Session 6:
A Modeling Approach to
Biochemistry
Tom Hsu, PhD.
Manos Chaniotakis, PhD.
Marina Dang, PhD.
Copyright © 2012 Chaniotakas and Hsu
1
Essential Questions
How are amino acids connected to form
a protein?
Does stoichiometry apply to macromolecules?
hemoglobin,
an oxygen-transporter
in red blood cells
Objectives
• Explain how a peptide bond is formed.
• Use the genetic code to translate an mRNA sequence
into an amino acid sequence.
• Describe some of the factors involved in protein folding.
• Use stoichiometry to analyze protein samples.
Assessment
• Write the amino acid sequence from this mRNA sequence:
AUGUUGCUGUUUUGCCAUUUUCCAACAGAC
The active form of insulin is a
5.8 kDa protein.
• What is the mass of insulin
(in g) of 0.81 mmol of insulin?
The body stores insulin as a
hexamer (6 molecules of insulin)
that contains two Zn2+ ions.
• What is the mass of zinc in
0.27 mmol of the hexamer
form of insulin?
TEKS correlations
112.35 (c)(8)(A)
Define and use the concept of the mole.
112.35 (c)(8)(B)
Use the mole concept to calculate the number of atoms,
ions, or molecules in a sample of material.
Review
Polymerization reaction
• Small building blocks (monomers)
come together to form a polymer.
• Proteins are polymers.
• The monomers are called amino acids.
Proteins in and around us
Why are proteins important?
Where do we find proteins and what to do they do?
20 amino acids, millions of proteins
Movement
Muscles are primarily made of proteins
Structure
Tendons, skin, bones, claws, and fibers such as wool and hair
Catalysis
Enzymes that catalyze chemical reactions
Transport
Storage
Hemoglobin, for example, transports oxygen to our tissues
Proteins store minerals needed by the body
Protection
Blood-clotting proteins which keep us from bleeding too much;
antibodies from our immune system protect us from infections
Energy
transfer
Cytochromes transfer electrons through a series of redox
reactions
Assembling amino acids
Each group builds one of the following
amino acids:
Valine
Alanine
Leucine
Serine
Asparagine
Methionine
Aspartic acid
Threonine
Glycine
Cysteine
Asparagine
(Asn)
Twenty amino acids
Use the amino acids chart.
Structure of an amino acid
On your model, find the following:
• Central carbon
• Amino group
• Carboxylic acid group
• R group (the side chain)
Structure of an amino acid
What part makes each amino acid different?
• Central carbon
• Amino group
• Carboxylic acid group
• R group (the side chain)
Structure of an amino acid
What part makes each amino acid different?
• Central carbon
• Amino group
• Carboxylic acid group
• R group (the side chain)
Naming amino acids
Write the 3-letter code for each amino acid.
What characteristic does the side chain give to the amino acid?
From DNA to mRNA to proteins
• The genetic information
contains “instructions” for
protein synthesis.
• DNA transfers the
information to mRNA.
Transcription
DNA molecule
Ex: ATG – GCC
mRNA molecule
AUG – GCC
From DNA to mRNA to proteins
• We use the genetic code
to translate from mRNA to amino acids.
Functional protein
Transcription
DNA molecule
Ex: ATG – GCC
Translation
mRNA molecule
Amino acid chain
AUG – GCC
Met – Ala
Understanding and using
the genetic code
Read the wheel starting from
the center.
AAU codes for
Asparagine (Asn)
Understanding and using the genetic code
• Each codon (group of 3 nucleotides) codes for one amino acid.
Understanding and using
the genetic code
Here is an mRNA sequence:
AUG/UCU/UGC/GAC/GGC/GCA/
ACC/GUC/AAC/CUA/UAG/
Build the protein chain that this
sequence codes for.
Building a protein chain
one amino acid
another amino acid
together form H2O
Building a protein chain
a peptide bond forms
between C and N
Building a protein chain
Building a protein chain from mRNA
AUG / UCU / UGC / GAC / GGC / GCA / ACC / GUC / AAC / CUA / UAG
one amino acid
another amino acid
together form H2O
Building a protein chain from mRNA
1. Why is this polymerization
reaction also called a
dehydration reaction?
2. How many water molecules did
you produce by connecting
these ten amino acids?
Building a protein chain from mRNA
1. Why is this polymerization
reaction also called a
dehydration reaction?
2. How many water molecules did
you produce by connecting
these ten amino acids?
A water molecule is produced or
“lost” every time a peptide bond
is made. “Dehydration” refers to
this loss of water.
There were 9 peptide bonds,
and 9 water molecules were
formed.
Building a protein chain from mRNA
This polypeptide chain has 10 amino acids.
Consider that real proteins can have hundreds of
amino acids:
• The active form in insulin has 51 amino acids, but it is stored as a
hexamer (6 insulin molecules): 306 amino acids.
• Cytochrome P450 3A4 in the human liver has 485 amino acids.
• The a and b chains of hemoglobin have 287 amino acids; hemoglobin
functions as a tetramer (4 hemoglobin molecules): 1148 amino acids.
Understanding and using
the genetic code
Translate these two sequences:
Sequence 1:
AUG/UCU/UGC/GAC/GGC/GCA/
ACC/GUC/AAC/CUA/UAG
Sequence 2:
AUG/AGU/UGC/GAU/GGG/GCU/
ACG/GUC/AAC/UUA/UAA
Understanding and using
the genetic code
Translate these two sequences:
Sequence 1:
AUG/UCU/UGC/GAC/GGC/GCA/
ACC/GUC/AAC/CUA/UAG
Sequence 2:
AUG/AGU/UGC/GAU/GGG/GCU/
ACG/GUC/AAC/UUA/UAA
Amino acid sequence:
Start – Met – Ser – Cys –
Asp – Gly – Ala – Thr –
Val – Asn – Leu – Stop
Understanding and using
the genetic code
Suppose there is a mistake in the mRNA sequence, and
GAC is replaced with GAU.
Is the protein chain affected?
Suppose there is a mistake in the mRNA sequence, and
UGC is replaced with UGA.
Is the protein chain affected?
Understanding and using
the genetic code
Suppose there is a mistake in the mRNA sequence, and
GAC is replaced with GAU.
Is the protein going to be affected?
No: Both codons code for aspartic acid.
Suppose there is a mistake in the mRNA sequence, and
UGC is replaced with UGA.
Is the protein going to be affected?
Yes: A cysteine amino acid is replaced with a stop codon.
This terminates the protein synthesis.
Protein folding
1. Look carefully at the amino acids in the polypeptide chain.
Determine which amino acids are polar and nonpolar.
2. How would you predict the polar amino acids to orient themselves in an
aqueous environment, such as the environment in our bodies?
Protein folding
1. Look carefully at the amino acids in the polypeptide chain.
Determine which amino acids are polar and nonpolar.
Polar:
Ser, Cys, Thr, Asn,
Nonpolar:
Met, Gly, Ala, Val, Leu
2. How would you predict the polar amino acids to orient themselves in an
aqueous environment, such as the environment in our bodies?
Polar amino acids would be on the outside and in contact with the
surrounding water; nonpolar amino acids would be protected in the center.
Demonstrate this with your model.
Protein folding
Factors in protein folding:
•
•
•
•
•
H bonding
Electrostatic forces
van der Waals
Disulfide bonds
Chaperone proteins…
Protein folding
1. Crack an egg into a cup or beaker.
2. Use a 3-mL plastic pipette to transfer some egg white into 3 test tubes.
3 mL of vinegar
3 mL of water
3 mL of water
+ a pinch of salt
#1
#2
#3
Protein folding
Precipitate
Precipitate
3 mL of vinegar
3 mL of water
No precipitate
3 mL of water
+ a pinch of salt
#1
#2
#3
Protein folding
Precipitate
3 mL of vinegar
#1
Some amino acids have side chains that are acidic
or basic. Do you think that adding vinegar to protein
will disrupt its 3D structure? Explain.
Protein folding
Precipitate
Some amino acids have side chains that are acidic
or basic. Do you think that adding vinegar to protein
will disrupt its 3D structure? Explain.
3 mL of vinegar
#1
Adding vinegar means that some of the basic side chains
may interact with the acid in the mixture. This can disrupt
the 3D structure of the protein.
Protein folding
Precipitate
No precipitate
3 mL of water
3 mL of water
+ a pinch of salt
#2
#3
If you are a protein biochemist,
would you stabilize proteins in
water or in water containing
some salt?
Protein folding
Precipitate:
protein aggregate
+ +
3 mL of water
–
–
+ +
#2
–
–
protein
–
–
protein
–
+
+
–
+
+
Electrostatic forces are involved in
protein folding. Some parts of the
protein are positive; others are
negative.
If “unprotected” surface charges
can cause proteins to aggregate
(“clump” together).
Protein folding
The salt ions help to stabilize the protein.
Precipitate:
protein aggregate
+ +
3 mL of water
–
–
+ +
#2
–
–
protein
–
protein
No precipitate:
stabilized protein
+
+
3 mL of water
+ a pinch of salt
–
+
+
–
Cl–
+ +
#3
Na+
–
Cl–
–
–
protein
–
Na+
Na+
–
+
+
Cl–
Stoichiometry in biochemistry
• Molar mass of large molecules are
expressed in daltons (Da).
• 1 Da = 1 g/mol
• 1 kDa = 1,000 g/mol
Hemoglobin
(64 kDa)
What is the mass of 1 mol of hemoglobin?
Stoichiometry in biochemistry
• Molar mass of large molecules are
expressed in daltons (Da).
• 1 Da = 1 g/mol
• 1 kDa = 1,000 g/mol
Hemoglobin
(64 kDa)
What is the mass of 1 mol of hemoglobin?
64 kDa = 64,000 g/mol
1 mol  64 kg
Note: The average North American adult has a mass of ~80 kg.
Stoichiometry in biochemistry
Lysozyme C has a molar mass of 16.5 kDa.
• What is the mass in grams of 1 mol of lysozyme?
Lysozyme
Stoichiometry in biochemistry
Lysozyme C has a molar mass of 16.5 kDa.
• What is the mass in grams of 1 mol of lysozyme?
g
16.5 kDa  16.5  10 Da  16.5  10
mol
3
3
The mass of 1 mol of lysozyme is 16,500 g or 16.5 kg.
Lysozyme
Stoichiometry in biochemistry
Lysozyme C has a molar mass of 16.5 kDa.
• A typical laboratory sample is most likely
to contain which amount of lysozyme:
• 1 mol?
• 0.1 mol?
• 0.0001 mol (0.1 mmol)?
Stoichiometry in biochemistry
165 apples
Lysozyme C has a molar mass of 16.5 kDa.
• A typical laboratory sample is most likely
to contain which amount of lysozyme:
• 1 mol?
• 0.1 mol?
• 0.0001 mol (0.1 mmol)?
16,500 g
1,650 g
1.65 g
Most likely amount
17 apples
Stoichiometry in biochemistry
Lysozyme C has a molar mass of 16.5 kDa.
A sample of lysozyme has a protein concentration of 1.8 mM.
• How many moles of lysozyme are in a volume of 1.5 mL?
Lysozyme
Stoichiometry in biochemistry
Lysozyme C has a molar mass of 16.5 kDa.
A sample of lysozyme has a protein concentration of 1.8 mM.
• How many moles of lysozyme are in a volume of 1.5 mL?
Convert from mM to mol/L:
Convert to moles:
Lysozyme
mol
1.8 mM  1.8  10 M  1.8  10
L
3
3
1.8  103 mol
 0.0015 L  2.7  106 mol lysozyme
L
Stoichiometry in biochemistry
Lysozyme C has a molar mass of 16.5 kDa.
A sample of lysozyme has a protein concentration of 1.8 mM.
• How many grams of lysozyme are in this sample?
Lysozyme
Stoichiometry in biochemistry
Lysozyme C has a molar mass of 16.5 kDa.
A sample of lysozyme has a protein concentration of 1.8 mM.
Lysozyme
• How many grams of lysozyme are in this sample?
Convert from kDa to g/mol:
g
16.5 kDa  16.5  10 Da  16.5  10
mol
3
3
Stoichiometry in biochemistry
Lysozyme C has a molar mass of 16.5 kDa.
A sample of lysozyme has a protein concentration of 1.8 mM.
Lysozyme
• How many grams of lysozyme are in this sample?
Convert from kDa to g/mol:
g
16.5 kDa  16.5  10 Da  16.5  10
mol
Convert from moles to grams:
3
16.5

10
g
6
2.7  10 mol 
 0.045 g  45 mg
mol
3
3
Assessment
• Write the amino acid sequence from this mRNA sequence:
AUGUUGCUGUUUUGCCAUUUUCCAACAGAC
Assessment
• Write the amino acid sequence from this mRNA sequence:
AUGUUGCUGUUUUGCCAUUUUCCAACAGAC
AUG – UUG – CUG – UUU – UGC – CAU – UUU – CCA – ACA – GAC
Met – Leu – Leu – Phe – Cys – His – Phe – Pro – Thr – Asp
Assessment
The active form of insulin is a
5.8 kDa protein.
• What is the mass of insulin
(in g) of 0.81 mmol of insulin?
Assessment
The active form of insulin is a
5.8 kDa protein.
Convert from kDa to g/mol:
Convert from mol to g:
• What is the mass of insulin
(in g) of 0.81 mmol of insulin?
g
5.8 kDa  5.8  10 Da  5.8  10
mol
3
3
3
5.8

10
g
3
0.81  10 mol 
 4.7 g
mol
Assessment
The body stores insulin as a
hexamer (6 molecules of insulin)
that contains two Zn2+ ions.
• What is the mass of zinc in
0.27 mmol of the hexamer
form of insulin?
Assessment
The body stores insulin as a
hexamer (6 molecules of insulin)
that contains two Zn2+ ions.
Mole to mole conversion:
• What is the mass of zinc in
0.27 mmol of the hexamer
form of insulin?
2
2
mol
Zn
0.27  103 mol hexamer 
1mol hexamer
 0.54  103 mol Zn2
Assessment
The body stores insulin as a
hexamer (6 molecules of insulin)
that contains two Zn2+ ions.
Mole to mole conversion:
• What is the mass of zinc in
0.27 mmol of the hexamer
form of insulin?
2
2
mol
Zn
0.27  103 mol hexamer 
1mol hexamer
 0.54  103 mol Zn2
Mole to gram conversion:
2
65.38
g
Zn
0.54  103 mol Zn2 
 0.035 g  35 mg
2
1mol Zn
Extracting DNA from strawberries
1. Place one strawberry in a
resealable bag and puree.
5. Filter the mixture into a new
cup.
2. In a cup, mix 2 tsp of dish
detergent, 1 tsp of salt, and ½
cup of water.
6. Add an equal amount of cold
rubbing alcohol.
3. Pour the mixture into the bag
of strawberry puree.
7. Observe what happens.
8. Stir with a wooden stick, and
remove it from the mixture.
4. Mix gently (avoid bubbles).
How big are macromolecules?
Note: One human DNA molecule contains 204 billion atoms.
60