The Chemistry of LifeIB Biology

Biochemistry Elements of lifeMost common elements of living things: (3.1.1)• Carbon (C)• Hydrogen (H)• Oxygen (O)Other elements both plants and animals have:

(3.1.2 & 3.1.3)• Nitrogen (N)

DNA and RNA

Amino acids (proteins)

• Calcium (Ca)

Component of cell walls

Component of bones and teeth

• Phosphorus (P)

ATP• Adenosine triphosphate stores energy in both plants and

animals

DNA and RNA

• Iron (Fe)

In hemoglobin (animals)

In cytochromes• Molecules in the electron transport chain (ETC) of:

– Photosynthesis (in plants)

– Cellular respiration (in plants and animals)

• Sodium (Na)

Ion used for osmosis – “salty roots”

Ion used for nerve transmission in animals

Atom vs. Ion

Ex: Hydrogen• Atom

• Ion – charged particle

1 p+

1 n0

1e-

1 p+1 n0

(no electron orbiting)

H

H+

Water (3.1.4)

1. Structure

-O H+

water is polar (has a positive and +H negative end)

Hydrogen BondO H 1. alone they are weak

2. together they are strong

H ex: slide on a desk

O H

H

Oxygen is very electronegative, which means it has an affinity for the electrons it is “sharing” in the covalent bond with hydrogen.

The hydrogen bond is the attraction between the slightly positive H and the slightly negative O

2. Thermal Properties of Water

(3.1.5, 3.1.6)

a) Water has a high heat of vaporization

• Takes a lot of heat to change the state of water from a liquid to a gas

• 60 times more energy to vaporize water than alcohol

• Because energy (heat) is required to vaporize water (even when it’s at its boiling point), evaporation of water cools down surfaces (SKIN, LEAVES)

a)

b) Water has a high specific heat• 2X that of alcohol• 4X that of air• 1 calorie raises 1 gram of water 1o C• Keeps temperature of water constant

c) Water changes density as it freezes

10oC 4oC 0oC

Less dense Most dense Least dense

(sinks) (ice floats)

3. Cohesive properties of water (3.1.5, 3.1.6)

• Molecules stick together (hydrogen bonds)• Due to polarity• Water moves up the xylem in plant stems

– Capillary action– Cohesion and adhesion

» Adhesion occurs when water clings to xylem tissue during plant transpiration

1.

2.

4. Solvent properties of water (3.1.5, 3.1.6)• Salt (ionic-ally bonded) is dissolved in water (because

it’s polar) and carried by blood

Na+ -O H+

+H

Cl-

Hydrophilic – has an affinity for water; “water-loving”

ex: glucose in blood

sucrose in plants

Hydrophobic – water fearing

ex: oil, grease

Question: When is it beneficial to have lipids be hydrophobic?

5. Significance of water to living organisms (3.1.6)

PLANTSANIMALS

A. Coolant evaporation evaporation-use of heat for on leaf causes of sweat causesevaporation cooling cooling(high heat ofVaporization)

B. Transport carries carries medium sucrose glucose-because itspolarity causesit to be a goodsolvent

PLANTSANIMALS

C. Good

habitat -water stays at a constant

-due to temperature high specific

heat

1. Keeps

temperature

constant

2. Transparency -photosynthesis -see prey

Organic – contains carbon (and usually hydrogen), and is found in a living organism

-ex: C6H12O6 glucose

• Exceptions:• Hydrogencarbonates – (a.k.a. bicarbonate) the anion

HCO3-

• Carbonates – the anion CO3-

• Oxides of carbon – carbon monoxide (CO), carbon dioxide (CO2)

(3.2.1)

(continuing… NOT talking about water anymore!)

4 Biological Molecules: 1. Carbohydrates (sugars)

• Monosaccharides – major nutrients for cells

glucose, galactose, fructose, ribose

Glucose circulates in animal blood and is used by cells for energy (3.2.4)

Fructose is the sugar in the fruit of plants

• Disaccharidesglucose + glucose maltose

glucose + fructose sucrose

glucose + galactose lactose

Lactose is the sugar in milk – gives energy (3.2.4)

Sugar is transported as sucrose through the vascular tissue of plants (3.2.4)

(3.2.3)

• Polysaccharides (3.2.3.& 3.2.4)

Energy-storing in plants: starch

Energy-storing in animals: glycogen

Structural in plants: cellulose

Structural in animals: chitin

All of these are made of chains of glucose molecules

2. Proteins (structure, enzymes)

Amino acids are the building blocks

2 amino acids – a dipeptide

Peptide Bonds

R R R R

H2N – C – C – N – C – C – N – C – C – N – C – C – OH || || || ||

H O H H O H H O H H OAmino

CarboxylThis is a ‘polypeptide’

3.2.5 Condensation & Hydrolysis Reactions

• When are joining subunits (monomers) of molecules together to make polymers, a water molecule is given off.

• This is a condensation synthesis.• When a polymer is broken into monomers, a water

molecule is used.• This is hydrolysis.

NH2 -–C—COOH + NH2—C—COOH NH2—C—CO—NH—C—COOH + H2O

R R R R

H H H H

Mono Mono Polymer Water

3. Lipids (fats; mainly for energy storage, thermal insulation, and structure)H GLYCEROL O 3 FATTY ACIDS | ||

H C OH HO C (CH2)n CH3

O ||

H C OH HO C (CH2)n CH3

O ||

H C OH HO C (CH2)n CH3 |

H

Hydrolysis vs. Condensation Synthesis (3.2.5, 3.2.6)

H O | ||

H C O C (CH2)n CH3

O ||

H C O C (CH2)n CH3

O ||

H C O C (CH2)n CH3 |

H +3 H2O Lipid + Water

Phospholipid

O-

|

R – O – P – O – CH2

|| |

O H – C – O – C – (CH2)n – CH3

|

H – C – O – C – (CH2)n – CH3

|

H

POLAR HEAD

(hydrophilic)

NON-POLAR TAIL

(hydrophobic)

O

O

This negative oxygen makes

this part of the molecule

hydrophilic

Energy Storage (3.2.7)

Carbohydrates vs. Lipids

Soluble in water, Insoluble in water, do not

easily transported in blood cause problems with osmosis

Broken down quickly Broken down for energy

for energy more slowly

Less energy per gram Twice as much energy

per gram

4. Nucleic Acids (DNA & RNA) (3.3.1, 3.3.2)

• Made of nucleotides (these are the monomers)

Phosphate

Sugar Nitrogen

Base

Nitrogen Bases• Adenine• Guanine• Cytosine• Thymine (*DNA only)

• Uracil (*RNA only)

Ribose or Deoxyribose sugar

• DNA (3.3.3, 3.3.4, 3.3.5)

P P

D A T D

P P

D G C D

P P

D C G D

P P

D G C D

-double stranded

-Helix (twisted)

-A-T and G-C are complementary

(weak) hydrogen

bond

One nucleotide

Covalent

bond

• RNA

P

R U

P

R A

P

R C

P -single strand

R G -U instead of T

You MUST be able to recognize the following molecules from diagrams showing their structure: (3.2.2)

• Amino acids

• Glucose

• Ribose

• Fatty acids