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Lecture 1

Biology 1002B Lecture Notes - Lecture 1: Blastomere, Thymine, Start Codon

Course Code
BIOL 1002B
Tom Haffie

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1.1 The Physical Nature of Light (p. 2-4)
2 functions of light: source of energy that directly or indirectly sustains all organisms, AND it
provides organisms with info about the physical world that surrounds them
The green alga Chlamydomonas is an organism that uses
light for both energy and information
o Single-celled photosynthetic eurkaryote
o Found in ponds and lakes
o Each cell contains a single large chloroplast that
harvests light energy and uses it to make nutrient-
rich molecules through the photosynthesis
o Each cell contains a light sensor called an
“eyespot” that allows individual cells to gather
information about the location and intensity of a
light source
Regardless of whether the light is used a source of energy or as a source of information, both
uses require light energy to be captured by the organism
What is light?
o By converting hydrogen into helium at an immensely high rate, the sun converts over 4
million tonnes of matter into energy every second
This energy is given off as electromagnetic radiation, which travels in the form
of a wave at the speed of light
Different types of ER are distinguished by their wavelength
o Light is defined as the portion of the electromagnetic spectrum that humans can detect
with their eyes (visible light 400 to 700 nm)
o Light both behaves as a wave that travels through space, AND a stream of energy
particles called photons (particle-wave duality)
o The longer the wavelength, the lower the energy of the photons it contains
Light interacts with matter
o Even though light has no mass, it can still interact with matter and cause change
This change is what allows the energy of light to be used by living things
o When a photon of light hits an object, the photon has 3 possible fates:
It can be reflected off the object
It can be transmitted through the object
It can be absorbed by the object
o Absorption must take place for the light to be used as a source of energy or information
o Absorption of light occurs when the energy of the photon is transferred to an electron
within a molecule
This excites the electron, moving it from its ground state to a higher-energy
level that is referred to as an excited state
o A photon can be absorbed by an electron of a molecule ONLY if the photon’s energy
equals the energy difference between the electron’s ground state and an excited state
If the energies don’t match, then the photon is transmitted through the
molecule or reflected
It is the excited-state electron that represents the source of energy required for
processes such as photosynthesis and vision
o Pigments are a class of molecules that are very efficient at absorbing photons

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E.g. chlorophyll a, retinal, indigo
Pigments are all very structurally different from each other, yet they all share a
common feature critical to light absorption: a region where carbon atoms are
covalently bonded to each other with alternating single and double bonds
This bonding arrangement is called a conjucated system, and it results
in the delocalization of electrons
None of these electrons are closely associated with a particular atom or
involved in bonding and are thus able to interact with a photon of light
Pigments absorb light and distinctly different wavelengths
This is because they differ in the number of excited states available to
the excitable electrons
While some pigments can absorb only blue photons because they have
only one high-energy state, others can absorb two or more different
wavelengths because they have two or more excited states
Pigment absorption is intimately related to the concept of colour
A pigment’s colour is the result of photons of light that it does NOT
Instead of being absorbed, these photons are reflected off the pigment
or transmitted through the pigment to reach your eyes
Proteins (p. F-29-35)
Proteins are polymers of amino acids and most diverse group of biological macromolecules
Generalized structure of an amino acid has a central atom attached to an amino group, a
carboxyl group and a hydrogen atom
The remaining bond of the central atom is to 1 of 20 different side groups (R group), which
ranges from a single hydrogen atom to complex carbon chains and rings
o Differences in side groups give amino acids their individual properties
o 20 amino acids are categorized into different groups:
Uncharged polar
Negatively charged (acidic) polar
Positively charged (basic) polar
Covalent bonds link amino acids into linear chains called polypeptides
o The link between each pair of amino acids is called a peptide bond and is formed by a
dehydration synthesis reaction between the NH2 group of one amino acid and the
COOH group of a second
o In cells, amino acids are added only to the COOH end of the growing peptide strand
o A protein is a polypeptide that has folded into the specific 3-D shape that is required for
most proteins to be functional
o One end of the chain has an N-terminus, and the other end has a C-terminus

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4 Levels of Protein Structure:
o Primary structure particular & unique sequence of amino acids forming a polypeptide
Determined by the nucleotide sequence of the coding region of the protein’s
corresponding gene
o Secondary structure twists and turns of the amino acid chain
Based on hydrogen bonds between atoms of the backbone
Form between the hydrogen atom attached to the nitrogen of the
backbone and the oxygen attached to one of the carbon atoms of the
Alpha helix and beta sheet are two highly regular structures
A third, less regular arrangement is a random coil or loops
Alpha helix coil shape formed when hydrogen bonds form between every N-
H group of the backbone and the C=O group of the amino acid
Beta sheet side-by-side alignment of beta strands, formed by hydrogen
bonds between atoms of each strand
o Tertiary structure folding of the amino acid chain, with its secondary structures, into
the overall 3-D shape of a protein
4 major interactions between R groups that occur are: ionic bonds, hydrogen
bonds, hydrophobic interactions and disulfide bridges
Protein undergoes conformational changes
o Quaternary structure optional structure that refers to the arrangement of polypeptide
chains in a protein that is formed from more than one chain
Cofactors/Prosthetic groups
o Non-protein chemical compounds that are bound to a protein and required for the
protein to function
o Can be either organic or inorganic molecules
o Vitamins are essential to life because they act as cofactors
o E.g. heme in hemoglobin is a cofactor as it is responsible for binding molecules of
In many proteins, folding of the polypeptide chains produces distinct, large structural
subdivisions called domains
o One domain of a protein is often connected to another by a segment of random coil
o The random coil is flexible and allows domains to move with respect to one another
o Different domains of a protein are both structurally and functionally distinct
Proteins (p. F-29-35)
We can detect energy only through its ability to do work move objects against opposing
forces, such as friction, gravity, or pressure, or to push chemical reactions toward completion
Energy the capacity to do work
Energy exists in different forms and states
Different forms of energy includes heat, chemical, electrical and mechanical
These forms can be converted or transformed readily from one form to another
All forms are categorized into one of two different types:
KINETIC energy energy possessed by an object because it is in motion
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