Chapter 12 - Reactions of biologically important compounds

Homopolymer

Has an amine and a carboxyl group

Has the same type of repeating monomer all throughout (with two different types of functional groups at the end)

Many biological polymers are built this way

Has an amine and carboxyl functional group

Condensation Reactions (In terms of the body)

Proteins, Carbohydrates, Lipids - all are formed by a condensation reactions

Heteropolymer

Two or more different kinds of monomers are used within the same polymer

They each have different functional groups

One monomer is a diol (two hydroxyl groups - can be internal (OH inside the carbon chain) or terminal (OH outside the carbon chain)

2nd monomer has two carboxylic acids - two carboxylic acid functional groups

Condensation Reaction By-products

Mainly water

Ammonia, hydrogen chloride and methanol - occasionally formed as byproducts of condensation reactions

Glycine and Alanine (Two of the simplest amino acid structures)

Both have amine group and carboxyl group

General Formula Of Amino Acids (Add picture here)

H₂N-CH(R)-COOH (amine group, carbon bonded with another chain, carboxyl group)

2-amino acids

The very next carbon after the carboxyl group is termed as the second carbon - 2nd carbon

The amine (amino) is bonded to the second carbon atom - hence is called (2-amino acid)

is also called a-amino acids

How properties of the side chain (R) affect the amino acid itself - Unclear

• Definition of R group:

  • The basic structure of an amino acid is:
    H₂N–CH(R)–COOH

  • The R group is the variable part attached to the central carbon (α-carbon).

• How R group affects the amino acid:

  • Polarity:

    • Polar R groups → hydrophilic (water-loving) → often found on the outside of proteins.

    • Non-polar R groups → hydrophobic (water-fearing) → often buried inside protein structures.

  • Charge:

    • Acidic R groups (e.g., –COOH) → negatively charged at physiological pH.

    • Basic R groups (e.g., –NH₂) → positively charged at physiological pH.

  • Size and shape:

    • Bulky R groups (like tryptophan or phenylalanine) can affect protein folding.

    • Small R groups (like glycine) allow flexibility in the protein chain.

  • Special properties:

    • Some R groups can form disulfide bonds (cysteine), hydrogen bonds (serine), or act as catalysts in enzymes (histidine).

How amino acids are denoted

In three-letter abbreviations

e.g. Alanine - Ala

Glycine - Gly

Amino acids in body #1

Amino acids in body #2

Amino acids in body - #3

How protein is formed (dipeptide)

When two monomers (amino acids) bond, a peptide link /amide is made(as two monomers are involved)

Called dipeptide

Amide is made (review) - CONH

Water is pushed off

How protein is formed (polypeptide)

When the process for a dipeptide occurs many times - over and over

Overall polymer is called polypeptide

Examples

The direction and the functional groups that interact dictate the product molecule made - can be different —→

Tripeptide

When three amino acids are formed

Where biological polymers are made between amino acids

In the ribosome - a biological synthesizing machine

One monomer unit = 4.2 million gmol^-1

Synthesizing proteins in labs

The synthesis occurs across solid state catalysts

In 85-90 degrees Celsius

Can have protein tailor made in few hours

They add amino acids one-by-one - making it into a polypeptide

How polypeptides are named (Need more attention)

The first three letters named together

e.g. Ala-Glu-Gly-Cys-Val-Lys

N terminal

The side which has the amine group (NH₂)

C terminal

The part which has the carboxyl group (COOH)

Insulin

Made up of 51 amino acid residues

Is formed through condensation polymer reaction

Has an N-terminal at the start (next to Phe - Phenylalanine), because it is not involved in the reaction

Has a C-terminal at the end (next to Thr - Threonine, because the COOH is not bonded to anything)

Sulfurs within the insulin

S - sulphur atoms

Are part of cytosine

When the sulphides form, they create a disulphide bridge/disulphide bond

Act like “molecular staples” and hold the insulin molecule in shape

Main structrual component of all plants

Polymer cellulose

Belongs to carbohydrates

Cabrohydrate Formula

C_x(H₂0)_y - x and y are whole numbers

Monosaccharides

Smallest carbohydrates

White, sweet-tasting and highly soluble in water

Glucose, Galactose, Fructose (Isomers of one another)

Are all isomers of one another, (e.g. the OH group in glucose and galactose are different)

All are C₆H₁₂O₆

All have polar hydroxyl groups - they can make hydrogen bonds with water - are highly soluble

Glucose

In all living things

Juice of fruits, sap of plants

Blood and tissue of animals

Product of photosynthesis - key energy source in most forms of life

Fructose

In many fruit juices and honey

Main role in body is an energy source

Most common sugar in fruit, especially berries

Galactose

Not found free in nature (Cells use galactose as a building block, not mainly as a fuel.

• Free galactose can be toxic in high amounts, so the body tightly controls it.

• It’s more chemically stable and biologically useful when attached to other molecules.)

Bonded with larger compounds (e.g. lactose- the main sugar in milk)

Disaccharides

Carbohydrates created by the reaction between two monosaccharide molecules

Are bonded through a condensation reaction - water is ejected

Leaves behind a glycosidic link/ether functional group

Glucose + Glucose = Maltose

Glucose + Fructose = Sucrose

Ether functional group/Glycosidic Link (Insert Visual Representation Here)

The link found between monosaccharide units in a carbohydrate

R-O-R’ - formula - Oxygen is between two carbon chains

Maltose

Used in beer fermentation (as it has a high concentration of glucose, which is used to make ethanol)

Derived from barley

Sucrose

Popular sweetener

High concentrations in sugarcane and sugar beet

Polysaccharides

Have a lot of monosaccharides (more than disaccharides - like a long chain)

Regulated by enzymes in the body

Are generally insoluble in water (unclear) + have no taste

Polysaccharides (Visual Representation)

Starch (In relation to polysaccharides)

Polysaccharides are formed through condensation of glucose (monosaccharide)

Is called amylose - the overall structure (polysaccharide of glucose structures)

Amylose

1. What amylose is

• Amylose is a type of starch.

• Starch is how plants store energy.

• Amylose is made only of glucose molecules (the same sugar in honey and fruit).

2. How it’s built (structure)

• Glucose molecules are joined together by α-1,4 glycosidic bonds (a type of ether bond).

• The chain is mostly straight (unbranched).

• Because of hydrogen bonding, the chain twists into a coil (helix). - the coil restricts OH groups to be exposed to water, thus preventing solubility

Think of it like: a long string of beads twisted into a spring.

3. Properties

• Insoluble in water because:

  • It’s very large,

  • The –OH groups are bonded to each other (hydrogen bonds), not free to bond with water.

• Can form a gel when heated with water (like when you cook rice or make jelly).

• Compact energy storage → plants can store a lot of energy in a small space.

4. Biological role

• Energy storage in plants.

• Slowly digested → gives long-lasting energy for humans and animals.

Condensation to become a starch

Amylose (Full Structure)

Amylopectin

A second form of starch

Can occur if the hydroxyl groups undergo condensation in different positions than from the ones in starch

Occasional branching occurs

Branching of the polymer restricts coiling (like starch) and allows more -OH groups to be exposed, interacting with water - is more soluble than starch

Amylopectin (Structure)

Glycogen

Similar structure to Amylopectin (but is even more branched - has very high solubility) - polymerization of only glucose - all of these are only polymerizations of glucose

Is formed due to excess glucose and is stored in the liver or in muscle tissue (as fat)

Energy can be taken from these stores, and then be used in cellular respiration - used for energy

Glycogen Structure

Lipids

Are fats and oils - in meat, fish, dairy products and eggs

Are a source of the unsaturated fatty acids

Triglycerides

Large, non-polar structures (fat)

fats - solids

oils are liquids

Unable to form hydrogen bonds with water (is non-polar) - are insoluble in water and are immiscible (cannot mix in water)

How triglcerides are formed (revision)

Monosatruated fatty acid

Has one C=C bond

“kink” in the bonds”

reduces close packing - lower boiling point

Saturated fatty acids

No kinks

Have close packing and are more crystalline - higher boiling point

Polyunsaturated fatty acids

More than one C=C bond

Multiple “kinks” in the carbon chain

Is least crystalline - and therefore less packing

Lower boiling point

Examples

Hydrolysis

Reducing molecules into smaller individual atoms

Used to rebuild into new substances that are required for the body

The deconstructed atoms are transported to different parts of the body to become reconstructed

Two main chemical reactions to reconstruct and break down nutrient molecules

Condensation and hydrolysis

Hydrolytic Reactions

Reactions involving hydrolysis

Condensation

Joining of two molecules with the elimination of water

Enzyme

A biological catalyst used to accelerate the rate of reaction in condensation and hydrolysis reactions

Some only catalyze one particular reaction, or only work is a specific functional group is present

Condensation Reaction Examples

Proteins (Hydrolysis and condensation)

Hydrolysis: The amide bond breaks and the amino acids are separated into their own parts

They undergo condensation later to form new proteins once they are transported to cells

Polysaccharides (Hydrolysis and condensation)

Hydrolysis: Hydrolyzed into monosaccharides and disaccharides by hydrolysis of ether bond

Condensation: Are converted back into polysaccharides such as glycogen for energy stores

Triglycerides (Hydrolysis and condensation)

Hydrolysis: Triglycerides are hydrolyzed back down to glycerol and fatty acids - through hydrolysis of ester bond

Condensation: Can be converted back to triglycerides to produce/use energy in cells

Summary (Hydrolysis and Condensation)

Metabolism

The overarching term that describes the hydrolysis and condensation of molecules within the body

Condensation (Endothermic)

Energy is required to fixate the bonds in between molecules

Hydrolysis (Exothermic)

Energy is released as the bonds are broken in the formation of smaller molecules

Digestion

1st phase of metabolism

Has many different enzymes throughout the sustem to break down the components of food

Overview of Digestion

Hydrolysis of carbohydrates in body through digestion

1) Chewing - Increases surface area of the food, allowing greater contact with the enzyme amylase (found in saliva) - breaks carbohydrates down into smaller disaccharides (two monosaccharides bonded together)

2) The disaccharides (e.g. maltose) - broken down in smaller monosaccharides by specific digestive enzymes

What does saliva do

Hydrolyses the starch within the food to maltose (a disaccharide - is also found within the lactate of milk - is also sweet)

Maltase

An enzyme is small intestine - aids in digestion and hydrolysis

Maltase (enzyme) hydrolyzes maltose(from the mouth) into glucose

Visual (Of Hydrolysis)

Why are glucose molecules highly soluble

Has a lot of hydroxyl groups —→ can easily make hydrogen bonds with the water present in the blood

Can easily be transported to different parts of the body

Are used to produce energy through respiration

Others are used to make energy storages (e.g. glycogen)

Cellulose Hydrolysis

Cellulose—→ is known as dietary fiber or roughage

Humans lack cellulase (the enzyme required to hydrolyze the cellulose)

Though we cannot digest cellulose, it aids in digestion and can prevent constipation, hemorrhoids and colon cancer

How does cellulose allow better digestion (Revew)

a) Adds bulk to your poop

• Fibre soaks up water and makes your poop bigger and softer.

• Bigger poop moves through your intestines faster, so you don’t get constipated.

b) Slows sugar absorption

• Some fibres form a gel in your gut.

• This makes sugar from food enter your blood slower, which is better for energy and blood sugar control.

c) Feeds good bacteria

• Some fibre is eaten by gut bacteria.

• These bacteria make healthy chemicals that help your intestines stay happy.

Hydrolysis Of Proteins

Happens in the stomach with the enzyme pepsin - activated by HCI

Pepsin breaks the protein into smaller polypeptides (smaller chains of amino acids)

Continue to break down into dipeptides (done with pancreatic protease) and then into amino acids (intestinal protease)

Protease

An enzyme that helps break down proteins

How HCI induced Pepsin (Unclear)

• The stomach secretes pepsinogen (inactive form of pepsin).

• HCl lowers the pH in the stomach and converts pepsinogen → active pepsin.

• Pepsin then breaks proteins into smaller peptides.

Visual representation of protein being broken down

Stomach—→ Pancreas—→ Intestines

Hydrolysis of triglycerides

Triglycerides, as they are non-polar (insoluble in water) - cannot be hydrolyzed directly

Bile (from the small intestine) is released and breaks the large triglyceride into smaller droplets

This increases the surface area for the lipase to interact with more triglyceride molecules aiding in a quicker, more effective hydrolysis

Emulsion

The process of breaking down fats and spreading them into small droplets

Lipase

A lipase is an enzyme that breaks down fats (triglycerides) into glycerol and fatty acids.

From the pancreas

Catalyzes the hydrolysis of three of the ester bonds in the triglycerides - forms glycerol and the fatty acids

Hydrolysis in the presence of lipase

The glycerol backbone is seperated from the fatty acids

Note: The fatty acids can be different hydrocarbons (can have different length and size) - is represented by R, R’ and R’’ (can be the same structure) - represents each branch of the fatty acids