Chapter 3 Protein Structure and Function
3.1 What do Proteins do?
Function of Protein/Role of Protein in the cell Protein Type
1. Defense: proteins called antibodies and Antibodies and complement protein
complement proteins attack and destroy viruses/
bacteria causing disease
2. Movement: contractile/motor proteins are Contractile/motor proteins
responsible for moving cell, moving large
molecules/other cargo in a cell.
e.g. actin/myosin slide past one another to create a
3. Catalyze chemical reactions: some proteins called Enzymes
enzymes function as a catalyst (speed up reactions).
e.g. carbonic anhydrase in red blood cells helps
move carbon dioxide from cells to lungs
- Salivary amylase in mouth starts process of
digestion of starch and is involved in the
breakdown of complex carbohydrates to simple
4. Acts as signal to help coordinate activities of cells Hormones/Receptor Protein
E.g. peptide hormones bind to receptor protein cells
resulting in a change in the activity of the cell with
the receptor protein
- Proteins responsible for receiving/ carrying
signals from cell to cell
5. Provide support for cell and tissues and form Structural proteins
structures (i.e. hair, cocoons, spider webs, finger
- Membrane red blood cells covered with
structural protein inside the cell
- Work together to keep cell flexible and normal
6. Move substances across cell membrane and Transport protein
throughout the body
e.g. hemoglobin is a transport protein used to carry
oxygen throughout the cell
- Other proteins embedded in the cell
permit/prohibit entry and departure of certain
3.2 Early origin of Life
Stanley Miller Spark Discharge Experiment
- Purpose- wanted to see if complex organic molecules can be synthesized from simple molecules present
in the Earth’s early atmosphere and ocean (wanted to see if he could start a chemical evolution by
stimulating earth’s earliest conditions in a laboratory)
- Experimental question- can simple molecules and kinetic energy lead to a chemical evolution?
- Experimental set-up: a. Large glass flask contained gases (NH 3 CH 4 H 2 and all had free energy)
b. Small flask held tiny ocean-200 mL of water (boiled water constantly, so water vapor added to
mixture of gases).As vapor cooled and condensed, it flowed back into small flask, where it was
c. With no charge- boiling water did not cause spontaneous chemical reactions because even at high
temperatures, molecules involved in a reaction are stable. When electricity added to electrode
inserted in atmosphere, lightening bolts assed to electrical energy in mix. One day past and flask
colour is pink and one week, the colour is red and cloudy.
d. Miller drew samples from apparatus in intervals and found large quantities of HCN (Hydrogen
cyanide)/ formaldehyde (H 2O). This is significant because HCN and formaldehyde is necessary
for synthesis of complex organic molecules like amino acids.
- Conclusion- chemical evolution occurs if simple molecules with high free energy exposed to source of
- -Alternative Theories –
o Hydrothermal Vents- sub-units found deep in the core of the ocean using submarine technology
o Murchison Meteorite- theory that sub-units came from outer space. They found carbohydrates
and other monomer sub units on the meteorite.
The counter argument- meteorite picked up sub units on the way to earth or sediment just
deposited/settles on meteorite.
3.3AminoAcids and Polymerization
1. Monomer- a sub unit of a polymer i.e. amino acids, simple sugars, nucleotides
2. Polymer- large molecule composed of several subunits i.e. proteins, carbohydrates, lipids, nucleic acids
3. Macromolecules- large organic polymers
4. Polymerization- process of bringing together monomers
- Proteins (i.e. bacteria) composed of 21 amino acids that have a common backbone structure
- Figure 3.2.a. – compare to ionized form in figure 3.2.b.
o Central carbon atom- attaches to an amino group, carboxyl group, a hydrogen, and a variable side
chain( R group)
o Presence of amino group and carboxyl group important in solution. In water, the amino group acts
as a base gaining a hydrogen (NH +) and carboxyl group loses hydrogen-forming COO-. Charges
on functional groups important to help amino acids stay in solution and interact with one another
and to add to their chemical activity.
- Nature of the side chains- R groups are variable and create the 21 different amino acids because each one
has a different R-group
o R-groups can be single hydrogen or carbon atoms linked in a ring structure.
o 3 main types of amino acids- polar, non-polar, electrically charged
o Non-polar- no electrically charged or electronegative e atoms, so cannot form hydrogen bonds in
water (hydrophobic). Hydrophobic chains coalesce in water.
o Polar molecules/electrically charged side chains- interact readily with water by forming hydrogen
bonds and can hydrophilic amino acids dissolve easily in water.
Examination question: look at figure 3.3 and distinguish between polar, non-polar, electrically charged by looking
at structure of amino acid
Optical Isomers - isomers- molecules with the same molecular formula, but have different structures
- 3 types of isomers:
o Structural isomers- have the same atoms but differ in the order in which they covalently bonded
to atoms are attached e.g. figure a on pg 51
o Geometric Isomers- have the same atoms but differ in the arrangement of atoms or groups on
either side of a double bond or ring structure i.e. figure b. on pg 51
o Optical isomers- have the same atoms but differ in the arrangement of atoms or groups around a
carbon atom that had 4 different groups attached i.e. figure c on pg. 51
Condensation and Dehydration Synthesis Reactions
- Condensation reactions (monomer in, water out)- also called dehydration synthesis reactions
o Monomers polymerize through condensation reactions where the newly formed bond results in a
loss of water
- Hydrolysis reactions (monomer out, water in)- breaks polymers by adding a water molecule. Water
molecule reacts with bond linking monomer and separating one monomer from polymer chain.
- Figure 3.6
- Amino acids when a bo