrier molecule picks up the molecule on the low side and releases it on the high side. It has
to use ATP to push the molecule.
Endocytosis/Exocytosis
page 79
These are mechanisms by which cells move things in and out the cytoplasm, but keeps whatever
is being moved in a vesicle.
Pinocytosis: cell drinking
Small vesicles form at the surface of the cell and pinch off inside the cell. This is how the cell
can bring in extracellular fluid.
Phagocytosis: cell eating
The cell forms pseudopodia, surround a particle, and engulf it, forming a large vacuole called a
phagosome. (eat/body).
This is used by macrophages to eat bacteria.
Receptor mediated endocytosis
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This is a selective process, not just any molecule will do.
1. Membrane contains protein receptors for a particular called a ligand.
2. The binding of the ligand and receptor causes the cell membrane to invaginate (just like the
other forms of endocytosis)
3. The vesicle will separate the ligand from the receptor.
4. The vesicle will split into two vesicles, one containing the ligand, one containing the
receptors.
5. The receptors will return to the surface to bind with some more ligands.
6. The vesicle containing the ligand will fuse with a lysosome and the ligand will be digested.
Exocytosis: This is basically the reverse of endocytosis. Those secretory vesicles formed by the
Golgi apparatus leave the cell by exocytosis.
Organelles of the cytoplasm
Cytoskeleton
page 88
Just like we use muscles and bones to move around, and to support us, individual cells have their
own "muscles and bones".
Three classes of fibers:
Microfilaments: small filaments (5nm), variable in length. Often composed of actin, usually
contractile.
Function: change the shape of a cell, cytokinesis
Location: in all cells to some degree, may be highly specialized like the actin and myosin
found in muscle cells.
Microtubules: long hollow tubes (20-30 nm in diameter) look like a soda straw, tend to appear
and disappear. They will self-assemble and disassemble. Sort of like a circulatory system.
Function: movement of organelles (mention escalator effect),
Including chromosomes during mitosis (cell division).
Movement of cilia and flagella (sperm tails), some support
Location: found in all cells, may specialize. Neurofibrils
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An interesting point, microfilaments and microtubules are nanomachines, tiny linear motors.
Intermediate filaments: Larger than microfilaments (10 nm), form a filamentous web that runs
throughout the cytoplasm. Very stable, don't contract, and don't disappear. Sorta like bones.
Function: Main support system of the cell, help hold it together, suspend the nucleus in
many cells, help anchor desmosomes.
Location: most cells, should be more prevalent in cells that have a lot of mechanical
stress like skin cells.
Centrioles
page 89
Structure: These are paired structures composed of microtubules, arranged in a cylinder
usually found near the nucleus
Function: the centrioles will form the spindle fiber apparatus, which will direct the
movement of chromosomes during meiosis and mitosis. Also act as a "seed" for the
formation of cilia and flagella.
Cilia and Flagella
page 90
Both cilia and flagella are motile processes (they wiggle) that are continuous with the cell
membrane. Structurally they are cylinders of microtubules covered by a membrane.
If there are many short processes, they are called cilia. These beat in a synchronized wave, and in
humans, are usually involved with the movement of materials like mucus.
If there is only one long process, it's a flagellum. Flagella (plural) are only found attached to
sperm in humans.
Mitochondria
page 83
structure: elongated oval sac, having an inner and outer membrane. The inner membrane
has folds called cristae.
function: generate ATP from glucose
ATP is the "electrical" energy of the cell. All the reactions in your body depend on ATP. ATP
works like a one shot rechargeable battery. ATP is converted into ADP + energy. The ADP is
recharged in the mitochondria.
Endoplasmic reticulum (E.R.)
page 84
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Structure: a complex network of interconnecting membranous canals; they may be
tubular or look like flattened sacs. They may also be interconnected with the nuclear
envelope.
Function: transport & manufacturing
Some areas of ER can be studded with ribosomes, which are small organelles made of protein
and RNA. Ribosomes direct the manufacture of all proteins in a cell. These areas are called
rough endoplasmic reticulum (rough ER). Rough ER makes protein. Cells that make a lot of
protein will have lots of RER.
The proteins are stored in the RER, and will travel from the ER to the Golgi apparatus.
Ribosomes can also be found loose in the cytoplasm. They are usually manufacturing the
proteins that stay inside the cell.
Areas of ER that are not associated with ribosomes are called smooth ER. Remember, smooth
and rough ER are interconnected, think of them as an assembly line.
Smooth ER is involved in transport & storage, and mainly lipid manufacture. (Remember that all
of these membranes can have enzymes attached).
Eventually, portions of the ER will pinch off vesicles, and these vesicles will travel to the Golgi
apparatus.
Golgi apparatus:
page 88
Structure: these appear as flattened stacks of membranes 4-8 layers thick. Picture them
as a stack of curved pancakes, with small vesicles traveling between the pancakes.
Function: Golgi takes the material from the ER vesicles and refines it (it may need
further enzymatic processing), packs it into new vesicles, and sends them off. These
vesicles may be secretory, may remain as lysosomes or join with the surface of the cell
membrane to add membrane and receptors
(Go over SER, RER and Golgi again)
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Lysosomes
page 86
Structure: small single walled sacs, filled with enzymes that breakdown carbohydrates,
proteins, and nucleic acids. They are full of nasty stuff!
Function: fuse with phagosomes and digest whatever is inside
why?
1. A form of digestion in single celled organisms
2. A way to recycle used cell organelles
3. A way to kill bacteria & other foreign invaders (WBC)
4. A way to commit suicide.
(Aged beef)
Peroxisomes
Structure and function: small single walled sacs, filled with enzymes that help destroy
some toxic molecules and neutralize free radicals.
Vacuoles & vesicles
Structure: these words are more or less synonymous. Vacuoles are single membrane
bags found in the cytoplasm and are big, vesicles are little bags of stuff.
Function: depending where they come from they may be secretory vesicles from the
Golgi, they could be pinocytotic vesicles, or phagosomes, they could be for storage, or
any other single walled sacs except lysosomes.
Nucleus
page 92
It's usually spherical, enclosed in a double membrane full of holes, think of a golf ball with the
dimples punched out. These holes are to allow things to go in and out of the nucleus.
Most cells have one nucleus, some have none, and some have more than one.
Inside the nucleus is the nucleoplasm, which consists of:
The nucleolus: a dark staining area easily seen in the light microscope. It consists of protein and
RNA. This is where ribosomes are assembled. (The ribosomal proteins are made in the
cytoplasm)
Chromatin: This is the DNA and it's associated proteins.
Intercellular junctions
page 67
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Many cells are held together by the sticky nature of the cell membrane. These membranes are
often intertwined so that the cells fit together like pieces of a jigsaw puzzle.
Some cells need more so they have specialized structures.
Tight junction: cell membranes are fused together with a "protein zipper"
Function: a leak proof cell junction.
Location: cells that line cavities that contain materials, which would cause trouble if they
leaked.
Example: epithelial cells lining the digestive tract and the bladder
Desmosomes: areas of the cell membrane are "spot welded" together with proteins. It's almost
like the cell membrane has rivets like you would find on blue jean pockets. These desmosomes
are also connected to the intermediate filaments of the cell.
Function: strength
Location: found in cells that have to resist mechanical forces
Examples: skin cells, heart muscle, and the cells of the digestive system again. Plus a
really full bladder!
Gap Junctions: membranes are connected with protein channels
Function: to facilitate communication between cells. Cells communicate with chemicals.
Location and examples: embryonic cells, excitable tissues like heart muscle and smooth
muscle, some nerve cells.
Questions
What type of organelles would be seen in a:
macrophage?
fibroblast?
muscle cell?
bone growing cell?
liver cell?
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