Option B
Biochemistry
Introduction to
Biochemistry
• The chemistry of living organisms is called biochemistry.
• Metabolism – the sum of all reactions happening in your
body/cells.
• Respiration – energy that is made in cells through a
complex series of oxidation reactions
• Bomb Calorimeter – special type of calorimeter used to
measure heat of combustion of certain reactions – can also
measure energy in food.
BOMB CALORIMETER
Watch
YouTube
video
Calorimetry
• Energy content of food can be determined by calorimetry.
• The food is burned in a calorimeter, and the increase in
temperature of surrounding water is measured:
q = mcΔT
q = heat (in joules)
m = mass of water (in grams)
C = specific heat of water (4.184 J g-1 ºC-1)
ΔT = temperature change of water (in ºC)
Calorimetry
• Example: 1.13 g of rice raises the temperature of 525 g of
water by 3.31ºC. Determine the energy content in kJ/g.
Q = mcΔT
= (525 g) (4.18 J g-1 ºC-1) (3.31ºC)
= 7260 J = 7.26 kJ
Energy content is 7.26 kJ / 1.13 g rice = 6.42 kJ per gram of rice
Calorimetry
1. A 0.78g sample of cheese is combusted in a bomb
calorimeter. The temperature of 105.10g raised from 15.4 ºC
to 30.6 ºC. Calculate the energy value of the cheese in kJ/g.
•Pay attention on the IB exam for units that the question is
asking for. If the question asks for J/mol you must multiply
your answer by the molar mass (g/mol)
Proteins
• Proteins are major groups of biological
molecules
• Two Types
• Structural – fingernails, hair, tendons,
muscles
• Act as tools – act as catalysts, transport
oxygen
Examples
Proteins
• Proteins are polymers made up monomers – amino
acids.
• They are made up of 2-amino acids. (this means that the
amine group is on carbon number 2, while the
carboxylic acid group is on carbon number 1)
Proteins
Structure of 2-Amino Acids
Carbon 2:
contains amine
group
H2N
H
O
C
C
R
Carbon 1: carboxylic group
OH
Name comes from
the face that the amine
Group is on C #1
Functional group – where one
amino acid differs from the
others
• There are about 20 amino acids found in most
proteins.
• Each amino acid is assigned a three-letter
abbreviation.
• Amino acids are listed in the IB data booklet
• Our bodies can synthesize about 10 amino acids.
• Essential amino acids are the other 10 amino acids,
which have to be ingested (part of our diet).
• The -carbon (carbon 2) in all amino acids (except
glycine is chiral) (has 4 different groups attached to it).
Examples of Amino Acids
H
H2N
H
O
C
C
OH
H2N
H
O
C
C
H2N
OH
C
O
C
CH 2
CH 2
CH 3
alanine
Ala
H
CH 2
glycine
Gly
NH
C
NH 2
arginine
Arg
NH
OH
Amino Acids
• Amino acids:
• have very high melting points (above 200C)
• high solubility in water
• A zwitterion has both positive and negative charge in
one molecule.
• The carboxyl group can behave like an acid and donate the
H+ (forming COO-); the amine can behave like a base and
accept an H+ (forming NH3+); if both occur at the same
time, a zwitterion is formed
• Therefore it is amphoteric
Zwitterions
Amino Acids
pH determines the net charge of the amino acid
Positive charge = low pH
Negative charge = high pH
Isoelectric point – the intermediate point at which
an amino acid is electrically neutral
Buffer Capability
Amino acids are able to maintain a relatively constant pH
despite the addition of small amounts of acid or base.
This is very important b/c many proteins can be destroyed
even in the slightest fluctuation of pH.
Example – Blood has a pH of 7.4. Even a fluctuation of 0.5
can be fatal.
Polypeptides and Proteins
• Amino acids react together in a condensation reaction
(water is eliminated)
• The new bond formed between amino acids is called a
peptide bond and they form dipeptides
H
R
O
N
C
C
H
H
OH
+ H
R'
O
N
C
C
H
H
OH
H
H2O
Dipeptides will continue to react forming polypeptides
R
O
N
C
C
H
H
R'
O
N
C
C
H
H
Peptide Bond
OH
Examples
2. If cysteine has an isoelectric point of 5.1,
what will the structure be when the pH is...
5.1
4.0
6.0
3. Draw a tripeptide with the following sequence:
Cys-Val-Asn
Protein Structure
• Primary structure is the number and
sequence of the amino acids in the
polypeptide chain (protein).
• Example: NH2-leu-his-ala-…-alaval-ser-COOH
• A change in one amino acid can alter
the biochemical behavior of the
protein.
Protein Structure
• Secondary structure is the regular
arrangement of segments of protein.
• The polypeptide chain folds as a result
of the hydrogen bonding between
peptide groups.
• One common secondary structure is the helix.
• Contains hydrogen-bonding parallel to
helix
• The polypeptide chain folds as a result
of the hydrogen bonding between
peptide groups four amino acids apart.
• It is flexible and elastic b/c H bonds
can break and reform as it is stretched
• Ex. keratin
… = H bond
• Another secondary structure is the β-pleated sheet.
• Contains H-bonding perpendicular to the sheet
• The helix or pleated sheet is held together by hydrogen
bonds between N-H bonds and carbonyl groups.
H bond
β-pleated is flexible but INELASTIC. Found in spider webs.
Protein Structure
Tertiary Structure is the overall shape of the protein. It
refers to the twisting, folding, and coiling of the the
polypeptide chain as a result of interactions between the R
groups (side chains). The 3-d compact structure that
results is know as the protein’s conformation.
Conformation is important in globular proteins. (enzymes and
hormones)
They are water soluble b/c the polar R groups are on the outer surface
where they can interact with water.
Forces Affecting Tertiary Structure:
•
•
•
•
Ionic Bonding – between side chains that have a charge
Hydrogen Bonding – between polar side chains
Hydrophobic interactions – between non-polar side chains
Covalent Bonds (disulfide bridges) – between sulfur in the
amino acid cysteine – very strong
(held together by INTRAmolecular forces)
• Proteins can be denatured – or
lose their tertiary structure due to
changes in pH or temperature.
hydrophobic
Protein Structure
Quaternary Structure – not very common
• This is the structure if a protein is made up of more than one
polypeptide chain. Ex. Collagen – found in skin and tendons
and Hemoglobin – carries oxygen in blood
Held together by INTERmolecular forces (H-bonds, dipoledipole, vdW)
collagen
hemoglobin
Analysis of Proteins – 2 ways
1. Chromatography
solvents final position
Amino acids will spread according to their different solubilities.
Analysis of Proteins – 2 ways
1. Chromatography
• Paper is removed and
sprayed with ninhydrin (a
reagent that makes the amino
acid turn purple since they are
colorless)
Each amino acid has a specific Rf value.
Analysis of Proteins
2. Gel Electrophoresis – Separate amino acids based
on isoelectric point (ip)
ip = isoelectric point = the pH at which positive and
negative charges are balanced (no net charge on
amino acid or polypeptide)
1. Mixture of amino acids placed on gel (or paper)
2. Gel (or paper) is saturated with a buffer of known
pH.
3. Electric Current is applied and amino acids move
towards oppositely charged electrodes.
4. UV light helps identify the position of the amino
acids.
Electrophoresis
•If pH = ip, amino acid does not move
•If pH > ip, amino acid moves toward “+”
– Amino acid loses H+ in basic solution and
becomes negative, moving toward anode.
•If pH < ip, amino acid moves toward “-”
– Amino acid gains H+ in acidic solution and
becomes positive, moving toward cathode.
•The further the pH is from ip, the faster the amino
acid will move.
****Note – Anode is + and Cathode is –
Just like electrolytic cell!****
Electrophoresis
• Example – A mixture of 5 amino acids
(shown below with pi values) is to be
separated by electrophoresis. A buffer
with a pH of 6.0 is used. What will happen
when the current is turned on?
Cys
Gln
Gly
His
Lys
5.1
5.7
6.0
7.6
9.7
+
What if the buffer used has a pH of 7.0?
-
Examples
4. Explain why in gel electrophoresis the
amino acid isoleucine migrates towards the
anode at high pH and the cathode at low pH.
5. You are attempting to separate a mixture
of glutamic acid and histidine by gel
electrophoresis. Give a suggested pH value
for the buffer solution and say which way
each acid will migrate.
Gel Electrophoresis
Go to:
http://learn.genetics.utah.edu/content/labs/
and click on gel electrophoresis. This will
give you a general idea of how it works.
Major Functions of Proteins
1. Structure – fibrous proteins
•
•
Muscle, cartilage, skin, bones, hair, nails
Collagen (skin), keratin (hair)
2. Enzymes – Catalyze specific chemical
reactions in the body.
3. Energy Source
4. Protection –antibodies (immunoproteins)
5. Control – hormones – ex. Insulin
6. Transport - hemoglobin