Biology 1001 unit 2: Carbon Atoms and Large Biological Molecules

carbon

an element with Atomic number 6 (=> 6 protons + 6 electrons)
The dominant isotope C-12 has ALSO 6 neutrons

• all life on earth is ______ based

all the large molecules

Ability to form 4 bonds makes carbon a good material to form the
backbone of ________________ that living
organisms are made of

inorganic compounds

non-living origin, subject to the laws of physics and chemistry

organic compounds

considered impossible to produce because they were imbued with a “life force”

Fredrich wohler

• trying to make ammonium cyanate using ammonium ions and cyanate ions

• however was shocked to see urea crystals form

• paved the way for synthesis of organic compounds

stanley miller

Tried to recreate conditions of Earth’s early environment.

produced a variety of organic
compounds including:

• amino acids and oily hydrocarbons

  Conclusion: Organic molecules, CAN be formed abiotically (in the
  absence of life) IF conditions are right

why carbon?

• it is small, allowing other atoms to get close enough to share electrons

• it has 6 electrons- 4 in the outer shell

  therefore it can connect up to 4 different atoms (takes 8 to fill its outer shell)

carbon can bond covalently with…

hydrogen, oxygen, nitrogen, Sulphur, phosphorus and other carbons.

junction

carbon acts as a ______ from which a molecule can branch off in 4 directions

• share single electrons- forming tetrahedrons

• or two electrons - double covalent bond

shapes of 3 simple carbon based molecules:

a) methane

b) ethane

c) ethene

methane

• tetrahedron

• CH₄

ethane

• two overlapping

• C₂H₆

ethene

• double bonds- flat/in the same plane

• C₂H₄

carbon skeletons

molecular diversity arises from variation in ____________

carbon skeleton variations:

a) length

b) branching

c) double bond position

d)presence of rings

isomers

compounds that have the same numbers of atoms of the same elements but different structures and hence different properties.

• structural, cis-trans, enantiomers

structural isomers

• differ in the covalent arrangements of their atoms

• have same molecular formula but different arrangement of carbon skeletons

• may also differ in the location of double bonds

cis-trans isomers

• differ in arrangement around a double bond- due to inflexibility of double bonds

• cis- xs are on the same side

• trans- xs are on opposite sides

enantiomers

• differ in spatial arrangement around an asymmetric carbon- mirror images, like left and right hands

• cannot be superimposed on each other

left handed enantiomers

• L or S

• 100 times more effective in ibuprofen

• ineffective in albuterol (counteracts)

right handed enantiomers

• D or R

• more effective in albuterol

• ineffective ibuprofen

thalidomide tragedy

• Marketed from 1957 -1961

• Sedative and drug for morning sickness in pregnancy

• 24,000 children born with severe birth defects

• Probably >120,000 babies died before birth due to teratogenic (affecting embryo or fetus) effects of the S enantiomer

hydroxyl group properties

• -OH

• is polar due to electronegative oxygen

• forms hydrogen bonds with water, helping dissolve compounds suchas sugars

• compound name: Alcohol

hydroxyl group form

carbonyl group

• >C=O

• sugars with ketone groups are called ketoses

• those with aldehydes are aldoses

  compound name: ketone- within a carbon skeleton

  aldehyde- at the end of a carbon skeleton

carbonyl group form

carboxyl group

• -COOH

• acts as an acid (can donate H+) because the covalent bond between oxygen and hydrogen is so polar

  compound name: carboxylic acid or organic acid

carboxyl group form

amino group

• -NH₂

• acts as a base- can pick up an H+ from the surrounding solution

  compound name: amine

amino group form

sulfhydryl group

• -SH

• two- SH groups can react, forming a “cross-link” that helps stabilize protein structure

• maintain straightness or curliness of hair

  compound name: thiol

sulfhydryl group form

phosphate group

• -OPO₃^2-

• contributes negative charge (1- inside, 2- when at the end)

• when attached , confers on a molecule the ability to react with water, releasing energy

  compound name: organic phosphate

phosphate group form

methyl group

• -CH₃

• affects the expression of genes when on DNA or in proteins bound to DNA

• affects the shape and function of male and female sex hormones

  compound name: methylated compound

methyl group form

organic molecule categories

• carbohydrates

• lipids

• proteins

• nucleic acids

momomers

• small molecules

• building blocks of big molecules

• can polymerize- link up to form macromolecules

polymers

• big molecules

polymerized

• linked together

• carried out by dehydration reaction

dehydration reaction

• two molecules become covalently bonded with the removal of water

how a polymer is produced:

• monomers are lined by enzymes

• enzymes remove a hydroxyl (-OH) group from one monomer and a hydrogen (-H) from the other

• then link the two monomers together and release a water molecule (H2O)

• process repeated over and over

dehydration reaction: synthesizing a polymer

hydrolysis: breaking down a polymer

hydrolysis

• to break down large polymers to monomers

• breaks bond between two molecules by the addition of H2O

• example: digestion

carbohydrates

• serve as fuel and building material

• include sugars and polymers of sugars

• monosaccharides/simple sugars

• disaccharides- double sugars

• macromolecules- polysaccharides

monosaccharide

• the simplest carbohydrate

• simple sugars

• monomers from which more complex carbohydrates are built

• all isomers of C₆H₁₂O₆

  ex. glucose, fructose, galactose

disaccharides

• two monosaccharides joined by a dehydration reaction- glycosidic linkage

  ex. maltose, sucrose, lactose

monosaccharide structure

• can be linear or ring

• tend to form rings in a solution- more stable

polysaccharides

• macromolecules- built from monomers

• energy store- storage material, hydrolyzed as needed to provide sugar for cells- ex. starch

• structural molecules- building material for structure that protect the cell- ex. cellulose

functions of sugars (little carbs):

1. energy supply

   • sugars→ major energy source for cells

   • glucose= fuel for cellular respiration →ATP production

2. carbon skeletons

   • provide raw materials for carbon framework, and synthesis of other small molecules

     ex. amino acids, fatty acids, and polysaccharides

starch

• the energy storing polysaccharide found in plants

• made up of glucose monomers linked together

• molecules are helical (spiral)

• different forms- amylose (branched) vs. amylopectin (unbranched)

glycogen

• the energy storing polysaccharide of animals

• polymerized glucose with extensive branching

  → stored in liver, muscle, etc

  → hydrolysis releases glucose on demand

• short term energy store

cellulose

• structural polysaccharide

• polymer of glucose

• essential component of plant cell walls

• leaves, wood

• most abundant organic compound on earth

• indigestible by most organisms

starch vs. cellulose- why the difference?

• glucose exists as two isomers- alpha and beta

• Starch and glycogen are polymers of a glucose→ helical form

• Cellulose is a polymer of β glucose monomers→ linked together- able to form straight close packed chains

• cellulose strong and tough, chemically stable

chitin

• structural polysaccharide

• found in animal exoskeletons and fungal cell walls

• long chain polymer of β glucose- with N-containing side group

lipids

• large (not macro) molecules

• not polymers- more diverse in structure

• commonly hydrophobic (water hating)- have large hydrocarbon regions

types of lipids:

1. fats- energy storage

2. phospholipids- structure

3. steroids and cholesterol- hormonal

fats

• energy storage

• more commonly known as triacylglycerols

  → glycerol’s with 3 fatty acid side groups

• TAGs or triglycerides

• consist of fatty acids joined at one end to glycerol

• main long term energy store in animals

animal fat vs. plant oils

• animal fat is solid because it doesn’t have double bonds meaning it can pack closer together

• plant oils are liquid at room temp because they have double bonds and cant pack as closely together- the fatty acid chains kink

saturated fats

• has no double bonds between C atoms

• all H positions filled

• chains are straight

• ex. dairy

mono-unsaturated fatty acid

• has one double bond in the chain

• chain is bent

• ex. plant oils

poly-unsaturated fatty acid

• more than one double bond

• very bendy

• ex. plant and fish oils

hydrogenation

the process that makes plant oils solid at room temp- margarine

1. take unsaturated fat

2. bubble H through it in the presence of a catalyst

3. double bonds will break, hydrogen will form covalent bonds with carbon

4. all chains will straighten out, making it solid

other functions of fats:

• padding- for internal organs

• insulation

• buoyancy in marine mammals

phospholipids

• structural lipid made up of glycerol joined to two fatty acids and phosphate group

• hydrocarbon chains act as nonpolar, hydrophobic tails

• and rest acts as a polar hydrophilic head

• form bilayers

phospholipids self aggregate into a bilayer because…

they have hydrophilic and hydrophobic parts

steroids

• lipid characterized by carbon skeleton with 4 fused carbon rings

• ex. cholesterol

cholesterol

• steroid

• common component of animal cell membranes

• molecule from which other steroids, including sex hormones are synthesized ex. progesterone, testosterone, estrogen

proteins

• =>50% of dry mass of most cells

• are all polymers of amino acids

• linked in unbranched chains

• made up of one or more polypeptides, each folded and coiled into a specific 3d structure

• =completed sweater

amino acids

• an organic molecule with both an amino group and carboxyl group

general formula for amino acids:

making a polypeptide:

• amino acids are linked together in dehydration reactions

• a peptide pair is formed between each AA pair

• result- polypeptide with amino end and carboxyl end

polypeptide

• a chain of amino acids

• linked together by peptide bonds

• =strand of yarn

four levels of protein structure:

• primary= AA sequence

• secondary= hydrogen bonding in the backbone

• tertiary= overall shape due to interaction of side chains

• quaternary= applies to proteins made up of 2 or more polypeptides

  correct shape is critical to function

when polypeptides are produced inside cells, correct folding is achieved by:

• the intrinsic order of amino acids

• the environment in the cell (pH, concentration, temp)

• other proteins

  misfolded proteins are no longer functional- can cause disease.

nucleic acids (DNA and RNA)

• polymers

• built up of monomers called nucleotides

• linked by dehydration reactions that form

• phosphodiester bonds

nucleotide

=molecule in 3 parts

1. nitrogenous base

2. pentose sugar

3. phosphate group

five nitrogenous bases:

• pyrimidines

  1. cytosine

  2. thymine -DNA

  3. uracil- RNA

• purines

  4. adenine

  5. guanine