Molecules of Life

Outcomes
 20–D1.2k
 describe the chemical nature of carbohydrates, lipids
and proteins and their enzymes; i.e., carbohydrases,
lipases and proteases
 20–D1.3k
 explain enzyme action and factors influencing their
action; i.e., temperature, pH, substrate concentration,
feedback inhibition, competitive inhibition
20–D1.2s
 perform experiments, using qualitative tests, to detect
the presence of carbohydrates, proteins and lipids
 Organic Compounds
 Carbon containing compounds found in
living organisms
 All organic compounds have a minimum
combination of C, H and O elements
 Includes proteins, carbohydrates, lipids,
nucleic acids (DNA & RNA) and vitamins
Other elements found in living
things:
 Fe – hemoglobin
 K, Na, Ca – nervous function
 P – phospholipids and nucleic acids
 N – proteins and nucleic acids
 S – proteins and DNA
 Nutrients – molecules, atoms and
ions required for life
 1. Macronutrients
 - required in large quantities
 - used as raw materials for metabolism
 - includes: carbohydrates, protein, and lipids
2. Micronutrients
- required in small quantities
- used in chemical reactions
- includes vitamins and minerals (minerals are
inorganic)
 3. Special nutrients
 Fibre
 From fruits, veggies, & whole grains
 undigestable cellulose
 Important for normal bowel function
 Linked to prevention of heart disease, colon cancer,
gallstones, obesity, etc
 Water
 Solvent of life
 Involved in transport
 Helps maintain body temperature
 Special Properties of Water
 High specific heat of capacity (can absorb a lot of
energy before it experiences a change in
temperature)
 Is cohesive and adhesive (sticks to itself as well as
other polar/ charged substances) – gives good
dissolving power of water
 Carbohydrates
 Contain C, H, and O, usually in the 1:2:1 ratio.
 Functions – first energy source for cellular
respiration – used first, most readily available
 Other functions: energy reserves (glycogen),
structural components, receptor sites, etc
 Vocabulary
 Monomer – 1 sub unit
 Polymer – many subunits bonded to each other
3 classes of Carbs
1. Monosaccharides
2. Disaccharides
3. Polysaccharides
Class Examples Composed of: Found in
Polysaccharides Starch Glucose Plants
Cellulose Glucose Plants
Glycogen Glucose Liver and muscles

Disaccharides Sucrose Glucose-fructose Plants

Lactose Glucose-galactose Milk
Maltose Glucose-glucose Seeds of plants
(nuts)

Monosaccharides Glucose Plants

Fructose Plants
Galactose animals
 Monosaccharides
 Simple sugar - 1 sub-unit, usually in ring structure
(monomers of large carbohydrates)
 3-7 carbons are possible
 Sugars end in “ose”
 Ex: Glucose – C6H12O6
 Disaccharides
 2 monosaccharides bonded together
 Formed when 2 monosaccharides undergo a
condensation reaction where water is
produced, forming a glycosidic bond
 Examples:
 Sucrose – glucose and fructose (plants)
 Lactose – glucose and galactose (milk sugar)
 Maltose – glucose and glucose (plant sugar)
 Condensation Synthesis Reaction
How all proteins and carbohydrates
are made - water out to form a
bond
 Polysaccharides
 Many monosaccharides bonded to each other
 Monomers forming a polymer
 Examples:
 Starch – many glucose monomers, made by
plants, consumed by humans
 Glycogen – many glucose monomers, storage of
sugars in humans in liver and muscles
 Cellulose – many glucose molecules – cell walls
of plants – undigestable by humans
 Test for Carbohydrates
 Benedicts Test
 Tests for reducing sugar
 Blue color is a negative result
 Green  brown is positive result
 Most simple sugars and some disaccharides will test
positive
 Iodine test
 Will turn from amber to dark blue in presence of
starch (this is review)
 Will turn darker reddish brown in glycogen
 Lipids – 4 types
 Insoluble in water, but soluble in non-polar
solvents
 Include: fats, phospholipids, steroids, oils
 Function:
 Energy storage
 Structural (membranes)
 Has most energy per gram than all other
macronutrients – used in CR if no sugars
available
 Types of Lipids
1. Fats (triglycerides)
- One glycerol molecule (backbone) and 3 fatty
acid chains
- Formed by 3 condensation reactions
- Saturated and unsaturated fats
- Unsaturated fats have 1 or more double bonds
– usually found in form or oil, plant derived
- Saturated fats have no double bonds, solids
are room temp – harder to digest
Triglycerides

+3 H2O(l)
Lipids Continued
2. Waxes
- functions
a. protective layer on plants, frogs, and insects
– prevents water loss
b. beehive structure
c. ear wax – cleanser
- fatty acid molecules linked to a different
alcohol
Phospholipids
 1 glycerol (3 carbons)
 2 fatty acid chains
 1 phosphate group (hydrophilic part)
 Main component of cell membranes
Steroids
 Examples – cholesterol, sex hormones
 Ring structures with linear carbon structure
 Insoluble in water
 Cholesterol
 LDL – bad cholesterol – cause build up in
arteries (atherosclerosis)
 HDL – good cholesterol – lowers bad
cholesterol
 Test for Lipids
Translucence test
Lipids on unglazed paper turn
translucent, even after drying
Sudan IV
Turns lipids red, floats on top of non-
lipids
Proteins
 Amino acids (A.A.) are the monomers or
sub-units of proteins
 2 A.A – dipeptide
 3 A.A. – tripeptide
 Many A.A = polypeptide
 1 or more polypeptides = protein
 A.A. have a –COOH group, NH2, and an R
group (functional group)
Protein Functions
1. Structural – claws, nails, collagen (skin)
2. Transport – channel & carrier proteins,
hemoglobin
3. Movement – actin and myosin in muscles
4. Regulatory – hormones
5. Catalyst – enzymes speeding up reactions
6. Immune system – antibodies, antigens
Protein Synthesis
 Amino acids can be absorbed by the digestive
system or some can be assembled by your body
 Those that cannot be assembled by your body are
considered to be “essential” A.A – must be taken
in by diet
 20 amino acids commonly found in human
proteins.
 Done by condensation reaction forming a peptide
bond (water produced)
Condensation Rx forming a peptide
bond
 Energy in Proteins
 Comparable to carbohydrates (17 kJ/g)
 Usually only used for energy once all available
sugar, glycogen and fat are used up.
 R on this diagram
is a functional group that
varies with each A.A.
Structure of Proteins
1. Primary Structure (1º)
- sequence of amino acids – chain of A.A.
- held together by peptide bonds (covalent)
2. Secondary Structure (2º) (structural)
- folding of polypeptide
- beta sheets (zig zag) or alpha (spiral)
- held together by H-bonds
 Globular proteins with specific
function
3. Tertiary Structure (3º)
- folding of beta sheet or alpha helix
- achieved by forming irregular bonds with R groups –
often disulfide bonds
- these bonds easily broken
4. Quanternary structure (4º)
- interaction of 2 or more polypeptide structures to
form a single protein
- ex: hemoglobin has four polypeptides
 Altering protein shape and
function
1. Denaturation
- exposure to heat, pH change can break H bonds
- changing shape changes function
- may be reversed if conditions change slowly
2. Coagulation
- extreme changes (heat and pH)
- irreversible protein change (cooking egg)
 3. deamination
- if you consume too much protein, excess A.A
broken down by liver
- A.A. deaminated (NH2 group removed)
- urea will be produced and excreted out by kidneys
- C, H, O left as raw materials
Test for Proteins
 Biruet test
 Blue solution turns pink, purple or
violet in presence of peptide bonds
 Enzymes
 Special proteins produced by different cells that
act as biological catalysts.
 Catalyst? = a molecule that is used in a reaction
but not used up & it increases rate of reaction by
reducing activation energy
for example… (don’t write
this down
 in your blood, CO2 is transported as it is converted to
carbonic acid

 without a catalyst, only about 200 molecules of

carbonic acid would be produced in 1 hour 

 the enzyme carbonic anhydrase increases the reaction

rate so that approx. 600 000 molecules of carbonic
acid are created – EACH SECOND!!! 

 Or 36 million molecules/minute with the help of the

enzyme
Enzyme properties
 Can catalyze synthesis or hydrolysis reactions
 Enzymes have an active site where the substrate
will bond
 Show specificity – one enzyme works only for one
substrate (substrate is a molecule an enzyme
works on)
 Names usually end in “ase”
 Ex: lipase, amylase, sucrase
Old theory (1890) – Lock and Key
 Temporary joining of the enzyme with the substrate
molecule forms the enzyme-substrate complex
 Enzyme is a ‘lock’ which requires a specific substrate
molecule ‘key’
Induced-Fit Model
 replaced lock and key in 1973
 Actual shape of the active site is altered slightly
when the substrate molecules are trapped
 Makes the fit between enzyme and substrate even
tighter during the formation of the enzyme-
substrate complex
 Enzymes need help:
Coenzymes – organic molecules which are made from
vitamins
Cofactors – non-protein, inorganic molecules or ions.
-Eg.O2, CO2, H2O, iron, zinc, potassium, minerals, not
produced by living things

- Both are required by certain enzymes to bind with

substrate molecules – not all though
- Coenzymes and cofactors can work with more than one
type of enzyme – not as specific
- Both may help with the molding of the enzyme to substrate
molecule
 Factors Affecting Enzyme
Reactions
1. pH
-enzymes are protein molecules that function
best within certain pH ranges
 2. Substrate Concentration:
 More substrate increases the rate of reaction, to a
point
Begins to level off, because there is a limited
amount of enzyme available
Substrates cannot join an active site until it is
free.
3. Enzyme concentration
 As [enzyme] , rate of rx
 As the enzyme concentration increases the rate of the
reaction also increases, because there are more
enzyme molecules (and so more active sites), available
to catalyse the reaction therefore more enzyme-
substrate complexes form.
 4. Temperature:
-increasing temperature  increase reaction
rates
- But too high temperature begins to change
the shape of the enzyme (denaturation)
-most enzymes function best within a
relatively narrow range of temperatures
- Human enzymes work
optimally at 37 degrees C
5. Presence of Competitive Inhibitors:
C.I. are molecules with a similar shape to an
enzyme’s substrate
-they hijack the active site blocking the
substrate from docking

 As long as the competitive inhibitor is bound to the

enzyme, it is prevented from functioning normally.
 This can be helpful or harmful
 Ex: carbon monoxide – competes with oxygen
and attaches to haemoglobin (not an enzyme
but same principle applies)

Ex: cyanide – attaches to an enzyme in the

mitochondria and prevents sugar break
down during cellular respiration

 Ex: penicillin – blocks enzyme for bacteria to

make protective walls
How are enzymes regulated?
 Feedback Inhibition:
- as the products of the enzymatic reaction
accumulate the end product attach to the
regulatory site of the enzyme inhibiting, or
turning off, substrate binding
Precursor Activity:
- as the initial substrate builds up, it binds at the
regulatory site of the last enzyme in a metabolic pathway
to improve the fit of the substrate into the enzyme to get
the whole sequence of events started
Summary:

Precursor activities turn “on”

metabolic pathways while
feedback inhibition turns “off”
metabolic pathways.
 Digestive System
 Heterotrophs must consume organic
compounds (nutrients) to survive
 Nutrients are:
1. Digested (gastrointestinal tract)
2. Absorbed
3. Transported (circulatory system) to
cells of the body
 Nutrients
 Once inside the cells, nutrients supply the
body with energy and raw materials for:

 Growth
 Maintenance
 Tissue repair
 Digestive system function
 Breaks down large, complex organic
materials  smaller components (used by
tissues)
 Every organ system depends on the
digestive system for nutrients
 The digestive system, in turn, depends on
other systems
 Processes of Digestion
1. Ingestion: taking in of nutrients
2. Digestion: breakdown of complex
organic molecules  smaller
components by enzymes
3. Absorption: the transport of digested
nutrients to the cells of the body
4. Egestion: the removal of food from the
body
Ingestion
 Digestive tract of adult humans is normally 6.5m to 9m
long
 Ingestion
Physical digestion
1. Mouth
 This breaks food into smaller pieces and
increases the surface area to help chemical
digestion
 Food bolus (the thing you swallow) formed by
using teeth and tongue
 Ingestion
2. Saliva
 Produced by salivary glands
 Contains amylase which break down complex
carbohydrates  simpler carbohydrates (first place
for chemical digestion of carbohydrates)
 Dissolves food particles so we can taste what we
are eating
 Lubricates food so it can be swallowed
 Ingestion
Saliva
 Taste buds located in our tongue and
cheeks allow distinguish flavour
 Sense of smell is involved in tasting
 Different receptors respond to different
flavours of food
 Ingestion
3. Esophagus
 Once swallowed food travels from mouth 
stomach (via esophagus)
 Bolus of food stretch the walls of the esophagus
 rhythmic, wave-like contractions of smooth
muscle  peristalsis (move food along GI
tract)
 The only point at which food moves voluntarily
is during swallowing and egestion
 Peristalsis activity

From: http://www.yksd.com/distanceedcourses/YKSDbiology/lessons/ThirdQuarterLessons/Chapter08/8-1Digestion/images/peristalsis.jpg
 Ingestion
4. Stomach
 Site of food storage and initial protein digestion
 Movement of food to and from stomach regulated by:
 Sphincters: constrictor muscles that regulate the opening
and closing of tube-like structures
 Contraction of lower esophageal sphincter(LES) closes
the opening to stomach and relaxation allows food to
enter
 LES prevents food and acid from being regurgitated
(heart burn)
 Pyloric sphincter regulates movement of food and
stomach acids into the small intestine
From: http://www.ahealingtouch.biz/images/digestive.jpg
 Stomach
J- shaped with numerous ridges,
allowing it to expand
Can store up to 1.5L of food
Contractions of the stomach mix the
food with the gastric juices – physical
digestion– increase surface area (SA)
of food
 Stomach
 Cells lining the interior of stomach secrete gastric
fluids that aid in digestion
 Mucus - alkaline mucus protects stomach lining
from being digested (not present in esophagus)
 Pepsinogen – enzyme released by peptic cells
into stomach
 breaks down proteins in food when activated
 HCl (aq) - makes pH in stomach between 2.0 - 3.0 from parietal
cells
 Kills pathogens, denatures proteins, converts
pepsinogen (inactive form) to pepsin (active
form)
 Peptic Ulcers
 When the lining of the stomach is broken down;
cell membrane is exposed to HCl(aq) and pepsin
 Destroys cell membrane, increases blood flow and
acid secretion, which burns more tissues….cycles!
 From this we get an ulcer
 Lesion on the surface of an organ

 Ulcers caused by bacteria (Heliobacter pylori)

 Diet and stress can play a role
From: http://www.medicinenet.com/images/illustrations/peptic_ulcer.jpg
From: http://www.mercksource.com/ppdocs/us/common/dorlands/dorland/chapters/images/w0146_u_04.jpg
 Small Intestine
 measures up to 7m in
length, but only 2.5 cm in
diameter, divided into
three sections
 duodenum – 25 cm long,
where most digestion
occurs
 focusing on absorption
 jejunum – 3 m long
 ileum – 4 m long
 Small Intestine
 the majority of digestion and absorption
(90%) takes place here – lipid digestion,
continuation of carbohydrate and protein
digestion
 the accessory organs of digestion, the
pancreas, gall bladder and the liver secrete
their juices into the duodenum to aid in
digestion
 as the chyme enters the duodenum, its
acidity and contents stimulates a number
of hormones release, which in turn
stimulate the secretion of digestive and
protective chemicals from accessory organs
and the intestinal epthelium itself
 Micro structures in the small intestine
 The small intestine is
 highly folded to increase surface area (by 600x);
 the folds are called villi, which are covered in small cytoplasmic
projections called microvilli,
 the structure of the small intestine (from the outer surface in)
includes:
 villi/microvilli – surface (epithelial) cells designed for
absorption
 lacteal – vessel projection of the lymphatic system, designed
to absorb fats
 capillaries – vessels of the circulatory system, for absorption
of all other nutrients for immediate transport to the liver for
processing
 Hormones
 Enteric gastrin
 stimulated by partially digested proteins to cause more gastric
juice secretion and promote stomach emptying
 Cholecystokinin (CCK)
 stimulated by partially digested proteins and irritants in the
chyme,
 stimulates pancreatic enzyme release and bile from the
gallbladder
 Secretin
 in response to acids in the duodenum,
 inhibits the secretion of gastric juice,
 stimulates sodium bicarbonate release by the pancreas and
stimulates bile secretion by the liver
Pancreas
 Pancreas
 a soft tubular gland that lies just behind the stomach
 connected to the duodenum by two ducts
 has both a exocrine (secretory) and endocrine
(hormonal) function
 its exocrine functions are to
 secrete digestive enzymes and
 sodium bicarbonate to neutralize the stomach acid and
establish a pH of 7.1-8.2
 which will not only neutralize the enzyme pepsin, but
activate the pancreatic enzymes
 Enzymes from the Pancreas
 pancreatic amylase – digest carbohydrates  maltose
 trypsin – protein digestion: peptones  small
polypeptides (activated by enterokinase, secreted by the
intestinal wall)
 chymotrypsin – protein digestion: small polypeptides
 peptides (activated by trypsin)
 carboxypeptidase – digests polypeptides  amino
acids
 lipase – digests fats into fatty acids and glycerol
 ribonuclease – digests RNA to nucleotides
 deoxyribonuclease – digests DNA to nucleotides
The Liver
 Liver
 the liver has over 500 functions, Four being
fundamental:
 production of bile
 storage of glucose in the form of glycogen ( fat if glycogen
limits exceeded),
 conversion of galactose and fructose to glucose
 detoxification of the blood
 (makes enzymes to break down toxins; ex: alcohol, caffeine,
nicotine, barbiturates, poisons, excess hormones)
 deamination of amino acids – removing nitrogen, producing
ammonia and eventually urea (excreted by the kidneys)
 Liver Connected
 it receives two separate blood
supplies
 via the portal vein –
bringing freshly absorbed
nutrients from the small
intestine
 via the hepatic artery –
bringing oxygenated blood
from the lungs/heart
 Bile
 consists of
 water,
 bile salts,
 cholesterol and
 bile pigments (made from bilirubin – yellow in colour)

 each day, the liver secretes between 800 – 1000 mL of bile

 stored in the gallbladder
 released on demand into the small intestine
 acts as an emulsifier,
 breaking large fat globules into small ones, allowing lipase
more surface area for digestion
Gall Bladder
 Gallbladder
 lodged in one of the lobes of the liver
 a light muscular bag that stores and releases bile
 why store bile?
 We eat large quantities of fats at a time, so
having a store of bile is useful
 problems – bile salts can crystallize in the
gallbladder forming gallstones
 Digestion in the Small intestine
 the combination of hormones and the presence
of certain foods leads to the secretion of
 pancreatic enzymes,
 bile and
 intestinal enzymes
 (maltase, lactase, sucrase and enterokinase)
 all of which are active in the slightly basic pH of
the duodenum
 Absorption of Nutrients
 the villi of the small intestine are specialized to absorb
the molecules of digestion:
 large surface area
 transport proteins on the epithelial cells move aa,
glucose, water soluble vitamins, etc.
 by facilitated diffusion and
 active transport into the capillary system,
 then on to the liver immediately for processing

 electrolytes by diffusion,
 water by osmosis
Absorption of Nutrients
 fatty acids and glycerol are absorbed into the epithelial
cells and are repackaged as triglycerides
 being hydrophobic, they are packaged into protein packs to
enable their transport through the body
 the packaged fats are absorbed into the lacteals in the
interior of the villi, and are transported through the bodys
lymphatic system
 fat soluble vitamins will move with fats into lacteals
for absorption in the body
Absorption of Glucose
 The digestion of starch:
 begins in the mouth with salivary amylase.
 In the stomach, hydrochloric acid (acidic pH) denatures the salivary amylase so
starch digestion is stopped.

 Chyme enters the duodenum; the pH rises to pH of 8.

 Pancreatic amylase completes the digestion of starch to disaccharides.
 Other carbohydrases hydrolyze the disaccharides into monosaccharides such as
glucose.

 Monosaccharides are absorbed by active transport (requires ATP) into the

intestinal villi.
 From the cells of the intestinal lining, the monosaccharides enter the
bloodstream and are transported directly to the liver.
 Monosaccharides other than glucose are converted into glucose by the liver.
 Glucose is circulated from the liver by the bloodstream to all the body cells
where it is used as a source of energy.
Absorption of Amino Acids
 The digestion of proteins:
 The polypeptides that are produced by the action of pepsin are
further digested in the small intestine by two proteases secreted
by the pancreas.
 These proteases, trypsin and chymotrypsin, are secreted as
inactive enzymes and then activated by a different enzyme
secreted in the small intestine.

 Both trypsin and chymotrypsin hydrolyze the peptide bonds

between specific but different amino acids, resulting in the
formation of short peptide chains.
 Different peptidases split the short peptide chains into single
amino acids.
 The amino acids are then absorbed by active transport into the
villi of the small intestine.
 From there, the amino acids diffuse into the blood capillaries and
are carried, like the sugars, directly to the liver.
Absorption of Lipids
 The digestion of fats:
 The arrival of fats in the duodenum stimulates the secretion of bile, which
emulsifies the fat droplets into a fine suspension.

 Emulsification is a physical process, not a chemical process. The bonds that join
the glycerol and fatty acids in fats are not hydrolyzed by emulsification.

 The breakdown of fats by hydrolysis is carried out by lipase secreted in the

duodenum.
 The resulting glycerol and fatty acids are absorbed into the cells of the villi by
simple diffusion.
 Inside the cells of the intestinal lining, the fat subunits are reassembled into
triglycerides and then coated with proteins to make them soluble before they
enter the lymph vessels in the villi.
 The lymph vessels carry the coated triglycerides to the chest region, where they
join the bloodstream.
 Once in the bloodstream, the protein coating is removed by lipase in the lining
of the blood vessels. Lipase hydrolyzes the triglycerides, making free fatty acids
and glycerol available for use by the body cells.
 Large Intestine
 about 1.5 m in length, a
diameter of 6.5 cm.
 at the junction of the
small and large
intestine, the ileum
exists the appendix,
which has no real
function given our diet
 Functions of the Large Intestine
 the large intestine has three main functions:
 absorption of water and electrolytes
 production of feces
 consisting of water, inorganic salts, cells from the GI
tract, bacteria, bacterial decomposition and
undigested food
 housing bacteria,
 that will use remaining unabsorbed nutrients or
undigested carbohydrates to make vitamin K and B
vitamins for us to absorb (as well as methane gas)
 Colon Functioning
 Material that is not absorbed in the small
intestine travels to the lumen of the large
intestine (colon)
 Functions of the Colon
 concentrates feces
 stores feces
 production of vitamin K by mutualistic
bacteria
 Feces

mixture of
water
undigested/ unabsorbed matter
bacteria
Storage of water

 Na+ ions are pumped out of

the lumen
 This draws water out via
osmosis
 Cells in the Large Intestine
 Cells in the lining of the wall secrete
 mucus
 for lubrication
 bicarbonate
 buffer the acidic fermentation process
Colonizers
 fermentation is performed by bacteria that
are ingested when eating
 Movement through the large intestine is
slow and thus allows for the growth of
bacteria.
 These bacteria are referred to as colonizers
 Expelling Food
 Upon eating the next meal
 signal sent to the colon
 feces moves ¾’s of the colon’s length to make way
for the new
 occurs within a few seconds
 Contents are stored in the Rectum until they
are expelled
 The rectal wall becomes distended
 a reflex action is triggered
 inhibition and contraction of the muscle sphincter
at the anus are controlled by the nervous system