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Concepts of Biology:
Chemistry of Life
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Concepts of Biology
Chapter 2:Chemistry of Life
•
Foods such as bread, fruit, and cheese are rich sources of biological macromolecules.
(credit: modification of work by Bengt Nyman)
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Concepts of Biology
Chapter 2:Chemistry of Life
• Students are often surprised that we need to go
down to the atomic level in this Biology course.
Organisms depend on the properties of
molecules and the shape of those molecules and
the property and shape depends on the nature of
the atoms and the way that they are bonded.
• There are a few specific aspects of atoms and
bonds that you will need to be familiar with.
These concepts will come up again when we talk
of enzymes, genes, nutrition, etc.
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Concepts of Biology
Chapter 2:Chemistry of Life
•
Atoms are made up of protons and neutrons located within the nucleus, and electrons
surrounding the nucleus.
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Concepts of Biology
Chapter 2:Chemistry of Life
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Concepts of Biology
Chapter 2:Chemistry of Life
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Concepts of Biology
Chapter 2:Chemistry of Life
• Protons define the element
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Concepts of Biology
Chapter 2:Chemistry of Life
•
Arranged in columns and rows based on the characteristics of the elements, the periodic
table provides key information about the elements and how they might interact with each
other to form molecules. Most periodic tables provide a key or legend to the information
they contain.
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Concepts of Biology
Chapter 2:Chemistry of Life
•
The age of remains that contain carbon and are less than about 50,000 years old, such as
this pygmy mammoth, can be determined using carbon dating. (credit: Bill Faulkner/ NPS)
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Concepts of Biology
Chapter 2:Chemistry of Life
• Whatever is living takes in C. A tiny
proportion is always C14. The ratio of C12 to
C14 shifts over time. Half-life of 5700 years.
• You are what you eat.
• Dead things don’t eat, therefore the clocks
start ticking.
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Concepts of Biology
Chapter 2:Chemistry of Life
CONCEPT IN ACTION VIDEO
• http://phet.colorado.edu/en/simulation/isot
opes-and-atomic-mass
• To learn more about atoms and isotopes, and
how you can tell one isotope from another,
visit the site (link above) and run the
simulation.
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Concepts of Biology
Chapter 2:Chemistry of Life
Orbitals and Bonding
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Concepts of Biology
Chapter 2:Chemistry of Life
•
Elements tend to fill their outermost shells with electrons. To do this, they can either
donate or accept electrons from other elements.
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Concepts of Biology
Chapter 2:Chemistry of Life
• Ionic bond – giving or taking electrons to fill
outer shells
• This giving and taking of electrons results in a
charge on the element and the charge
differential creates attraction.
• Know NaCl as the example
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Concepts of Biology
Chapter 2:Chemistry of Life
• A covalent bond is a sharing of a pair of elements
to fill their outer shells.
• Electrons can be shared equally when the atoms
are identical (O-O, C-C), and also in the C-H bond.
This is a nonpolar covalent bond. Equal sharing
creates a nonpolar bond.
• Electrons can be shared unequally, as is the case
with H-O-H (water), and this is a polar covalent
bond.
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Concepts of Biology
Chapter 2:Chemistry of Life
•
The water molecule (left) depicts a polar bond with a slightly positive charge on the
hydrogen atoms and a slightly negative charge on the oxygen. Examples of nonpolar bonds
include methane (middle) and oxygen (right).
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Concepts of Biology
Chapter 2:Chemistry of Life
Oxygen
• Oxygen exerts a powerful pull on electrons, hence the
unequal sharing of electrons.
• This property makes it both essential and deadly.
Essential in cellular respiration as you will learn later –
to create ATP to sustain order and life. But deadly in
its destruction of key molecules.
• Skin test – collagen. Oxygen and aging.
• Dog with a cloudy eye.
• Beauty products are antioxidants – vitamins, drinks
etc.
• (Catalase Lab) – link to products catalase
pseudoscience link
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Concepts of Biology
Chapter 2:Chemistry of Life
•
Hydrogen bonds form between slightly positive (δ+) and slightly negative (δ–) charges of
polar covalent molecules, such as water.
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Concepts of Biology
Chapter 2:Chemistry of Life
• The partial charges across a polar bond give
rise to hydrogen bonding which gives water
its peculiar properties, like adhesion,
cohesion.
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Concepts of Biology
Chapter 2:Chemistry of Life
• Hydrophilic
• Hydrophobic
• Lipids are defined by being hydrophobic.
• Lipids are hydrocarbons made up of nonpolar
covalent bonds.
• Hence, oil and water do not mix.
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Concepts of Biology
Chapter 2:Chemistry of Life
•
As this macroscopic image of oil and water show, oil is a nonpolar compound and, hence,
will not dissolve in water. Oil and water do not mix. (credit: Gautam Dogra)
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Concepts of Biology
Chapter 2:Chemistry of Life
•
(a) The lattice structure of ice makes it less dense than the freely flowing molecules of
liquid water. Ice’s lower density enables it to (b) float on water. (credit a: modification of
work by Jane Whitney; credit b: modification of work by Carlos Ponte)
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Concepts of Biology
Chapter 2:Chemistry of Life
Water
• Water is the strangest substance. You can’t
name another in which the solid floats on the
liquid, that has a surface tension, and that
dramatically shapes climate and life on earth.
• Water is most dense at 4 degrees C.
• Releases energy (and heat) and molecules
move apart upon freezing.
• Problem – plants on a balcony.
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Concepts of Biology
Chapter 2:Chemistry of Life
CONCEPT IN ACTION
• http://www.janewhitney.com/Ice_Movie_Re
sources/ice_movie.mov
• View the 3-D animation of the structure of an
ice lattice. (credit: image created by Jane
Whitney using Visual Molecular Dynamics
(VMD) software1)
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Concepts of Biology
Chapter 2:Chemistry of Life
•
When table salt (NaCl) is mixed in water, spheres of hydration form around the ions.
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Concepts of Biology
Chapter 2:Chemistry of Life
Water
• Life is mostly water and all charged and partially
charged molecules are soluble in water.
• Since water has positive and negative charges it
can create a shell of water around charged
entities.
• That is water happens when you put salt in water
– it disappears and is said to be soluble.
• This will be an important point when we discuss
osmosis.
• Would there be a limit to how much salt you
could dissolve in water – why or why not?
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Concepts of Biology
Chapter 2:Chemistry of Life
• Can you explain why water does not act as a
solvent for fats?
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Concepts of Biology
Chapter 2:Chemistry of Life
•
The weight of a needle on top of water pulls the surface tension downward; at the same
time, the surface tension of the water is pulling it up, suspending the needle on the surface
of the water and keeping it from sinking. Notice the indentation in the water around the
needle. (credit: Cory Zanker)
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Concepts of Biology
Chapter 2:Chemistry of Life
• Trillions of weak hydrogen bonds gives structure to
water.
• This allows a needle to float, pulls water from roots to
a treetop, makes water hard to heat and slow to cool.
• What is temperature and what does temperature
measure?
• Why is water hard to heat compared to other
substances?
• Why is Victoria’s climate better than Edmonton’s?
• How specifically does sweating cool you?
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Concepts of Biology
Chapter 2:Chemistry of Life
•
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The pH scale measures the amount of
hydrogen ions (H+) in a substance.
(credit: modification of work by Edward
Stevens)
Concepts of Biology
Chapter 2:Chemistry of Life
pH
• Normal blood pH is 7.38.
• Changes +/- 0.5 pH would be fatal.
• Homeostatic mechanisms, including respiration
rate and buffers, keep pH in a tolerable range.
• The pH scale is orders of magnitude – like the
Richter scale.
• Acids add H+ (protons); bases add OH-.
• Buffers can add or eliminate H+ to stabilize pH.
• Bicarbonate equation here (double arrows)
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Concepts of Biology
Chapter 2:Chemistry of Life
•
Carbon can form four covalent bonds to create an organic molecule. The simplest carbon
molecule is methane (CH4), depicted here.
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Concepts of Biology
Chapter 2:Chemistry of Life
Carbon
• All life is carbon-based.
• Carbon is fundamental because of the vast
variety of shapes that the molecules made
from it can assume.
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Concepts of Biology
Chapter 2:Chemistry of Life
Biological molecules
• All life is made of these 4 categories of
molecules:
• Carbohydrates
• Proteins
• Lipids
• Nucleic Acids
• All fulfill similar functions in all organisms.
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Concepts of Biology
Chapter 2:Chemistry of Life
•
These examples show three molecules
(found in living organisms) that contain
carbon atoms bonded in various ways to
other carbon atoms and the atoms of
other elements.
(a) This molecule of stearic acid has a long
chain of carbon atoms.
(b) Glycine, a component of proteins,
contains carbon, nitrogen, oxygen, and
hydrogen atoms.
(c) Glucose, a sugar, has a ring of carbon
atoms and one oxygen atom.
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Concepts of Biology
Chapter 2:Chemistry of Life
Carbohydrates
•
•
•
•
Built on the (CH2O)n formula.
C6H12O6
They function as energy sources.
They also have structural functions, play a
role in cellular identification (blood type).
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Concepts of Biology
Chapter 2:Chemistry of Life
•
Glucose, galactose, and fructose are isomeric monosaccharides, meaning that they have
the same chemical formula but slightly different structures.
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Concepts of Biology
Chapter 2:Chemistry of Life
• Sugars are soluble because they are more
than hydrocarbons – the OH groups make for
partial charges.
• Which has more calories per gram? Frosted
Flakes or Special K?
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Concepts of Biology
Chapter 2:Chemistry of Life
Disaccharides
• Sucrose and lactose are common
disaccharides.
• (Lactase, lactose, lactose intolerance)
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Concepts of Biology
Chapter 2:Chemistry of Life
•
Although their structures and functions differ, all polysaccharide carbohydrates are made
up of monosaccharides and have the chemical formula (CH2O)n.
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Concepts of Biology
Chapter 2:Chemistry of Life
• Starch vs. Cellulose
• (enzymes, termites, why can’t we eat
cellulose for energy?)
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Concepts of Biology
Chapter 2:Chemistry of Life
•
Hydrophobic lipids in the fur of aquatic mammals, such as this river otter, protect them
from the elements. (credit: Ken Bosma)
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Concepts of Biology
Chapter 2:Chemistry of Life
Lipids
• Diverse non-polymeric molecules common
feature is being hydrophobic – fats, earwax,
steroid hormones…
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Concepts of Biology
Chapter 2:Chemistry of Life
•
Lipids include fats, such as triglycerides, which are made up of fatty acids and glycerol,
phospholipids, and steroids.
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Concepts of Biology
Chapter 2:Chemistry of Life
• Why are there more calories in fats than
proteins or carbohydrates?
• Saturated and unsaturated fats and
behaviour at RT.
• Hydrogenation of vegetable oils in processed
foods.
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Concepts of Biology
Chapter 2:Chemistry of Life
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Concepts of Biology
Chapter 2:Chemistry of Life
Phospholipids
• This shape is crucial in their functioning in
cell membrane bilayers.
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Concepts of Biology
Chapter 2:Chemistry of Life
•
During the hydrogenation process, the orientation around the double bonds is changed,
making a trans-fat from a cis-fat. This changes the chemical properties of the molecule.
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Concepts of Biology
Chapter 2:Chemistry of Life
• Trans fats – we don’t have the enzyme
machinery to break them down.
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Concepts of Biology
Chapter 2:Chemistry of Life
CONCEPT IN ACTION
• https://www.wisc-online.com/learn/naturalscience/life-science/ap13204/biomolecules-the-lipids
• For an additional perspective on lipids,
explore “Biomolecules: The Lipids” through
the interactive animation (link above).
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Concepts of Biology
Chapter 2:Chemistry of Life
Proteins
• You are expected to know the basic structure
of an amino acid.
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Concepts of Biology
Chapter 2:Chemistry of Life
Proteins
• Proteins have the most diverse range of
functions, in part from their being 20
different amino acids as building blocks and
the diversity of shapes such polymers can
assume.
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Concepts of Biology
Chapter 2:Chemistry of Life
•
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Amino acids are made up of a central
carbon bonded to an amino group (–
NH2), a carboxyl group (–COOH), and a
hydrogen atom. The central carbon’s
fourth bond varies among the different
amino acids, as seen in these examples of
alanine, valine, lysine, and aspartic acid.
Concepts of Biology
Chapter 2:Chemistry of Life
Protein functions
•
•
•
•
•
•
Transport
Enzymes
Structural
Energy storage
Immunoglobulin
Etc.
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Concepts of Biology
Chapter 2:Chemistry of Life
•
The four levels of protein structure can
be observed in these illustrations.
(credit: modification of work by National
Human Genome Research Institute)
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Concepts of Biology
Chapter 2:Chemistry of Life
• Sickle cell anemia as an example of mutation
effecting protein structure and function.
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Concepts of Biology
Chapter 2:Chemistry of Life
• Temp, pH – why are they closely regulated?
• Protein tertiary structure is fragile.
• Environmental induced protein shape
changes is called denaturation and is
irreversible.
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Concepts of Biology
Chapter 2:Chemistry of Life
Gene protein connection
• Genes code for the primary sequence of
proteins.
• Mutations introduce alternative amino acids
that disrupt tertiary structure and function.
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Concepts of Biology
Chapter 2:Chemistry of Life
CONCEPT IN ACTION
• https://www.wisc-online.com/learn/naturalscience/life-science/ap13304/biomolecules-the-proteins
• For an additional perspective on proteins,
explore “Biomolecules: The Proteins”
through the interactive animation (link
above).
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Creative Commons Attribution 4.0 International License (CC-BY).
Concepts of Biology
Chapter 2:Chemistry of Life
Nucleic acids
• DNA nucleotides – A,T,G & C
• Nucleotides have 3 components
• All cells use DNA as the genetic material
(with the same genetic code)
• RNA acts as messenger for the reading of
genes and their translation into amino acid
entities.
• RNA nucleotides – A, U, G & C
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Concepts of Biology
Chapter 2:Chemistry of Life
•
A nucleotide is made up of three components: a nitrogenous base, a pentose sugar, and a
phosphate group.
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Concepts of Biology
Chapter 2:Chemistry of Life
•
The double-helix model shows DNA as two parallel strands of intertwining molecules.
(credit: Jerome Walker, Dennis Myts)
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Concepts of Biology
Chapter 2:Chemistry of Life
LTS activity
http://outreach.letstalkscience.ca/component/
zoo/item/diy-activities.html?Itemid=652
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Concepts of Biology
Chapter 2:Chemistry of Life