Grade 12 Biology - Biochemistry TEST #1

You will get that 95+

Biochemistry

the study of chemical processes in
living organisms.

Elements

A pure chemical substance that cannot be broken
down into simpler substances.

Compounds

Substances that contain two or more elements
chemically combined

Molecules

A type of compound made by covalently
bonding two or more atoms together

Organic Molecules

A carbon-containing molecule in which
carbon atoms usually are bonded to hydrogen

Inorganic Molecules

Molecules that do not contain carbon

Atom

The smallest unit of an
element which retains all of
the properties of the element

Representing Atoms

Element symbol

Atomic Number & Atomic Mass

Atomic Number = # Protons = # Electron
Atomic Mass = Protons + Neutrons

Isotopes

Atoms of the same element that have the same
number of protons

Radioactivity

Radioactive decay involves the spontaneous
transformation of one element into another.

Radioisotopes

Isotopes that have unstable nuclei and undergo radioactive decay.

Half-Life

The time it takes for one half of the
nuclei to decay

Radioactive Dating (for Carbon-14)

Plants absorb a mixture of radioactive (C-14) and non-radioactive (C-12) carbon dioxide from the air and water for photosynthesis and then Scientists can calculate the time that has passed since an organism's death by measuring the ratio of C-12 to C-14 in a dead or fossilized organism

Radioactive Tracers

Radioactive isotopes are used in biological

Nuclear Medicine

Uses radioactive materials either to image a patient's body or to destroy diseased cells

Orbital

Electrons occupy volumes of space (3-D) around
the nucleus called orbitals or energy levels
Valence shell full of electrons = HAPPY =
STABLE ATOM

Electronegativity

A measure of an atom's ability to attract/pull a shared electron pair in a covalent bond
Electronegativity number (EN) - the larger the number

Intramolecular Bonds

Forces that hold atoms together
within a molecule

Non-Polar (Pure) Covalent Bond

Two atoms SHARE electrons (nearly) EQUALLY
Occurs between:
Atoms of the same element (∆EN = 0) *All H O F Br I N Cl elements.
Atoms of of different elements (∆EN < 0.3)
Single

Polar Covalent Bonds

Two atoms SHARE electrons
UNEQUALLY
∆EN = 0.4 - 1.7
One atom is slightly negative (δ -) and the
other is slightly positive (δ +)
Polar molecules have dipoles because of oppositely charged ends

covalent bond

Covalent bonds are bonds formed between two nonmetal elements that share electrons.

Ionic Bond

• Formed by a TRANSFER of electrons from atom to atom (usually metal to non-metal)
• ∆EN= 1.7 - 3.3
• Ions are atoms that have obtained a stable valence shell by losing or gaining electron

Atom losing electrons

→ (+) charge → cation

Atom gaining electrons

→ (-) charge → anion

Electronegativity scale

0-0.3 = Non polar covalent
0.4-1.7 = Polar covalent
1.7-3.3 = Ionic

Intermolecular Bonds

Forces of attraction between molecules
They are weaker than intramolecular bonds

Hydrogen Bonding

A weak association between an atom with
partial negative charge and a hydrogen with
partial positive charge

Hydrophobic Interactions

Polar Molecules = hydrophilic ("water-loving")
Non-Polar molecules = hydrophobic ("water-hating")
Non-polar molecules have a tendency to clump together when mixed with polar molecules

Carbon Chemistry

Compounds that contain carbon (a few exceptions) are
called organic compounds

Carbon

• Carbon can form up to 4 bonds with other atoms (contains 4 valence electrons) giving it covalent compatibility with many different elements
• May form single

Synthetic Organic Chemistry

• The biomaterials industry develops synthetic substances that can
  integrate well with living tissues
• Biomedical engineers design

Molecular Formula

Shows the number of each atom in an
element or compound

Structural Formula

Shows how the different atoms are bonded together

Skeletal Formula

Shows each carbon atom as an end or bend in the chain of the molecule

Hydrocarbons

Molecules containing only carbon and hydrogen
atoms

Functional Groups

• Parts of molecules involved in chemical
  reactions

• Elements like H, O, S, N, and P (and form reactive clusters)

• Often make a molecule polar

R - Group

• "Radical" group
• An abbreviation for any group where a carbon or hydrogen is attached to the rest
• It is NOT a specific functional group

Hydroxyl (-OH)

• Polar due to the electronegative oxygen atoms

• Water molecules are attracted to hydroxyl group

• Names usually end in -ol

Carbonyl (-CO)

• Carbon is joined to the oxygen by a double covalent bond

• Polar (hydrophilic)

• Aldehyde is formed when this group

  is on the end of a carbon skeleton

  and the carbon is bonded to a

  hydrogen (R-CHO)

• Ketone is formed when a

  carbonyl group is

  not on the end of a (R-CO-R’)

Aldehyde

is formed when this group

is on the end of a carbon skeleton

and the carbon is bonded to a

hydrogen (R-CHO)

Ie. Formadehyde (CH₂O)

Functional Group?

Carbonyl - Aldehyde

Functional group?

Carbonyl - Ketone

Ketone

is formed when a

carbonyl group is

not on the end of a chain

(R-CO-R’)

Ie. Acetone (CH3COCH3)

Carboxyl (-COOH)

• Carbon atom double bonded to an oxygen atom

and single bonded to a hydroxyl group (-OH)

• Polar (hydrophilic)

• Source of hydrogen ions (H+), which makes a

  molecule acidic. These organic acids are called

  carboxylic acids.

Functional Group?

(-COOH) Carboxyl - acids

carboxylic acids.

Source of hydrogen ions (H+), which makes a molecule acidic.

Amino (-NH2)

• Nitrogen atom bonded to a hydrocarbon radical and two

  hydrogen atoms

• Polar (hydrophilic)

• Molecule is basic. These molecules are organic bases

  called amines.

• Act as a base, picking up protons (H+) from the surrounding

  solution.

Functional Group?

Amino group = molecule is basic + bases are called amines

Sulfhydryl (-SH)

• Sightly polar (hydrophilic)

• Help stabilize structures of

  proteins

Phosphate (PO₄⁻³)

• Polar (hydrophilic)

• Negatively charged

• Molecule is acidic

• Found in molecules that make up the

  cell membrane, as well as DNA and

  RNA

• Transfer of energy between organic

molecules (ATP)

Functional group in these molecules?

Aldehyde

Functional group in these molecules?

Carboxylic acid

Functional group in these molecules?

Ketone

Functional group in these molecules?

Alcohol

Macromolecules

large organic molecule

polymer

large molecule consisting of many identical or similar subunits connected

together

monomer

subunit or building block molecule of a polymer

4 classes of macromolecules

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

Catabolic Reaction

Breakdown of large molecules into smaller ones

Releases energy in the process

Anabolic Reaction

Buildup of smaller molecules into larger ones

Requires energy input

Condensation (Dehydration Synthesis) Reaction

Joining smaller molecules into larger ones with the input of energy (e.g.:

ANABOLISM)

Releases a WATER molecule as a result

An H atom from the functional group of one molecule combines with an OH group from another molecule to form H-OH (i.e.: Water)

The resulting molecules are linked together

Hydrolysis Reaction

• This process involves the ADDITION of water to break the bonds between large molecules to form smaller molecules (i.e.: Catabolism)

• Releases energy in the process

• The H atom from water is added to one molecule, while the OH group is added to the other

• Enzymes are involved as well to help speed up these reactions (catalyst)

Neutralization Reactions

ACIDS

Release H+ ions when dissolved in water

Proton donors

Ex. HCl 🡪 H+ + Cl-

BASES

Release OH- ions when dissolved in water

Proton acceptors

Ex. Ca(OH)2 🡪 Ca2+ + OH-

What happens when you mix an acid and a base?

Acid + Base 🡪 Water + Salt

Oxidation Reduction (Redox) Reactions

Transfer of electrons between molecules

OXIDATION = loss of electrons by a molecule

REDUCTION = gain of electrons by another molecule

These reactions occur at the same time - when one molecule undergoes oxidation, the opposite must also occur

In biological systems, redox reactions involve the removal of H

atoms from one molecule and the addition of H atoms to

another molecule

Function of Carbohydrates

• Used as sources of ENERGY

• Cell surface markers for cell-to-cell communication

• Building materials

Carbohydrates

• Contain C, H, O in a 1:2:1 ratio

• Formula: (CH2O)n (n = # of Carbons)

• Sugar names end in –ose

Simple Carbohydrates:

Monosaccharide and Disaccharide

Complex Carbohydrates:

-Polysaccharide and Oligosaccharide

MONOSACCHARIDE

Single sugar molecule (smallest monomer of a carbohydrate)

Formula: C6H12O6

Examples: Glucose, Fructose, Galactose

What is this?

Glucose

What is this?

Galactose

What is it?

Fructose

Carbohydrates are Characterized

1.) Number of carbons

ie. ribose has 5 carbons, glucose has 6

carbon

2.) Functional Groups

An –OH group is attached to each carbon

except one, which is double bonded to a

carbonyl group (=O)

glucose and galactose have an aldehyde

group while fructose has a ketone group

Isomers

are monosaccharides with the same chemical formula but

different arrangement of atoms

What is it?

Alpha glucose

What is it?

Beta Glucose

Disaccharides

composed of two monosaccharides (monomers) joined through a

condensation (dehydration synthesis) reaction, forming a

glycosidic linkage (covalent bonds)

Link between C1 of a glucose molecule and C4 of a second

glucose

Glucose + Glucose

Maltose

Glucose + Fructose

Sucrose

Glucose + Galactose

Lactose

FORMATION OF A DISACCHARIDE:

DEHYDRATION SYNTHESIS: Hydroxyl group (-OH) of 1 sugar is combined with a Hydrogen atom (-H) of another

sugar, forming a water molecule

FORMATION OF A DISACCHARIDE (2)

HYDROLYSIS

Opposite of dehydration synthesis

In order to separate disaccharides back into their

component monosaccharides, 2 things are needed:

Water

A specific ENZYME (biological chemical that speeds up reaction

rates)

Maltase (separate maltose into 2 glucose)

Sucrase (separate sucrose into glucose & fructose)

Lactase (separate lactose into glucose & galactose)

Oligosaccharides

3-10 monosaccharides linked

glucose + galactose + fructose = Raffinose

Found in beans, peas, lentils, broccoli,

asparagus

*Humans lack enzymes to digest oligosaccharides (causes bloating,

cramps, gas)

Polysaccharides

More than 10 monosaccharides linked

Most are made up of hundreds of monosaccharides bonded together

- Types:

Starch: glucose storage in plants *long term energy

2. Glycogen: glucose storage in animals *short term energy

3. Dietary Fiber: not used for energy (not digestible by humans)

-Cellulose: structural support in plants

-Chitin: structural support in organisms

Glycosidic bonds in Starch

Starch

A starch molecule contains hundreds of glucose molecules in

either

branched chains: Amylopectin or

unbranched (coiled) chains: Amylose

Straight chain polymer of α glucose 1-4 glycosidic

linkages

Glycogen

Found in liver and skeletal muscles

Many branch points allows for rapid break down

for glucose to be released and used for energy

Cellulose

Structural support in plant cell walls

Difficult for humans to digest so used as fibre in diets

Also used by humans in

wood for lumber and paper

cotton and linen for clothing

Straight chain polymer of β glucose 1-4 glycosidic

linkages

Chitin

Add nitrogen containing group to C2

Structure support - exoskeleton of insects,

crabs, lobsters, fungi cell wall

Also used in medicine: contact lenses,

surgical thread

What is the function of lipids?

• composed of carbon, hydrogen, and oxygen atoms

higher proportion of non-polar C-H (high energy) bonds

makes lipids extremely hydrophobic (insoluble in water)

• Provides long-term energy storage, cushions and insulates

organs, cell membrane structure, synthesis of hormones

• Gram for gram, fats contain more stored energy than

carbohydrates - due to high proportion of C-H bonds

Fat

38 kJ or 9kcal of energy/g

Carbs:

17 kJ or 4kcal of energy/g

Lipids (Types)

1) Triglycerides (fats)

2) Phospholipids

3) Steroids

4) Waxes

Fatty Acids

The building block

(monomer) of lipids

Chain of carbon atoms

Carboxyl group (-COOH)

at alpha (α-) end

Methyl group (-CH3) at

omega (ω-) end

Lipids yield double the

amount of energy as

carbohydrates per gram

Glycogen is more accessible

to break down; carbs are

used up before lipids are

broken down

How are fatty acids characterized?

Length of carbon chain

Saturation

Degree of Saturation

Location of double bonds

Hydrogenation

Orientation of hydrogen around double bond

Length of Carbon Chain (Lipids Characterization)

-Short-chain fatty acids (<8 carbons)

- Medium chain fatty acids (8-12 carbons)

- Long chain fatty acids (>12 carbons)

Saturation (Lipids Characterization)

Saturated fatty acids:

• have only single bonds between C atoms

contain maximum # of H atoms possible

Unsaturated fatty acids:

• have one or more C-C double bonds

fewer than maximum # of H atoms possible

formed by removing H atoms from molecule

• Double bonds create a “kink” or bend in

shape

Double bonds create oils/liquids because

they prevent molecules form packing

together closely enough to solidify

Saturated fatty acids:

have only single bonds between C atoms

contain maximum # of H atoms possible

Unsaturated fatty acids:

have one or more C-C double bonds

fewer than maximum # of H atoms possible

formed by removing H atoms from molecule

Double bonds create a “kink” or bend in

shape