BIOLOGY

Unit 1: Metabolism
Biomolecules
Chemical compounds that are found in living organisms, including both organic and
inorganic compounds.
Organisms get energy and nutrients from food in the form of biomolecules

Monomer
A monomer is the individual unit, like a building block

Polymer
A polymer is many interconnected monomers

Organic Biomolecules
●​ They all contain Carbon and Hydrogen
●​ They are formed by multiple molecules bonding together
●​ All organic molecules are built from a single type of building block

Macromolecules
Macromolecules are larger organic biomolecules, with a weight greater than 1000
daltons (da)
●​ Carbohydrates
○​ Monomer: Sugar
○​ CHO
○​ Stores energy and makes structural material
●​ Lipids
○​ Monomer: Fatty acids tails and glycerol heads
○​ CHO
○​ Stores energy and forms membrane and plays a role in signaling
○​ Lipids generally don’t dissolve in water
●​ Proteins
 ○​ Monomer: Amino acid
○​ CHON
○​ Creates Enzymes, structural material and peptides
○​ For growth and tissue repair
○​ Transport nutrients
○​ Act as Antibodies
○​ Act as Receptors
○​ Some are hormones
●​ Nucleic Acid
○​ Monomer: Nucleotide
○​ CHONP
○​ Stores genetic information

Micromolecules
Micromolecules are smaller biomolecules, both organic and inorganic that are less
than 800 Da.
●​ Amino Acids
○​ Compound formed with an amino group (NH2), an acid group (COOH),
hydrogen, a central carbon and a variable group (r)
○​ Every amino acid has another atom bonded to the carbon called the R
group
○​ There are 21 amino acids in proteins, each one with a different R group
○​ The two types of amino acids are essential amino acids and non-essential
amino acids
■​ Essential amino acids cannot be synthesized by the body and need
to be supplied by the body
■​ Non-essential amino acids can be synthesized by the body
●​ Sugars
○​ Sugars are sweet and water soluble
○​ They are formed of C, H, and O in a 1:2:1 ratio
■​ E.g. Ribose -> C5H10O5
○​
●​ Nitrogen Bases
 ○​ Nitrogen-based molecules that are found in DNA and RNA. They can be
classified into
■​ Purines - Two ring structure
●​ Adenine (A)
●​ Guanine (G)
■​ Pyrimidines - One ring structure
●​ Cytosine (C)
●​ Thymine (T) [Only in DNA]
●​ Uracil (U) [Only in RNA]

Nucleosides
Compounds that are formed by combining a nitrogen base and a sugar
E.g. Adenine + Sugar -> Adenosine
Cytosine + Sugar -> Cytidine

Nucleotides
Compounds that are formed by combining a nitrogen base, a sugar and a phosphate
that make up Nucleic Acids
E.g. Adenine + Sugar + Phosphate -> Adenylic Acid
Cytosine + Sugar + Phosphate -> Cytidylic Acid

Deoxyribose Sugar
Deoxyribose sugar is sugar that makes up DNA. It has 5 carbons and 3 oxygens.

DNA
●​ Deoxyribonucleic acid
●​ Consists of 2 polynucleotide strands arranged in a double helix
●​ Deoxyribose sugar has hydrogen which is less reactive than OH

RNA
●​ Ribonucleic acid
●​ has a single helix structure
 ●​ Ribose sugar is more reactive than deoxyribose because it has OH which is
more reactive than hydrogen

Nitrogen Base Bonds

Only in DNA: A = T (2 hydrogen bonds)
Only in RNA: A=U (2 hydrogen bonds)
RNA & DNA: C = G (3 hydrogen bonds)

Phosphodiester Bond
The bond that connects nucleotides to form DNA or RNA, by connecting the
phosphate of one nucleotide to the pentose sugar of the next

Monosaccharides
●​ Monosaccharides are simple carbohydrates that cannot be broken down
further
●​ Monosaccharides contain either an aldehyde or ketone group
●​ They do not need to be broken down during digestion
●​ E.g. Glucose, Fructose, Galactose

Disaccharides
Disaccharides are formed when two monosaccharide molecules are joined with a
glycosidic bond

Polysaccharides
Polysaccharides are long chains of monosaccharides linked by glycosidic bonds
Digestible polysaccharides such as starch are broken down in the mouth and small
intestine

Reducing Sugars
A reducing sugar is any sugar that can act like a reducing agent. A reducing agent is a
substance that gives away electrons during a chemical reaction
Peptides
Peptides are amino acids that are linked together by a peptide bond

Polypeptides
Polypeptides are chains of amino acids linked together by peptide bonds

Collagen
Collagen is a structural protein that binds the whole body together. It is the main
structural protein in the outer layers of the skin. Collagen levels start dropping at the
age of 20, and our bodies stop making it at 40.

Primary Structure of Protein

The linear sequence of amino acids in peptides or proteins

Secondary Structure of Protein

The secondary structure of protein is the three dimensional form of protein, that
exists in two structures - ɑ-helix and ß-pleated Sheets

Tertiary Structure of Protein

The tertiary structure of protein is the helical polypeptide further folding in on itself
like a hollow woolen ball

Quaternary Structure of Protein

The quaternary structure of protein is assembled sub units

Glucose
Glucose is the sugar used in cellular respiration that makes ATP which is important
for energy

Types of Lipids
Triglycerides - Fats and Oils
Phospholipids
Steroids - Sterols-cholesterol

Triglycerides
●​ Most common form of lipids
●​ Three fatty acids and a glycerol backbone
●​ High levels increase risk of heart disease and health issues
●​ When we eat, our bodies convert excess calories into triglycerides which are
stored in fat cells
●​ Important for metabolic roles
●​ Stores energy
●​ Regulates body temperature
●​ Insulates vital organs
●​ Builds membrane of the cell
●​ Absorption of some essential minerals and vitamins
●​ Aids clotting

Phospholipids
●​ The main component of the cell membrane
●​ Made up of two fatty acids, a phosphate group and a glycerol molecule
●​ Semipermeable

Steroids
●​ They have a ringed structure unlike the other lipids
●​ Steroids have four linked carbon rings
●​ Steroids with OH are classified as alcohols called sterols

Saturated Fatty Acids

●​ Saturated fatty acids lack carbon-carbon double bonds
●​ They have a higher melting point than unsaturated fatty acids of the same size
●​ They can pack their molecules together in a straight rod-like shape
●​ Increase both good and bad cholesterol levels
●​ Don’t spoil easily
Unsaturated Fatty Acids
●​ Unsaturated fatty acids have more than one double bond
●​ Their double bonds create a structure that stops them from being able to group
their molecules in a straight rod-like shape
●​ Unsaturated fatty acids are healthier than saturated acids
●​ Increases only good cholesterol
●​ Spoil easily
●​ Our body requires around 25-30% unsaturated fatty acids in our diet
●​ Decreases bad cholesterol

Trans Fats
Trans fats increase the levels of bad cholesterol and lower the levels of good
cholesterol leading to severe blockage of the arteries

Cholesterol
●​ The most common steroid mainly synthesized in the liver
●​ Precursor to vitamin D and hormones like estrogen and testosterone
●​ Cholesterol is used in regulating cortisol (Stress hormone) and aldosterone
(regulates water and salt balance)
●​ Excess cholesterol (Hypercholesterolemia) can increase the risk of heart disease
and stroke
Food Tests
Iodine - When Iodine is added to Starch, it turns Blue-Black
Biuret - When Biuret Solution is added to Protein, it turns Purple-Violet
Benedict’s - When Benedict’s Reagent is added to a Reducing Sugar and the solution
takes a water bath, it turns yellow-orange
Ethanol - Add 2cm3 of ethanol to fat, shake, then add 2cm3 of water, it will create a
white emulsion

Enzymes
●​ Enzymes are biocatalysts which speed up metabolic reactions
●​ They occur inside cells or are secreted by cells
●​ They are made of proteins
 ●​ They can be reused repeatedly
●​ Enzyme speed is impacted by temperature, pH and pressure
●​ Enzymes reduce activation energy

Catalyst
A substance that speeds up the rate of a chemical reaction but is not changed by the
reaction

Substrate
Substrates are the chemical compounds that enzymes work on

Intracellular Enzymes
Enzymes that are synthesized and kept in a cell for the cell itself to use

Extracellular Enzymes
Enzymes that are synthesized in the cell but work externally

Nomenclature of Enzymes
●​ Enzymes are named according to the substrate it works on
○​ Lactose-Lactase, Lipid-Lipase, Protein-Protease

●​ Some enzymes were named before the system was put in place
○​ Pepsin, Trypsin

Activation Energy
●​ Activation energy is the minimum amount of energy required for a chemical
reaction to occur
●​ The activation energy is much higher without an enzyme to catalyze the
reaction

Enzyme Action
Enzyme action is how enzymes speed up reactions by binding substrates, lowering
activation energy, and releasing products
Active Site
The region or groove on the enzyme where the substrate binds with it
​ Active sites are divided into binding sites and catalytic sites
Binding site: The substrate binds to the active site
Catalytic site: Where the reaction occurs

Lock and Key Model

Active site shapes specifically match the shape of a substrate, making it highly specific

Induced Fit
Enzymes are specific but not rigid, which means they can slightly move around for the
substrate to fit well, but they cannot change shape

Factors affecting the Rate of Enzyme Controlled Reaction

Temperature - As the temperature increases, kinetic energy increases, so the rate of
reaction increases
​ ​ - 40o c is the optimum temperature, where the rate of reaction is at its
fastest
​ ​ - After 40o the enzyme begins to denature and loses its active site

pH level - Different enzymes work best at different pH levels, meaning the optimum
pH depends on the enzyme
​ - The rate of reaction increases until reaching optimum pH after which the
enzyme begins to denature
Substrate/Enzyme concentration - As substrate/enzyme concentration increases, more
enzyme/substrate molecules are bound increasing the rate of reaction.
​ ​ ​ - After a certain point all enzymes and substrates are bound,
so the rate of reaction cannot increase further

Enzyme use in the food industry

●​ Pectinase breaks down substances in apple cell walls to enable greater juice
extraction
 ●​ Lactase breaks down lactose in milk to make milk that lactose intolerant
people can eat
●​ Proteases ‘pre-digest’ some of the proteins in baby food
●​ Enzymes are also used in baking bread, cheesemaking and brewing
Other uses of Enzymes
●​ Enzymes are used to help cure disease
●​ Enzymes are used in seed germination
●​ Enzymes are used to make food with fewer calories

Lactose Intolerance
Lactose Intolerance and Lactose Allergy are not the same thing
Lactose intolerance occurs when a person has insufficient amounts of lactase, so
lactose cannot be broken down

Photosynthesis
●​ Photosynthesis is the process by which plants, algae, and some bacteria make
their own food using sunlight​ ​ ​ ​
●​ Carbon Dioxide + Water ⇒ Glucose + Oxygen
●​ 6𝐶𝑂2 + 6𝐻2𝑂 ⇒ 𝐶6𝐻12𝑂6 + 6𝑂2
●​ Light and Chlorophyll help convert carbon dioxide and water into glucose and
oxygen
●​ Carbon Dioxide diffuses into the leaf through the stomata
●​ Water is taken up by the roots and transported to the leaves by xylem
●​ Oxygen diffuses out of the leaf through the stomata
●​ You can tell photosynthesis has taken place by detecting the presence of
glucose (starch)
●​ It takes place in the chloroplast
●​ Photosynthesis takes place in two steps
○​ The light-dependent reaction
■​ Happens only in sunlight
■​ Light energy is used to make ATP and NADPH
■​ Water is split and oxygen is given off as waste
 ■​ 2H₂O + 2NADP⁺ + 3ADP + 3Pi → O₂ + 2NADPH + 3ATP
○​ The light-independent reaction, or Calvin cycle
■​ Also known as dark reaction
■​ Sugar molecules are formed from the water and CO2 Molecules
■​ The NADPH and ATP from light reaction are used to convert
carbon dioxide into glucose

Chlorophyll
Chlorophylll is a green pigment that is found within plant cells that absorbs light
energy and transfer that energy into chemicals for the synthesis of carbohydrates. It
does not absorb the green wavelengths of white light, giving plants their green color

Glucose
●​ Glucose is used in respiration to release energy for cells
●​ Glucose forms cellulose for strength in the cell wall
●​ Glucose forms insoluble starch for storage
●​ Converts into fats and oils for energy storage in seeds
●​ Combines with nitrates from the soil to form proteins
●​ Converts into sucrose for transport around the plant

Factors affecting the Rate of Photosynthesis

Internal Factors
-​ Number, size, age and orientation of leaves
-​ Mesophyll cells and chloroplasts
-​ Internal carbon dioxide concentration
External factors
-​ Sunlight
-​ Temperature
-​ Carbon Dioxide concentration
-​ Water

Blackman’s Law of Limiting Factors (1905)

If a biochemical process depends on many factors, the one that is closest to running
out decides the rate of the process
For example, a plant with green leaves, optimal light and CO2 may not
photosynthesize in a low temperature

Limiting Factors
●​ A plant has a certain minimum amount it needs of its raw materials to
complete photosynthesis. If it has less than that, it will not be able to complete
the process
●​ The three factors which limit the rate of photosynthesis are
○​ Temperature
■​ The rate of photosynthesis is controlled by enzymes, so after a
certain point the enzymes begin to denature and the rate of
reaction decreases
○​ Light intensity
■​ The more light a plant receives, the faster the rate of
photosynthesis
■​ After a certain point the rate will not increase further because
another factor will start limiting the rate
○​ Carbon Dioxide concentration
■​ The more carbon dioxide that is present, the faster the reaction
can occur
■​ This continues until another factor prevents the rate from
increasing further
○​ Water
■​ If there is too much water, the stomata closes which reduces the
CO2 availability
■​ This also wilts leaves which reduces the surface area of the leaves
and their metabolic activity

Parts of a Leaf
Wax Cuticle: Protective layer on top of the leaf to prevent water from evaporating
Upper epidermis: Allows light to enter the palisade mesophyll layer underneath
Palisade Mesophyll: Tightly packed cells with chloroplasts to absorb more light
Spongy Mesophyll: Contains internal are spaces to increase surface area
Lower Epidermis: Contains guard cells and stomata
Guard cell: Absorbs and loses water to open and close the stomata
Stomata: Where gas exchange and water evaporation takes place
Vascular bundle: Contains xylem and phloem
Xylem: Transports water into the leaf
Phloem: Transports sucrose and amino acids around the plant

Chloroplasts
●​ Chloroplasts are present in the walls of mesophyll cells of leaves
●​ It contains grana, stroma, lamellae and fluid stroma
●​ Oval shaped
●​ Two membranes, outer and inner
●​ The space in the inner membrane is the stroma, the dense fluid with the
chloroplasts
●​ Chlorophyll is located in chloroplasts

Metabolism
The chemical processes that take place inside a living organism for it to survive
​ Catabolism - Breaking down of complex molecules into smaller parts
​ Anabolism - The synthesis of molecules