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Chemistry of Life

Chapter 2: Biochemistry
by

Brett Meyerhoefer

on 27 August 2014

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Transcript of Chemistry of Life

The Chemistry of Life
Water
Water is a Polar Molecule
Hydrogen Bonds form between slightly - O and slightly + hydrogen
Cohesion vs.
Adhesion
Cohesion
= Water molecule attracted to other water molecules
Ex.
Surface tension
is a result of this property
Adhesion
= water clings to another substance
Ex. meniscus formed when water adheres to glass.
Transpiration
- movement of water up xylem and their evaporation from stomata. H2O clings to each other by cohesion and to xylem walls by adhesion
Water has High Specific Heat
Specific Heat
- amt. heat needed to inc. 1 g of water by 1 deg C.
Ex. High specific heat of water makes temperature of oceans relatively stable and able to support life
The human body (72% water) can withstand drastic temp changes.
Specific Heat - Heat Capacity Demo
Heat of Fusion & Heat of Vaporization
Heat comes out of the body to vaporize water. In return, heat is carried away from body, cooling the body off.
water is less dense solid than liquid. Because ice floats, this keeps large bodies of water from freezing solid. Ice on top on lake insulates water below and keeps it from freezing
Water is a Universal Solvent
salt crystal being dissolved in water
Solute
- the thing being dissolved.
Solvent
- the thing doing the dissolving
What is the importance of water as a solvent?
transport of oxygen and nutrients in blood
transport around cell
excretion of wastes and more
pH

Acids
= (0-6.9) excess H+ ions

Bases
= (7.1-14) excess OH - ions

Neutral
= (7) H+ = OH-
Buffers
- minimize changes in pH by donating H+ when depleted or accepting H+ from solution when it is in excess.
Hydrophobic - Hydrophilic
By rubbing your finger with superhydrophobic aerogel powder you can make it superhydrophobic. Then, when sticking the finger into water no water droplet will stick on the finger. All water is completely repelled. A thin air layer forms between the finger and the water.
Hydrophobic
do not dissolve in water
(ex. nonpolar molecules like oils)
Hydrophilic
- substances that are typically water soluble
(ex. ionic compounds. polar molecules )
All organic compounds contain
Hydrogen and Carbon
(C +H)
C,H,N,O make up 96% of all living matter
Carbon is King!
C has 4 valence electrons
can form 4 covalent bonds (single , double, or triple bonds)
can from chains, rings, branches.
Organic Compounds
Functional Groups
- attach to carbon skeleton and have diverse properties.
Methyl
bound to DNA affects expression of genes
Monomers & Polymers
Monomer
- smaller units ("building blocks") of organic compounds that can be linked together to make larger molecules
Polymer
- long chain molecules made of repeating subunits (monomers)
Dehydration Synthesis
- removal of
water
to create polymers from a set of monomers.
synthesis

- means to build
Hydrolysis
- water is added to split large molecules (polymers) in smaller units
lyse
- means to split
http://nhscience.lonestar.edu/biol/dehydrat/dehydrat.html
Carbohydrates
Monomers
all have C, H, and O in a ratio of
1:2:1 or CH2O
Polymers
Two monosaccharides together make
disaccharides.
Three or more monosaccharides linked together make a
polysaccharide
Examples of Polysaccharides
in plants -
Starch
(used for energy storage)
in humans -
Glycogen

(energy storage)
How are carbohydrates held together?

-Answer:
Glycosidic Linkages
different bonding brings about different function of molecules.
Ex. Cellulose vs Starch - same chemical formula, different orientation of bonding
cellulose broken down by bacteria in rumin
because the y have the right enzymes
cow can absorb energy once
cellulose broken down
cellulose used for structure in tree,
but not for energy like starch
Humans do not have enzymes to break down cellulose. Therefore they cannot extract energy from it. Cellulose is considered fiber and helps to keep you 'regular.'
Chitin
steroid molecule -
Lipids are
hydrophobic
organic compounds made of C, and H

Examples include
Fats, Oils, Waxes,
&
Steroids
molecules
Lipids
Fats - are made of
1 glycerol
and
3 fatty acids
(large hydrocarbon chains)

F.A. bind to Glycerol using
Ester Linkage
(type of bond)
Phospholipids
glycerol backbone is
hydrophilic
fatty acid tails are
hydrophobic
When placed in water, hydrophobic tails face inward, while hydrophilic heads face outward.
In cells, phosoplipds arrange into
lipid bilayers
to make cell membranes.
Functions
Energy Storage
- fats store 9kcal/gram of energy vs only 4kcal/gram in carbohydrates. Have many high energy chemical bonds
Protection of vital organs and insulation. Fat stored in adipose cells
Saturated vs Non Saturated Fatty Acids
Saturated F.A.
all single bonds between carbons
remain solid at room temperature, can pack together closer
increase heart disease - create solid plaques in blood vessels
Non-Saturated F.A.
have at least one double bond between carbons (results in kink in chain)
tend to be liquid at room temperature (ex. oils)
monounsaturated F.A. - 1 C=C
polyunsaturated F.A. - 2 or more C=C
Steroid
made of 4 rings fused together
many hormones are hydrophobic hormones
Ex. Cholesterol - hormone on cell membrane
Estrogen and Testosterone are steroid hormones
Nucleic Acids
genetic instructions for how to build polypeptide chains (proteins)

DNA & RNA are the two nucleic acids
Nucleotide
3 parts
Phosphate group
pentose (5 sided) sugar
nitrogenous base
building block (monomer) for building RNA & DNA
Composed of C, H, O, N, & P
Function
Directionality
pentose sugars bind with 3' end of one to the 5' end of another.

directionality tells cells how to read the DNA / RNA molecule
Differences between DNA & RNA
DNA - Thymine N.B , RNA - Uracil N.B.
(both share Guanine, Adenine, Cytosine)
DNA - deoxyribose sugar, RNA - Ribose Sugar
DNA - double stranded, RNA - single stranded
Remember - N. bases hydrogen bond together
A-T, G-C, and A-U
Proteins
C, H, O, N
amino acids are the building blocks of proteins

AAs contain alpha carbon , amino group, carboxyl group, R group (side chain)

there are 20 different side chains, therefore 20 different AA
Directionality- amino end always binds with carboxyl end to form chain of AA (polypeptide)
Structure of Proteins

Primary structure -
sequence of AA

Secondary structure -
hydrogen bonding
between AAs creates Beta pleated sheet , or Alpha helix

Tertiary structure- sheets and helices interact and bond. Side chains interact. (hydrogen bonding, hydrophoic interactions, ionioc bonds, disulphide bridge)

Quaternary structure- some proteins have
several polypeptide chains interacting
with one another. Ex. hemoglobin - globular structure with 4 structure

Structure of protein determines function!!!
Chaperonins
Amino Acids
R Groups (side chains) can be polar, non-polar, acidic, basic, hydrophobic, hydrophilic.
All which affect the folding of the final protein.
AA link together through dehydration synthesis to form
peptide bonds
.
Amino Acids Bonding
Protein Structure
Functions of Proteins
Enzymes,
structural proteins, transport proteins, etc.
Shape Determines Protein Function
Example: Sickle Cell Anemia
Bonds that affect 3' structure
single AA change causes difference in folding of protein at all levels.

causes hemoglobin molecules to clump together in long chains, bending the RBC

Result: RBCs carry less oxygen, are more fragile and can block blood vessels.
Denaturation
change of the shape
of a protein, ultimately changing its function.

hydrogen and other bonds break and protein unravels
Change of shape can be caused by
heat
, changes in
pH,
physical perturbation, etc
Denaturation w. Acid
Cooking is a good example of denaturation
protein molecules that assist in proper folding of proteins. Provide isolating environment in which polypeptide can achieve final conformation.
Why can't denatured proteins reform back to original shape?

Answer:
chaperonins are not present
, therefore the polypeptide will interact with other molecules (polar non-polar, acidic, etc) and cause change in shape.
Enzymes
Catalyst - alters speed of chemical reaction
without being altered in the process.


Enzymes are (usually)
proteins
that act as
biological catalysts
Enzymes
decrease

the amount of

activation energy
needed to start a reaction. However, they
do not
alter the free energy change of the reaction.
Activation energy- amount of energy needed to break the bonds of the reactant molecules
Energetics
Substrate
- the reactant an enzyme binds to

Active Site
- region of enzyme substrate binds to

Remember - Enzymes are specific!

Lock and Key model -
one type of substrate for one enzyme

Enzyme substrate complex
- when substrate and enzyme are held together often by weak interactions. enzyme holds substrate in a favorable orientation which decreases activation energy.

enzyme converts substrate into
products
which are that released leaving enzyme unchanged and ready to grab more substrate.
each enzyme has an optimal temperature and pH at which it works best.

Remember- high temperatures and extreme pH levels can denature proteins and thus inactivate enzymes.
Things that Affect Enzyme Reaction Rate
How Enzymes Work
Activation Energy
Catalysts
Temperature and pH
Cofactors and Coenzymes
Cofactors - non protein, inorganic helpers that allow enzyme to catalyze reactions (ex. Iron, Magnesium, Zinc)

Coenzymes - organic cofactors that bind to enzyme and help it perform its task. Vitamins are coenzymes
Competitive Inhibitors & Noncompetitive Inhibitors
competitive Inhibitors -
compete with the substrate
for the active site, often blocking substrate from binding

noncompetitive inhibitors - do not directly compete w/ substrate They inhibit enzyme by
binding to a different part
of it, in turn
changing its shape
.
Allosteric Site Regulation
Sites other than active site where molecules can bind, thus changing the shape of the enzyme. This can either work to activate or inhibit the enzyme.
(Like the key to a car. Insert key and turn before engine starts. Or like boot on car tire inhibiting movement)
feedback inhibition
(negative feedback) - end product of a enzymatic pathway, binds to allosteric site and decreases enzyme activity. Cells ensure that product is not overproduced.
Kinetic Energy - energy of motion

Potential Energy - particle or system of particles derived from position, or condition, rather than motion.
In Biology, related to potential energy in bonds of molecules.
Every bond has the potential to release energy and do work.

Energy can be converted from one form to another.
ENERGY
1st Law - energy can neither be created of destroyed, only converted from one form to another.
Ex. convert food energy into energy of movement.
2nd Law - Entropy (a measure of disorder) increases in the universe
food is broken down into heat and smaller molecules like CO2 and water.
Laws of Thermodynamics
Free Energy
dG = dH -TxdS
delta G - Gibbs free energy
More organization means more free energy.
a spontaneous process
always
has a decrease in free energy.
it would be spontaneous to fall off a diving board, but it would not to walk back up to it.
Endergonic vs Exergonic Reactions
Exergonic - happen spontaneously. - delta G. Energy is released.
Spontaneous reactions don't always happen immediately
Endergonic - do not happen spontaneously. require an input of ernergy. + delta G
less free energy
more free

energy
no change in free energy once equilibrium is reached
keep food coming in
keep powering your body
Wastes going out
In many reactions, energy is released in stages as molecules are changed from one form to another. This is more realistic metabolic pathway in the body.
ATP - adenosine triphosphate
major energy source of the body. Type of nucleotide
ATP is used to power the unfavorable, endergonic reactions and make them proceed.
very high
energy bond
more free energy
less free energy
Free Energy Budget
not going to happen spontaneously
Have to expend free energy in terms of ATP to make reaction proceed in the body.
Enough free energy to cover the energy requirements for the reaction to take place.
What is ATP used for?
movement of molecules across membranes
movement inside cells
muscle movement
cell division
etc
To make more ATP (
catabolism
), we break down food molecules in an exergonic reactions.
eat food - recharge ATP
Hydrolyze ATP - release
energy for other reactions
Isomers
compounds with the same number of atoms of the same elements, but different structures
3 Types of Isomers
Structural
Geometric
Enantiomers
Example how isomers have
differnt properties

- Thalidomide
one type used to cure morning sickness
the other caused birth defects
both isomers where Incorporated into drug.
Ex. digestive system breaks down polymer to be absorbed by cells
Free Energy -is the portion of a system's energy that can perform work
Complex molecules (ex. sugar) with high free energy are less stable than simpler molecules (ex. CO2, water) with less free energy
Bonds of molecules need to be contorted to unstable state before they will break. This is activation energy (which is typically supplied in th form of heat which reactants absorb from thier surroundings)
ex. Vitamin C - coenzyme for some enzymes that synthesize collagen. Vit C deficiency leads to scurvy.
Metabolism
Catabolic Pathways (Catabolism) - release energy by breaking down complex molecules to simpler compounds

Anabolic Pathways (Anabolism) - consume energy to build complex molecues form simpler ones.
the totality of chemical reactions in an organism
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