Biological Molecules

Water

Water makes up 70-80% of a cell.
FUNCTIONS

• It's a reactant in important chemical reactions, including Hydrolysis.
• It's a Solvent - which means substances can dissolve in it. Most biological reactions take place in a solution.
• It Transports substances. it is good at this because it is a Liquid and is a Solvent.
• It helps with Temperature Control because it has a High Specific Heat Capacity and a High Latent Heat of Evaporation.
• Water is a Habitat. many organisms can survive and reproduce in it.

STRUCTURE

• H₂O is the chemical formula for water. This means that in every molecule of water, there are 2 Hydrogen atoms, and 1 Oxygen atom. The hydrogen atoms are joined to the oxygen atom by a Covalent Bond, which simply means it Shares Electrons.

• Because the Shared Negative Hydrogen Electrons are pulled Towards the Oxygen atom, each hydrogen atoms are left with a Slight Positive Charge.
• The Unshared Electrons on the Oxygen atom give it Slight Negative Charge.
• This makes water a Polar Molecule. its slightly negatively charged on one side, and slightly positively charged on the other.

• The δ sign is called 'Delta' and just means 'Slight', so δ- is delta negative, so it has a slightly negative charge. δ+ is delta positive, so it has a slightly positive charge.
• The slightly negatively charged Oxygen atoms Attract the slightly positively charged Hydrogen atoms of Other Water Molecules. this is called Hydrogen Bonding and gives Water some of its useful properties.

PROPERTIES

• High Specific Heat Capacity
• specific heat capacity is the energy needed to increase the temperature of 1 gram of a substance by 1°C.
• Hydrogen Bonds between water molecules can Absorb a lot of Energy
• Basic terms - it takes a Lot of Energy to Heat It Up.
• Water doesn't have rapid temperature changes, meaning it is a Good Habitat - the temperature underwater is likely to be more stable than it is on land.
• High Latent Heat of Evaporation
• It takes a Lot of Energy to Break the Hydrogen Bonds between water molecules.
• Therefore, lots of energy is used up when it evaporates.
• this is great for organisms because water is Good at Cooling things down. This is why some mammals sweat when they're too hot. when sweat evaporates, it cools the surface of the skin.
• Very Cohesive
• Cohesion is the Attraction Between Molecules of the Same Type. Water molecules are very cohesive because they are polar.
• This helps water to Flow, making it good for Transporting Substances.
• It also helps water to be Transported Up Plant Stems in the transpiration stream.
• Good Solvent
• Lots of important substances are Ionic (e.g. salt) which means they consist of one positively charged atom or molecule, or one negatively charged atom or molecule
• Because water is polar, the delta positive end of a water molecule will be attracted to the negative ions and vice-versa. (Opposites Attract!)
• This means the Ions will get Completely Surrounded by Water Molecules, i.e. they dissolve.
• Less Dense When Solid
• At low temperature, water freezes - it turns from liquid to solid.
• In ice, Water Molecules are Held Further Apart than they are in a liquid state, because each molecule forms four hydrogen bonds to other water molecules, making a Lattice Shape. because of this, ice is less dense than water and this explains why ice floats.
• This is useful for organisms because, in cold temperatures, Ice Forms an Insulating Layer on top of the water, which is why the Water Below Doesn't Freeze. So organisms that live in water don't freeze and can still move around when it's cold.

Carbohydrates

Carbohydrates are Polymers. This simply means it is a molecule made up of many similar, smaller molecules (Monomers) bonded together.
The monomers that make up carbohydrates are called Monosaccharides.
Glucose is a monosaccharide with Six Carbon Atoms. This means it is a HEXose monosaccharide.
There are two forms of glucose, Alpha (α) and Beta (β). They both have a Ring Structure.

In this diagram, each line represents a bond between atoms or molecules. As you can see, the H and OH, highlighted in blue and pink, are opposite in the Alpha and Beta Glucose Molecules.
The structure of Glucose is related to its function as the Main Energy Source in animals and plants. the ring structure makes it Soluble so it can be Easily Transported. the bonds contain a lot of energy.
Ribose is a structure with 5 Carbon Atoms - so it is a Pentose Monosaccharide. Unfortunately, this is another silly diagram we need to know how to draw. (NOTE: WE DO NOT NEED O LEARN ABOUT DEOXYRIBOSE! ... I couldn't crop the picture...Also, we can ignore the numbers, that's chemistry stuff!)

Monosaccharides are joined together by Glycosidic Bonds.
During synthesis, (The combination of components to make a connected whole), Hydrogen atom on one monosaccharide bonds to a hydroxyl Group (OH) on the other Releasing a Molecule of Water. this is called a Condensation Reaction. The opposite of this is called Hydrolysis. This is where a Molecule of Water Reacts with the Glycosidic Bond, breaking it apart.
A Disaccharide is when Two Monosaccharides join together.
There are a few more disaccharides we need to know about:
Maltose - When Two Alpha Glucose molecules are joined together by a glycosidic bond.
Sucrose - Alpha Glucose and Fructose
Lactose - Beta Glucose and Galactose
Amylose - Lots of Alpha Glucose joined by glycosidic bonds, this is a Polysaccharide (when More Than Two Monosaccharides are joined together).

The three main Polysaccharides we need to know about are:

STARCH

1. Cells get energy from glucose. Plants Store Excess Glucose as Starch. So when a plant needs more energy, it Breaks Down Starch to Release the Glucose
2. Starch is a mixture of two polysaccharides, Amylose and Amylopectin:

Amylose	Amylopectin
A Long, Unbranched chain of Alpha Glucose.	A long, Branched chain of Alpha Glucose.
Angles of the glycosidic bonds make a Coiled Structure, almost cylindrical	The Side Branches allow the Enzymes that break down the molecule to get to the Glycosidic Bonds Easily.
This makes it Compact, so it's really Good for Storage because you can fit more in a small space.	This means the Glucose can be Released Quickly

  3.  Starch is Insoluble In Water, so it doesn't enter cells by osmosis, which would make them swell. This makes it good for storage.

GLYCOGEN

1. Animal cells get energy from glucose too. But Animals Store Excess Glucose as Glycogen, which is another polysaccharide of alpha glucose.
2. The structure of glycogen is very similar to amylopectin, except it has Lots more Side Branches, which allows stored glucose to be Released Quickly when it is needed.
3. It's also very Compact, making it Good for Storage.

CELLULOSE

1. Cellulose is made of long Unbranched Chains of Beta-Glucose.
2. When Beta-Glucose molecules bond, they Form Straight Cellulose Chains.
3. The chains are linked together by Hydrogen Bonds to form strong fibres called Microfibrils. The strong fibres mean cellulose provides Structural Support for cells, i.e. in Cell Walls.

Lipids

Simple terms: Fatty Oily Things. Some of them are just straight-forward fats, but others have additional parts. We need to know about 3 types of lipids:

• Triglycerides
• Phospholipids
• Cholesterol

All Lipids contain Carbon, Hydrogen and Oxygen atoms.

TRIGLYCERIDES

• Triglycerides are Macromolecules - they're complex, with a relatively large molecular mass.
• Triglycerides have one molecule of Glycerol, with 3 Fatty Acids attached to it.
• The Fatty Acids have a Long Tail made of Hydrocarbons (hydrogen and carbon only) which are Hydrophobic, so they repel water molecules. this makes them Insoluble in Water.

• All fatty acids have the same basic structure, but the hydrocarbon tail varies. 
• The picture below shows the chemical structure of a fatty acid: C is carbon, O is oxygen, H is hydrogen. As you can see, there is a double bond between the C and the O. The rest are single bonds. The R represents the Variable Hydrocarbon Tail.

• Triglycerides are Synthesised by the formation of an Ester Bond between each Fatty Acid and the Glycerol molecule.
• The Ester Bond is Formed by a Condensation Reaction (water molecule released) This process is called Esterification.
• Triglycerides Break Down when the Ester Bonds are Broken. Each Ester Bond is Broken by a Hydrolysis Reaction (when a water molecule is used up).

There are two types of fatty acids: Saturated, and Unsaturated.

SATURATED

• Saturated means it has No Double Bond between Two Carbon Atoms. 
• The General formula is something we just have to learn and know how to use it. 
• For Saturated fatty acids, the formula is C_nH_(2n+1)COOH

UNSATURATED

• Unsaturated means it has, At Least One Double Bond between Two Carbon Atoms.
• The General Formula is the same as saturated fatty acids, so the only real difference is the double bond.

PHOSPHOLIPIDS

Phospholipids are also Macromolecules, so they look pretty similar to triglycerides, but instead of having one glycerol to 3 fatty acids, they have One Glycerol to Two Fatty Acids and One Phosphate Group

The Phosphate Group is Hydrophilic, so it attracts water molecules.

Structures & Functions of Triglyceride, Phospholipids and Cholesterol.

TRIGLYCERIDES	PHOSPHOLIPIDS	CHOLESTEROL
Energy Storing molecules	Found in the Cell Membranes of all Eukaryotes and Prokaryotes.	Hydrocarbon Ring  attached to  a Hydrocarbon Tail.
In Bacteria, it is used to Store Carbon too	They make up the Phospholipid Bilayer	Has a Polar Hydroxyl (OH) Group. (polar means it has a slightly negatively charged bit and a slightly positively charged bit).
They  are good for storage because: Long Hydrocarbon Tails  contain lots of Chemical Energy which is released when broken down Hydrophobic Tails  forces Triglycerides to bundle together as Insoluble Droplets with tails facing inwards, shielding themselves from water with their glycerol heads.	Phospholipid Heads are Hydrophilic, and their Tails are Hydrophobic, so they make a Double Bilayer with their heads facing outwards.	Small in size and Flattened shape - allowing Cholesterol to fit In Between the Phospholipid molecules in the Membrane
	The Centre of the Bilayer is Hydrophobic, so water soluble substances can't pass through easily.	They Bind to the Hydrophobic Tails of the Phospholipids, causing them to Pack more closely together - this makes the Membrane Less Fluid and More Rigid.

^^^Triglyceride - Insoluble droplets^^^

^^^Phospholipid Bilayer ^^^

^^^Cholesterol in the Bilayer^^^

Proteins
There are Millions of different proteins and they are essential to life.

• Proteins are Polymers.
• Amino Acid is the Monomer.
• A Dipeptide is when Two Amino Acids join together.
• A Polypeptide is when More Than Two Amino Acids join together.
• Proteins are made of one or more Polypeptides.

Amino Acids
All amino acids have the Same General Structure.

• 1 Carboxyl Group (-COOH)
• 1 Amino Group (-NH2)
• All attached to a Carbon Atom
• The only difference is the part labelled 'R' which is a Variable Atom

Peptide Bonds join Amino Acids together to form Dipeptides or Polypeptides. A Molecule of Water is Released during the reaction and the reverse of this reaction breaks the peptide bond (hydrolysis)

Primary Structure - The Sequence of amino acids:

Secondary Structure - The chain does not stay straight and flat. Hydrogen Bonds form Between the Amino Acids making it either coil into an α Helix or it folds into a β Pleated Sheet.

Tertiary Structure - The coiled and folded chain of amino acids is Coiled and Folded Further. For proteins made out of a single polypeptide chain, this phase forms their final 3D structure.

Quaternary Structure - Some proteins are made of more than one polypeptide chain. This phase is where the Different Polypeptide Chains are Assembled. i.e. haemoglobin is made of 4 polypeptides.

Different bonds hold together different structures of proteins:

1. Primary Structure - Peptide Bonds
2. Secondary Structure - Hydrogen Bonds between amino acids
3. Tertiary Structure - there's a few:
1. Ionic Interactions - Weak Attractions between the Positive and Negative parts of the molecule.
2. Disulphide Bonds - only when Two Molecules of an amino acid called Cysteine come Close Together, a Sulphur atom from Each Cysteine Join together.
3. Hydrophobic and Hydrophilic Interactions - when Hydrophobic Groups are Close together, they tend to Clump together, Pushing the Hydrophilic groups to the Outside
4. Hydrogen Bonds
4. Quaternary Structure - All of the above.

The shape of proteins relates to its function. There are two examples we need to know:

COLLAGEN

• A Fibrous protein
• Forms Supportive Tissues in animals, so it needs to be Strong.
• Made of 3 Polypeptide Chains Tightly Coiled into a Triple Helix.
• Chains are Interlinked by Strong Covalent Bonds
• Minerals can Bind to the Triple Helix to Increase its Rigidity.

HAEMOGLOBIN

• A Globular protein
• Contains a Haem Group with Iron in it that Binds to Oxygen, carrying it around the body.
• It has a Curled Up Structure.
• Hydrophilic Side Chains are on the Outside of the molecule, and Hydrophobic Side Chains face Inwards.
• This makes it Soluble in Water which makes it Good for Transport in the Blood.

Microscopes and Magnification

Magnification & Resolution
Magnification = Image Size / Actual Size. (How much bigger the image is compared to the specimen.
Resolution = The point at which a microscope can distinguish between two points that are close together.
Increasing the magnification, will not make the image clearer.

Light Microscopes

• It uses light (duh)
• Maximum resolution: 0.2 micrometres.
• Usually used to look at whole cells or tissues
• Maximum magnification: 1500X

Transmission Electron Microscopes

• Uses electrons instead of light.
• Produces more detailed images
• Uses electromagnets to focus a beam of electrons which are transmitted through the specimen.
• Denser parts of the specimen absorb more electrons, so they appear darker on the image produced.
• they are often used to look at organelles.
• they can only be used on thin specimens.

Scanning Electron Microscopes

• Scans a beam of electrons across the specimen.
•  This knocks electrons off the specimen, which are collected in a cathode ray tube to form an image. 
• The image produced shows the surface of the specimen and can be a 3D image. 
• However, they give a lower resolution that TEMs.

	Light Microscope	TEM	SEM
Maximum Resolution	0.2µm	0.0002 µm	0.002 µm
Maximum Magnification	X1,500	X1,000,000 +	X500,000

Prokaryotic Cells

PRO KARY NO CARRY!

Prokaryotes	Eukaryotes
Small (2 µm)	Larger (10-100 µm)
Circular DNA	Linear (usually double helix)
No Nucleus (DNA is free in cytoplasm)	Nucleus present with DNA inside
Cell wall made of polysaccharides, no cellulose or chitin	No cell wall (in animals). Cellulose cell wall (in plants) Chitin cell wall (in fungi)
No membrane bound organelles	Many organelles
Flagella (when present) is made of flagellin, arranged in a helix	Flagella (when present) is made of microtubule proteins arranged in 9+2 formation
Small ribosomes	Larger ribosomes
Example: E.coli bacterium	Example: Human Liver Cell

Bacterial Cells

Cytoskeleton

The Cytoskeleton is a Network of Protein Threads running through the Cytoplasm. In Eukaryotic cells, the protein threads are arranged as Microfilaments (small solid strands)  and Microtubules (tiny protein cylinders. The best way I can think of to remember this is microTUBUles are shaped like tubes!

The cytoskeleton has 4 main functions:

1. Microtubules and microfilaments Support the Organelles,  keeping them in place.
2. They Strengthen the cell and Maintain its Shape.
3. They're responsible for the Movement of Materials within the cell. i.e. during cell division, microtubules contract the Spindle Fibres to separate the chromosomes.
4. The proteins in the cytoskeleton cause the cell to Move. For example, the movement of Flagella or Cilia is caused by the cytoskeletal proteins. so in the case of sperm cells, the cytoskeleton propels the whole cell.

Protein Synthesis

• Proteins are made at ribosomes.
• The ribosomes on the RER make proteins that are attached to the cell membrane.
• The free ribosomes in the cytoplasm make proteins that stay in the cytoplasm.
• New proteins produced at the RER are folded and processed in the RER.
• They are then transported from the RER to the Golgi apparatus in vesicles.
• At the Golgi Apparatus, the proteins are processed again (sugar chains are trimmed or more are added. 
• The proteins enter more vesicles to be transported around the cell. For example, glycoproteins move to the cell surface and are secreted from the cell.

Cell Structure and Organelles

Prokaryotic - no nucleus - single celled - much smaller and simpler. e.g. bacteria

Eukaryotic - has a nucleus- multicellular organisms - plant and animal cells

Organelles

Round in shape, surrounded by a membrane, with no clear internal structure,

ORGANELLE	DIAGRAM	DESCRIPTION	FUNCTION
Plasma Membrane		Found on the surface of animal cells, and just inside plant cell walls and prokaryotic cells. It is made of proteins and lipids.	Regulates the movement of substances entering and exiting the cell. It also has receptor molecules so it can respond to chemicals such as hormones.
Cell Wall		Rigid structure that surrounds plant cells and mostly consists of cellulose.	Mostly for support.
Nucleus		A large organelle surrounded by a nuclear envelope, which  contains some pores. The nucleus contains chromatin (DNA and Proteins) and also contains a structure called a nucleolus	Controls what the cell does. The pores allow substances (RNA) to move between the nucleus and the cytoplasm. The nucleolus makes ribosomes.
Lysosome		Contains digestive enzymes, which are kept separate from the cytoplasm ---------------> They can be used to digest invading cells, or to break down worn-out components of the cell.
Ribosome		Very small, and floats free in the cytoplasm, or can be found attached to the RER. It's made up of proteins and RNA. It has no membrane.	The site of protein production.
Rough Endoplasmic Reticulum (RER)		A system of membranes enclosing a fluid-filled space. The surface is covered with ribosomes.	Folds  and processes proteins that have been made at the ribosomes.
Smooth Endoplasmic Reticulum (SER)		Similar to RER, but with no ribosomes.	Synthesises and processes lipids.
Vesicle		A small fluid-filled sac found in the cytoplasm, surrounded by a membrane	Transports substances in and out of the cell (across the cell membrane), and between organelles. Some are formed by the Golgi Apparatus or the ER while others are formed at the surface
Golgi Apparatus		A group of fluid filled, membrane bound, flattened sacs. Vesicles are often seen at the edges of the sacs.	Processes and packages new lipids and proteins. It also makes lysosomes
Mitochondrion		Usually oval-shaped, they have  a double membrane. The inner membrane is folded to form structures called cristae, inside is the matrix, which contains enzymes involved in respiration.	The site of aerobic respiration where ATP is produced. They're found in large numbers in the cells that are very active and require a lot of energy.
Chloroplast		A small, flattened structure found only in plant cells. It has a double membrane and has membranes inside called thylakoid membranes. These stack up in some parts of chloroplasts to form grana. Grana are linked together by lamellae - thin, flat pieces of the thylakoid membrane.	Where photosynthesis takes place. Some parts of photosynthesis take place in the grana, other parts take place in the stroma (thick fluid found in chloroplasts).
Centriole		Small, hollow cylinders made of microtubules (tiny protein cylinders). They are found in most animal cells, but only some plant cells.	Involved in the separation of chromosomes during cell division.
Cilia		Small, hair-like structures found on the surface membrane of some animal cells. In cross section, they have an outer ring made of pairs of protein microtubules, with two microtubules in the middle. (9+2 formation)	The microtubules allow the cilia to move. This movement is used by the cell to move substances along the cell surface.
Flagellum		Flagella on eukaryotic cells are like cilia, but longer and found in fewer numbers. They stick out from the cell surface and are surrounded by the cell membrane. Inside, they are similar to cilia. They are also in the 9+2 formation.	The microtubules contract to make the flagellum move. The flagellum is used like outboard motors to propel cells forward (Sperm cells).

Tissues, Organs and Systems

Multicellular organisms are made of lots of different cell types, organised to work together. Cells that carry out the Same Function are organised into Tissues (i.e. epithelial), and Different Tissues are organised into Organs, and organs Work Together as Organ Systems.

Tissues

Tissue - A Group of Cells specialised to Work Together to carry out a Particular Function. A tissue can contain more than one cell type.

Examples:

Tissue Type	Explanation
Squamous Epithelium	Single Layer of Flat Cells lining a surface. It's found in many places, including the Alveoli and the Lungs
Ciliated Epithelium	A layer of cells covered in Cilia. It's found in places where things need to be   i.e. the trachea, to Waft Mucus.
Muscle Tissue	Bundles of Elongated cells (Muscle Fibres). There are 3 different types: Smooth, Cardiac, and Skeletal. They're all Slightly Different in structure.
Cartilage	A type of Connective Tissue found in the joints. It also Shapes and Supports the Nose and Windpipe. It is found where cells (chondroblasts) Secrete a Jelly-like substance containing Protein Fibres which become trapped inside.
Xylem Tissue	Two jobs - Transports Water, and Supports the plant. It contains hollow xylem vessel cells (dead) and parenchyma cells (living)
Phloem Tissue	Transports Sugars around the plant. It's Arranged in Tubes and is made up of Sieve Cells, Companion Cells and Regular Plant Cells.

Organs and Organ Systems

Organ - a Group of Different Tissues that Work Together to perform a Particular Function.

LUNGS - Contain squamous epithelial tissue (alveoli), Ciliated epithelial tissue (bronchi), and elastic connective tissue and vascular tissue (blood vessels).

LEAVES - Contain palisade tissue for photosynthesis, epidermal tissue to prevent water loss from the leaf, and xylem and phloem tissues in the veins. 

Each system has a particular function. The respiratory system is made up of the lungs, trachea, larynx, nose, mouth and diaphragm.

The circulatory system consists of the heart, arteries, veins and capillaries.

Stem Cells

Stem Cells & Differentiation
Multicellular organisms are made up of many different cell types which are Adapted for their Function. i.e. blood cells, muscle cells e.t.c. All of these originated from Stem Cells. Stem cells are Unspecialised, but can develop into different types of cell. All multicellular organisms have stem cells in some form. In Humans, they are found in early Embryos and in a few places in adults. Stem cells in embryos can develop into Any Type of cell. However, Adult stem cells can only develop into a Limited Range of cells

The process where stem cells become specialised for their function is called Differentiation. In adults, stem cells can be used to Replace Damaged Cells, i.e. skin cells or blood cells. Plants are always growing, so stem cells are needed to Produce New Shoots and Roots. Stem cells in plants can also differentiate into Xylem and Phloem Cells.
Stem cells can also divide to produce more Unspecialised Stem Cells.

BONE MARROW
Bones are living organs. They contain Nerves and Blood Vessels. The main bones of the body have Bone Marrow in the Centre. It is here that adult stem cells can differentiate to Replace Worn Out Blood Cells - Erythrocytes (Red) and Neutrophils (White).

MERISTEMS
Meristems are the part of the plant where Growth takes place. In the Root and the Stem of the plant, stem cells of the Vascular Cambium Divide and Differentiate into Xylem Vessels and Phloem Sieve Tubes.

STEM CELL TREATMENT
As stem cells can differentiate into different types of cell, Scientists think we can Replace Damaged Tissue Cells to cure diseases, mostly neurological disorders like Alzheimer's and Parkinson's.

Alzheimer's	Parkinson's
Alzheimer's is where Nerve Cells in the Brain Die in increasing numbers.	People with Parkinson's suffer from Uncontrollable Tremors
This results in Severe Memory Loss.	The disease causes the loss of a particular type of nerve cell located in the brain.
In this case, researchers want to Replace Damaged Nerve Cells with re-grown nerve cells that have been differentiated from stem cells.	These cells release a chemical called Dopamine, which is needed to Control Movement
	It is thought that transplanted stem cells will help to Regenerate the dopamine-producing cells.

Stem cells are also used for Developmental Biology (studying how cells grow and develop). This can help us understand developmental disorders and cancer.

DIFFERENTIATION

Once cells differentiate, they have a Specific Function. Their structure is then adapted to perform that function.

Below is a table of cell types that are specialised for their specific function.

Cell Type	Function	Adaptations
Neutrophil	Defends the body against disease	Flexible shape to engulf foreign particles or pathogens More lysosomes contain digestive enzymes to break down engulfed particles
Erythrocytes	Carry oxygen in the blood	Biconcave shape provides large surface area for gas exchange No Nucleus to allow more haemoglobin
Epithelial Cells	Cover the surfaces of organs	Ciliated epithelia have cilia that beat to move particles away Squamous epithelia are very thin to allow  efficient diffusion of gases
Sperm Cells	Fertilisation of ovum cells	Flagellum so they can swim to the ovum Lots of mitochondria to provide energy to swim The acrosome contains digestive enzymes to enable the sperm to penetrate the surface of the egg.
Palisade Cells	Photosynthesis	Lots of chloroplasts to absorb more sunlight Thin walls so CO2 can easily diffuse into the cell.
Guard Cells	Open and close the stomata	Thin outer walls and thickened inner walls force them to bend outwards opening the stomata, allowing the leaf to exchange gases for photosynthesis
Root Hair Cells	Absorb water and mineral ions from the soil	Large surface area for absorption Thin permeable cell wall for entry of water and mineral ions More mitochondria to provide energy needed for active  transport