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Biochemistry
Biochemistry Main Idea 1
The basic unit of matter is the atom. An
element is a pure substance made of only
one kind of atom. Atoms of an element
that have different numbers of neutrons
are called isotopes.
ATOM- Building block of matter
PROTON: (+) In nucleus; NEUTRON: (0) In nucleus
ELECTRON: (-) In orbitals around nucleus
How do we know?
Early humans easily
distinguished
between materials
that were used for
making clothes,
tools, or foods.
They developed
words to describe
them.
Empedocles (492 BCE) –One of 1st theories that
attempted to describe things around us. He argued that
all matter was composed of 4 elements: fire, air, water, &
earth. But--Using the example of stone, which was
commonly used for making tools, there is a problem with
this explanation. No matter how many times you break a
stone in 1/2 , the pieces never resemble fire, air, water,
or earth.
This theory was an important
development in scientific thinking
because it was among the 1st to
suggest that some substances that
looked pure, like stone, were
actually made up of a combination
of different "elements."
Democritus (460 BCE) knew that if
you took a stone and cut it in ½,
each ½ had the same properties as
the original. If you continued to
cut the stone into smaller &
smaller pieces, at some point you
would reach a piece so tiny that it
could no longer be divided.
Democritus called these
infinitesimally small pieces atoms.
Democritus reasoned that each
material’s atoms were unique to
that material.
Torricelli (1643) showed
that air had weight & was
capable of pushing down
on a column of liquid
mercury (thus inventing
the barometer). This was
a startling finding. If air this substance that we
could not see, feel, or
smell - had weight, it
must be made of
something physical.
Bernoulli, a mathematician,
proposed an answer. He
developed a theory that air
& other gases consist of tiny
particles that are too small
to be seen, & are loosely
packed in an empty volume
of space. The particles could
not be felt because, unlike a
solid stone wall that does
not move, the tiny particles
move aside when a human
hand or body moves
through them.
Priestly experimented with red mercury calx in
1773. Mercury calx, a red solid stone, was
coveted because when it is heated, it appears to
turn into mercury, a silver liquid metal. Priestley
had observed that it does not just turn into
mercury, it actually breaks down into two
substances: liquid mercury & a strange gas.
Priestley carefully collected this gas in glass jars &
studied it.
He burned a candle in this gas and noted it had
a remarkably vigorous flame. Also, a mouse
placed in a sealed container of the gas lived for
a longer period of time than a mouse placed in
a sealed container of ordinary air. Priestley’s
discovery revealed that substances could
combine together or break apart to form new
substances with different properties.
Lavoisier (1778) experimented with dephlogisticated air (the air from Priestly’s
earlier experiments) & theorized that the gas made some substances acidic. He
renamed Priestley’s gas oxygen, from the Greek words that loosely translate as
"acid maker".
Lavoisier named hydrogen from the Greek words
for "water maker“ because when hydrogen is
mixed with oxygen water is formed.
Lavoisier also burned other substances such as
phosphorus & sulfur in air, & showed that they
combined with air to make new materials. These
new materials weighed more than the original
substances, & Lavoisier showed that the weight
gained by the new materials was lost from the
air in which the substances were burned. From
these observations, Lavoisier established the
Law of Conservation of Mass, which says that
mass is not lost or gained during a chemical
reaction.
Scientific experiments showed that some substances could combine with
others to form new materials; other substances could be broken apart to form
simpler ones; and a few key “elements” could not be broken down any
further.
John Dalton, a teacher & scientist, put together the pieces and developed the
first modern atomic theory in 1803.
Through his observations of morning fog and other weather patterns, Dalton
realized that water could exist as a gas that mixed with air and occupied the
same space as air. Solids could not occupy the same space as each other; for
example, ice could not mix with air. So what could allow water to sometimes
behave as a solid and sometimes as a gas? Dalton realized that all matter must
be composed of tiny particles. In the gas state, those particles floated freely
around and could mix with other gases, as Bernoulli had proposed. But Dalton
extended this idea to apply to all matter – gases, solids and liquids. Dalton
first proposed part of his atomic theory in 1803 and later refined these
concepts in his classic 1808 paper A New System of Chemical Philosophy.
ELEMENT- Substance that cannot be broken down
into a simpler substance by ordinary chemical
means
Most abundant in life:
Carbon (C)
Hydrogen (H)
Oxygen (O)
Nitrogen (N)
CARBON
HYDROGEN IN
PLASMA STATE
LIQUID OXYGEN
LIQUID
NITROGEN
Biochemistry video 1 goes here.
Atoms are neutral.
The outer shell of electrons = Valence Electrons
Biochemistry video 2 goes here.
An ionic bond forms when an electron from one atom “jumps” to another atom.
COVALENT BOND- Atoms held together by sharing
electrons
Bonding sites: Carbon (4)
Hydrogen (1)
Oxygen (2)
Nitrogen (3)
*see formula sheets
Hydrogen bond- Chemical bond in which a
hydrogen atom is attracted to another atom.
Here are some hydrogen bond examples:
•Water molecules. When one molecule of water attracts another
the two can bond together; adding more molecules results in more
and more water sticking together. This bond is responsible for the
crystal structure of ice, which allows it to float.
•Human DNA. The hydrogen bonding that occurs between base
pairs in a strand of DNA results in DNA’s familiar double helix shape.
This hydrogen bond actually enables the replication of DNA strands.
Oxygen Atom has
8 protons & 8
electrons
Hydrogen Atom has
1 proton & 1
electron
The Water Molecule: Polar Bond, Covalent Bond, Hydrogen Bond
Biochemistry video 3 goes here.
https://www.youtube.com/watch?v=_M9khs87xQ8
Biochemistry video 4 goes here.
http://www.vevo.com/watch/right-saidfred/Im-Too-Sexy/GBBRL9290469
Biochemistry Main Idea 2
Carbon atoms have the ability to form
millions of different large and complex
compounds. Four groups of organic
compounds found in living things are
carbohydrates, lipids, nucleic acids, and
proteins.
COMPOUND- Chemical combination of two or more
elements in definite proportions
ORGANIC COMPOUND: Contain carbon with bonded
hydrogen
Types: Carbohydrates
Lipids (Fats)
Proteins
Nucleic acids (DNA & RNA)
*will look at in Genetics
*not now*
Nutrients Packet
CARBOHYDRATES- The energy compounds (-ose)
Sugars: Simple carb’s
Glucose
Fructose
Starches: Complex carb’s
Cellulose (plants)
Glycogen (animals)
LIPIDS (FATS)- The storage compounds
PROTEINS- The growth compounds
Contain nitrogen (N) and sometimes sulfur (S)
AMINO ACIDS- Building blocks of protein
* see diagrams
Lab 9
Pattern Matching: Organic Molecules
Black
Blue
Red
White
Lab 10
Organic Molecule Construction
H O N C
1 2 3 4----Covalent Bonding Sites
1 Bonding Site
4 bonding sites
#7: C2H6
Lab 11
Identifying Organic Compounds
Organic Elements:
Oxygen
Nitrogen
Hydrogen
Carbon
Organic Molecules:
Carbohydrates
Lipids
Proteins
Nucleic Acids
Building Blocks:
Monosaccharides
Glycerol & Fatty Acids
Amino Acids
Foods:
Organic Molecules are held together by chemical bonds.
Hydrogen Bond- has hydrogen
Covalent Bond- has shared electrons
Ionic Bond- electrons move from one atom to another
and form ions
Polar Bond- has an uneven distribution of electrons
Water has the following bonds:
Hydrogen
Covalent
Polar
Water is cohesive- attracted to itself
adhesive- attracted to other things
Substances made of water demonstrate capillary action because of water’s
adhesive quality. They move through narrow areas against gravity.
The pH scale is based on water’s ability to form multiple bonds.
Lab 12
Using an Acid-Base Indicator
pH: Potential of Hydrogen- measures the concentration
of H+ ions in solution. The pH scale goes from 0-14. 7 is
neutral.
Fluids in organisms each have varying pHs’. Enzymes
(special proteins) in organisms need certain pHs’ to
work. If the pH is wrong, the enzyme will denature
(change shape) and fail to work.
If the pH of a substance is high---adding a weak acid will
bring the pH closer to neutral. If the pH of a substance
is low---adding a weak base will bring the pH closer to
neutral. A weak acid or base can act as a buffer to help
maintain homeostasis in a living organism.
Biochemistry Main Idea 3
Nutrients provide activation energy
necessary for chemical reactions that drive
life processes. Cells use enzymes to speed
up chemical reactions. Enzymes lower the
activation energy needed to get a reaction
started. Enzymes may be affected by pH
value, temperature, and enzyme
concentration.
Enzymes are Proteins that Lower Activation Energy Needed
to get a Reaction Started
ENZYMESChange the rate of reactions in living things (-ase)
SUBSTRATE- Substance that enzyme acts on
SUBSTRATE
ENZYME
Lactose………………………………………………………………..Lactase
Maltose……………………………………………………………….Maltase
Proteins……………………………………………………………….Protease
ENZYMES-SUBSTRATE COMPLEX- Lock - &- Key Model
Lock & Key Model of Enzyme Action
FACTORS INFLUENCING ENZYME ACTION
pH
Temperature
(Concentration)Amount of Enzyme
(Concentration) Amount of Substrate
F
Concentration
Rate Of
Enzyme
Action
Chemical Reactions
Energy Releasing
Reaction
Energy Absorbing
Reaction
https://www.youtube.com/watch?v=XTUm-75-PL4
Biochemistry video 5 goes here.
Biochemistry video 6 goes here.
https://www.youtube.com/watch?v=ok9esggz
N18
Lab 13: Enzyme- Catalase