the essence of life...biology 1

outline

• Water: the most important molecule in the equation of life?

• Inorganics• Organics

H2O• Earth is misnamed - in fact, the earth’s surface

is covered by 70% water• Living cells are 70–95% water• Life evolved in water• Search for life on other planets can be

simplified as a search for other planets containing water

• The vitally important fluid nature of water is due to hydrogen bonds, as a result of the covalent bonding between H and O2

• The polar nature of the covalent bond between hydrogen and oxygen is critical in forming the known properties of water– Solvency - H2O is the universal solvent– Cohesiveness - leads to adhesion,

capillary action and surface tension– Buffer - H2O can mediate processes by

acting as a buffer– Heat capacity - H2O can absorb heat,

resisting temperature changes

Solvency of H2O• Polarity of water causes it to be an efficient

solvent of ionic compounds, termed hydrophylic compounds– Most biochemical reactions involve solutes

dissolved in water– Water is an essential medium for transport of

reactants and products for biochemical reactions

• Non-polar molecules tend not to dissolve in H2O—termed hydrophobic

Cohesion of H2O molecules

• Transient hydrogen bonding causes water molecules to ‘stick’ together

• Allows water to ‘stick’ to a substrate (adhesion)—e.g., a plant vessel wall

• Cohesion results in capillary action• Cohesion causes a surface tension at

air/water interface, causes water to bead

H2O as a buffer

• Water can protect cells from environments of dangerously high chemical concentrations

• By acting as a buffer (e.g., acid/base environments), water minimizes fluctuations in pH

The high heat capacity of H2O• Hydrogen bonds require extra energy to

break—thus, H2O has an unusually high heat capacity

• A large body of H2O can act as a heat sink (reducing greenhouse effect?)

• Evaporative cooling is a major mechanism in keeping organisms from overheating

• The marine environment has a relatively stable temperature

Other inorganics

• Life requires other inorganic molecules and elements to mediate biochemical processes– In some cases they are reactants – In other cases they are an defining part of

an organic molecule

• For example, Na+Cl-, K+, Mg+, HCO3-

Organics• Involve carbon, which has an outer shell

of 4 electrons, leaving 4 free spaces• Organic molecules are thus generally

based on a unit shape of a triangular based pyramid

• Organic molecules are generally defined by the elements other than carbon in them, and by the types of bonds they form with carbon

– Organic molecules are often formed of monomers (small, basic units) which may join together to form polymers (long chains of monomers).

– One typical method of polymerization is by the condensation reaction (removal of an OH- group and an H+ group from two respective monomers to form water, leaving a bond between the two monomers

– Condensation reactions can be reversed via hydrolysis (the addition of water to a bond within a polymer

– Condensation and hydrolysis reaction are common mechanisms in metabolism

Biologically important organic molecules

• Carbohydrates (for short term energy)• Lipids (for long-term energy and

membrane structure)• Proteins (for membrane and other

organelle structure• Nucleic acids (for the construction of

DNA and RNA—the cell “management”)

Carbohydrates• Monomer form is the monosaccharide (in the ratio

of CH2O). For example, – 6-carbon sugar (hexose): e.g., Glucose (C6H12O6)– 5-carbon sugar (pentose): e.g., Ribose

• Two monosaccharides can join together to become a disaccharide via a condensation reaction that creates a glycosidic linkage. For example– Sucrose (Glucose + Fructose)– Maltose (Glucose + Glucose)

• Many monomers joined together form the polymer polysaccharide– Polysaccharides are a good source of

medium term energy. For example,• Starch (a helical glucose polymer with 1-4

linkages, either unbranched (amylose) or branched (amylopectin)

• Glycogen (highly branched form of amylopectin)– Polysaccharides are also structurally

important. For example, • Cellulose (D-glucose unbranched chain using

1-4 linkages)• Chitin (in fact an amino sugar)

Lipids• Typically hydrophobic compounds• Fats are important for long term energy

stores, and consist of 3 fatty acid chains joined at one end by a molecule of glycerol via an ester link– Fatty acid chains vary in length, and may have

double bonds (unsaturated) or not (saturated)• Saturated fats are usually solid at room temp., and

are found in animals• Unsaturated fats are usually liquid at room temp.,

and are found in plants

– Phospholipids have one of the fatty acids in a triglyceride replaced by a phosphate group

• The fatty acid hydrocarbon tails are hydrophobic• The phosphate group (ionic) is hydrophillic

– Phospholipids thus show ambivalent behavior to water

– Phospholipids are a major component in the structure of a biological membrane

– Biological membranes can be argued to play perhaps the most important role in cellular metabolism

• A third group of lipids are the Steroids– Steroids play an important role in the

regulation of metabolism. For example, • Cholestrol

• All fats have high energy bonds. Hydrolysis reactions thus yield high energy. Fats are typically broken down for their high energy content

Proteins– Proteins are made of monomers termed Amino Acids

which:• have both an amine (NH2) and a carboxyl acid (COOH)

group• A third group (given the symbol ‘R’) defines the amino acid

– Amino acids join together via condensation to form polypeptide chains (linked by peptide bonds). Components of these chains then interact to give a unique 3-dimensional structure, vital for the macromolecule’s reactivity

– Such a 3-dimensionally shaped polypeptide is termed a protein

• There are only 20 common amino acids• Proteins are defined by 4 types of

structure• Primary structure refers to the sequence

and the types of amino acids linked together. Polypeptide chains are typically very long)

• Secondary structure refers to linkages between carbons within the polypeptide backbone ( pleating, helix coiling) by hydrogen bonds

• Tertiary structure refers to linkages between R-groups, including– Hydrogen bonds– Sulphur bridges– Others

• Quarternary structure refers to incorporation of other polypeptide chains. For example,– Hemoglobin consists of 4 polypeptide

chains around Fe

Nucleic Acid• Nucleic acids store and transmit

hereditary information• This information ultimately is expressed

through the production of goal-specific proteins, including enzymes and structural molecules

• There are two types of nucleic acid:– DNA (deoxyribonucleic acid)– RNA (ribonucleic acid)

• Nucleic acids are polymers, the individual unit (monomer) of which is the nucleotide

• Nucleotides have:– A “backbone”

• A pentose sugar– Ribose– Deoxyribose

• A Phosphate group

– A nitrogenous base

Purine Pyrimidine

DNA only ThymineDNA and RNA Guanine

AdenineCytosine

RNA only Uracil

DNA• Is a double stranded helix (model first proposed by

Watson and Crick). Deoxyribose lacks an OH group on the 2nd carbon– Nitrogenous bases always pair purine to pyrimidine.

Specifically,• Adenine-Thymine (A-T)• Guanine-Cytosine (G-C)

• Contains coded information to program all cell activity• Makes up genes, which in turn group into

chromosones• Is responsible for the manufacture of mRNA

RNA• Is a single stranded nucleic acid that is the

intermediate agent in production of proteins• Components of RNA are similar to that of DNA,

except uracil (U) is substituted for thymine (T)• There are several kinds of RNA, including

– Messenger mRNA– Transfer tRNA– Ribosomal rRNA

• Other uses for nucleotides include chemical transfer agents (ATP) and electron transfer agents (NAD)