Unit 1 Biochemistry
Unit 1 Biochemistry
Properties of water
Water is deemed the medium of life
Solvent
Can dissolve a variety of molecules
Water dissolves reactants and enzymes so they can come together
Catabolic reaction → break down larger molecules into smaller molecules
Anabolic reaction → build larger molecules from smaller molecules (and a another)
Dissolved solutes can be transported around the body of an organism
Ex. dissolved sugars in photosynthesis are transported in the phloem from source to sink
Ex. dissolved mineral ions are transported in the xylem from roots to leaves
Helps multicellular organisms transport molecules around a body
Medium in which chemical reactions occur
Metabolite
Water is a metabolite by being a reactant or product of a reaction
Ex. condensation → water is formed
Ex. hydrolysis → when water reacts with a chemical and breaks into smaller molecules
Cystol
Liquid part of the cytoplasm
Mostly water and contains dissolved salts, fatty acids, sugars amino acids and proteins
Needed to carry out metabolic processes to keep the cell alive
Temperature buffer
High specific heat capacity
Intermolecular hydrogen bonds to maintain a narrow range of temperature that accommodates the enzymes
Maintains biological structures
Contributes to the formation of cell membranes
Hydrophillic heads and hydrophobic tails in the bilayer
Impacts the folding of proteins
As amino acids avoid water they fold to perform their functions
Suppports the double helix by surrounding DNA
Atomic structure
Protons - positive charge
Neutrons - no net charge
Electrons - negative charge
Ions - unequal charges in the atom
Ionic bond
Transfer of electrons between non-metal and metal
Attraction between a positively and a negatively charged ion
Atom with a lost electron is a positive cation
Atom with a gained electron is a negative anion
Covalent bond
Sharing of electrons between two non-metal elements
Nonpolar covalent
Share electrons equally
Polar covalent
Share electrons unequally
+ → slight positive charge because less electrons
- → slight negative charge because more electrons
The nucleus has more pull on the electrons (stronger)
Hydrogen bond
Attraction between 2 polar molecules with unequal charges
Represented by a dotted line
Each water molecule can bond with up to 4 other water molecules
Bonds are made and broken quickly though is stable as there is a very large amount of bonds
Cohesion, adhesion, solvency, and high specific heat make water the primary median of life
Cohesion
Molecules that stick to each other
Allows plants to move water under tension in xylem
Retains water on earth’s surfaces for habitats
Contributes to physical properties of water important to living organisms
Transpiration occurs because of the evaporation of water which pulls water in a sunction against gravity (also adhesion)
Surface tension
Molecules on the surface are more attracted to each other than the molecules in the air
Allows organisms to “walk on water” and for seeds to disperse
Adhesion
Attraction of water to other polar molecules
Hydrophilic
Polar molecules dissolve as they are charged ions
Water is electrostatically attracted to ions
Allows plants to move using capillary action
Permits water to move against gravity
Ex. water sticking to the xylem cell wall in transpiration
Ex. water adheres to soil particles that plant take in via osmosis
Capillary actions
Glucose is polar due to the unequal sharing of electrons
Water can form hydrogen bonds with glucose to allow it to be transported around the body
Negative charge attracts to positive
Meniscus
Capillary action as adhesion puts on upward force of the liquid on the edge of the vessel creating the meniscus
Water sticks to tube and cohesion makes water stick to itself
Water molecule
Polar covalent bonding within the water molecule
Polar because the oxygen molecule has more protons and attracts the shared electrons more creating an unequal charge
The electrons are pulled towards the oxygen atom
Solvation
Interaction of a solute molecules separating from each other when dissolving in water and becoming surrounded by water molecules
Hydration shell
Layer of water molecules surrounding an ion in an aqueous solution
Shell around the solute in a hydrogen bond
Hydrophobic
Nonpolar molecules that don’t have a charge are insoluble in water
Don’t attract water
Attracted to other hydrophobic molecules so they clump together when exposed to water
Ex. oil
Hydrophobic tails aren’t exposed to water and form bilayers
Lipoprotein
Lipids can’t be transported in solution
so they are coated in proteins and phospholipids to form lipoprotein to be able to be transported in blood
Physical property
Measurable behaviour or characteristics of matter that exists without the matter reaction or interacting with other things
Observable things
Water is the medium of life = water is the substance that life exists and depends upon
Buoyancy
Upward force applied to an object that is immersed in a fluid
Object will float if the buoyancy force of the fluid is greater than the objects weight
Depends on density
If the object’s density is lower than the fluids density the buoyancy force will be greater than gravity and the object will float
Even if objects have the same mass, the density is different and can affect
Ex. birds limb bones are hollow and are strong but no dense and allows them to float
Ex. fish can move up and down by changing their density by filling their swim bladder and moving up or removing the air and become more dense and move downwards
Viscosity
Measure of a fluid’s tendency to flow
Amount of friction the molecules of a liquid experience as they flow over each other
Thick fluid → more viscous
Thin fluid → less viscous
Water is more viscous than some substances due to hydrogen bonds that increase the friction and reduce the tendency to flow
Water is more viscous than air
Blood is even more viscous because cells and dissolved solutes increase viscosity
Thermal conductivity
Measure of a materials ability to move heat across a temperature gradient
Determined by how easily energy transfers throught the material
Less conductive
Heat moves slowly through the material
Better insulation and prevents heat loss
Ex. styrofoam
Keeps warm things inside warm
Ex. fat or fur on animals
More conductive
Heat moves rapidly though the material
Better for absorbing and transferring heat
Ex. pots and pans
Get hot quick
Ex. people get hypothermic in water more than air as water rapidly conducts body heat away from the body
Specific heat capacity
Quantity of energy needed to raise the temperature of a chemical per unit of mass
Water has the highest specific heat capacity of any liquid
Takes a lot of heat to raise water temperature
Good for temperature regulation
Good environment for habitats since the temperature doesn’t change fast
Caused by numerous hydrogen bonds
Each bond is weak but together it takes a lot of energy to break them all
Animal examples of physical properties
Ringed seal
Buoyancy allows the seal to float without spending a lot of its energy
Since water is viscous they can streamline and swim through it
Seals insulate themselves with blubber to maintain body temperature due to the great thermal conductivity water has
Lives in a stable habitat since water temperatures don’t change quickly due to specific heat
Black-throated loon
Buoyancy allows the bird to float without spending a lot of its energy
When flying the bird must expend energy to stay aloft
Can easily move through the air due to the low viscosity
Since air has low thermal conductivity the loon doesn’t lose as much body heat to the air
Air temperature changes rapidly since it has a low specific heat
Carbohydrates and Lipids
Carbon
“Backbone of every single organic molecule”
Very strong covalent bonds
Can form bond with 4 other atoms due to 4 valence electrons
Very stable
Can form long chains, rings or branched molecules
Macromolecules of life
Carbohydrates
starch
Lipid
Triacylglycerol
Protein
Enzyme
Nucleic acid
DNA
Macromolecule → large molecule
They are all polymers
Molecules made up of monomer subunits
Nanometer
0.001 m
1.010-6 mm
1.010-7 cm
1.010-9 m
1.010-12 km
Monosaccharides
Glucose
C6H12O6
Hexose (6 carbon)
Sugar that fuels respiration
Monomer for many polymers
Alpha
HO on bottom sides
Beta
HO on bottom, OH on top
Most common in nature
Primary source of energy for life
Brain needs x2 glucose to function compared to other cells
Isomers
Alpha-glucose and beta-glucose
Have different properties due to differences in hydroxyl group orientation on carbon 1
Soluble
Bc it’s polar due to many polar hydroxyl (OH) groups
Oxygen ring has a partial negative charge and the carbon-hydrogen (C-H) groups have a partial positive charge
Can easily be transported in blood plasma and form H-bonds with water
Chemical stability
Cyclic structure and the orientation of the OH groups make it a stable molecule
Key feature
for the structural role of the polysaccharide cellulose in plants
For starch and glycogen in the storage of glucose in plant and animal cells
Oxidation
Chemical reaction → the loss of electrons from an or molecule
Losses an electron → oxidised
Gain an electron → reduced
Occur through the addition of oxygen, removal of hydrogen atoms, or loss of electron
Involves the production of energy
Glucose is broken down by losing electrons to oxygen to produce carbon dioxide (CO2) and water
Products
Water, carbon dioxide and energy is released
Galactose
C6H12O6
Hexose
Found in milk and cereals
OHs on opposite heights of sides
Fructose
C6H12O6
Isomer formula as glucose and galactose
Pentose
Found in fruit, honey and is the sweetest
Ribose
C5H10O5
Pentose
Backbone of RNA
Differs in representation
Condensation reactions
Polymerization reaction joining two monomers and producing water
Two glucose example
Hydroxyl group being removed from one and a hydrogen being removed from the other to make water
The other product is disaccharide maltose
When more than 2 monosaccharides combine it’s called a polysaccharide
Anabolic reaction
Building up
Hydrolysis
Catabolic reaction
Breaking down
Water is used to break down bigger molecules into smaller molecules
Ex.
Maltose molecule into two glucose molecules
Similarities
Reversible processes that can create and break down polymers
Essential for proper functioning of biological systems
Allow for recycling of monomers and synthesis of new polymers needed for cellular processes
Complex carbs
polysaccharide polymers that have repeating glucose monomers
Starch
Amylose
Linear polysaccharide
Made up alpha glucose monomers
Alpha-1, 4-glycosidic bonds
Coiled structure composed of 300 and 3000 glucose units
Amylopectin
Highly branched
Alpha-1, 4-glycosidic
Occasional alpha-1, 6-glycosidic bonds
Create branches
Allows for more efficient storage of glucose
Major component of starch (80-85%)
Large molecular size
Starch is insoluble
Helps maintain osmotic balance within cells
Glycogen
Primary storage of glucose in animals and fungi
Coiled and branched polymer of glucose
Alpha-1, 4-glycosidic bonds
Frequent alpha-1, 6-glycosidic bonds
More extensively branched and compact
Efficient storage and mobilization of glucose
Insoluble due to large molecular size
Maintain osmotic balance within cell
Stored in the liver and muscle cells of animals
Liver stores glycogen to maintain blood glucose levels and can break down glycogen and release glucose to bloodstream when blood glucose levels drop
Muscle cells store glycogen to provide energy for muscle contractions
During exercise
Cellulose
Complex polysaccharide composed of beta-glucose molecules
Component of the cell wall
Forms a straight chain
Because beta-glucose molecules alternate in direction
Allows cellulose molecules to form long chains that can be grouped into microfibrils (bundles)
Held together by hydrogen bonding occurring between cellulose molecules
Creates strong and astable lattice structure
Tensile strength
Glycoproteins
Proteins that have 1+ carbohydrates attached
Form branched or linear chains that extend from the protein surface
Found in extracellular matrix, cell membranes, secreted proteins
Roles:
Cell-to-cell recognition
Act as markers → allow them to identify and interact with each other
Ex. immune system recognize and attack foreign cells (virus, bacteria)
Ex. immune system recognises incompatible blood types as foreign molecules and attack
Leads to red blood cells clumping → organ failure or death
Receptors
Receive signals from other cells or molecules
Ex. insulin binds to glycoprotein receptor triggering events leading to glucose uptake by the cell
Ligands
Binding to specific receptors on other cells to initiate signalling pathways
Structural support
Contribute to the structural integrity of cells and tissues
Can form part of the extracellular matrix, providing support for the cell
Glycoproteins on the surface of red blood cells determine the compatibility of ABO blood system based on recognition and interactino
Glycoprotein A and B antigens
Type O → universal donour
Type AD → universal recipient
Lipids
Mostly non-polar molecules that have low solubility
Exception for the phospholipid bilayer
Held together by estro bonds
Non-triglyceride lipids
Waxes → completely insoluble, high melting point
Steroids → hydrophobic, don’t contain fatty acids
Ex. cholesterol, progesterone, estrogen, testosterone
Naturally occuring hormones that regulate a wide range of physiological functions in the body
Composed of four carbon-based rings
Cholesterol
Provides the phospholipid bilayer with stability and flexibility
Oestradiol and testosterone
Development of female and male reproductive development
Hydrophobic
Can pass throught the phospholipid bilayer
Allows cells to have faster response to the presence of steroids
Efficient signalling
Triglycerides
Category of lipids for fats and oils
Can be consumed in food or manufactured in the liver
Composed of a glycerol molecules + 3 fatty acids (picture)
General structure:
All living organisms require lipids
Plants store fats or oils as a source of energy in seeds used by the germination seedling to grow until it can photosynthesize
Mostly unsaturated fatty acids
Endotherms
Human, mammals, birds
Rely on metabolic reaction to generate heat to maintain a body temp.
Require constant supply of energy (food)
Fat is stored in adipocytes as liquid droplets and can be broken down to ATP, used in cellular processes
Thermal insulators
Help regulate body temperature and protect against the cold
Ex. blubber in whales composed of triglycerides in adipose tissues
The layer serves as an insulator in cold waters
Also serves as an energy reserve so that they can survive long periods without food
Also makes them more buoyant
Lipids release twice as much energy in cell respiration per gram of lipids compared to carbohydrates
Fat doesn’t retain water so it is more efficient to store
Carbohydrates add 6 times more body mass for the same amount of energy
Fats are stored as pure droplets
1g of glycogen is stored with 2g of water
Critical for active animals that need energy storage
For the same energy
= 1g of lipids OR
= 2g of carbohydrates + 4g of water
Fatty acid types
Saturated (straight)
Straight chain with no double bonds
No more hydrogen atoms can be added
Chains are compact
Solid at room temperature
Higher melting point because it is harder to break the bonds since they are compact
Ex. butter
Unsaturated
Gaps between molecules → less compact → liquid
Membrane fluidity
Monousaturated
One double bond
Polyunsaturated
Multiple double bonds
The more double bonds there are, the lower the melting point
Easier for the bonds to break apart and turn liquid
Ex. oil
Cis-isomers
Common in nature
Hydrogen atoms on the same side of the double bonded carbon atoms
Each one causes a bend
Loosely packed
Low melting point triglycerides
Liquid
Trans-isomers (straight)
Rare in nature, artificially produced
Margarine from oil
Hydrogen atoms on opposite sides of the double bond
No bend
Closely packed
High melting points
Solid
Proteins
Amino acid
Monomers that make up proteins
21 found in eukaryotes
General structure
Amino group
R side chain (differs in each type)
Carboxyl group
Identifier for acids
Alpha carbon
Orientation can differ
Dipeptide
Two amino acids covalently bonded together by condensation (anabolic )
Amino acid + amino acid → dipeptide + water
Carboxyl group of the first amino acid bonds with the amino group of the second
The covalent peptide bond is very stable
Polypeptide
Has more amino acids bonded together by condensation
String of amino acids that didn’t form a protein conformation yet
Protein
Very large polypeptide chain that is folded into a function shape
Essential amino acids
Amino acids your body can’t produce
Must get them from the food you eat
Necessary for proper growth, maintenance and repair of body’s tissues and organs
Balanced diet is important to consume the appropriate combination of protein
Complete proteins
Contain all 9 essential amino acids
Ex. quinoa, soy, fish, eggs, dairy
Non essential amino acids
Can be produced by the body from other amino acids or the breakdown of proteins
Necessary for your body to function
Infinite peptide possibilities
Genes contain codes to build proteins that our traits result from, the genetic codes are read by the ribosomes in 3-nucleuotide sections (codons)
Our genetic code has codons for 20 different amino acids
To calculate the number of possible polypeptides
20 to the power of the amount of amino acids
Common polypeptides
Lysozyme (lysosome)
129 amino acids
In tears and saliva
Has antimicrobial properties
Distrupts the cell walls of certain bacteria
Provides a defence mechanism against microbial infections
Alpha-neurotoxins
60-75 amino acids
In snake venom
Target and disrupt the nervous system
Bind to and inhibit specific receptors and induces neurotoxic effects, paralysis, and death
Glucagon (think glucose → blood sugar levels)
29 amino acid residues
Bits removed
Hormone
Regulates blood sugar levels
Secreted from the pancreas when glucose levels in the blood are low, stimulating the liver to release stored glucose into the bloodstream
Raises blood sugar levels
Myoglobin (think my oxygen-globin)
153 amino acid residues
Found in muscle tissues
Oxygen-binding protein
Facillitates the storage and release of oxygen to muscle fibres
Particularly during periods of low oxygen availability (excersize)
Amino acid R group
Dictates the unique character of the amino acid and polypeptide once assembled (differentiates them)
Can be negatively charged, positively charged, polar or hydrophobic
Reason for the high diversity of protein form and function
Proteins can adapt a vast array of three-dimensional shapes
Protein conformation
Result of chemical character in R side chains
As the polypeptide is constructed by ribosomes, the R groups start to chemically interact with their aqueous environment and each other
Protein folding leading to protein conformation
If the sequence of amino acids is correct (no mutation), the protein folds into the correct 3D shape and will function correctly
If not → genetic disorders could be harmful or lethal
Primary structure of proteins
Primary
Polypeptide
The order of amino acids that the protein is composed of
Chain series of covalent peptide bonds between adjacent amino acids
Made by ribosomes
Controls all subsequent levels of structure
Secondary
Hydrogen bonding between the carboxyl group of one amino acid and the amino group of the other in a different part of the polypeptide chain
Forms alpha helix (curved) and beta-pleated sheets
Hydrogen bond is weak, though together hydrogen bonds are strong enough to old the conformation of the protein
Tertiary
Complex 3D shape
Further interactions between R-groups
More H-bonds form
Between polar R-groups
Covalent disulphide bridges
Between cysteine amino acids (contain sulfur atoms)
Ionic bonds
Between oppositely charged R-groups
Play an important role in determining the final conformation of the protein
Hydrophobic interactions
Non-polar amino acid R-groups
Non-polar amino acids clump together away from water to minimize contact
Hydrophilic interactions
H-bonds with polar amino acids
Interactions further stabilize the structure
Quaternary
2+ folded polypeptide subunits
Can be identical or different
Have one or more prosthetic groups
Non-peptide component attached to a protein
Crucial role in the protein’s function
Ex. hemoglobin
Composed of 2 alpha and 2 beta subunits
The alphas are coded by genes (HBA1 and HBA2) that are close on the chromosome 16
Beta subunit is coded by gene HBB on chromosome 11
Prosthetic group is a ring-shaped iron molecule (heme group)
Ex. fetal hemoglobin
Composed of 2 alpha and 2 gamma subunits
pH, temperature, and proteins
Data analysis question
Video on L3 slide 26
As temperature increases there is more particle movement → more collisions
Has a maximum temperature limit where they start to break down
Prefers an acidic environment
Starts to break down at a certain pH
Controlled variables
pH, temperature, concentration
Denaturation
If bonds or interactions between R-groups of amino acids (are weak) are broken and there is a change to the conformation of the protein
Denatured protein doesn’t return to its former structure
Permanent
Soluble protein become insoluble
2 liquids that form a solid
Change to a proteins tertiary or quaternary structure
Change in secondary structure in very extreme conditions
Enzymes can be denatured
Can’t perform its function
With minor denaturation reversible change are possible
Ex. heat
Vibrations within the molecule breaks intermolecular bonds (H-bonds)
Ex. extremes of pH
Changes the charges of R groups and breaks the tertiary structures ionic bonds or causes new bonds to form
Ex. presence of heavy metals
Ex. hydrothermal vent
Certain bacteria, thermophiles, live in hot conditions and their proteins are stable at the higher than normal temperature
Enzymes
Metabolism
Interdependent and interacting chemical reactions occurring in living organims
Doesn’t happen without enzymes
Enzymes
Speed up chemical reactions and can indirectly slow them down
Help regulate the duration of metabolic processes
Complex globular proteins
Dissolve easily in water
Have many hydrophilic amino acid residues on their surface
Biological catalysts
Increases the rate of a reaction by having a lower activation energy for the reaction to occur
Active site
Specific area composed of a few amino acids
Where the catalytic reaction takes place
The active site has the necessary properties due to interactions between amino acids within the 3D conformation
Substrate
Smaller piece
Chemical on which enzyme acts
Binds to the active site of the enzyme
Catabolism
Breakdown of complex molecules into simpler molecules
Hydrolysis of macromolecules into monomers
Ex. breakdown of sugars or fats to release energy
Energy is released
Anabolism (build up)
Synthesis of complex molecules from simpler molecules
Requires energy
Forms macromolecules from monomers by condensation
Ex. amino acids → protein
Ex. glucose → starch
Ex. Monosaccharides → carbohydrate
Both
Metabolic reactions catalyzed by enzymes
Induced fit binding
Previous school of thought (lock and key)
Believed that one substrate could only bind to one enzyme due to conformation and unique complementary chemical properties (charge, hydrophobicity …)
Evidence that some enzymes could bind to multiple substrates
Both the substrate and the enzyme change shape in order for the substrate to bind properly to the active site
Enzyme + substrate
The enzyme and substrate mix and bump into each other
Collisions allow the substrate to bind to the active site
Enzyme-substrate complex
When the substrate is binded it triggers a change in the 3D shape of the enzyme and the substrate
Transition state
The binding weakens the bonds in the substrate
Lower activation energy
Enzyme-product complex
Bonds are broken and the substrate is converted to the product
Enzyme + product
Product is released
Enzyme’s active sit returns to its original conformation, ready to bind to another substrate
Kinetics
Most enzyme reactions occur when substrates are dissolved in water
Collisions are know as substrate and active site coming together
Dissolved molecules are in random motion, each molecule moving separately
If not immobilized (bound to a cell membrane) the enzyme can move
Enzymes are larger than substrates and move slower
Collisions are the result of random movement of both substrate and enzyme
The substrate may be at any angle to the active site when collisions occur
Successful collision happen with correct orientation and enough energy for binding to occur
Exceptions
When the substrate is immobillised
The enzyme has to move in relation to the substrate
Ex. enzymes catalysing peptide bond between amino acids
When enzymes are immobilized
Ex. embedded in membranes
The substrate has to move to the enzyme
Industrial enzymes can be made immobile to increase their stability and reusability
Ex. enzymes in lactose-free milk
Ex. pepsin in the stomach (used to very low pH environments)
Ex. amylase in saliva
Ex. trypsin in the small intestine
Enzyme substrate specificity
Matching chemical and physical properties between the substrate and the active site
The level of enzyme-substrate specificity can vary
Certain enzymes are capable of binding to a single substrate exclusively
Others can bind to a range of similar substrates
Enzyme activity
Low temperature
Molecules move slowly
The chance of collision between substrate and enzyme is low
Rising temperature
Molecules move more rapidly
More likely for collisions to occur
Optimum temperature
Each enzyme has one
Rate of enzymatic reaction is the highest at this point
Higher temperature than optimal, enzyme can denature
Enzymatic reaction rapidly decreases
Enzymes work in different pH environments
Low pH → acidic (ex. stomach)
A change in pH from the optimum affects the enzyme activity
Affects the amino acid charges
Amino acids may not be attracted to each other anymore
Gradually decreases the rate of reaction
Extreme pH
Denature the enzyme by altering the 3D confirmation of the activity site
Substrate concentration
Low concentration → more enzyme molecules available than substrate
Low rate of reaction
Increase concentration
More chances of collisions → rate of enzymatic reaction rises gradually
Increase in rate of reaction stops when all active sites are occupied by substrate molecules (adding more substrate no longer affects the rate of reaction)