Protein structure and function STRUCTURE RELATES TO FUNCTION
Subunit of a polymer FIND REAL WORLD EXAMPLES FOR THE PROTEIN
Large molecule composed of several connected subunits
Large organic polymers
Stanley millers spark- discharge experiment (figure 3.1)
a large flask containing methane, ammonia and hydrogen (these have high free energy), was connected to a smaller flask
containing 200 mL of liquid water (meant to act as a small ocean)
miller boiled the water constantly to connect the mini atmosphere with the mini ocean. This added water vapour to the
as the vapour cooled and condensed, it flowed back to the smaller flask, where it boiled again. this way, the vapour
circulated continuously through the system.
This was important – if the molecules in the atmosphere reacted with eachother, the “rain” would carry them to the ocean,
forming a simulated version of the prebiotic soup (a hypothetical solution of sugars, AAs, nitrogenous bases, and other
building blocks of larger molecules that may have formed in shallow waters or deep ocean vents of ancient Earth and given
rise to larger biological molecules)
NOTE: even at 100C, the starting molecules are stable and therefore do not undergo spontaneous chemical reactions
Miller sent electrical discharges across the electrodes he’d inserted into the atmosphere
These mini lightening bolts added a crucial element to the reaction mix – pulses of intense electrical energy
After a day of boiling and sparking boiling flask solution turned pink
After a week deep red and cloudy
When he analyzed the ocean, he found large quantities of hydrogen cyanide (HCN) and formaldehyde (H2CO). key
components in chemical evolution b/c when reacted, they lead to synthesis of more complex organic molecules
The complex molecules were found in the ocean AMINOACID (building blocks of protein)
purple box things in textbook titled experiments are VERY important
Question: Can simple molecules and kinetic energy lead to chemical evolution?
Hypothesis: if kinetic energy is added to a mix of simple molecules with high free energy, reactions will occur that produce
more complex molecules, perhaps including some with C-C bonds
Null hypothesis: Chemical evolution will not occur, even with an input of energy
How things change over time
Where do these building blocks come from?
Why was his experiment soo significant? Stanley Miller’s experiment simulated the early earth conditions
His results and those of other subsequent researchers supported chemical evolution
3.2 AMINOACIDS AND POLYMERIZATION
Other alternative perspectives regarding chemical evolution. HOW DID WE GET THE SUBUNITS ON EARTH? ALL OF THESE
Hydrothermal Vents – collecting samples here have subunits
Murchison Meteorite – landed inAustralia. The outer surface had diff types of carbohydrates and diff types of subunits associated with
AA. Meteorite picked up macromolecules as it was coming through the atmosphere.
SCIENCE ONLYTESTS THINGS. THEY NEVER PROOVE THINGS
The structure ofAmino Acids
the cells in your body produce tens of thousands of distinct proteins. Most of these molecules are composed od just 20 diff
building blocks called AMINOACIDS. All 20 amino acids have a common structure
central carbon atom that can form 4 bonds
NH2 the amino functional group
COOH the carboxyl functional group
H hydrogen atom
An “R-group” an atom or group of atoms called a side chain
In water NH2 act as base and attracts a proton, making it NH3+
In water COOH is acidic because the oxygen is VERY electronegative and loses an electron, making it COO-
The charges helpAAstay in solution, where they can interact with one another and with other solutes
The charges also alter amino acid chemical reactivity
The nature of side chains
The properties ofAAs vary because R groups vary
functional groups affect reactivity
o several of the side chains found inAAs contain the carboxyl (COOH), sulphydryl (SH), hydroxyl (OH)or amino
(HN2) functional groups. Under the right conditions, these functional groups can participate in chemical reactions
o Ex. AAs with sulfur in side chains can form bonds that help link diff parts of large proteins
o However, side chain with just C and H atoms rarely participate in chemical reactions.As a result, the chemical
behavior of theseAAs depends primarily of their size and shape rather than reactivity
The polarity of side chains affect solubility
o 3 categories (polar, nonpolar and electrically charged)
o AAs with nonpolar side chains lack charged or electronegative atoms capable of forming hydrogen bonding with
o AAs with polar or charged side chains interact readily with water (hydrophilic) How doAmino Acids link to form protein?
Amolecular subunit such as an AAacid, a nucleotide, or a sugar is called a monomer (“one part”). When monomers bond
together polymer (“many parts”) formed. The process of linking monomers together is called polymerization. Thus,AAs
polymerize to form proteins.
Aprotein is a macromolecule (large molecule made up of smaller molecules). Protein is a polymer that consists of linked
The theory of chemical evolution states that monomers in the prebiotic soup polymerized to form proteins and other
macromolecules this is a difficult step because monomers do not spontaneously self assemble into macromolecules.
According to the second law of thermodynamics, complex and highly organized molecules are not expected to form
spontaneously from simpler constituents because polymerization organizes the molecules involed into a more complex,
ordered structure. polymerizations decreases the disorcer, or entropy, of the molecules involved.
Also, polymers are energetically much less stable than their component monomers
POLYMERIZATION REACTIONS ARE ENDERGONIC AND NONSPONTANEOUS
> Could polymerization occur in the energy rich environment of early earth?
A) make something larger condensation or dehydration synthesis
a. monomer in and water out
B) make is smaller hydrolysis
a. water in and monomer out
- in a solution such as the prebiotic soup, hydrolysis dominates because it is exergonic increases entropy and favourable
the C – N bond that results from condensation reaction is called a peptide bond.
Because water is lost in the condensation reaction, the carboxyl group of theAAis converted to a carbonyl functional group
in the polymer
Peptide bonds are unusually stable because the electrons involved are partially shared between the peptide bond and the
neighbouring carbonyl functional group The degree of electron sharing is great enough that peptide bonds actually have some of the characteristics of a double bond
peptide bond is planar
POLYPEPTIDE: when amino acids are linked by peptide bonds into a chain, theAAs are referred to as residues and the
resulting molecule is called a polypeptide.
FIG 3.7 shows how the chain of peptide bonds in a polypeptide gives the molecule a structural framework, or a “back-bone”
o polypeptide chain
There are 3 key points to note about the peptide-bonded backbone of a polypeptide:
o R-group orientation: the side chains present in each residue extend out from the backbone, making it possible for
them to interact with eachother and with water
o Directionality: there is an amino group (NH3+) on one end of every polypeptide chain and a carboxyl group (COO-)
on the other. By convention, biologists always write amino acid sequences in the same direction
End of sequence with free amino group is placed on left N-terminus or amino terminus
End with free carboxyl group is placed on right C-terminus or carboxy terminus
AAs in the chain are always numbered starting from N-terminus because that is the start of the chain when
proteins are synthesized in cells
o Flexibility: peptide bond is double bond so cannot rotate. The single bonds on either side of the peptide bond can
rotate the structure as a whole is flexible.
3.3 PROTEINS ARE THE MOST VERSATILE LARGE MOLECULES IN CELLS
- proteins perform more types of cell functions than any other type of molecule does. It makes sense to hypothesize that life began
with proteins, simply because proteins are so vital to the life of today’s cells.
- Hemoglobin – carries oxygen from your lungs to cells throughout body. Each RBC contains about 300 million copies of this protein.
- Each RBC also has thousands of copies of carbonic anhydrase which is important for moving CO2 from cells back to the lungs,
where it can be breathed out
Proteins are crucial to most tasks required for cells to exist. These tasks include:
Catalysis: many proteins speed up chemical reactions enzyme. Carbonic anhydrase is a catalyst. Most chemical reactions
that make life possible