1.4: Properties of Biological Macromolecules

Structure and function of polymers depends on the chemical properties and assembly of their monomers
Macromolecule: chains of polymers linked together
Polymers: large molecule made up of monomers joined by covalent bonds
Monomer: single repeating subunit

Nucleic Acids:

Biological information is encoded in sequences of nucleotide monomers
DNA & RNA are polymers of nucleotides; nucleotides named by nitrogenous base

Structural Components of Nucleotides

Nitrogenous Base: has 2 types;
- Purines: Adenine and Guanine with double ring structure
- Pyrimidines: Thymine, Cytosine, Uracil with single ring
Phosphate Group: (-) charged
Five-carbon sugar: deoxyribose or ribose; nonpolar

DNA and RNA synthesis

DNA nucleotides form single-stranded DNA when phosphate group joins to sugar of another nucleotide → covalent
Two of the strands are paired by weak HB between bases → form double-stranded DNA
Nucleotides are added to the 3’ end of the strand; nucleotides linked by sugar-phosphate covalent bonds

Sugar-Phosphate Backbone

Composed of alternating sugar and phosphate groups that defines directionality & structure of nucleic acids
The sugar-phosphate backbone is polar

Antiparallel

The DNA Molecule has directionality, otherwise known as Antiparallel ⇒ double helix
The two strands run in opposite directions
- One strand is arranged 5’ → 3’ end & other is 3’ → 5’
- Antiparallel: gives DNA stability and allows for replication–if wasn’t then nucleotides wouldn’t be complementary
Binding of the nitrogenous bases
- Cytosine + Guanine with 3 hydrogen bonds = stronger
- Adenine + Thymine with 2 hydrogen bonds
Purine + Pyrimidine = only uniform diameter suitable for double helix

5’ End

The phosphate group is bound to the carbon at the 5th position on sugar

3’ End

Starting from the 5’ end, the positions alternate until it reaches the open -OH attached to 3’ carbon (where phosphate will attach to)

DNA vs RNA

DNA has:

– Double strand

– Deoxyribose 5-carbon sugar

– Functional group lacks O2

– Thymine not Uracil

– Antiparallel in directionality

RNA has:

– Single strand

– Ribose 5-carbon sugar

– Hydroxyl functional group

– Uracil not Thymine

DNA and RNA

DNA and RNA are primary sources and carriers of genetic information.
Have all 3 components of nucleotides joined together w/ dehydration synthesis
Bases perpendicular to the sugar-phosphate backbone

Proteins

Function:

Structural: ex: keratin in hair, collagen in tissues
Storage: ex: casein in milk
Transport: ex: membrane of cells and oxygen carrying hemoglobin in red blood cells
Defensive: Ex: antibodies that protect against foreign substances
Enzymes: regulate the rate of chemical reactions

Protein Combination and Separation

Peptide Bond: Covalent bond that holds amino acids together (dehydration synthesis)
Polypeptide Chain: Multiple combinations of amino acids bonded together

Structure

Proteins differ from each other by number and arrangement of 20 types of amino acids that vary in polarity

Always contains amino group (basic), carboxyl (acid), R group, H

R Group:
- “Random group” → determine chemical properties & differences of amino acids
  - R groups determine if they are polar or nonpolar
- The interaction of these R groups determine structure and function of that region
- Polar R groups have N, S or O while non-polar have C or H
Proteins have directionality: one end is a carboxyl group and the other an amino group
- Amino acid are added onto the carboxyl end thru dehydration synthesis
Dimer: protein with two tertiary structures

The 4 Structural Levels of Proteins

PRIMARY STRUCTURE

Order of amino acids connected by covalent bonds which determines the overall shape and function of a protein

SECONDARY STRUCTURE

Local folding of the amino acid chain (polypeptide) into elements such as alpha-helices and beta sheets thru hydrogen bonding
- Misfoldings lead to prions

TERTIARY STRUCTURE

The overall 3D shape of the protein as a result of different interactions between amino acids
- Usually makes up structure of globular proteins; minimizes free energy & increases stability
Components of a tertiary structure:
- Hydrogen bonds and ionic bonds between R groups of amino acids
- Disulfide bonds: sulfur atom in amino acid cysteine bonds to sulfur atoms in another cysteine
  - Helps maintain folds of amino acid chain
- Hydrophobic interactions/effect: occurs when hydrophobic R groups move toward the center of protein (away from water in which protein is usually in)

QUATERNARY STRUCTURE

Arises from non-covalent interactions between multiple polypeptide units (ex: hemoglobin)
- Basically, two or more polypeptides (2nd) into single protein; not all proteins have it
Most proteins are made of a single polypeptide chain but some have multiple chains called subunits that allow for 4th structure.

Carbohydrates

Function: main source of energy (for ATP) and cell structure
- Carbs (+fats, lipids) are high energy bcuz have many hydrogen atoms with e-
Contain carbon, hydrogen and oxygen (1:2:1) held by covalent bonds
Pentoses: (5-carbon sugars) include ribose and deoxyribose & make up nucleic acids
Hexoses: (6-carbon sugars) are in the food that we eat and include glucose, fructose, and galactose (monosaccharides)

Simple: Monosaccharides and Disaccharides

Dehydration synthesis of two monosaccharides makes a disaccharides
glucose, frutose, galactose
- Structural isomers → placement of carbon atoms are diff → different functions
  - Alpha glucose (storage) and beta-glucose (structure) differ by reversal of H and OH
- Monosaccharides provide immediate energy bcuz don’t need hydrolysis
- Simple carbs are polar bcuz of -OH functional group which makes them hydrophilic
  - Some polysacch like cellulose & starch are insoluble
- Disaccharides include…
  - Glucose + Glucose = Maltose
  - Glucose + Fructose = Sucrose
  - Glucose + Galactose = Lactose

Complex: Polysaccharides → energy storage

Polymer made of repeating monosaccharide monomers; usually consisting of glucose
Cellulose: make up plant wall, non digestible (fiber) in humans, long chains of glucose
Chitin: fungi cell wall
Glycogen: energy storage in liver and and stomach cells (animals)
Starch: long term storage carb for plants, quick energy for humans

Lipids: Fats, Steriles, Phospholipids

Function: cell membrane (phospho,) insulation, protection, fat is long term and high energy
Structure: Nonpolar, hydrophobic
- Not true macromolecules bcuz not large enough

Triglycerides: fats and oils

Structure: 3 acid groups from fatty acids (sat or unsat) + one glycerol.
Fatty acids: hydrocarbon with carboxyl group → nonpolar
- Vary in structure by number of carbons and placement of single/double covalent bonds
- Saturated fatty acid: single bonds between carbons and two H (is saturated with H)
  - No double bonds/kinks in chain = molecule can compact together = solid/rigid → build up in bloodstream
Unsaturated Fatty Acids: Two or more double covalent bonds

Stops carbon from packing together and hydrogen from saturating them which makes fat more flexible/liquid

Monounsaturated Fatty acid: one double bond and each has only one H
**differences in saturation determine the structure and function of lipids**

Steroids: are characterized by four linked carbon rings

cholesterol, hormones
Cholesterol maintain cell structure and cell fluidity, used in nervous system & insulation
Hormones: long distance, nonpolar molecules that control bodily activities
- Ex: Testosterone & estrogen made with cholesterol

Phospholipids: Like a triglyceride except one of fatty acids chain replaced by phosphate group (PO₄); part of every cell membrane lipid bilayer

Hydrophilic Head → Has phosphate group with R (random) group attached
Hydrophobic tail → Nonpolar bcuz made up of carbon and hydrogen atoms

The 4 Carbon Compounds

Name	Carbohydrates	Protein	Lipids	Nucleic Acids
Bond (Covalent)	Glycosidic	Peptide	Ester	Phosphodiester
Monomers	Monosaccharides	Amino acids	Glycerol & fatty acids	Nucleotides
Elements	C, H, O	C, H, O, N, *S	C, H, O, *P	C, H, O, N, P