Biochemistry Basics

Chapters 2 and 3

Subatomic Particles and the Atom• Protons (+ charge) and

neutrons (neutral)– found in the nucleus

• Electrons (- charge)– Surround the nucleus in a

“cloud” or orbital

• Orbital– the 3D space where an

electron is found 90% of the time

– Each orbital can only fit only 2 electrons

Isotopes• Different forms of the same

element• Have the same number of

protons, but different number of neutrons

• May be radioactive spontaneously giving off particles and energy

Radioactive Decay and Half-Life• The decay of radioactive elements occurs

at a fixed rate. • The half-life of a radioisotope is the time

required for one half of the amount of unstable material to degrade into a more stable material.

• For example, a source will have an intensity of 100% when new. At one half-life, its intensity will be cut to 50% of the original intensity…. Etc.

• The half-life pattern is the same for every radioisotope, the length of a half-life is different. For example, Co-60 has a half-life of about 5 years while Ir-192 has a half-life of about 74 days.

• May be used to:– date fossils– as medical tracers – to follow a

metabolic process or locate a substance within an organism

6

APPLICATION

In this example, radioactive tracers are being used to determine the effect of temperature on the rate at which cells make copies of their DNA.

DNA (old and new)

Ingredients includingRadioactive tracer (bright blue)

Human cells

Incubators1 2 3

4 5 6

987

10°C 15°C 20°C

25°C 30°C 35°C

40°C 45°C 50°C

TECHNIQUE

2

1

The cells are placed in test tubes, their DNA is isolated, and unused ingredients are removed. 1 2 3 4 5 6 7 8 9

Ingredients for making DNA are added to human cells. One ingredient is labeled with 3H, a radioactive isotope of hydrogen. Nine dishes of cells are incubated at different temperatures. The cells make new DNA, incorporating the radioactive tracer with 3H.

7Temperature (°C)

The frequency of flashes, which is recorded as counts per minute, is proportional to the amount of the radioactive tracer present, indicating the amount of new DNA. In this experiment, when the counts per minute are plotted against temperature, it is clear that temperature affects the rate of DNA synthesis—the most DNA was made at 35°C.

10 20 30 40 50

Optimumtemperaturefor DNAsynthesis

30

20

10

0

Co

un

ts p

er

min

ute

(x 1

,00

0)

RESULTS

3

RESULTS

A solution called scintillation fluid is added to the test tubes and they are placed in a scintillation counter. As the 3H in the newly made DNA decays, it emits radiation that excites chemicals in the scintillation fluid, causing them to give off light. Flashes of light are recorded by the scintillation counter.

Figure 2.5

8

Energy LevelsThird energy level (shell)

Second energy level (shell)

First energy level (shell)

Energyabsorbed

Energylost

An electron can move from one level to another only if the energyit gains or loses is exactly equal to the difference in energy betweenthe two levels. Arrows indicate some of the step-wise changes inpotential energy that are possible.

(b)

Atomic nucleus

Figure 2.7B

Electrons have more potential energy the farther they are from the nucleus.

Bonding – Covalent Bonds

• Atoms bond through interaction of their valence (outer orbital) electrons

• Covalent bond– electrons are

shared between atoms and the valence orbitals overlap

Hydrogen atoms (2 H)

Hydrogenmolecule (H2)

+ +

+ +

+ +

In each hydrogenatom, the single electronis held in its orbital byits attraction to theproton in the nucleus.

1

When two hydrogenatoms approach eachother, the electron ofeach atom is alsoattracted to the protonin the other nucleus.

2

The two electronsbecome shared in a covalent bond,forming an H2

molecule.

3

Name(molecularformula)

Electron-shell

diagram

Structuralformula

Space-fillingmodel

Methane (CH4). Four hydrogen atoms can satisfy the valence ofone carbonatom, formingmethane.

Water (H2O). Two hydrogenatoms and one oxygen atom arejoined by covalent bonds to produce a molecule of water.

HO

H

H H

H

H

C

Polarity

• Electronegativity– Is the attraction of an atom

for electrons

• The more electronegative an atom– The more strongly it pulls

electrons toward itself

•

This results in a partial negative charge on theoxygen and apartial positivecharge onthe hydrogens.

H2O

–

O

H H+ +

Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen.

Ionic Bonds

Cl–

Chloride ion(an anion)

–

The lone valence electron of a sodiumatom is transferred to join the 7 valenceelectrons of a chlorine atom.

Each resulting ion has a completedvalence shell. An ionic bond can formbetween the oppositely charged ions.

Na NaCl Cl

+

NaSodium atom(an uncharged

atom)

ClChlorine atom(an uncharged

atom)

Na+

Sodium on(a cation)

Sodium chloride (NaCl)

• Covalent bonds are stronger than ionic bonds• Covalent and Ionic bonds are intramolecular

forces of attraction because they are within molecules

Intermolecular Forces• intermolecular forces of attraction exist

between molecules

• Van der Waals Interactions– Forms when atoms and molecules are very

close together– Occurs because electrons are in constant

motion and may accumulate by chance on one part of the molecule. The result is “hot spots” of positive and negative charge.

– very weak

• hydrogen bonds – form when the slightly negative O or N that is

bonded to a slightly positive H is attracted to the slightly positive H of a neighbouring molecule

– strongest intermolecular forces

–

+Water(H2O)

Ammonia(NH3)

OH

H +

–N

HH H

A hydrogenbond results from the attraction between thepartial positive charge on the hydrogen atom of water and the partial negative charge on the nitrogen atom of ammonia.+ +

Figure 2.15

18

Morphine

Carbon

Hydrogen

Nitrogen

Sulfur

OxygenNaturalendorphin

(a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds toreceptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match.

(b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine.

Naturalendorphin

Endorphinreceptors

Morphine

Brain cell

Figure 2.17

Morphine affects pain perception and emotional state by mimicking the brain’s natural endorphins

Bicarbonate Buffer SystemWhen excess hydrogen ions are added to the reaction is shifted to the left. This means that some of the added hydrogen ions will react with the bicarbonate ions to produce

carbonic acid and the carbonic acid will dissociate into carbon dioxide and water as shown below.

When hydrogen ions are removed from the reaction, the reaction will shift to the right. More carbon dioxide will combine with water and more carbonic acid will be

produced and more hydrogen ions and bicarbonate ions will be produced.

Water

• highly polar because of asymmetrical shape and polar covalent bonds

• The polarity of water molecules results in hydrogen boding

Hydrogenbonds

+

++

+

–

–

– –

Figure 3.2

High heat of vaporization: In order for water to reach a gaseous state, it must absorb a great deal of heat from surroundings

High Specific Heat Capacity: the amount of heat required to raise the temperature of a substance by 1C. It takes a lot of energy to increase or decrease temperature. Large bodies of water moderate the temperature on land.

Universal Solvent: able to dissolve many polar substances (e.g. salt, sugar, etc.)

Density: Water is most dense at 4C, which is less dense than water. Aquatic life can survive throughout the winter

Adhesion: water molecules are attracted to other molecules (e.g. nutrients)

Cohesion: Water molecules are attracted to one another (between O and H of neighbouring molecules) so water evaporating from leaves of a plant will pull up other water molecules

Surface Tension: A force that occurs at the surface of the water so it behaves as if there is a film on top.

“Like Dissolves Like”• ionic compounds dissolve in water because

the ions separate• Hydration shell

• However, molecules do not need to be ionic to dissolve in water

• polar covalent molecules (eg: sugars, alcohols) can dissolve in water, but large nonpolar molecules (eg: oils) do not

• small nonpolar molecules (eg: O2, CO2) are slightly soluble and need soluble protein molecules to carry them (eg: hemoglobin transports oxygen through the blood)

• hydrophilic – “water-loving;” dissolves in water – e.g. polar or ionic molecules, carbohydrates, salts

• hydrophobic – “water-fearing;” does not dissolve in water – e.g. non-polar molecules, lipids

Acids and Bases

• acid – donates H+ to water; pH 0-7• base –donates OH- to water (or H3O); pH 7-14• neutralization reaction – the reaction of an

acid and a base to produce water and a salt (ionic compound)

Strong and Weak Acids/Bases

• strong acids and bases – ionize completely when dissolved in water– HCl(aq) (100% H3O+

(aq))

– NaOH(aq) (100% OH-(aq))

• weak acids and bases – ionize only partially when dissolved in water– CH3COOH(aq) (1.3% H3O+

(aq))

– NH3(aq) (10% OH-(aq))

27

Functional Groups• Functional groups are

the parts of molecules involved in chemical reactions

• They Are the chemically reactive groups of atoms within an organic molecule

• Give organic molecules distinctive chemical properties

CH3

OH

HO

O

CH3

CH3

OH

Estradiol

Testosterone

Female lion

Male lionFigure 4.9

28

• Six functional groups are important in the chemistry of life– Hydroxyl– Carbonyl– Carboxyl– Amino– Sulfhydryl– Phosphate

29

Some important functional groups of organic compounds

FUNCTIONALGROUP

STRUCTURE

(may be written HO )

HYDROXYL CARBONYL CARBOXYL

OH

In a hydroxyl group (—OH), a hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule. (Do not confuse this functional group with the hydroxide ion, OH–.)

When an oxygen atom is double-bonded to a carbon atom that is also bonded to a hydroxyl group, the entire assembly of atoms is called a carboxyl group (—COOH).

C

O O

C

OH

The carbonyl group ( CO) consists of a carbon atom joined to an oxygen atom by a double bond.

30

Names of Compounds

Acetic acid, which gives vinegar

its sour tatste

NAME OF

COMPOUNDS

Alcohols (their specific

names usually end in -ol)

Ketones if the carbonyl group is

within a carbon skeleton

Aldehydes if the carbonyl

group is at the end of the

carbon skeleton

Carboxylic acids, or organic

acids

EXAMPLE

Propanal, an aldehyde

Acetone, the simplest ketone

Ethanol, the alcohol

present in alcoholic

beverages

H

H

H

H H

C C OH

H

H

H

HH

H

H

C C H

C

C C

C C C

O

H OH

O

H

H

H H

H O

H

Figure 4.10

HYDROXYL CARBONYL CARBOXYL

31

Functional Groups

The amino group (—NH2) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton.

AMINO SULFHYDRYL PHOSPHATE

(may be written HS )

The sulfhydryl group consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group in shape.

In a phosphate group, a phosphorus atom is bonded to four oxygen atoms; one oxygen is bonded to the carbon skeleton; two oxygens carry negative charges; abbreviated P . The phosphate group (—OPO3

2–) is an ionized form of a phosphoric acid group (—OPO3H2; note the two hydrogens).

N

H

H

SH

O P

O

OH

OH

Figure 4.10

Chemical Properties of Functional Groups

• Functional groups possess certain chemical properties that they impart to the molecules to which they are attached.

Hydroxyl Polar – hydrophilic– Water molecules are attracted to hydroxyl group, dissolves in

water (e.g. sugars have hydroxyl groups)

Carboxyl Polar – hydrophilic– Carboxyl group is a source of hydrogen ions (H+) and therefore

makes the molecule acidic

32

δ- δ+

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

solution

• Sulfhydryl Help stabilize structures of proteins

• Phosphate Transfer of energy between organic molecules (ATP)

33

Test your Knowledge

1. Identify the functional groups in the following molecules.

G3P Aspartame Aspirin2. Which of the above molecules are soluble in water? Explain.3. Which of the above molecules can act as a base? an acid? Explain.4. Explain the significance of one of the functional groups on G3P.