2.1
Molecules to Metabolism
Biology Journal 8/25/2014
Complete the table!
Molecule
Type
Monomer
Dimer
Polymer Examples
Carbohydrates
Proteins
Lipids
(aka fats)
Starch…
Enzymes,
collagen,
elastin, keratin
Monopeptide
(one amino acid)
CH2
n/a
lipid
Biology Journal 8/25/2014
Molecule Type
Monomer
Dimer
Polymer
Carbohydrates Monosaccharide Disaccharide Polysaccharide
Monopeptide
Proteins
(one amino
acid)
Dipeptide
Polypeptide,
Protein
Lipids
(aka fats)
CH2
n/a
lipid
Examples
Starch,
lactose,
glucose,
ribose
Enzymes,
keratin,
elastin,
Fatty acids,
triglyceride
Biology Journal 8/25/2014
1. What kind of reaction is shown?
2. Write out the reaction as words:
Sucrose + _______ → ________ + _______
3. When might this reaction be happing in your
life?
+
H2 O
→
+
Biology Journal 8/25/2014
1.
2.
3.
What kind of reaction is shown? Catabolism
(breaking down) through hydrolysis
Write out the reaction as words:
see below
When might this reaction be happing in your life?
This happens whenever you eat sucrose (sugar)!
+
sucrose
H2 O
→
+ water →
+
fructose
+
glucose
We will now learn how the digestive
system makes this happen!
Biology Journal 8/27/2013
What is the name of the monosaccharides shown below?
These 2 molecules bond in a condensation reaction to form a
disaccharide called lactose. Show this reaction by circling the
atoms that are “released” as water, and draw the product.
Biology Journal 8/27/2013
What is the name of the monosaccharide below? These 2
molecules bond in a condensation reaction to form a
disaccharide called lactose. Show this reaction by circling the
atoms that are “released” as water, and draw the product.
+
→
+
H2O
Biology Journal 8/19/2014
What is a monomer?
What is a dimer?
What is a polymer?
glucose
lactose
starch
Biology Journal 8/20/2014
Label each drawing with its name. Annotate the pictures with
a description of the elements found in them, and their relative
amounts. (you don’t have to draw the pictures in your
notebook, just write the names and describe them)
Fatty acid
Has 2 O’s (carboxyl)
Long chain of C’s and H’s
Glucose
General formula = CnH2nOn
Amino acid
Complex C and H structure
Has O’s (carboxyl)
Has N (amino)
R group can be many things
Fatty acid (again!)
Ribose
General formula = CnH2nOn
Biology Journal 8/21/2014
A chemical reaction occurs, synthesizing 5 glucose molecules.
a. What is the name of this chemical reaction?
b. What is the name of the product?
c. What is the other product and how many molecules of it are
made?
H
OH
H2 O
H
OH
H2 O
OH
H
H2 O
(a) Condensation anabolism (building up)
(b) starch or cellulose
(c) 4 H2O molecules are made
H
OH
H2 O
Topic 2: Molecular biology (21 hours)
2.1 Molecules to metabolism: Living organisms control their composition by a complex web of chemical
reactions.
Nature of science: Falsification of theories—the artificial synthesis of urea helped to falsify vitalism.
Understandings:
 Molecular biology explains living processes in
terms of the chemical substances involved.
 Carbon atoms can form four covalent bonds
allowing a diversity of stable compounds to exist.
 Life is based on carbon compounds including
carbohydrates, lipids, proteins and nucleic acids.
 Metabolism is the web of all the enzymecatalysed reactions in a cell or organism.
 Anabolism is the synthesis of complex molecules
from simpler molecules including the formation
of macromolecules from monomers by
condensation reactions.
 Catabolism is the breakdown of complex
molecules into simpler molecules including the
hydrolysis of macromolecules into monomers.
Applications and skills:
 Application: Urea as an example of a compound
that is produced by living organisms but can also
be artificially synthesized.
 Skill: Drawing molecular diagrams of (alpha-D and
beta-D) glucose, D-ribose, a saturated fatty acid
and a generalized amino acid (using R).
 Skill: Identification of biochemicals such as sugars
(mono- and di-saccharides), lipids (triglycerides
and phospholipids, saturated and unsaturated) or
amino acids (R groups do not need to be
memorized) from molecular diagrams.
 Skill: Food tests such as the use of iodine to
identify starch or Benedict’s reagent to identify
reducing sugars could be carried out.
Biology Journal 8/18/2014
2.1 Homework Quiz!
1. What are the 4 most common elements found in living
things? (you can use their atomic symbols to answer)
2. Glucose and cellulose are examples of:
a. Carbohydrates
b. Lipids
c. Proteins
d. Nucleic acids
3. True or false: In the process of anabolism, polymers are
broken down into their component monomers.
4. What are the names of any 2 nucleic acids?
5. Give the names of 2 common examples of proteins.
All of these represent the same substance:
glucose. There are many ways of expressing
the idea of a molecule.
C6H12O6
Chemical
Formula
Lewis-stick
drawing
Spacefilling
model
Skeletal-line Drawing
Ball and Stick
model
Skeletal Line Drawings are often used when
representing large, complex biological molecules.
1.
2.
3.
4.
Rules for Skeletal Line Drawings:
Lines are covalent bonds
C’s are “corners”
H’s attached to C’s are not drawn
(remember: C makes 4 bonds)
Other elements, and H’s attached
to them, are shown with their
symbol
This is nicotine. What’s its
chemical formula?
H
C10H14N2
H
C
HC
C
C
H
C CH
C
H2
CH2
C
H2
Rules for Skeletal Line Drawings:
1.
2.
3.
4.
Lines are covalent bonds
C’s are “corners”
H’s attached to C’s are not drawn (remember: C makes 4 bonds)
Other elements, and H’s attached to them, are shown with their symbol
This is Cocaine. It can be turned
into crack. What’s its chemical
formula?
C10H14N2
H
C
C H
C
C
C
C
C
H C H
H
H
C
H2
Rules for Skeletal Line Drawings:
1.
2.
3.
4.
Lines are covalent bonds
C’s are “corners”
H’s attached to C’s are not drawn (remember: C makes 4 bonds)
Other elements, and H’s attached to them, are shown with their symbol
This is adrenaline, which is stored in your adrenal glands, and released as
part of the “fight or flight response.”
C
C
H
C
C
H
C
C H C H2
C
H
C9H13NO3
C
H3
These are the same molecule, called
a fatty acid. They are represented in
different ways.
All of these represent the same substance:
glucose. There are many ways of expressing
the idea of a molecule.
C6H12O6
Chemical
Formula
Lewis-stick
drawing
Spacefilling
model
Skeletal-line Drawing
Ball and Stick
model
The process of science is based on a system of:
• Making hypotheses
• Testing them through rigorous collection of
empirical evidence (can be measured and
recorded)
• Peer-review of data
• Statistical analysis
• Replication
• Acceptance
THEORY!
Highest level of certainty in science
acceptance
corroborated
unquestionably
repeated
corroborated
?
observations
hypothesis
hypothesis
?
“It’s only
a theory”
testing
not corroborated
(evidence does not
support hypothesis)
The scientific process
Falsifiability
• The purpose of science is to explain and predict.
• Falsifiability is the possibility that an statement
could be proven false.
• This does not mean it is false; rather, it means
that if the statement were false, then its
falsehood could be demonstrated.
No human
lives forever.
Is this falsifiable?
No.
• It does not seem possible to
prove wrong.
• In theory, one would have to
observe a human living
forever to falsify that claim.
All humans
live forever.
Is this falsifiable?
Falsifiable.
• Observing just one dead
human could prove the
statement wrong.
• A hypothesis, proposition, or theory is "scientific"
only if it is, among other things, falsifiable.
• Unfalsifiable statements are non-scientific.
The theory that the molecules of living things came only from a special
“vital principal” was proven false, when urea was synthesized artificially.
Urea was
discovered
in the 1720’s
in urine.
In 1828 Friedrich Wohler synthesized urea!
Silver isocyanate
It was assumed
to be a product
of the kidneys.
At the time, it was thought that these
compounds could only be made with
the help of a “vital principle”.
Ammonium chloride
Yea, I like pee.
So what?!
This “vital principle” causes the
phenomena of life to happen, rather
than chemical or physical forces.
If urea had been synthesized without a “vital principle” then other organic compounds
could as well.
Molecules can be represented in lots of different ways.
Look at the following diagrams, they all represent the same
thing.
How?
Molecules can be represented in lots of different ways.
Look at the following diagrams, they all represent the same
thing.
How?
2.1 Draw a molecular diagram of alpha-D glucose, D-ribose, a saturated fatty acid, and a
generalized amino acid (showing R group)
Glucose
C6H12O6
2.1 Draw a molecular diagram of alpha-D glucose, D-ribose, a saturated fatty acid, and a
generalized amino acid (showing R group)
Ribose
C5H10O5
We put the D in DNA
DNA is deoxyribonucleic acid.
A form of ribose with one
fewer oxygen called
“deoxyribose” is part of DNA’s
structure.
2.1 Draw a molecular diagram of alpha-D glucose, D-ribose, a saturated fatty acid, and a
generalized amino acid (showing R group)
Saturated Fatty Acid
2.1 Draw a molecular diagram of alpha-D glucose, D-ribose, a saturated fatty acid, and a
generalized amino acid (showing R group)
Generalized Amino Acid
This is an an amino acid.
(this one is called asparagine)
R group
(in this case CH2CONH2)
Amine
(NH2)
Carboxyl
(COOH)
Alpha carbon
(the middle C where the R group is attached)
Drawing structures
Glucose – C6H12O6
• 6-membered ring with a side chain
• 5 carbons in the ring, one carbon in the
side chain
• #C’s with 1 on the right, then clockwise
• Hydroxyl’s (-OH) on C’s 1, 2, 3, 4 point
down, down, up, down
Ribose – C5H10O5
• 5-membered ring with side chain
• 4 carbons in the ring, one carbon in the
side chain
• #C’s with 1 on the right, then clockwise
• Hydroxyl’s (-OH) on C’s 1, 2, 3, point up,
down, down
Generalized amino acid
• C atom in the center is bonded to four
things
• Amine group –NH2
• Carboxyl group – COOH
• Hydrogen atom –H
• R group
Saturated fatty acid
• C’s form an unbranched chain
• All single bonds in a saturated fatty acid
• # of C’s is between 14 and 20
• At one end of the chain, the C is part of
a carboxyl group
• At the other end of the chain, the C is
bonded to three H atoms
• All other C’s are bonded to two H atoms
Lipids (aka fats) have repeating CH2 units. This gives
them lots in energy (calories) in the numerous C-H
bonds.
•
Most mammals (humans included), store their
extra energy as the lipid triglyceride, shown
below.
Saturated fats have the maximum number
of H’s.
•
•
They are crammed, or “saturated” with H’s
Thus, they have the most calories
Animal fats are
usually saturated.
Unsaturated fats have one
(monounsaturated) or more
(polyunsaturated) double bonds.
•
•
With double bonds, there is fewer room for H’s
Thus, they have fewer calories, and are generally
“healthier.”
Plant fats are usually
unsaturated.
What is condensation?
Condensation is the formation of water
Model how fatty acids and glycerol combine to
form triglycerides through condensation reactions
OH + H =
Build Triglyceride through a
condensation reaction!
1. Cut out the molecules
2. Label each molecule with a marker
3. “Chop” off the H and OH from the appropriate
molecules, and attach them together.
4. Put the H and OH on a water drop. It’s H2O!
Attach it to the molecule nearby, to show that
water was created through this process.
Carbohydrates and Sugars
•
•
•
•
General formula of CnH2nOn
Monomer = sugar or monosaccharide
Polymer = carbohydrate or polysaccharide
Plants often store their extra energy as
carbohydrates, rather than lipids.
Disaccharides
Sucrose =
glucose +
fructose
Monosaccharides
Lactose =
glucose +
galactose
Glucose
Polysacchardies
Starch = glucose +
glucose +glucose +
glucose…
Ribose
Galatose
Model how monosaccharides combine to form
disaccharides through condensation reactions
OH + H =
Build Maltose through a
condensation reaction!
1. Cut out the molecules
2. Label each molecule with a marker
3. “Chop” off the H and OH from the appropriate
molecules, and attach them together.
4. Put the H and OH on a water drop. It’s H2O!
Attach it to the molecule nearby, to show that
water was created through this process.
Build Starch through a
condensation reaction!
1. Cut out the molecules
2. Label each molecule with a marker
3. “Chop” off the H and OH from the appropriate
molecules, and attach them together.
4. Put the H and OH on a water drop. It’s H2O!
Attach it to the molecule nearby, to show that
water was created through this process.
5. Make a starch polymer, consisting of 4
monomers!
Amino Acids
• Have amine group
(NH2), carboxyl group
(COOH), alpha carbon,
and side chain (R).
• Make polymers called
polypeptides, or
proteins.
Tyrosine
Serine
Glutamine
There are 20
(or more,
depending on
how you
count) amino
acids used in
the human
body.
Anabolism = building a polymer from monomers.
Makes H2O (condensation)
Ex: your body making hair
Catabolism = Breaking down a polymer into
monomers. Consumes H2O (hydrolysis).
Ex: digesting a muffin
Build a Protein through condensation anabolism!
1. A maximum of 4 students in a group.
– (more than 4 names on a model will result in ½ credit)
2. Look at your sequence and ID the amino acids
you need. Label each amino acid with a marker.
3. “Chop” off the H and OH from the appropriate
molecules, and attach them together, show 1
molecule “drop” of H2O is made and attach it
nearby.
4. Bond all of the amino acids in the correct
sequence. Label what sequence number you
have is on your model!
2.1 Skill: Food tests such as the use of iodine to identify starch or Benedict’s reagent to
identify reducing sugars could be carried out.
An Iodine Solution (yep, the element) can be
used to identify if starch is present.
Iodine
Solution
+
Starch
Solution
→
Positive
Test
Starch Test:
https://www.youtube.com/watch?v=ebaQkkw2DCs
2.1 Skill: Food tests such as the use of iodine to identify starch or Benedict’s reagent to
identify reducing sugars could be carried out.
Benedict’s Reagent can be used to identify all
monosaccharides, and many disaccharides. It
must be mixed, then heated.
Benedict’s Reagent Test:
https://www.youtube.com/watch?v=Lt7RCIfudYQ
Question from Paper 1
Which molecule represents ribose?
What is molecule B?
What is molecule C?
Question from Paper 1
Which structure represents an amino acid?
Question from Paper 1
Which molecule is:
i. ribose
ii. Generalized fatty acid
ii. Generalized amino acid
Discuss which two molecules are most similar in structure.
a. What kind of molecule is this?
b. Label its parts.
R group
(in this case CH2CONH2)
Amine
(NH2)
Carboxyl
(COOH)
Alpha carbon
a) amino acid (in this case asparagine)
a. What is the name of this molecule?
b. Label its parts
Carboxyl groups
Glycerol
a. triglyceride
3 Fatty acids
What kind of molecule is this?
It’s a lipid! Specifically, a phospholipid.
a. Name this molecule.
b. Describe it’s structure in as much detail as you
can.
a. Fatty acid.
b. It is a lipid, it has a carboxyl group
(COOH), and it is unsaturated (it has
a double bond), which makes it have
fewer calories than a saturated
version.
1. What kind of reaction is shown?
2. Write out the reaction as words:
Sucrose + _______ → ________ + _______
3. When might this reaction be happing in your
life?
+
H2 O
→
+
1.
2.
3.
What kind of reaction is shown? Catabolism
(breaking down) through hydrolysis
Write out the reaction as words:
see below
When might this reaction be happing in your life?
This happens whenever you eat sucrose (sugar)!
+
sucrose
H2 O
→
+ water →
+
fructose
+
glucose
A chemical reaction is shown below.
1. Name each reactant and product.
2. What kind of reaction is this?
3. Where should water be present in the reaction?
How many molecules of water?
→
A chemical reaction is shown below.
1. Name each reactant and product.
2. What kind of reaction is this?
3. Where should water be present in the reaction?
How many molecules of water?
Catabolic Hydrolysis Reaction
Monopeptide
(amino acid)
Dipeptide
+ H2O
Monopeptide
(amino acid)
→
• Hydrolysis (water is split)
• It “fills in” each monomer
A chemical reaction occurs, synthesizing 5 monomers.
a. What could be two terms to describe this reaction?
b. What is the name of the product?
c. What is the other product and how many molecules of it are
made?
H
OH
H2 O
H
OH
H2 O
OH
H
H2 O
(a) Condensation anabolism (building up)
(b) starch or cellulose
(c) 4 H2O molecules are made
H
OH
H2 O