Please enable JavaScript.
Coggle requires JavaScript to display documents.
Unit 1: Biological Molecules - Coggle Diagram
Unit 1: Biological Molecules
Water
Chemical
Formula - H2O
Covalent bond
Bond is polar. Meaning it will create hydrogen bonds, where multiple 'H2O's bond with one another
Highest cohesion of any non-metal liquid
This is why you see water droplets when you pour some water on wax paper. This is because the cohesion forces are stronger than the adhesion forces
This is ALSO why you see water 'defy' gravity. When you suck on a straw, water will climb up due to it's cohesion to itself, and the adhesion to the straw
Great solvent
Hydrophillic - Can dissolve in water
Hydrophobic - CANNOT dissolve in water
Denser when in liquid state, as opposed to solid state
Very high heat capacity
Only substance that naturally occurs in all 3 states
Info
Polarity and Intermolecular Forces of Attraction
Intermolecular Forces of Attraction (Ranked from strongest to weakest)
An interaction between two molecules that can be attractive or repulsive
Ionic - The electrons are unequally shared so the functional group is negatively charged or positively charged. Oppositely charged functional groups attract.
Hydrogen Bonding - A special case of dipole involving functional groups containing H bonded to N or O because electrons are more unequally shared. The partial negative and positive charges are stronger. Oppositely charged ends of functional groups on two different molecules attract.
Dipole - The electrons in a covalent bond in a functional group are not shared equally. This causes a partial negative charge to exist on one end of the functional group, and a partial positive charge on the other. Oppositely charged ends of functional groups on two different molecules attract.
Dispersion - The electrons around an atom in a molecule are, on average, evenly distributed around the nuclei, but at any time they could all be found on one side of a molecule. At this instant, a mini-negative charge would result which can repel electrons in a nearby molecule. The two molecules attract.
Polarity
Some elements, like carbon and hydrogen share electrons almost equally. We describe this as Non-Polar.
Some elements, like carbon and hydrogen share electrons almost equally. We describe this as Polar
Functional groups
Biological molecules are characterized by common groups of atoms. These groups of atoms are called Functional Groups , as they are the locations are interact and react with other molecules.
Ketone
Found in keto- type sugard
CO is polar because O attracts electrons strongly compared to C
CO
Carboxyl
Found in organic acids such as amino acids and fatty acids
COOH is polar, because O attracts electrons more strongly than C or H
C
Aldehyde
Found in aldo- type sugars
CO is polar because O attracts electrons strongly compared to C
COH
Amine
Found in amino acids, proteins, and other N-containing compounds
NH3 is polar, because N attracts electrons strongly compared to H
NH2
Phosphate
Found in nucleic acids (DNA, RNA). ADP, ATP, phospholipids
PO4 can’t be defined as polar or non-polar because the functional group is an ion so electrons were donated from another functional group
PO4
Sulfhydryl
Found in the amino acid: cysteine. Also found in most proteins
SH is polar, because S attracts electron strongly compared to H
SH
Hydroxyl
OH is polar because O attracts electrons strongly compared to H
Found in carbohydrates and many other cellular compounds
OH
They determine how they interact with each other. Do they attract, or do they repel? Is this a strong attraction or weak attraction? This will determine if a substance is a liquid because it melts easily, or a solid because the molecules are attracted tightly together. Or if it’s hard or soft. Soluble or insoluble.
Nutrition and Macromolecules
Essential nutrients - Nutrients that an organism can only get from their environment
We must ingest as much as we can, and include as much as we can into a balanced diet.
One of these nutrients are carbohydrates
Without carbohydrates, we would run out of energy fast
Various foods have distinct flavors and textures because they contain different types of carbohydrates.
We convert these nutrients into biological molecules
How all biological molecules are used by cells and the body depends on the structure of those molecules.
The functional groups that make up different biological molecules are related to the types of intermolecular force of attraction
Shape and size of the molecule is also important
Four main types of nutrients we need in large amounts. These are called macronutrients/biomolecules.
Macronutrients are unique because they are made of smaller molecules called monomers
These monomers put together to create polymers
Monomers
Small chemical molecules that can be connected together to make larger molecules
Polymers
A chemical molecule made from many smaller monomer molcules
4 Macronutrients/Biomolecules
Lipids ("Fats")
Glycerol and Fatty acids are the monomers of Lipids
Ex. Butter, oil, cholesterol
Great source of long term energy. We use them after we burn up all of our carbohydrates
Lipids make up cell membranes
Major elements
Carbon
Oxygen
Hydrogen
Proteins
Ex. Meats and beans
Amino acids are the monomers of Proteins
They contribute to muscle building, working in immune system, acting as enzymes (enzymes are made of proteins)
Major elements
Carbon
Hydrogen
Oxygen
Nitrogen
Carbohydrate
Fast source of energy
Ex. Pasta and bread are heavy in carbohydrates
Monosaccharides are the monomers of Carbohydrates
Major elements
Carbon
Hydrogen
Oxygen
Nucleic acids
Nucleotides are the monomers of Nucleic acids
Makes up the DNA in the nucleus of all cells
Major elements
Carbon
Hydrogen
Oxygen
Nitrogen
Phosphorus
Carbohydrates
A type of neutral compound made of carbon, hydrogen, and oxygen. Mostly formed by green plants and is a major class of animal foods.
4 types
Disaccharides
Made up of 2 Monosaccharides
Ex. 2 Alpha Glucose molecules form a bond together to create Maltose through condensation/removal of water. You can reverse this by adding water (hydrolysis)
Alpha Glucose + Alpha Glucose ->(Condensation) Maltose (C1 of Galactose and C4 of Glucose bond together)
Beta Galactose + Beta Glucose ->(Condensation) Lactose (C1 of Galactose and C4 of Glucose bond together)
Alpha Glucose + Beta Fructose ->(Condensation) Sucrose (C1 of Glucose and C2 of Fructose bond together)
Sucrose is formed by plants, not animals
Oligosaccharides
Short chain of Monosaccharides, less than 20 monosaccharides
Maltose + Alpha Glucose ->(Condensation) Maltotriose [3 Alpha Glucose, can keep growing with more glucose molecules] (C1 and C4 being bonded)
Monosaccharides
Simple sugars
3 main monosaccharides
Galactose
Glucose
Main source of energy for humans
Contains 6 carbon atoms
Types of Glucose
Alpha Glucose - The OH of C1 (Carbon 1) is pointing in the opposite direction to the CH2OH (C6)
Beta Glucose - The OH of C1 and the CH2OH of C6 are pointing in the same direction
Isomers - Molecules that have the same amount of elements, but different configurations and placements of
Fructose
Makes up all carbohydrates
Polysaccharides
Homopolysaccharide
1 type of Monosaccharides
Branched
Uses 1-4 and 1-6 glycosidic bonds
Amylopectin
Unbranched
Only bonded through 1-4 glycosidic bonds (C1 and C4 bonds together)
Amylose
Serves as storage forms of monosaccharides
Starch
Found in bread, cereal and rice
Only made of Glucose
Contains Amylose AND Amylopectin
Branch points occurse every 24-30 glucose residues
Glycogen
Storage form of glucose in animals
Only made of Glucose
Branch points occurs every 8-12 glucose residues (More branch points than Starch)
Dextrans
Structural component in bacteria and yeast
Made of 1-3 and 1-6 glycosidic bonds (may contain 1-2 and 1-4)
Made of Glucose
Cellulose
Made of Beta Glucose
1-4 glycosidic bonds
Heterosaccharides
Two or more Monosaccharides
Branched
Unbranched
aka. Glycans
Saccharides come from the Greek word for sugar
Types of saccharides/carbohydrates
Alpha - The OH of C1 and the CH2OH of C6 are pointing in the same direction
Beta - The OH of C1 (Carbon 1) is pointing in the opposite direction to the CH2OH (C6)
Lipids
Most energy dense nutrient
20 different fatty acids in food. 2 are essential to Humans.
These 2 fatty acids are used for biological processes like cell membrane structure and hormone production. Not energy production.
Predominantly non-polar molecules
The molecule of oleic acid, for example, is made of a long chain of 18 carbon atoms. Carbon and hydrogen share electrons relatively equally so it’s true to describe this section of oleic acid as non-polar or hydrophobic. Yet oleic acid also has a polar, hydrophilic, carboxyl group to the left. Clearly our current definitions aren’t adequate to describe the whole molecule.
Instead, we can use the term amphiphatic to describe a molecule with both polar and non-polar functional groups.
Hydrophobic interactions
We’ve already seen amphipathic molecules when we looked at the folding of polypeptide chains. Hydrophobic amino acids come together because of Hydrophobic interactions and dispersion forces between non-polar side chains.
Hydrophilic amino acids tend to attract to each other, or watery environments. Hydrophobic amino acids, tend to be excluded from this attraction and stay together because of weaker dispersion forces
Hydrophilic amino acids come together because of stronger dipole-dipole, hydrogen bonding, and ionic-dipole interactions between polar and charged side chains. The hydrophilic amino acids also make strong intermolecular forces of attraction with water so they are located around a core of hydrophobic amino acids.
Uses
Energy
Insulation
Lubrication
Protection
Precursors of some hormones
Key components of cell membranes
Memorize trick
S - Storage and Source of energy
H - Hormonal roles
I - Insulation
P - Protection
S - Structural components
Types of Lipids
Phospholipids
Molecular
Glycerol and 2 Fatty acids + a Phosphate group that attaches to the 3rd Carbon
Hydro-stuff
Glycerol + Phosphate = Hydrophillic
Fatty acids = Hydrophobic
So they arrange themselves like this
Major component of plasma membranes of the cell
Hydrophilic head on outside
Steroids
4 fused rings of carbon to which different functional groups attach
Ex. Cholesterol
Present in plasma membranes
Testosterone
Estrogen
Vitamin D
Cortisone
Triglycerides
Insoluble in water
Oils
Liquid at room temperature
Used by plants as long term energy storage
Unsaturated
Fats
Solid at room temperature
Used by animals as long term energy, protection, and insulation
Saturated
https://youtu.be/QhUrc4BnPgg
Molecular
Glycerol
3 Fatty Acids
Hydrophobic chain (Chain of Hydrogen and Carbon)
Methyl group
Acid group
Saturated
Only single carbon to carbon bonds. This makes the Carbon saturated with Hydrogen bonds.
Unsaturated
1 or more double bonds
Trans fats
Unsaturated fatty acid, but the Hydrogen atoms are opposite of one another at the double bonds
Cis Fatty Acids
Carbon chain is arranged on the same side of the double bond. As a result, the molecules make a concave shape at the double bond. This kink in the shape is important in the increased fluidity between these fatty acid molecules.
Trans Fatty Acids
There is, however, a chemical method of arranging the double bond such that the molecule makes a zigzag shape. This type of fatty acid is called a trans fatty acid.
They come together (Glycerol and the 3 Fatty acids) by Dehydration synthesis (So take H2O out of the 3 Fatty acids)
Waxes
Non-polar. Repels water
Found on leaves and animals
Micelles
A spherical arrangement of amphipathic molecules, hydrophobic side on the inside, hydrophilic side on the outside
Phospholipid bilayer
Phospholipid bilayers are found in the membranes in the cell. Membranes define the compartments of the cell. These include the cell membrane and cell organelles: the nucleus, endoplasmic reticulum, vacuoles, lysosomes, golgi apparatus, mitochondria and chloroplasts
These membranes create fluid mosaics, having proteins and components within the cell membrane that aid in the filtration of molecules and structures coming in and out of the cell membrane
Proteins
Structures
Secondary structures
Primary structures fold into beta-sheets and alpha-helices to create secondary structures due to intermolecular forces
Tertiary structures
Multiple secondary structures fold together and make structures depending on intermolecular forces
Primary structures
Polypeptide/Multiple amino acids bonded together
Quaternary structures
Multiple tertiary structures bonded together
Progression
Amino acids are made up of an amine, carboxyl, and a side-chain/R group
Peptide bonds
The amino acids then bond together to create dipeptides using peptide bonds
Dipeptides
2 amino acids bonded together
Polypeptides
The dipeptides bond together to create polypeptides/primary structures
Later structures
This primary structure then folds in different ways to make secondary structures and finally a whole 3D tertiary structure.
Functions
Hormones
Antibodies
Receptors - Helps in cell membranes
Enzymes
Transports
Essential amino acids - In humans, we can make 11 of the 20 amino acids in our cells. The other 9 amino acids must come from our diet and are called essential amino acids
Nucleic Acids
ATP
In autotrophs , like plants, sunlight energy is captured first as ATP. Most of this energy is used by the autotroph in its daily biological processes, such as growing new tissue like cellulose or storing energy in the form of amylose or fatty acids.
As matter is passed to heterotrophs in the next trophic level in the food chain only about 5-20 % of the original energy the autotroph received is passed on. In the consumers, enzymes convert the energy consumed into ATP.
Monomers
Nucleotides
one or more phosphate functional groups, a 5-carbon sugar, and a nitrogenous base.
There are five common nitrogenous bases: guanine, adenine, cytosine, thymine and uracil.
Purines (Double ring) - Adenine and Guanine
Pyrimidines (single ring) - Cytosine, Thymine, Uracil
Structuring
Like proteins, polymer forms of nucleic acids can make 3D structures as a result of intermolecular forces of attraction. Unlike proteins, though, nucleic acids have more predictable rules for which nitrogenous bases are attracted to each other.
DNA
Deoxyribose is used to make polymers of deoxyribonucleotides, also called DNA
DNA and RNA can exist as either single strands of one polymer or double strands made of two polymers.
When two strands come together, though, they always line up and connect with one strand inverted compared to the other. This orientation is called antiparallel
RNA
Ribose, on the other hand is used to make polymers of ribonucleotides, also called RNA
Nucleotides are connected between their phosphate group and a hydroxyl group on the 5-carbon sugar to make a phosphodiester bond
In other nucleic acids, like dinucleotides, cyclic AMP (cAMP), and ATP, the phosphate is connected differently to the ribose sugar.
NADP+
NAD+
FAD
CoA
Cellular structures
Imaging
Eye: The eye is the easiest tool for viewing biological samples. The ability to be able to tell two separate objects apart is called resolution. For the trained naked eye, our resolution is about 75 μm;
Light Microscopy: Improvements to optical microscopy over the past 300 years have increased magnification up to 1,500x and allowed optical microscopes to resolve objects as small as 200 nm. This resolution is a physical limit dictated by the wavelength of light
Electron Microscope: Electron microscopes (EM) use accelerated electrons and magnetic coils to make an image instead of light and glass lenses. Electrons have a wavelength (size) that is 104 to 105 times smaller than the wavelength of light. EMs can resolve objects that are 103 times smaller than the smallest resolvable object in a light microscope. The high-resolution transmission EM can magnify a sample up to 50,000x and provide a resolution of 0.1 nm. In cryo-EM, specimens are frozen rapidly to eliminate ice crystals from forming that can distort the specimen’s structure. Samples are then viewed at temperatures as low as –185ºC. Two- and three-dimensional models of the sample can be reconstructed using a computer program that averages many electron micrographs taken from different angles. Electron microscopy requires a sample thin enough to allow electrons to pass through. Samples smaller than 1/500th the diameter of a human hair are used
X-ray Crystallography: X-rays, with wavelengths approximately the same size as the spacing between atoms, are directed through a crystal of the substance under study. The X-rays are bent by the electrons surrounding the atoms in the crystal. The scattered X-rays produce a pattern as they exit the crystal. Sophisticated computer programs use measurements of the angles of the scattered X-rays and their intensities to calculate the three-dimensional positions of the atoms in the crystal. By rotating the crystal and making many two-dimensional images, it is possible to combine results to produce a three-dimensional picture of the molecule
Cell Tagging: In many cases, it can be difficult to pick out a cellular structure in a light microscope or electron microscope image. Cell tagging takes advantage of being able to follow individual molecules that make up a part of the cell. There are different methods of tagging biomolecules. For example, radioactive isotopes of atoms can be introduced to cells. Isotopes are used the exact same way as regular atoms except that their radioactive emissions can be detected with X-ray film. As cells consume the isotopes, they incorporate them into their cell structures. Another method involves adding a coloured or fluorescent chemical that binds to specific functional groups. In all cases, the final result is that the cell structure is highlighted compared to the rest of the cell.
Experimenting
Variables
Independant
The one thing you change
Dependant
The change that happens because of the Independent variable
Controlled
Everything you want to remain constant and unchanging
