Human Biology (BIOL 104)
Talk two:
The Chemistry of life
Chapter Two
Don’t Panic!
WHY?!!!!!!!!!!!!
• In studying human biology, it’s useful to understand
some basic chemistry
– Chemical reactions explain the effects – harmful or helpful – of
substances we take into our bodies
• This will actually help you to identify structures,
functions, and processes of many of the human
body systems.
• It will help you understand how everything in the
human body works together for healthy life to
exist.
– In other words – it will help you connect up all the dots
Atoms and Elements
• Matter: Anything
that takes up space.
• Element: Substance
composed of one
type of atom.
• Atom: Smallest unit
of an element that
retains the chemical
and physical
properties of that
element
• Neutron: atomic
particle with one mass
unit and no charge.
• Proton: atomic particle
with one mass unit and
a positive charge.
• Electron: atomic
particle with a negative
charge and “no” mass.
Chemical Bonding and Molecules
• Atoms want to fill their outer shells with electrons!
• Chemical reactions enable atoms to give up or
acquire electrons in order to complete their outer
shells
• These interactions usually result in atoms staying
close together
• Interactions between outer shells of atoms
= chemical bonds
1) Ionic Bonds
• When an atom loses or
gains electrons, it becomes
electrically charged
– Charged atoms are
called ions
– Ionic bonds are formed
between oppositely
charged ions (transfer
of electrons)
Sodium atom (Na)
Chlorine atom (Cl)
Complete
outer shells
Sodium ion (Na) Chloride ion (Cl)
Sodium chloride (NaCl)
2) Covalent Bonds
• A covalent bond forms when two atoms share
one or more pairs of outer-shell electrons
The number of covalent bonds an atom can
potentially form = number of additional electrons
needed to fill its outer shell.
Water
• Water - one of the most important molecules in life.
 70% of the bodies mass is water
 2/3 of total body water is intracellular (55-66% body
weight of men and 10% less for women)
 The rest is interstitial fluid of which 25% is in the
blood plasma.
• pH - The body tightly controls both the volume and pH of
water.
 The bicarbonate system is crucial for blood
maintenance
 changes of pH greater than 0.1 are dangerous and can
lead to coma -diabetics
Life on Earth would not be
possible without water
Its chemical and physical
properties actually defy some
fundamental laws of physics
Almost all biochemical reactions
require water!
How does water support life?
– Water is cohesive
– Water can moderate
temperature of surrounding
environment
– Ice floats
– Versatility of water as a
solvent
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Water is a polar molecule
•
When electrons are not shared equally in
a covalent bond, the molecule is
described as polar.
•
Water molecules are polar. This means
that while water molecules are neutral as
a whole, one end of the water molecule
tends to have a positive charge while the
other has a negative charge.
•
The oxygen end has a slight negative
charge while the hydrogen end has a
slight positive charge.
•
Each end of a water molecule is
attracted to the opposite charged end of
another water molecule.
•
Water's polarity is responsible for the
"stickiness" or cohesion between the
molecules.
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Water
Water is a polar molecule
•Water has a dipole
moment
•“like dissolves like”
Oxygen is more electronegative than
hydrogen so there is an uneven distribution
of charge in this H-O bond
Uneven distribution is called a dipole and
the bond is said to be polar
Water has hydrogen bonding
potential
• H-bonds are non-covalent,
weak interactions
• H2O is both a Hydrogen
donor and acceptor
• One H2O can form up to
four H-bonds
• (A) Hydrogen bonds
between water
molecules results in
local aggregations of
water molecules
• (B) Theses are very
short lived, break up
rapidly to form more
random
configurations
• Due to temperature
variations in water
Water
Density
• Another property of water is
density during phase changes.
– The density of most
substances increases when
a liquid becomes a solid.
Solid water is actually less
dense than liquid water.
• It is for this reason that ice
floats.
– The fact that ice floats is
essential for the survival
of many aquatic
ecosystems and ultimately
life on Earth.
Hydrogen bond
Ice
Stable hydrogen bonds
Liquid water
Hydrogen bonds
constantly break
and re-form
Capillary Action & Surface tension
• Cohesion of water causes capillary
attraction, which is the ability of water to
move upward in small spaces.
• Cohesion makes it possible for water to
move up the fibers of a plant.
•
– This is how plants get the water they
need to survive.
– In addition, it moves water upwards in
soil.
– Allows water to be taken into human
cells attached to other molecules
• Cohesion of water also causes surface
tension, water's invisible skin which allows
water striders to walk on water
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Water is a solvent
• Water is the Universal Solvent.
– Water “dissolves” polar molecules
– Water allows chemical reactions to
occur
• Any dissolved substance is known as a
solute.
• When a substance dissolves, water
molecules cluster around it forming
spheres of hydration.
• This is what happens to solutes in
blood and other body fluids.
• Almost all chemical reactions in the
human body occur in water-based
solutions.
Used with permission from
compchemmpi.wikispaces.com/
Water is nucleophilic
• Water participates in many chemical
reactions
– it is electron rich
– it is a weak nucleophile
– it is present in high concentration
Water weakly ionizes
pH and buffers
• Measure of the acidity or basicity of an aqueous solution.
– Solutions with a pH less than 7 are said to be acidic
– Solutions with a pH greater than 7 are basic or alkaline.
– Pure water has a pH very close to 7
•
•
•
•
Acid
A chemical compound that donates H+ ions to solutions.
Base
A compound that accepts H+ ions and removes them from solution.
• Remember H3O+ and OH-?
• The H3O+ donates H+ to a solution and the OH- removes H+ from a
solution
• If an equal number of these ions are present in a solution the pH
will not change as it is said to be buffered.
H20 helps buffer our blood
•Water reacts with CO2 to form an
important blood buffer
•We breath in and out gaseous CO2
•In the blood, CO2 reacts with water to
form the buffering compound H2CO3 –
carbonic acid
•Disturbances in blood buffering system
leads to acidosis (pH below 7.1) or
alkalosis (pH above 7.6)
•Bleeding in lungs – death!
•
“a few good men”
The pH scale
• To describe the acidity of
a solution, we use the pH
scale.
• Acids have a low pH, so
they have a high
concentration of H+
• Bases have a high pH, so
they have a low
concentration of H+
Used with permission from purewaterproducts.com
The Biomolecules
• These are the molecules of life
– Carbohydrates
– Lipids
– Proteins
• Glycoproteins
– Nucleotides and Nucleic acids
• These molecules are involved in the chemical reactions
that allow us to live.
• Remember the levels of biological organization?
• Understanding the molecules allows you to understand
how the cell works
– Which is the fundamental unit of life
Carbohydrates
• Carbohydrates constitute more than 1/2 of organic
molecules
• Main role of carbohydrates in nature:
 Storage of energy
 Structural support
 Lipid and protein modification:
 membranes asymmetry, recognition by IgG/fertilization/virus
recognition/cell cell communication
Definition: Carbohydrates, Sugars and Saccharides- are
all polyhydroxy
 (at least 2 OH) Cn(H20) n = hydrate of carbon
Basic facts
Monosaccharides - Simple sugars
• Single polyhydroxyl
 Can’t be hydrolyzed to simpler form
Trioses - Smallest monosaccharides have three carbon atoms
Tetroses (4C) Pentose (5C) Hexoses (6C) Heptoses (7C) etc…
Disaccharide - two sugars linked together. Can be the same molecule
or two different sugars. Attached together via a glycosidic linkage
Oligosaccharide - 2 to 6 monosaccharides
Polysaccharides - straight or branched long chain monosaccharides.
Bonded together by glycosidic linkages
Classification of monosaccharides
• The a and b anomers of glucose.
• Note the position of the hydroxyl
group (red or green) on the anomeric
carbon relative to the CH2OH group
bound to carbon 5:
•
Either on the opposite sides (a)
•
Or the same side (b).
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Important disaccharides
• Maltose
• Malt sugar or corn sugar consists
of two glucose molecules linked
by an a-1,4-glycosidic bond
• It comes from partial hydrolysis
of starch by the enzyme amylase,
which is in saliva.
• Maltose is an important
intermediate in the digestion of
starch.
• In humans, maltose is broken
down by the enzyme maltase so
that there are two glucose
molecules from which the glucose
metabolism obtains energy.
Important disaccharides
• Sucrose (table sugar)
• Sugar beets, fruits and vegetables all
contain sucrose.
• When sucrose is consumed, it is broken
down to glucose and fructose.
• The body will use glucose as its main
energy source
• The excess energy from fructose, if
not needed, will be poured into fat
synthesis, which is stimulated by the
insulin released in response to glucose
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Sucrose (table sugar)
• Human health
• Tooth decay has become a prominent health hazard
associated with the consumption of sugars, especially
sucrose.
– Oral bacteria such as Streptococcus mutans live in dental plaque and
metabolize sucrose into lactic acid.
– The resultant lactic acid lowers the pH of the tooth's surface, stripping it
of minerals in the process known as tooth decay
• Obesity
•
A United Nations report (2011) stated that obesity may correlate
better with sugar consumption than with fat consumption, and that
reducing fat consumption while increasing sugar consumption may
increase the level of obesity.
Year
Sex
Carbohydrate
Fat
Protein
Obesity
1971
Male
42.4%
36.9%
16.5%
12.1%
1971
Female
45.4%
36.1%
16.9%
16.6%
2000
Male
49.0%
32.8%
15.5%
27.7%
2000
Female
51.6%
32.8%
15.1%
34.0%
Important
Derived from galactose and glucose
linked by an b-1,4-glycosidic bond and disaccharides
• Lactose
•
makes up around 2–8% of milk (by
weight).
• Lactose Intolerance is the inability or
insufficient ability to digest lactose.
Lactose intolerance is caused by
reductions in the production of the
enzyme lactase by the cells of the
small intestine.
• Lactase production is at its highest in
infants at birth regardless of
ethnicity. This allows infants to digest
breast milk.
• Primary lactase deficiency occurs when
a person’s body decreases the
formation of lactase.
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Important disaccharides
• Lactose
• Symptoms of lactose intolerance can
be mild to severe, depending on how
much lactase your body makes.
Symptoms usually begin 30 minutes to
2 hours after you eat or drink milk
products.
• If you have lactose intolerance, your
symptoms may include
–
–
–
–
–
–
Bloating.
Pain or cramps.
Gurgling or rumbling sounds in your belly.
Gas.
Loose stools or diarrhea.
Throwing up.
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Important disaccharides
• Lactose
•
Primary lactose intolerance appears to have a genetic component with
specific populations showing high levels of intolerance.
Ethnicity
American Indians
Asians
African Americans
Ashkenazi Jews
Hispanics
Caucasian Americans
Northern European
Origin
% Adults with Primary Lactose
Intolerance
80 to 100 %
90 - 95%
60 – 80 %
60 – 80%
50 – 80%
13%
1 - 2%
Lactose Intolerance: Information for Health Care Providers. U.S. Department of
Health and Human Services. NIH Publication Number 05-5305B. 2006
• Starch - energy reservoir in plants
- made of two polysaccharides
• Glycogen – same as starch – animals
• Both starch and glycogen made up
of:
• Amylose -long unbranched glucose a
(1,4) with open reducing end large
tight helical forms.
• Amylopectin is like amylose, but has
extensive branching, with the
branches using a-1,6-glycosidic
bonds.
• A very highly coiled complex,
allowing hundreds of thousands of
glucose moieties to be stored in the
smallest possible physical space.
Important
Polysaccharides:
Important Polysaccharides:
- energy reservoir in plants - made of two polysaccharides
– Amylose -long unbranched glucose a (1,4) with open reducing end large tight
helical forms. Test by iodination.
– Amylopectin - polymer of a(1,4) and a (1,6) branches. Not helical.
Glycogen
• Mix both of these two types of
polysaccharides together and you get
glycogen.
• In humans, glycogen is made and stored
primarily in the cells of the liver and the
muscles, and functions as the secondary
long-term energy storage.
• In the liver cells (hepatocytes), glycogen
can compose up to 8% of its fresh
weight (100–120 g in an adult) soon after
a meal.
• Only the glycogen stored in the liver can
be made accessible to other organs.
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Plant Starch (Amylose and Amylopectin)
•
Starch contains a mixture of amylose and amylopectin
•
Amylose is an unbranched polymer (forms a-helix) of D-glucose molecules linked by a1,4-glycosidic bonds
•
Amylopectin is like amylose, but has extensive branching, with the branches using a-1,6glycosidic bonds
Cellulose
• Linear glucan chains of
unbranched (1-4)-blinked-D-glucose in which
every other glucose
residue is rotated 180°
with respect to its two
neighbors and contrasts
with other glucan
polymers such as:
• starch (1-4-a-glucan)
• callose (1-3-b-glucan).
Cellulose
• This means that cellobiose, and not glucose, is the basic
repeating unit of the cellulose molecule. Groups of 30 to 40
of these chains laterally hydrogen-bond to form crystalline
or para-crystalline microfibrils.
Lipids
Lipids fats oils…. Greasy molecules, mmmmm donuts.
Several levels of complexity:
• Simple lipids - a lipid that cannot be broken down to smaller
constituents by hydrolysis.
– Fatty acids, waxes and cholesterol
• Complex lipids - a lipid composed of different molecules held
together mostly by ester linkages and susceptible to cleavage
reactions.
– acylglycerols - mono, di and triacyl glycerols ( fatty acids and
glycerol)
– phospholipids - lipids which are made of fatty acids, glycerol, a
phosphoryl group and an alcohol. Many also contain nitrogen
General Structure
• glycerol (a type of alcohol with a
hydroxyl group on each of its three
carbons)
• Three fatty acids joined by
dehydration synthesis.
• Since there are three fatty acids
attached, these are known as
triglycerides.
• The longer the fatty acids the higher
the melting point.
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Saturated or not – the power of H
•
The terms saturated, monounsaturated, and poly-unsaturated
refer to the number of hydrogens
attached to the hydrocarbon tails of
the fatty acids as compared to the
number of double bonds between
carbon atoms in the tail.
•
Oils, mostly from plant sources, have
some double bonds between some of
the carbons in the hydrocarbon tail,
causing bends or “kinks” in the shape of
the molecules.
•
Because some of the carbons share
double bonds, they’re not bonded to as
many hydrogens as they could if they
weren’t double bonded to each other.
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Trans and Cis
•
In unsaturated fatty acids, there are two
ways the pieces of the hydrocarbon tail can
be arranged around a C=C double bond.
•
TRANS
– The two pieces of the molecule are on
opposite sides of the double bond, that is,
one “up” and one “down” across from each
other.
•
CIS
– the two pieces of the carbon chain on
either side of the double bond are either
both “up” or both “down,” such that both
are on the same side of the molecule
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Trans and Cis
•
Naturally-occurring unsaturated vegetable
oils have almost all cis bonds
– but using oil for frying causes some of the
cis bonds to convert to trans bonds.
•
If oil is used only once like when you fry an
egg, only a few of the bonds do this so it’s not
too bad.
•
However, if oil is constantly reused, like in
fast food French fry machines, more and
more of the cis bonds are changed to trans
until significant numbers of fatty acids with
trans bonds build up.
•
The reason this is of concern is that fatty
acids with trans bonds are carcinogenic!
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Phospholipids:
• Two fatty acids covalently
linked to a glycerol, which
is linked to a phosphate.
• All attached to a “head
group”, such as choline, an
amino acid.
• Head group POLAR – so
hydrophilic (loves water)
• Tail is non-polar –
hydrophobic
• The tail varies in length
from 14 to 28 carbons.
• A lipid molecule known as a Sterol and is
biosynthesized by all animal cells
Cholesterol
• Essential structural component of animal
cell membranes that is required to
maintain both membrane structural
integrity and fluidity.
• Has no fatty acid tail – instead have four
fused together carbon rings.
•
•
•
•
Essential derivatives include:
Vitamin D – bones and teeth
Bile salts – fat digestion
The sex hormones - estrogen and
testosterone
• Mineralcorticoids – Na+ and K+ balance in
the blood
• Glucocorticoids - involved in reducing
inflammation
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Proteins:
Peptides & Primary Structure
Protein Functions:
– Enzymes -Catalyze a thermodynamically favorable reaction
– Storage/transport - binding proteins fatty acids w/albumin
– no catalytic activity but do form chemical bonds with ligands
– Structure - Several levels
– cytoskeleton, collagen, bone ...
– Receptors
– Growth factors
– Antibodies
Amino acids
• -20 common amino acids there are others
found naturally but much less frequently
• Common structure for amino acid
• COOH, -NH2, H and R functional groups all
attached to the alpha carbon
Peptides
When amino acids are linked together it is through
the formation of a peptide bond
The formation of a
peptide bond occurs
by the loss of a water
or dehydration of
water from the a
carboxyl and of one
amino acid and the a
amino of another
amino acid
Proteins: Three-dimensional structure
• Background on protein composition:
• Two general classes of proteins
 Fibrous - long rod-shaped, insoluble proteins.
These proteins are strong (high tensile strength).
 Globular - compact spherical shaped proteins
usually water-soluble. Most hydrophobic amino
acids found in the interior away from the water.
Nearly all enzymes are globular…
 Proteins can be simple - no added groups or modifications, just
amino acids
 Or proteins can be conjugated. Additional groups
covalently bound to the amino acids. The naked
protein is called the apoprotein and the added group is
the prosthetic group. Together the protein and
prosthetic group is called the holoprotein. Ex.
Hemoglobin
Four levels of protein structure
• Primary structure: amino acid only. The actual amino
acid sequence is specified by the DNA sequence. The
primary structure is used to determine genetic
relationships with other proteins - AKA homology. Amino
acids that are not changed are considered invariant or
conserved.
Primary sequence
is also used to
determine
important
regions and
functions of
proteins domains.
Four levels of protein structure
• Secondary structure: This level is only concerned with the
local or close in structures on the protein - peptide
backbone. The side chains are not considered here,
even though they have an affect on the secondary
structure.
Two common
secondary
structures - alpha
helix and beta
pleated sheet
Non- regular
repeating structure
is called a random
coil.
- no specific
repeatable pattern
Four levels of protein structure
Tertiary structure - the overall three-dimensional shape
that a protein assumes. This includes all of the secondary
structures and the side groups as well as any prosthetic
groups. This level is also where one looks for native vs.
denatured state. The hydrophobic effect, salt bridges
And other
molecular
forces are
responsible
for
maintaining
the tertiary
structure
Four levels of protein structure
• Quaternary structure: The overall interactions of
more than one peptide chain. Called subunits.
Each of the subunits can be
different or identical
subunits, hetero or homo – x
mers
(ex. Heterodimer is a protein
composed of two different
subunits).
Glycoproteins
• Proteins that contain oligosaccharide chains covalently attached
to polypeptide side-chains.
• The carbohydrate is attached to the protein in a cotranslational or posttranslational modification. This process is known
as glycosylation.
– In proteins that have segments extending extracellularly, the
extracellular segments are often glycosylated.
• Glycoproteins are often important integral membrane proteins,
where they play a role in cell-cell interactions.
• Glycoproteins also occur in the cytosol, but their functions and the
pathways producing these modifications in this compartment are less
well-understood
Examples of glycoproteins found in the
human body
• Mucins
•
secreted in the mucus of the respiratory and
digestive tracts.
•
The sugars attached to mucins give them
considerable water-holding capacity and also
make them resistant to proteolysis by
digestive enzymes.
• In the immune system
•
white blood cell recognition molecules such
as antibodies which interact directly
with antigens
•
Molecules of the major histocompatibility
complex (or MHC), which are expressed on
the surface of cells and interact with T
cells as part of the adaptive immune response.
Examples of glycoproteins found in the
human body
• glycoprotein IIb/IIIa
– an integrin found on platelets that is
required for normal platelet
aggregation and adherence to
the endothelium.
• The zona pellucida
–
which surrounds the oocyte, and is
important for sperm-egg interaction.
• connective tissue.
– These help bind together the fibers,
cells, and ground substance
of connective tissue.
– They may also help components of the
tissue bind to inorganic substances,
such as calcium in bone.
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Examples of glycoproteins found in the
human body
• Hormones that are glycoproteins
include:
• Follicle-stimulating hormone
– Stimulates the follicle to produce
estrogen
• Luteinizing hormone
– Stimulates the corpus leuteum to
produce progesterone.
• Thyroid-stimulating hormone
• Human chorionic gonadotropin
– maintains the corpus luteum and
allows the production of progesterone
and estrogen until the placenta takes
over this task.
Nucleic Acids
• Composed of 4
nucleotide bases, 5
carbon sugar and
phosphate.
• Base pair = rungs of a
ladder.
• Edges = sugarphosphate backbone.
• Double Helix
• Anti-Parallel
The bases
• Chargaff’s Rules
• A=T
• G=C
• led to suggestion of a
double helix structure
for DNA
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The Bases
• Adenine (A) always base pairs with thymine (T)
• Guanine (G) always base pairs with Cytosine (C)
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The Bases
• The C#T pairing on the left suffers from carbonyl dipole
repulsion, as well as steric crowding of the oxygens. The
G#A pairing on the right is also destabilized by steric
crowding (circled hydrogens).
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The structure of RNA
• Formed from 4
nucleotides, 5 carbon
sugar, phosphate.
• Uracil is used in RNA.
– It replaces Thymine
• The 5 carbon sugar has
an extra oxygen.
• RNA is single stranded.
Adenosine triphosphate (ATP)
• Often called the "molecular unit of
currency" of intracellular energy
transfer.
• Transports chemical energy within
cells for metabolism.
• Transfers a phosphate group to many
molecules in the cell.
• It is one of the end products of
photophosphorylation, cellular
respiration, and fermentation and
used by enzymes and structural
proteins in many cellular processes,
including biosynthetic reactions,
motility, and cell division
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The End!
Any Questions?