Download ECA Biochemistry Gizmos

Science 10 – Biochem
Last time we focused on
Vocab, this time on
function within the system
Classifying Matter
• Substance v Mixture
• Elements v Compounds
• Homogeneous v Heterogeneous
Chemistry of Life
Element - any substance that is comprised of
one type of atom and cannot be broken
down into another substance.
Examples
Hydrogen
Oxygen
Carbon
Gold
Silver
http://facstaff.gpc.edu/~pgore/PhysicalScience/periodic-table.gif
Chemical bonds
http://kentsimmons.uwinnipeg.ca/cm1504/Image57.gif
• Ionic bonds - formed through the transfer of
electrons between two atoms. The bond is due to
the attraction of oppositely charged ions (atoms
with a negative or positive charge).
Chemical bonds
http://cache.eb.com/eb/image?id=96904&rendTypeId=4
• Covalent bonds - formed through the sharing of
atoms between atoms.
Matter Flow Chart
MATTER
yes
MIXTURE
yes
Is the composition
uniform?
Homogeneous
Mixture
(solution)
Colloids
no
Can it be physically
separated?
PURE SUBSTANCE
no
Heterogeneous
Mixture
yes
Can it be chemically
decomposed?
Compound
Suspensions
Element
no
Water is the solvent of
life
Chemical elements and
water
• Elements of life (most common)
o Carbon, hydrogen, oxygen
• Other necessary elements & function
o
o
o
o
o
Nitrogen (amino acids),
Calcium (bones, teeth),
Phosphorous (ATP, DNA),
Iron (hemoglobin),
Sodium (nerve transmision)
Like no other common substance, water exists
in nature in all three physical states:
– as a solid
– as a liquid
– as a gas
Properties of water
• Transparency:
o Light can easily pass through
o Reach inside cytoplasm (water) to
• chloroplast, retina
o Reach organisms in water
• Cohesion:
o Water molecules stick together (surface)
• Water can be pulled up trees
• Small animals can live on water surface (mosquito)
• Solvent Properties
• Thermal Properties
Properties of Water
Hydrophobic
http://asia.cnet.com/i/r/2006/dc/39304504/pearls_sc.jpg
Hydrophilic
http://dl.clackamas.edu/ch104-02/images/104vol07.jpg
• Cohesion - attraction between molecules of the same
substance.
• Adhesion - attraction between molecules of different
substances.
Cohesion:
Water molecules stick together
surface
tension
Polarity
• Polar: Uneven distribution of
charge within the molecule.
Example: H2O (water)
• Non-polar: Even distribution of
charge within the molecule.
Example: BF3 (boron trifluoride)
• Like dissolves like
o Something polar dissolves
something polar
o Something nonpolar dissolves
something nonpolar
Biochemistry
• The chemistry of Life
• Bio-molecules
o Proteins
o Saccharides
o Carbohydrates
o Lipids (fats, membranes…)
o Nucleic Acids (DNA…)
Organic Compounds
• Contain carbon & found in living organisms
o Inorganic Carbon compounds: CO2,
o Many inorganics found in living organisms
• Iron in blood
Macromolecules - large molecules formed
through the joining of many monomers (small
molecular units) into polymers (larger molecules).
We will be studying 4
important
macromolecules:
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids.
http://hsc.csu.edu.au/senior_science/option
s/polymers/2973/images/Fig_9513.jpg
Carbohydrates (saccharides) - sugars which
contain C, H and O and are the main energy
source for all living things (some organisms also
use carbohydrates for structural purposes).
• Monosaccharides - single sugar molecules (glucose, galactose).
• Disaccharides - carbohydrates composed of two sugar molecules
(lactose).
• Polysaccharides - large carbohydrates composed of many
monosaccharide monomers (starch, cellulose, glycogen).
Carbohydrates Gizmo
• Tutorial on Carbohydrates.
http://www.wisconline.com/objects/index_tj.asp?objID=AP13104
The building blocks!
1
1+1=2
2+2=4, etc..
http://chemistry2.csudh.edu/rpendarvis/1feb23.gif
Condensation (Dehydration) Reaction: monomers
form chains
o Remove water to form bonds
o Protein synthesis
o Fatty acid synthesis
Building Bonds!!
1
1
1
1
Short polymer
Unlinked monomer
Removal of
water molecule
1
Figure 3.3A
1
1
Longer polymer
1
• Hydrolysis - reverse process of condensation
polymers are broken down to monomers
o Using water
Breaking Bonds!!
1
1
1
1
Addition of
water molecule
1
1
1
1
Condensation
(dehydration) and
Hydrolysis Gizmo
• Animation on Condensation & Hydrolysis reactions.
http://www.tvdsb.on.ca/westmin/science/sbioac/b
iochem/condense.htm
Functions of Lipids (fats)
A group of organic compounds, including fats
oils, and waxes that are soluble insoluble in
water.
Energy storage:
Insulation:
Protection:
Membranes (phospholipids):
Glycerol & fatty acid
Structure of Triglycerides
Building Bonds = Condensation or Dehydrolysis
Saturated v. Unsaturated
Which is better for you?
In general….
• Unsaturated are better for you than Saturated
o Saturated fats clog arteries and raise bad cholesterol (LDL)
o Synthetic unsaturated fats are not necessarily better
• Contain artificially hydrolyzed bonds that are ineffective
• Liquids are better for you than solids
o If it is a solid at room temperature it is most likely not good
for you.
o Fats (lipids) are necessary – omega-3-fatty-acids like fish
and flax seed oil are very good for you, reducing risk of
heart disease and increase immune system
Lipid Gizmo
• Tutorial on lipids. Info about saturated and
unsaturated fatty acids you need. http://www.wisconline.com/objects/index_tj.asp?objID=AP13204
Enzymes
• Enzyme
o Protein
o Biological catalyst
o Example: amylase
• Active Site
o Location where substrate (reactant) binds
Proteins - macromolecules that contain N, H, O and C. Are
comprised of amino acid (the order and combination of these
amino acids determines the role of the protein) subunits.
Types of proteins:
• Enzymes - carry out the
chemical reactions in the
organism (lactase, DNA
helicase, catalase).
• Structural Proteins - aid in
building muscles, bones and
other components of the
organism (keratin, collagen).
• Functional Proteins - assist in
organism’s daily functioning
such as messengers
(hemoglobin, insulin), defense or
transport.
http://www.tikirobot.net/wp/wpcontent/uploads/2007/11/0143.gif
Proteins have levels of organization.
Proteins can be denatured.
Structure of Proteins
• Primary – sequence of amino acids
Chain of
1 GLYILE -VAL- GLU -GLN -CYS • Secondary – the folding
the chain
of amino acids into a helix or a
pleated sheet
• Tertiary – a higher level of folding in
which the helices and sheets of the
secondary structure fold upon
themselves
• Quaternary – polypeptide chains are
bound together usually by hydrogen
bonds
Amino Acids = the building
blocks of proteins
Protein Synthesis
• amino acids link
o dipeptides
o polypeptide chains (Proteins)
• The bonds are called peptide bonds
Dehydration
synthesis
Figure 3.13
Protein Gizmo
• Tutorial on Proteins (contains more info on
structure than we need right now but the idea of
denaturation is important when we talk about
Enzymes - which are proteins.) http://www.wisconline.com/objects/index_tj.asp?objID=AP13304
Enzymes – Lock and Key
Lock and Key Model
(enzyme-substrate specificity)
Effects of variables on
enzymes
• Temperature
• pH
Enzyme Gizmos
• What is an enzyme:
http://www.northland.cc.mn.us/biology/Biology1111/animations/
enzyme.html
• How an enzyme works: http://highered.mcgrawhill.com/sites/0072495855/student_view0/chapter2/animation__h
ow_enzymes_work.html
• Enzyme Specificity:
http://www.wiley.com/legacy/college/boyer/0470003790/animati
ons/enzyme_binding/enzyme_binding.htm
• Enzymes:
http://www.bbc.co.uk/schools/gcsebitesize/science/add_aqa/en
zymes/acidsbasesact.shtml
Nucleic Acids - macromolecules that contain H, O, N, C and P.
The 2 kinds of nucleic acids are DNA and RNA which store and
transmit genetic information (the “blueprint” to make you).
http://www.scfbio-iitd.res.in/image/nucleotide.jpg
http://faculty.uca.edu/~johnc/RNA%20DNA.gif
• Comprised of nucleotide (5-C sugar, phosphate group
and nitrogenous base) monomers.
Review Sites
• Biochemistry: http://www.scool.co.uk/alevel/biology/biological-moleculesand-enzymes.html
• Enzymes: http://www.scool.co.uk/gcse/biology/enzymes.html
• Biochemistry: http://www.scool.co.uk/alevel/biology/biological-moleculesand-enzymes.html
• Enzymes:
http://www.bbc.co.uk/schools/gcsebitesize/scienc
e/add_aqa/enzymes/