Transcript UNIT 1 - MsBragg

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.
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Pure water never only contains only H2O
molecules
Two H2O in every 550 million react with each
other.
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Compounds other than water can increase or decrease [H3O+] or [OH-]
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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.
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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
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Pure water contains equal numbers of
hydonium and hydroxide ions
◦ [H3O+] = [OH-]
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 Neutral
Neutralization reaction:
◦ Acid and base mixed
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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.
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Bonding Capacity: number of covalent bonds an
atom can form.
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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.
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For carbs, proteins, and Nas, the subunit can
also be called a __________________.
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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.
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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.
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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)
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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.
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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
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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.
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α – glucose
◦ Hydroxyl group at carbon 1: above plane of ring:
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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
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Plants store the Sun’s energy mostly in the form
of glucose by photosynthesis.
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 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.
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Humans do not have the digestive enzymes able
to break linkages between β-glucose subunits.
◦ Therefore, can not digest cellulose.
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Animals such as cows, sheep, and rabbits can
digest cellulose
◦ Symbiotic bacteria and protists in digestive tract produce
enzymes that break the linkages.
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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
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Hydrophobic – composed of H, C and O
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Functions
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◦ 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.
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Condensation reaction between glycerol and fatty
acid: ester linkage.
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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).
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Glycerol molecule + two Fas + highly polar
phosphate group.
◦ Polar head (hydrophillic)
◦ Non-polar tails (hydrophobic).
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When added to water, phospholipids form
spheres called micelles.
◦ Hydrophyllic heads orient themselves towards the
water while the hydrophobic tails orient towards
themselves.
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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.
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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