Transcript Introduction to Molecular forces and Macromolecules

Introduction to Molecular forces
and Macromolecules
Announcements
•There will be a quiz in next lab. Session. Like
always, it will cover materials from the previous
lab and from upcoming lab.
• Next lab. is cell biology,
• Instead of the BLC project for this lab, I’m giving
the choice to write a report on amino acids and
nucleotides. However, you may choose to do the
project and in all cases it is a total of 12 points
Today
atoms and how they behave
chemical bonds
biological macromolecules and their building
blocks.
in class exercises
BLC project
Atoms
-smallest part of any element
-made up of a positively charged central nucleus
surrounded by negatively charged cloud of
electrons.
-the nucleus contains protons (positively charged)
and neutrons (electrically neutral).
-number of protons equal the number of electrons, so
any atom is electrically neutral.
-atoms of the same element but with different
number of neutrons are termed isotopes
Atoms
-electrons are arranged in shells around the nucleus,
with the inner most (1st) able to hold two electrons
and 2nd and 3rd able to hold eight electrons.
-the outer most shell of determines how chemically
an element is active and how
it will behave in chemical
reaction.
…Helium and Neon are
chemically inert
… Carbon, Nitrogen,
oxygen and fluorine
Molecules
-molecule is a collection of atoms that are held
together.
-carbon is a major molecule forming atom (all life
forms contain carbon)
-molecular weight of any molecule is the sum of
the atomic weights of all its atoms.
Chemical bonds
-forces that hold atoms and molecules together
-Intramolecular bonds
1-covalent bond
.electron(s) sharing between two non metallic atoms.
.electron(s) either shared
evenly between the atoms
or not (this create ionic
character).
H2O… OH+
H+
Chemical bonds
2-ionic bond
.attraction for an anion and a cation after an
electron is transferred from
the metal to the non-metal
3-metallic bond
. a sea of electrons
Chemical bonds
Intermolecular bonds
1-hydrogen bonds
.attraction of the partially positive end of one highly
polar molecule for the partially negative end of
another highly polar molecule is called a hydrogen
bond
Chemical bonds
2-van der Waals Forces
.weak attractive forces that hold non-polar
molecules. H2, He, Ne
3-Molecule-Ion Attractions
.a molecule (water) is attracted
to an ion (sodium)
Chemical bonds
4-hydrophobic bond
.Force that bring two non-polar molecules together
when they exist in polar environment.
…oil in water
Experiments
1-hydrogen bonds and surface tension
.water, mineral oil, and ethanol
.fill eppendorf tubes (by submerging into the
beaker) with different types of liquids supplied.
Invert the tubes while still submerged and determine
which one resist pouring out.
2- hydrophobicity (1)
.veg. oil, detergent, water.
.fill petri dish with water and/or detergent and add
drops of oil
Hydrophobicity (2)
Magic sand and/ or ethanol
3- diffusion, temperature, osmosis
.agar plates
.dye (three different molecular weight dyes)
Biological Macromolecules
amino acids
monosaccharides
carbohydrates
proteins
fatty acids
DNA/RNA
nucleotides
lipids
Carbohydrates
-polymers of monosaccharides.
-short term energy storage material
-cell wall in bacteria and plants are complex
carbohydrates.
-they contain C, H, and O
-interaction between carbonyl group (>C=O) and
hydroxyl group (COOH) result in ring structure.
monosaccharides…glucose, fructose
polysaccharides…cellulose, starch, glycogen
Experiment
4- starch and amylases
.use the small Petri dishes to mix starch and
a source of amylases.
.incubate at room temp. for 15 min.
. Test for the presence of monosaccharides using
Benedict’s reagent
Proteins
-composed of one (or more) poly peptide chain.
-each polypeptide chain is a polymer of amino acid
-amino acids are tied together by covalent bond
termed; peptide bond. The reaction leading to
peptide bond formation is termed dehydration
reaction because it exclude a water molecule
-each amino acid has an amino group (NH2) at one
end and a carboxyl group (COOH ) at the other end.
this makes proteins have amino terminal end and
carboxyle terminal end.
-there are 20 a.a. and some of them are essential ones
proteins
-proteins are the architectural and functional unit of
the cell. They are parts of membranes and all
enzymes are proteins in structure.
-the amino acid sequence in any protein is termed
primary structure. This primary structure can fold
on itself forming a secondary structure and this in
turn can fold on itself forming a tertiary structure.
-protein function is dependant on correct folding
of this protein.
Experiment
5-enzymes/ protein folding
. Ready made jell-o (on ice), fruits pieces,
.add a piece of raw or heated fruit (cooled on ice)
onto jello surface.
.examine during next two hours (effect of gelatinase
from plant origin on the jell-O .
Lipids
-they are diverse in their structure, not true polymer
-contain primarily C and H
-hydrophobic
-four major groups
.fats or triglycerides
.phospholipid
.steroids
.trepens
….lipoproteins
Nucleic acids
-these include DNA and RNA
-DNA store the genetic code. The genetic code is
translated into amino acids (proteins).
-RNA store also the genetic code but it has an
enzymatic function (ribozyme catalyze the peptide
bond formation in cell).
-both are polymere of nucleotides. Each nucleotide
contain sugar molecule, 1 phosphate group
attached to carbon # 5 and a nitrogenous base
attached carbon # 2
Nucleic acids
-nitrogenous bases either purines ( adenine,guanine)
and pyrimidines (cytosine, thymine, uracil)
-RNA is single stranded and some RNA species can
fold in a similar manner to proteins.
-DNA exist in a double helix
Nucleic acids
Nucleic acids
purines
pyrimidines
Experiment
6- DNA is a large molecule
. Add equal amount of salmon sperm DNA and
absolute ethanol and try to spool using pasteur pipette.
.repeat the same after shearing the DNA using syringe.
.dispose the syringe while the needle still attached in
sharps discard
.dispose glass pasteur pipettes
Experiment
7-Detecting co2 using BaOH2
.use the designated flask and mix dry ice with
water and direct the pipette into BaOH2. Observe
what happens
BLC project
-get acquainted to molecules
-make a typed report identifying 6 a.a. and
2 nucleotides.
-nucleotides……!
-Amino acids
“http://www.chemie.fu-berlin.de/chemistry/bio/
amino-acids_en.html”