UNIT 1BIOCHEMISTRY

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.

Acids, Bases and Buffers(pg. 20)

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

Acids and Bases

Pure water contains equal numbers of hydonium and hydroxide ions◦ [H3O+] = [OH-] Neutral

Neutralization reaction:◦ Acid and base mixed

Acids and Bases (2)

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

pH

Carbon◦ Can form four covalent bonds◦ Attach to each other to form strait and branched

chains and ringed structures. 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.

The Chemicals of Life(1.2)

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.

Functional Groups and Reactivity

PP, page 27, #1

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.

Biological Macromolecules

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.

Anabolic Reactions & Condensation Reactions

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

Catabolic Reactions & Hydrolysis Reactions

Hydrolysis and condensation require the assistance of special protein molecules called enzymes – more on enzymes later.

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

Carbohydrates (in detail)(pg. 29)

“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.

Monosaccharides

Trioses◦ Glyceraldehyde (intermediate compound in carbohydrate

metabolism)◦ Dehydroxyacetone (ingredient in sunless tanning products)

Pentoses◦ Ribose (component of RNA)◦ Ribulose (used in photosynthesis)

Hexoses ◦ 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).

Common Monosaccharide Uses

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

Shapes of Monosaccharides

◦ 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.

Oligosaccharides

‘complex carbohydrates’ Monosaccharide polymers several hundred to

several thousand monosaccharides.◦ Energy storage and structural support. ◦ Starch: _________________________(amylose +

amylopectin)◦ Glycogen: _____________________________◦ Cellulose: _____________________________◦ Chitin: ________________________________

Polysaccharides

Amylose Unbranched α-glucose polymer α 1-4 glycosidic linkages

Amylopectin 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!)

Plants and Polysaccharides

Heterotrophs use enzymes to hydrolyze amylose and amylopectin into individual glucose molecules and then respirate to extract energy to glucose:

Cellular Respiration:

______________________________________________ Excess glucose molecules are linked to one

another to form glycogen.

Glycogen 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 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).

Corn in your Poop?

Chitin Exoskeleton of insects and crustaceans and cell

walls of many fungi. Monomer is a glucose molecule with a nigrogen-

containing group attached to carbon 2. Second most abundant organic material found in

nature. Used in contact lenses and biochemical stitches.

Building Carbohydrates with Molecular Modelling Set

Building Carbohydrates with Molecular Modelling Set

PPs, page 34. # 2-10

Hydrophobic – composed of H, C and O◦ Insoluble in water but soluble in other nonpolar substances.

Functions◦ 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:◦ Triglycerides◦ Phopholipids◦ Sterols◦ Waxes

Lipids (in detail) (page 35)

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.

Triglycerides

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

Solid consistency at room temperature. More difficult to catabolize.

Saturated Fatty Acids

Examples: plant oils: olive oil, corn oil, peanut oil. ◦ 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).

Unsaturated/Polyunsaturated Fatty Acids

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.

Phospholipids

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.

Phospholipid Bilayer

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.

Sterols

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.

WAXES

Pg. 40#11-13,15-18

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. ◦ 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!

Proteins (in detail) (Pg. 40)

Genetic information in DNA codes specifically for production of proteins and nothing else.

All copies of the same gene produce the same protein.

DNA to 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).

Protein Structure

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.

Formation of a Polypeptide

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.

Polypeptides

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?

__________________________________________________________________________________

Primary Structure

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.

Changing the sequence.

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.

Secondary Structure

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.

α-helix

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.

β-pleated sheet

Spiders are Crazy Cool!• silk contains large amounts of betapleated sheets spiders secrete silkin liquid form and then solidify when exposedto air. Many H-bonds. Strength!

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.

Tertiary Structure

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.

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:◦ Hydrogen bonds◦ Ionic bonds◦ Disulfide bridges◦ Hydrophobic interactions

Will usually return to original orientation if denaturing agent is removed.

Denaturation

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.

Denaturing (2)

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.

Nucleic Acids (in detail) (pg.52)

DNA (deoxyribonucleic acid) RNA (ribonucleic acid) protein.

Monomer: nucleotide◦ Nitrogenous base◦ Pentose sugar◦ Phosphate group.

DNA vs. RNA (both are helical)

Nucleic Acid Monomer

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

Nucleic Acid Sugars

Pyrimidine: single-ringed. Purine: double ringed.

Nitrogenous Bases

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).

Phosphodiester Bond

Double-stranded Strands held together by hydrogen bonds

between nitrogenous bases.◦ A-T: two hydrogen bonds◦ G-C: three hydrogen bonds.

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.

DNA

A nucleotide used to drive energy-requiring reactions.

More on thislater.

Adenosine triphosphate (ATP)

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.

DNA and Evolution

Table on Pg. 54: Summary of Macromolecules.

Work together to fill in the blanks.

Biological Macromolecule Summary

Complete:

#1-9, 11, 13-16, 18-19.

Test on Macromolecules: carbs, lipids, proteins, and nucleic acids.

Next Class:

I have decided to move onto ENZYMES next.

Unit 1, Part 2

First, we need to learn about energy.

ENZYMES.

“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: _________________________________.

An organism is the ‘sum of its parts’

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.

Energy

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.

First Law of Thermodynamics

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.

Bond Energy

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)

Endothermic/Exothermic Reactions

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

Entropy

How do each of the following statements make sense when thinking about Entropy?