Transcript BIOCHEMISTRY

BIOCHEMISTRY
the chemistry of life
Chpt. 3
Matter, energy
&
organization
1. Water
2. Carbon
compounds
3. Molecules of life
WATER
The molecules that make
you you are NOT water…
(Proteins, Carbohydrates,
Lipids & Nucleic Acids)
why then is water
important for life? Why will
you die w/out it?
• Somehow, it has properties that
other molecules don’t…
properties that are vital for life.
• But what is it about a water
molecule that makes it so
special???
• LET’s FIND OUT TODAY!!!!
Water molecule? Or…
A: WATER IS A POLAR MOLECULE…
it has a partial positive & partial negative
side to it… call them “poles”.
This gives it some unique properties.
Polarity means
separation of + & - charges
• Oxygen is a more
electronegative element
than hydrogen- it’s pull on
the electrons is greater.
• The shared electrons
spend more time around
the OXYGEN than they do
around the HYDROGENS.
Water is formed via
• OXYGEN is partially polar covalent bonds
between the hydrogen • HYDROGENS are partially +
and oxygen atoms.
Oxygen gas
Is O=O
This happens
when one
atom is more
electronegative
than another
in the covalent
bond.
Because of it’s
polarity… water is a
great solvent!
Polar substances will readily dissolve
in water.
• Sugars
• Proteins
• Ionic
compounds
ex. Table salt
(Na+Cl-)
Watch the salt disappear…
IT’S MAGIC!!!
No matter what the charge is on the solute, it can be
completely surrounded by water molecules. The partially
negative OXYGEN is attracted to the positive ion OR the
partially positive HYDROGENS are attracted to the - Cl
Salt crystals dissolve in water
when Na+ and Cl- ions are
separated and surrounded by water
The polarity of water
makes hydrogen bonding
possible
• A HYDROGEN Bond extends
from the + hydrogen atom in
one molecule to the partially
negative atom in another
molecule (N, O, S).
• N (nitrogen) O (oxygen) and
S (sulfur) are all electroneg.
• Shown as a dotted line.
Hydrogen bonds are weak
bonds that hold water
molecules together or to
other charged substances.
This results in COHESION
between water molecules.
(water-water H bonds)
• Jesus lizard
• Water Strider
The high surface tension of water allows for these two miracles.
Increased habitat for organisms. Water resists being pulled
apart from other water molecules.
Surface tension is molecules
resisting being pulled apart
because of their hydrogen bonds!
BIOLOGICAL MOLECULES
LIKE DNA ARE HELD
TOGETHER BECAUSE OF
HYDROGEN BONDS
ADHESION attractive
force between unlike
polar substances
Adhesion
of water
molecules to
the xylem
in these Giant
Sequoia trees
lets it rise
275 ft.by
capillary
action.
Capillarity or capillary action
is the rising of water up small tubes w/out the use of
Energy (this happens in XYLEM tubes).
TRANSPIRATION
• When water climbs through Xylem
tubes in plants, from soil to the roots
to the leaves to the atmosphere this
is called transpiration.
• A continuous water chain is
“yanked” up w/ each evaporated
water molecule from the leaf.
• This is called the COHESIONTENSION MODEL and it explains how
plants transport water and minerals
without using any ATP/energy.
BECAUSE OF IT’S HYDROGEN
BONDS, WATER IS A GREAT
TEMPERATURE MODERATOR
Where would you like to be on a hot day?
Water absorbs energy into it’s HYDROGEN
BONDS before it starts gaining energy itself.
Important for life/cells which are 90% water.
Helps to maintain homeostasis.
Water is excellent at preventing
temperature swings (getting too hot
or too cold under normal
circumstances)because it has an
extremely high SPECIFIC HEAT.
=‘s
the amount of energy needed to
change 1 g of the substance by 1
degree celcius.
WATER BOILS AT A
HIGHER TEMPERATURE
THAN ALCOHOL. WHY?
Water is MORE
polar & has more
hydrogen bonds.
Because of hydrogen
bonding WATER IS LESS
DENSE AS A SOLID…
• Hydrogen bonding
between water
molecules at low
energy levels
places them farther
apart than as a
liquid or gas.
• This means ice
(solid water) floats.
• An important
reality for aquatic
organisms.
RECAP OF THE PROPERTIES OF WATER
THAT MAKE IT ESSENTIAL FOR LIFE
1. Polarity:
good solvent.
2. Hydrogen Bonding:
surface tension,
cohesion,
adhesion,
capillarity.
3. Hydrogen Bonding:
temperature
moderation &
expands upon
freezing.
THE WATER LAB
1.
Magic Salt Disappearing Trick
2.
Drops on a Penny
3.
4.
Sprinkle a spoon-full of salt into a beaker/glass of water. Stir it
around and make it “disappear”. Where did it go? How do you
explain this using your knowledge of water chemistry?
Place as many drops of water on the face of a penny as you
can without them spilling over the side. Explain how you can
make this snow-globe shaped dome at the top!
Can you Break these Bonds
Take two flat pieces of glass (microscope slides work well)
and hold them flat sides together. Pull them apart. Now put a
film of water between them and try to pull them apart. Can
you? Explain what’s going on.
Rainbow Tree Simulation
Take a piece of chromatography paper and use a vis-à-vis
(water soluble ink) marker to draw a line near the bottom of
the strip that is horizontal to the paper. Put the paper in a
shallow cup of water with the end of the paper w/ the line in
the water. The water should be lower than the drawn line.
Watch as water creeps up the paper and see what it does to
the ink!!!! Explain this in terms of cohesion and adhesion.
Matter, energy
&
organization
1. Water
2. Carbon
compounds
3. Molecules of life
II. CARBON COMPOUNDS
ORGANIC COMPOUNDS are:
• Molecules formed by the
actions of living things.
• Molecules containing
CARBON & HYDROGEN.
• Molecules with a carbon
backbone-carbon atoms
covalently bonded to
other carbon atoms & to
other elements as well.
• The other clusters of
atoms attached to the
carbon backbone are
called functional groups.
• Ex. Alcohol functional
group
Organic molecules must be
made of carbon. Why carbon?
Carbon
(atomic #6)
• Abundance on Earth.
• Makes 4 covalent bonds
because 2 electrons in
first shell and 4 in the 2nd
shell… needs 4 more e• Versatility of carbon
allows for complex
shapes & arrangements
-Straight chains
-Branched chains
-Rings
• Single, double, or triple
bonds too!!!!
some carbon
compounds
glucose
Ethyne
benzene
Glycogen
GLUCOSE
FUNCTIONAL GROUPS
are clusters of atoms attached to the
carbon skeleton that influence the
properties of the molecules they
compose.
FUNCTIONAL GROUPS:
know this for the SAT subject test
• Hydrogen (-H)
polar or nonpolar; involved in condensation
and hydrolysis.
• Amino (-NH2)
Basic; involved in peptide bonds
• Phosphate (-H2PO4)
acid; links nucleotides; energy carrier group
ENERGY
• Methyl (-CH3)
nonpolar, makes molecules hydrophobic
CONTROL OF GENE EXPRESSION
• Carboxyl (-COOH)
acidic (carboxylic acids)
BESIDES WATER…WHAT MOLECULE
IS INVOLVED IN ALL CHEMICAL
REACTIONS???
THIS IS THE ENERGY MOLECULE
ASSISTING “coupled to” ALL
BIOCHEMICAL REACTIONS???
ATP
adenosine tri-phosphate
• Energy molecule
• Energy is stored in
the bonds between
the phosphate
groups.
• Energy is released
when the
phosphatephosphate bond is
broken!!!!!
ATP --> energy + ADP + Pi
Adenosine TRI phosphate can be broken
down into Adenosine DI phosphate…
When this happens, energy is released
to power ENDERGONIC reactions.
NAD+ + H+ + e- + e- = NADH
WHAT TYPES OF
MOLECULES ARE LIVING
THINGS MADE OUT OF ???
(hint: there’s 4 categories)
THERE ARE 4 TYPES OF
LARGE MOLECULES…
each is made from
specific kind of smaller,
“building block” .
1. PROTEIN
2. CARBOHYDRATES
3. NUCLEIC ACIDS
4. LIPIDS
(POLYMERS)
1.
2.
3.
4.
amino acids
glucoses
nucleotides
glycerol + fatty
acids
(MONOMERS)
Monomers & Polymers
MONOMERS are simple
molecules “chemical
building blocks” used to
construct larger carbon
compounds called
POLYMERS.
Ex. Nucleotides form DNA
amino acids form
PROTEIN
How do we build
polymers from
monomers?
How do we break down
polymers into
monomers?
CONDENSATION REACTION
(dehydration synthesis)
BUILDS LARGER MOLECULES
monomer in, water outyou get a polymer!!!
HYDROLYSIS or
DISSOCIATION
splitting of a polymer by
adding a water molecule.
- Means “to CUT w/ water”.
Macromolecule
(polymer)
Chemical
building
block
(monomer)
carbohydrate
s
simple
sugars
(ex. glucose)
proteins
Amino acids
(20 types)
lipids
Glycerol &
fatty acids
nucleic acids
(DNA, RNA)
Nucleotides
(A,T,G,C)
#1 CARBOHYDRATE functions:
1. Short term energy storage
&
2. Provide structure for cell
walls
cellulose
Plants- Starch
ex.amylose
Animals- glycogen
•
•
•
•
CARBOHYDRATES
Made of C, H, & O.
Ratio is 1 Carbon:2 hydrogens:1 Oxygen
The number of carbons varies.
Can exist as monomers or polymers.
1. Monosaccaride (single sugar)
ex.
Glucose- metabolized to make ATP
Fructose- fruit sugar
Galactose- milk sugar
2. Disaccharide
(double sugar)
ex.
Sucrose = fructose + glucose
Maltose = glucose + glucose
Lactose = galactose + glucose
3. Polysaccharide (3 or more)
ex.
Glycogen = millions of glucoses in
animal cells
Starch = millions of glucoses in plant cells
Cellulose = millions of glucoses in plant
cell walls
ISOMERS
are molecules with the same
molecular formula but different
shapes.
•C
6
H 12 O6
• Glucose (used
for cell energy)
• Fructose (fruit
sugar)
• Galactose (milk
sugar)
#2 LIPIDS
FUNCTIONS:
1)long-term, light weight, energy
storage
2) communication & 3) structure
#1 triglyceride
#2
Steroidhormone
#3
phospholipid
phospholipid bilayer
Cell membrane
LIPIDS are:
large, nonpolar, organic
molecules that don’t dissolve
in water.
• C,H, 0 but with a
higher ratio of
carbons & hydrogen
than carbohydrates.
• Carbon-Hydrogen
bonds store energy.
• Monomers of LIPIDS
are:
1) glycerol &
2) fatty acid(s)
Water
fearing
FATTY ACIDS
2 SIDES:
An unbranched carbon
chain (12-28 carbons) at
one end
That is HYDROPHOBIC
water fearing
Water
loving
And a -COOH carboxyl
group at the other end
That is HYDROPHILLIC
water loving
COMPLEX LIPIDS
TRIGLYCERIDE
3 fatty acids + 1 glycerol
Saturated ones have a high
melting points & solid at
room temperatureshortening.
Unsaturated ones have lower
melting points, are liquid at
room temp and are found in
plant seeds and fruits.
saturated vs.
unsaturated
Saturated means each
carbon is “full of
hydrogens”.
BAD FOR YOUR HEALTH
(beware of hydrogenated
products like margarine,
shortening and CRISCO)
Unsaturated means the
carbons have some
double bonding and fewer
hydrogens.
Best = polyunsaturated fats
These may lower your
PHOSPHOLIPIDS
Two fatty acids
joined by a
molecule of
glycerol.
A double layer of
phospholipids
provide a stable
and effective
barrier for cells.
WAXES
Long fatty acid joined
to a long alcohol
chain.
Highly waterproof
Protective coating in
STEROIDS
• Four fused carbon
rings with various
functional groups
attached.
• Not made of fatty
acids.
• Many animal
hormones are
steroids.
• Ex. Cholesterol,
testosterone,
progesterone etc.
#3) NUCLEIC ACIDS function is to store and
transmit genetic information and use that
information to direct the synthesis of new protein
DNA
RNA
NUCLEOTIDES are the basic building
block of Nucleic Acids
NUCLEOTIDE STRUCTURE:
All contain a
1. sugar (ribose or deoxyribose) a
2. phosphate… & a
3. nitrogen containing base .
- Adenine
- Cytosine
- Guanine
- Thymine (Uracil in RNA
nucleotides)
DNA’s sugar is DEOXYRIBOSE
RNA’s sugar is RIBOSE
DNA… stores genetic
information.
• THE sugars and phosphates
make the “uprights” of the
ladder.
(joined by covalent bonds)
• The nitrogenous bases
make the “rungs” of the
ladder.
(joined by hydrogen bonds)
• STORES information used in
the manufacture of proteins.
• RNA molecules are
assembled based on a
“gene” (1 side of DNA)
Two polymer chains, twisted ladder, spiral staircase,
double helix
RNA does the work of
building proteins!!!
• mRNA is the messenger
(directions)
• tRNA brings the amino acids
(transfer RNA)
• rRNA builds the RIBOSOME
(huge enzyme where the
polypeptide chains are built)
#4) PROTEINS provide structure & hormonal control
and they transport materials like oxygen or materials
across cell membranes.
PROTEINS
POLYPEPTIDE
Amino Acid
(monomer)
• organic compounds made of carbon,
hydrogen, and nitrogen.
• Ex. Skin, muscles, hair, enzymes, and
some hormones.
• Made from Amino Acids joined by
PEPTIDE bonds.
• 20 types
• AMINO ACIDS consist of:
a central CARBON w/ 4 fun groups
1. hydrogen -H
2. amino group -NH2
3. carboxylic acid -COOH
4. R group (variable x 20)
4 levels of STRUCTURE OF PROTEINS
are due to interactions of the amino acids.
1) PRIMARY STRUCTURE
Amino acid chain (peptide bonds)
2) SECONDARY STRUCTURE
Alpha helix, Beta pleated sheet
(due to hydrogen bonds)
3) TERTIARY STRUCTURE
3-D clump (R group interactions)
4) QUATERNARY STRUCTURE
Two or more 3D proteins.
ENZYMES
•
•
•
•
Are catalytic PROTEINS
Names end in -ase.
Biological Catalyst
Lower the amount of required
activation energy to start RXN.
• Thus… speeds up reactions!
• Unlike inorganic catalysts which
are consumed in the RXN,
enzymes are RECYCLED
(don’t get used up).
Enzymes are catalytic proteins… the
protein’s unique primary sequence & the
environment of the solution (pH, salts,
polarity) results in a unique tertiary globular
structure or shape of the protein.
• The SUBSTRATE fits into the
ACTIVE SITE of the enzyme.
• Shape dependent- very
specific
• LOCK & KEY model means
one enzyme works w/ one
substrate.
• INDUCED FIT model says the
enzyme “hugs” the substrate
once it binds.
• Ex. CATALASE breaks
HYDROGEN PEROXIDE into
WATER and OXYGEN
Temperature
Effects rate
Of RXN.
Think about kinetic energy.
• Work best under specific
conditions of
temperature, pH, and salt
concentration.
• High temperature or
changes in pH, solvent
polarity, or Salt
concentration can
DENATURE the enzyme
(now it won’t work)
• DENATURE = CHANGE
SHAPE
Which enzyme works best at acidic pH?
• Ubiquitous!
• they are
everywhere
• every reaction
has a specific
enzyme to
catalyse it!
3 DIGESTIVE ENZYMES
• Amylase- breaks
carbs to sugar
• Peptidasebreaks peptide
bonds… breaks
proteins down
into amino
acids.
• Lipase- breaks
lipids apart.