Download UNIT 1 - MsBraggSummer

BIOCHEMISTRY
Note:
1) bonds repel each other so that there is the maximum space
between them.
2) lone pairs also repel bonds as well as other lone pairs.


Pure water never only contains only H2O
molecules
Two H2O in every 550 million react with each
other.

Compounds other than water can increase or decrease [H3O+] or [OH-]

ACIDS
◦ Increase the concentration of H3O+ ions in a solution.
◦ Acidic solutions: sour taste, ability to conduct electricity.
◦ Contain at least one ionizable hydrogen atom.

BASES
◦ Increase the concentration of OH- ions in a solution.
◦ Basic solutions: bitter taste, slippery feel, conduct electricity.
◦ 2 reactions:
 1) Ionic base containing OH- ion dissociate to produce OH-
 2) Base not containing OH combines with H+ ions

Pure water contains equal numbers of
hydonium and hydroxide ions
◦ [H3O+] = [OH-]

 Neutral
Neutralization reaction:
◦ Acid and base mixed

Concentration of a solute in aqueous solution is
measured in moles of the solute per litre of
solutions  mol/L
◦ A mole is the amount of any substance that contains
6.02 x 1023 particles of the substance.
◦ A [H3O+] of 2.0 mol/L contains
__________________________________ H3O+ ions.
◦ A neutral solution has [H30+] = 1.0 x 10-7 mol/L.
◦ The pH of an aqueous solutions is equal to the negative
logarithm of the hydronium ion concentration.
 Acidic solutions, 0 < pH < 7
 Basic solutions, 7 < pH < 14
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Carbon
◦ Can form four covalent bonds
◦ Attach to each other to form strait and branched chains
and ringed structures.
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Hydrocarbons: contain only carbon and hydrogen
 non-polar.
Functional groups: reactive clusters of atoms
containing hydrogen, oxygen, nitrogen, sulfur,
and phosporus.
◦ Attach to the carbon backbone.

Bonding Capacity: number of covalent bonds an
atom can form.

FGs are more reactive than the hydrocarbon
portions of biological molecules.
◦ Eg. –OH and –COOH are polar due to the
electronegative oxygen atom they contain.
Therefore, sugars and alcohols are highly soluble in
water.
◦ Eg. –COOH makes a molecule acidic. –NH2 makes a
molecule basic.
PP, page 27, #1
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Complex carbohydrates, proteins, and nucleic
acids are polymers.
Lipids (triglycerides and phospholipids) are
not polymers but are relatively large molecules
composed of several smaller parts.

For carbs, proteins, and Nas, the subunit can
also be called a __________________.

Anabolic Reaction: result in the construction of
large molecules from smaller subunits.
◦ ‘formation’
◦ Cells use this process to form proteins (ex//cytoskeleton
( strength), carbohydrates (ex//membrane, glycogen for
energy storage), lipids (ex//phospholipid bilayer), etc.

Condensation/Dehydration Synthesis: creates a
covalent bond between two subunits, removing
(forming) a water molecule in the process.
◦ An –OH group is removed from one subunit, an H is
removed from another. OH + H  H2O.
◦ Process requires energy.

Catabolic Reactions: reactions that break
macromolecules into smaller units.
◦ ‘digestion’
◦ Cells may use this process to break apart larger
unusable macromolecules into their subunits in
order to re-build them into functional/required
macromolecules. (Lego)

Hydrolysis: water molecule is used to break a
covalent bond holding subunits together.
◦ Release of energy
Hydrolysis and
condensation
require the
assistance of
special protein
molecules
called enzymes
– more on
enzymes later.
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Millions of tonnes are produced by plants and
algae every year through process of
___________________________.
Functions:
◦ Sources/storage of energy for organisms.
◦ Building materials
◦ Cell surface markers for cell-to-cell identification.

Types (“saccharide”  sugar)
◦ Monosaccharide
◦ Oligosaccharides
◦ Polysaccharides
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“mono” + “saccharide”  single sugar.
Contain a single chain of carbon atoms to
which hydroxyl groups and a carbonyl group
is attached.
◦ Can be distinguished by
 the carbonyl group they possess: aldehyde or ketone.
 Aldoses: contain aldehyde
 Ketoses: contain ketones.
 Number of atoms in their backbone.
 Pentose: five carbons
 Hexose: six carbons.
 Etc.
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Trioses

Pentoses
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Hexoses
◦ Glyceraldehyde (intermediate compound in carbohydrate
metabolism)
◦ Dehydroxyacetone (ingredient in sunless tanning
products)
◦ Ribose (component of RNA)
◦ Ribulose (used in photosynthesis)
◦ The hexoses are isomers: contain same chemical
formula but with a different arrangement of atoms.
Possess different shapes and different physical and
chemical properties.
 Glucose (source of energy in cells)
 Galactose (component of lactose, milk sugar)
 Fructose (fruit sugar).
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Monosaccharides with five or more carbons are linear molecules in the DRY state.
Ring structure: when dissolved in water.
Ex// Glucose: carbons 1 & 5 react.
◦ Hydroxyl group at carbon 1: below plane of ring.

α – glucose
◦ Hydroxyl group at carbon 1: above plane of ring:

β - glucose
◦ Contain two or three simple sugars.
 Attached by special condensation rxn: glycosidic
linkage.
 Disaccharides: contain two monosaccharides.
 Important dissacharides
 Maltose: α–glucose + α–glucose (α 1-4 glycosidic linkage)
 Found in grains – use in the production of beer.
 “maltose”
 Sucrose: α–glucose + α-fructose (α- 1-2 glycosidic linkage)
 Table sugar
 Use by many plants to transport glucose from one part of a plant
to another.
 Found in high concentrations in sugar cane, sugar beet, and
sugar maple trees.
 Lactose: α-glucose + α-galactose
 Sugar found in milk.
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‘complex carbohydrates’
Monosaccharide polymers  several hundred to
several thousand monosaccharides.
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Energy storage and structural support.
Starch: _________________________(amylose + amylopectin)
Glycogen: _____________________________
Cellulose: _____________________________
Chitin: ________________________________
Amylose
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Unbranched
α-glucose polymer
α 1-4 glycosidic linkages
Amylopectin
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Branched
α-glucose polymer
Main-chain: α 1-4 linkages
Brances: α 1-6 linkages
Angles of glycosidic linkages causes polymers to
twist into coils: insoluble in water.
AMYLOSE + AMYLOPECTIN = STARCH

Plants store the Sun’s energy mostly in the form
of glucose by photosynthesis.
______________________________________________
 Glucose is then broken down when energy is
needed by the plant: for anabolism, catabolism
(formation of proteins, carbs, other processes)
◦ Usually produce more glucose than needed.
◦ Enzymes link together glucose into amylose and
amylopectin (polysaccharides), which mix to form starch.
 Potato: “starchy”.
 Roots in the winter: deciduous trees store energy in roots
during the winter so when spring bloom arrives, they are
ready to use energy to bud new leaves (beginning
photosynthesis!)
Heterotrophs use enzymes to hydrolyze amylose
and amylopectin into individual glucose
molecules and then respirate to extract energy to
glucose:
Cellular Respiration:
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______________________________________________
 Excess glucose molecules are linked to one
another to form glycogen.
Glycogen
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Similar to amylopectin (same linkages and
branched), but more branches.
Stored in muscle and liver cells.
Depleted in about a day if not replenished.
Cellulose
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Primary structural polysaccharide of plants.
Major component of cell walls.
Most abundant organic substance on Earth.
Strait-chain polymer of β-glucose held together by β1–4
glycosidic linkages
Neither coiled nor branched.
Strait shape allows hydroxyl groups of parallel monomers to
form many hydrogen bonds, producing microfibrils.

Humans do not have the digestive enzymes able
to break linkages between β-glucose subunits.
◦ Therefore, can not digest cellulose.

Animals such as cows, sheep, and rabbits can
digest cellulose
◦ Symbiotic bacteria and protists in digestive tract produce
enzymes that break the linkages.

Roughage
◦ Cellulose fibres – found in fresh fruit, vegetables, and
grains – we are unable to digest.
◦ Pass through our DT undigested  scrape walls of DT 
stimulates intestinal cells to secrete mucus  lubricates
feces and aids in elimination of solid waste (decreases
chance of back-up).
Chitin
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Exoskeleton of insects and crustaceans and cell
walls of many fungi.
Monomer is a glucose molecule with a nigrogencontaining group attached to carbon 2.
Second most abundant organic material found in
nature.
Used in contact lenses and biochemical stitches.
PPs, page 34. # 2-10

Hydrophobic – composed of H, C and O

Functions

◦ Insoluble in water but soluble in other nonpolar substances.
◦ Long-term storage of energy (more than twice the amount of energy in carbohydrates).
◦ In animals, excess carbohydrates are converted into fat and stored as droplets in the cells
of adipose (fat) tissue.
◦ Thermal insulation: layer of fat under skin (penguins, polar bears, walruses, etc).
◦ Plants also store energy in the form of fat: triglyerides.
Main types:
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Triglycerides
Phopholipids
Sterols
Waxes
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Made of:
◦ A glycerol (3-C molecule with three hydroxyl groups)
◦ Three fatty acids (long H chains containing –COOH)
 Usually even number of Cs and around 16-18 C long.
 Saturated FAs: all single bonds, max # H
 Unsaturated FAs: one or more C=Cs, not max # H.

Condensation reaction between glycerol and fatty
acid: ester linkage.

Examples: animal fats: butter and lard.
◦ Contain only saturated fatty acids.
◦ Strait hydrocarbon chains allow for many van der
Walls attractions
 Dipole-dipoles, dispersion forces
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Solid consistency at room temperature.
More difficult to catabolize.
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Examples: plant oils: olive oil, corn oil,
peanut oil.
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Bent at double bonds.
Reduced number of van der Waals attractions.
Liquids at room temperature.
Hydrogenation: process of adding hydrogen atoms
to double bonds in unsaturated triglycerides to
form semisolid material (margarine).

Glycerol molecule + two Fas + highly polar
phosphate group.
◦ Polar head (hydrophillic)
◦ Non-polar tails (hydrophobic).

When added to water, phospholipids form
spheres called micelles.
◦ Hydrophyllic heads orient themselves towards the
water while the hydrophobic tails orient towards
themselves.

Separate two water compartments
(extracellular fluid and cell’s
cytoplasm/intracellular fluid).
◦ Heads can mix with water and tails can mix with
one another in the center of the bilayer.
◦ Water/polar molecules: can not pass through
bilayer due to the highly nonpolar center.
 Proteins and hydrophillic pores form channels through
which charged materials can pass.
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Also called steriods
Compact hydrophobic molecules containing four
fused hydrocarbon rings and several different
functional groups.
Cholesterol: important in cell membrane  aid in
fluidity.
Cholesterol in bloodstream and diet rich in saturated
fats  artherosclerosis.
◦ Fatty deposits (plaque): line blood vessels and block the
flow of blood to tissues
 Body tissue dies
 Heart tissue: heart attack
 Brain: stroke.

Other Sterols:
◦ Sex hormones: testosterone, estrogen, and progesterone.
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Long-chain fatty acids linked to alcohols or carbon
rings.
Hydrophobic
◦ Waterproof coating on various plant and animal parts
◦ Cutin: wax produced by epidermal cells of plants, forming
water-resistant coating on the surfaces of stems, leaves,
and fruit  conserve water and barrier to infections.
◦ Birds: secrete waxy material to help keep feathers dry
◦ Bees: produce beeswax to construct honeycombs.
Pg. 40
#11-13,
15-18

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The most diverse molecules in living organisms and
among the most important: gelatin, desserts, hair,
antibodies, spider webs, blood clots, egg whites, tofu, and
fingernails, etc.
Make up 50% of dry mass of most cells.
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Structural building blocks
Functional molecules
Involved in almost anything that cells do.
3D shape is directly related to their function.
Enzymes: catalysts  speed up chemical reactions so cells can
sustain life.
Immunoglobins: protect animals against foreign microbes and
cancer cells.
Hemoglobin: transports oxygen.
Protein carriers: move substances across cell membranes.
And much more!
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Genetic information in DNA codes specifically for
production of proteins and nothing else.
All copies of the same gene produce the same protein.

Monomer: amino acid.
◦ Central carbon atom with an amino group, a carboxyl
group, a hydrogen atom, and a side chain (R).
◦ 20 different R groups, therefore 20 different AAs.
◦ Amphiprotic: both acidic (carboxyl) and basic (amino)
functional group.
 When dissolved in water, carboxyl group donates an H+ ion
to the amino group
 Causes the carboxyl group to become (-) and amino (+).
 Amino acids may have side chains that are polar (hydrophillic)
or nonpolar (hydrophobic), acidic (contain a carboxyl) or basic
(amino).
Nonpolar amino acids
Polar Amino Acids
Electrically charged (acidic/basic) amino acids
Note: there are 8 essential amino acids: body
cannot synthesize from simpler compounds:
Tryptophan, methionine, valine, threonine,
phenylalanine, leucine, isoleucine, lysine.
HW (to do for Monday):
Amino Acid Memory Cards
 1) take a cue card and place it in `portrait` orientation
towards you.
 2) fold the top down and bottom up about 1 inch from the
edges.
 3) Draw an amino acid on the blank side of the cue card.
 4) write the name of the amino acid on one of the folded
parts, and the short-hand notation on the other fold.
 5) write a few things about the amino acid on the side with
lines.
 6) use these cue cards to study. Do not lose them! (attach
them to your binder, put them in your pencil case, etc).
You will be required to know all of the amino acids as well
as their properties.

Proteins consist of one or more amino acid
polymers (polypeptides) that have twisted and
coiled into a specific shape.
◦ Final shape: conformation  determined by the
sequence of amino acids it contains.
◦ Peptide bond: condensation reaction between
amino group of one amino acid and carboxyl group
of another amino acid, forming an amide
 Functional group linkage is called an amide bond.
◦ Polypeptides: constructed in the cytoplasm of cells
through process called protein synthesis.
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Amino terminus: amino group at one end.
Carboxyl terminus: carboxyl group at other
end.
Can be between a few to more than a
thousand amino acids.
Sequence determines polypeptide’s 3D
conformation  determines function.
◦ Structural proteins: roughly linear: forms strands or
sheets.
◦ Globular proteins: 1+ polypeptide chains that coil
and bend to form rounded, spherical shape
 Many enzymes are globular.

Primary Structure: unique sequence of amino
acids in a polypeptide chain.
◦ Amino acid referred to as a ‘residue.’
◦ First protein to be ‘decoded’ in terms of residue
was insulin: Fredrick Sanger, 1958.
◦ Determined by the nucleotide sequence of DNA.
◦ Possible arrangement of polypeptides:
 The number of possible arrangements of residues in a
polypeptide are 20n .
 Example: How many different 40- residue
polypeptides are possible?
__________________________________________________________________________________

Changing the sequence by one amino acid could alter the
3D shape  protein loses it’s function, is rendered
useless, or has a different function (rare).
◦ Ex// Sickle cell anemia: single AA change in hemoglobin causes
red blood cell to change shaped: flow is hindered, vessels clog.


During protein synthesis, AAs added to growing
chain one at a time  coils, folds, bends at various
locations.
Two main shapes form:
◦ α-helix & β-pleated sheet.

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α-helix: hydrogen bond forms between the electronegative O of (C=O)
of one peptide bond and the electropositive hydrogen of the amino
group (N-H) four peptide bonds away
Ex// fibrous proteins - α-keratin: protein in hair.


Two parts of polypeptide chain lie parallel to one another.
Hydrogen bonds form between oxygen atoms of C=O on
one strand and hydrogen atoms of amino groups on
adjacent strand.
Spiders are Crazy Cool!
• silk contains large amounts of beta
pleated sheets  spiders secrete silk
in liquid form and then solidify when exposed
to air. Many H-bonds. Strength!

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Strong forces of attraction and repulsion between the polypeptide and
its environment force it to undergo additional folding.
Chaperone proteins: aid growing polypeptide to fold into tertiary
structure: deficiency: cystic fibrosis.
◦ AAs with polar R groups (ex// serine, tyrosine, and glutamine) are attracted to
water.
◦ AAs containing nonpolar R groups (ex//valine and phenylalanine) are ‘repelled’
by water. Congregate in the interior of folded polypeptide, away from water.
◦ Structure stabilized by number of R-group interactions.
 H-bonds
 ionic bonds (between oppositely charged side chains)
 van der Waals forces between nonplar R groups.
 Disulfide bridges: covalent bond between sulfur-containing R groups of
cysteine residues.
 Proline kinks: R group is attached to the amino group  forms a kink in the
polypeptide.

Sometimes 2+
polypeptide subunits
combine to form a
functional protein.
◦ Collagen (skin, bones,
tendons, ligaments)
◦ Keratin (hair)
◦ Hemoglobin (transports
oxygen): four polypeptides
in quaternary structure.


Proteins are made within a cell, in a mostly
neutral pH.
Different environmental conditions may cause
unravelling.
◦ pH
◦ temperature
◦ Salt concentrations

Various chemicals and heat disrupt:
◦
◦
◦
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Hydrogen bonds
Ionic bonds
Disulfide bridges
Hydrophobic interactions
Will usually return to original orientation if
denaturing agent is removed.

Enzymes work within specific ranges of conditions
◦ Thermophiles: (archaebacteria: live in water at about 100
degrees celcius)
 Would die at room temperature  enzymes would denature.
◦ Gastrin: digestive enzyme in the stomach works best at pH
= 2, and denatured in small intestine where the pH = 10.
◦ Fevers: prolonged fevers can denature proteins in brain and
lead to seizures/death.
◦ Preservatives: salt, sugar, curry, pickling  denatures
proteins in bacteria that spoil food.
◦ Straitening hair: temporarily denaturing proteins with heat.
◦ Cooking meat: to denature fibrous proteins in muscle
tissue.
PPs, Page 50. #19-29
ON MONDAY, MAKE SURE YOU HAVE THE
FOLLOWING COMPLETED:
 Any PPs from the text that I have assigned
throughout the powerpoint.
 Carbohydrate worksheet
 Lipid worksheet.
MONDAY: quiz on Carbohydrates and Proteins.

Informational macromolecules
◦ Store hereditary information.
◦ Determines structure of proteins  determines
function.
◦ Only molecules that produce identical copies.
◦ Reason why organisms can reproduce.

Monomer: nucleotide
◦ Nitrogenous base
◦ Pentose sugar
◦ Phosphate group.

DNA vs. RNA (both are helical)
Characteristic
DNA
RNA
Location
Nucleus
Nucleus & Cytoplasm
Sugar
Deoxyribose (one less
oxygen)
Ribose
Nitrogenous Bases
G, C, A, T
G, C, A, U
Strands
Double
Single
Pyrimidine: single-ringed.
Purine: double ringed.

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Nucleotides are linked together by a specific enzyme
into a strand.
NA Condensation reaction: phosphodiester linkage.
◦ Between phosphate group and hydroxyl group (on carbon #3).

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Double-stranded
Strands held together by hydrogen bonds
between nitrogenous bases.
◦ A-T: two hydrogen bonds
◦ G-C: three hydrogen bonds.

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Strands are antiparallel: free phosphate end
of one strand lines up with the free sugar end
of the adjacent strand.
Complimentary pairs: every pair of nucleotide
pair is composed of a purine facing a
pyrimidine.
A nucleotide used to drive energy-requiring
reactions.
 More on this
later.
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All organisms pass on their DNA to offspring.
Organisms that share similar features are
more closely related.
◦ THIS IS BECAUSE OF DNA!

Therefore, more closely related organisms
contain more closely related sequences of
nucleotides.
REMEMBER: DNA  RNA  PROTEIN.
Table on Pg. 54: Summary of Macromolecules.
Work together to fill in the blanks.
Complete:
#1-9, 11, 13-16, 18-19.

Test on Macromolecules: carbs, lipids,
proteins, and nucleic acids.

I have decided to move onto ENZYMES next.

First, we need to learn about energy.
“the ability to do work” = ______________
 Living organisms must continually capture,
store, and use energy in order to function =
live.
 Organisms do all their work at a molecular
level  highly controlled chemical reactions.
Anabolic Reactions: __________________________.
Catabolic Reactions: _________________________.
Matabolism: _________________________________.

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All forms of energy can be classified as kinetic or
potential energy
Kinetic Energy: ____________________________
◦ Heat, mechanical, electromagnetic, or electrical energy.

Potential Energy: __________________________.
◦ Gravitational, chemical.
◦ Ex// A diver. (Gained this energy because he WORKED to
get to the height that he is at).
WHEN THE DIVER DIVES, HE WILL GAIN KINETIC ENERGY
AND LOSE POTENTIAL ENERGY. Potential energy is
converted into kinetic energy.
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The total amount of energy in the universe is
constant.
Energy cannot be created nor destroyed.
Energy can only be converted from one form
to another.
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Atoms form molecules because they achieve
greater stability. (Think about it  atoms
want to have full valence shells).
Bond energy: measure of stability of a
covalent bond. ___________________________.
◦ The more energy needed to break a bond, the more
stable the bond is.

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First Law of Thermodynamics?
For any reaction that gives off energy, there
must be another reaction that absorbs
energy.
◦ Exothermic Reactions: ___________________________
◦ Endothermic Reactions: __________________________

Most living things absorb or release energy in
the form of heat (thermal energy)
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Measure of randomness/disorder.
Entropy increases as disorder increases.
The Universe favours an increase in entropy.
Put the following in order as entropy
increases:
_ Liquid
_ Gas
- Solid
How do each of the following statements make
sense when thinking about Entropy?