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SBI4U Biochemistry Notes
Biology (High School - Canada)
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Unit 1: Biochemistry
Importance of Water:
-
Water is polar and forms hydrogen bonds with other water
molecules
Universal Solvent:
- Dissolves more substances than any other
- Solutes dissolve into the spaces between the molecules
High Heat Capacity:
- Ensures temperature regulation and homeostasis
- Water requires large amounts of energy to heat it up, and it retains heat very
well once it has been warmed
- Release of sweat helps expel a source of warmth from the body
Cohesion and Adhesion:
- Cohesion is two water molecules bonded together (hydrogen bond)
- Adhesion is a water molecule bonding with another substance
Lower Density as Solid than as Liquid:
- Once water reaches below 4ºC, the amount of hydrogen bonds
continues to increase; it creates a more structured lattice of water
molecules which lowers the density of the water
- Helps to spread the weight of the water out, giving it
buoyancy
Types of Molecules:
Organic
-
Contains carbon, oxygen, hydrogen,
nitrogen; carbon is the basis of all life
Larger in size
Complex structures containing rings or
long chains
Eg. Glucose, Haemoglobin, DNA,
Starch
Inorganic
-
Usually doesn’t contain carbon (if it
does it doesn’t have hydrogen or is
simple)
Smaller in size
Simple structures containing 2 to 10
atoms
Eg. Carbon dioxide, Oxygen gas,
Sodium chloride, Calcium phosphate
Molecules:
- A large, complex, molecule (eg. protein, DNA)
- Polymer: a molecule composed of smaller, repeating
components (individual strand of DNA)
- Monomer: the smallest repeating portion of a polymer (eg.
nucleotide)
Dehydration Synthesis:
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Also known as condensation
When a water molecule is removed, it forms a new
bond as a hydrogen and a hydroxyl, creating two new
and longer polymers
Hydrolysis:
- When a water molecule is formed (from a hydrogen
and hydroxyl), it breaks bonds and forms longer
polymers
Functional Groups:
-
Functional groups are the active sites on molecules
Responsible for determining the chemical and physical properties of a molecule
Group
Chemical
Formula
Chemical Structure
Part of molecules
Hydroxyl
OH
Alcohols, carbohydrates
Carboxyl
COOH
Fatty acids and amino
acids
Carbonyl
C=O
Lipids
Amino
NH​2
Amino acids
Phosphate
PO​4
Phospholipids, nucleic
acid
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Carbohydrates:
-
Carbohydrates are used for storing energy (glucose), providing structure (cellulose),
cell identification and communication
- Monosaccharides are the monomers of carbohydrates; similar ring-like
structure, building block of all carbohydrates
- Found in foods like bread, pasta, fruit, vegetables
Glucose:
- The difference between glucose alpha and glucose beta is that
on C​1​, the hydrogen and the hydroxyl are flipped
- Alpha glucose: hydrogen on top
- Beta glucose: hydroxyl on bottom
- Galactose: C​4​ has the hydroxyl on top and hydrogen on
the bottom
Dehydration Synthesis:
- Water molecules are being removed,
which forms new bonds and creates
longer polymers
- In carbohydrates, monosaccharides are
joined together to form a disaccharide
to form a ether bond
- An ether bond is formed by the removal of water from two hydroxyl groups
- One water molecule is removed when a disaccharide is formed
Disaccharide Reactions:
- Glucose + Glucose = Maltose + Water
- Glucose + Fructose = Sucrose + Water
- Glucose + Galactose = Lactose + Water
Polysaccharides:
Molecule
Monomer
Location
Function of
molecule
Starch
Alpha glucose
Plants
Glucose storage in
plants
Glycogen
Alpha glucose
Liver and muscle
cells
Glucose storage in
animals
Cellulose
Beta glucose
Plant cell walls
Structural support
for plant cells
Lipids:
Function of Lipids:
- Used for long-term energy storage (triglycerides), cushioning, protection, vitamin
absorption
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- Used to make cell membranes (phospholipids)
- Used to make hormones (steroids)
- Used to make waterproof coatings (waxes)
Glycerides:
- A bond between glycerol and one fatty acid
- Diglyceride has one glycerol and two fatty
acids, triglyceride has three
- Carboxyl and hydroxyl are responsible for
combining a glycerol to a fatty acid by creating one
water molecule (two if diglyceride, three if tri…)
- Forms an ester bond
Saturated and Unsaturated Fatty Acid:
Molecule
Bonding
Physical State
Example
Saturated Fatty Acid
Only single bonds
between atoms
Solid at room
temperature
Butter, meat, cream,
cheese
Unsaturated Fatty
Acid
One or more double
bonds between
carbon atoms
Liquid at room
temperature
Vegetable oil, fish,
nuts, avocados
Types of Fats:
Molecule
Monomer Units
Location
Triglycerides
Glycerol and three fatty acids.
Used for long-term energy
storage in plants and animals
Phospholipids
Glycerol, two fatty acids,
phosphate group
Cell membranes (phospholipid
bilayer); phospholipids have a
polar head (hydrophilic) and
nonpolar tails (hydrophobic)
which causes them to form layers
Steroids
Synthesized from cholesterol,
composed of four carbon-based
rings
Don’t contain glycerol or fatty
acids, but they’re hydrophobic
Cholesterol in the cell
membranes
Estrogen and testosterone (sex
hormones)
Fatty Acids:
- Essential fatty acids are lipids that can’t be produced in the body and therefore must
be consumed; they’re found in linoleic acid and omega
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Trans-fatty acids are unsaturated fatty acids that have undergone hydrogenation in
order to become saturated and solid at room temperature
- The body can’t dispose of trans-fatty acids
properly so it sits in the body
- Hydrogenation is the process of breaking the
double carbon bonds in unsaturated acids so that
they only contain single bonds and can bond with
more hydrogen to become saturated
Proteins:
- Found in foods like meat, tofu, eggs, nuts
Function:
- Structure components of all cells (support, movement, transport)
- Enzymes (catalysts in chemical reactions)
- Regulators of cell processes (hormones, gene control)
- Defense from disease (antibodies)
Amino Acids:
- Amino acids are the monomers of all proteins
- There are twenty different varieties of amino acids, differing
only by their R groups
- R-groups are side chains that affect bonding and make each
amino acid unique from one another
- When two amino acids undergo dehydration synthesis, they produce a
dipeptide and one water molecule
- Held together by a peptide bond of the amino and carboxyl
functional groups
Protein Structure:
- Primary: the order of amino acids
- Secondary: Alpha helix or beta-pleated sheet
- Tertiary: Bends and kinds in secondary structure
due to interaction of R groups
- Quaternary: two or more polypeptide chains join
together to make a globular-shaped structure
Essential Amino-Acids:
- These are proteins that are needed by the body
but can’t be synthesized in it
- Non-essential amino acids can be produced in the body
Complete Protein Foods:
- A complete protein food contains all 9 essential amino acids; it doesn’t require you to
eat any other food in order to reach this full balance
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Nucleic Acid:
- Includes DNA, RNA and adenosine triphosphate (ATP)
Functions:
- DNA: makes up genetic material, making instructions for proteins
- RNA: involved in making proteins
- ATP: energy used for the cell (created in the mitochondria
through cellular respiration)
Nucleotide:
- Monomer unit for all nucleic acid
- Composed of sugar, phosphate group, and nitrogen base
(adenine, thymine, guanine, cytosine)
- Adenine and guanine are similar in shape, as are thymine
and cytosine
- Adenine and thymine bond through a double hydrogen
bond
- Guanine and cytosine bond through a triple hydrogen bond
DNA and RNA:
DNA
-
Double-stranded helix
Composed of deoxyribose sugar
Contain nitrogen bases of adenine,
cytosine, guanine and thymine
RNA
-
Single-stranded helix
Composed of ribose sugar
Contain nitrogen bases of adenine,
guanine, cytosine and uracil
Adenosine Triphosphate (ATP):
- Composed of three phosphate groups, one ribose (sugar)
and one nitrogen base
- Dehydration synthesis of ATP from ADP + P uses energy
since bonds are created (endergonic reaction)
- Hydrolysis of ADP + P from ATP releases energy since
bonds are broken (exergonic) reaction
Enzymes:
Biochemical Reaction:
- Process that changes biochemical substances into others
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Reactant: starts the chemical reaction
Product: result from the chemical reaction
Catalyst:
- Substances that speed up chemical reactions without being consumed in the reaction
- Enzymes are protein catalysts that reduce the activation energy required in biological
reactions
- Orient molecules towards each other or apart so that they
can synthesize/decompose by using less energy
Exergonic Reaction:
- There’s a net-release of energy during the chemical reaction
- Energy is consumed during the activation of the reaction,
but more energy is released during the process of breaking
bonds
Endergonic Reaction:
- There’s a net-input of energy into the chemical reaction
- Energy is absorbed so the reaction can occur, with some
being released after the formation of bonds
Functioning of Enzymes:
- Enzymes lower activation energy by reducing the amount of
energy needed for the reactants to come together and react
- Bind substrates tightly and specifically to an active site on
the enzyme
- Forms an enzyme-substrate complex
- Products are released from the active site, allowing the
enzyme to continue catalyzing additional reactions
Influences on Enzymes:
- Have optimal temperatures and pH
- Any changes to these conditions will change the
shape of the enzyme, altering the shape of the active site and their ability to
catalyze reactions
- Denaturation can be caused by heat, extreme cold, change in pH, chemicals
- Bonding between R-groups is disrupted (eg. hydrogen bonds are disrupted in
acidic environments since [H​+​] is high, meaning additional hydrogen are
bonded to molecules)
- Secondary, tertiary, and quaternary structures are modified
- Protein loses its 3D shape and becomes non-functional
Enzyme Inhibition:
- Competitive Inhibitors: Substances that compete with a
substrate for a spot on the enzyme’s active site (eg. CO
bonds stronger to haemoglobin than oxygen does).
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Noncompetitive Inhibitors: Substances that attach to a binding site on an enzyme
other than the active site; results in change of the enzyme’s shape and its loss of
affinity for substrate
Allosteric Regulation:
- Allosteric Site: Receptor sites, located far
away from the active site, which binds
substances that inhibits or stimulates an
enzyme’s activity
- Allosteric Activator: substance that binds to
an allosteric site on an enzyme and stabilizes
the protein conformation that keeps all the
active sites available for their substances
- Allosteric Inhibitor: A substance that binds to an allosteric site on an enzyme and
stabilizes the inactive form of the enzyme
- Feedback Inhibition: When a product of a sequence of reactions inhibits an enzyme
that catalyzed it in an earlier reaction
- Cofactors: Non-protein components that are needed for some enzymes to function
(often ions, et Zn​+2​, Mn​+2​)
- Coenzymes: Organic nonprotein cofactors that are needed for some enzymes to
function (eg. NAD​+​ from vitamin B​3​)
Cell Structure and Organelles:
Cell Wall:
- Not vital to cells (not all cells have them, eg. animal cells)
- Responsible for determining cell shape, controlling turgor
pressure (outward water pressure), adds strength to cell
- High turgor pressure (turgid) is when the cell walls are
pushed out and the cell is filled with water
- Low turgor pressure (flaccid) is when the cell walls
shrivel with little water inside the cell
- Cell walls are composed of cellulose (β glucose) in plants,
chitin in fungi and protists, glycoprotein in bacteria
Cell Membrane:
- Protects the cell from the outside environment, keeps
cell contents in place, controls which substances can
enter and exit the cell
- Phospholipids:
- Hydrophilic, polar head (phosphate and glycerol)
- Hydrophobic, nonpolar tails (fatty acids)
- Form a phospholipid bilayer
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Proteins:
- Float around within or on the surface of the membrane
- Used for structural support, surface binding sites for molecules (eg.
hormones), recognition sites for cell to cell communication and interaction,
transport molecules through the
membrane, transport electrons and
protons within the membrane
- Glycocalyx:
- Carbohydrate chains attached to proteins
(glycoproteins)
- Used for recognition and
communication of proteins, site for cell
to cell attachment
- Cholesterol:
- Keeps the phospholipids stable and retains the membrane’s shape; too much
cholesterol makes the membrane solid, too little makes it liquid
Nucleus:
- Region of the cell containing the genetic information
- Nucleolus
- A dense area within the nucleus containing
RRNA (ribosome RNA) and proteins; ribosomes
are produced here
- Nuclear pore:
- Openings in the nuclear membrane allowing for
the passage of molecules in and out of the
nucleus
- Chromatin:
- Stringy material made of proteins and DNA that takes up the majority of the
nucleus
- Chromosomes:
- Condensed chromatin; condenses into chromosomes shortly before cell
division begins
- DNA is important since it contains all the instructions to make
proteins
Ribosomes:
- Microscopic spheres attached to the endoplasmic reticulum or
free-floating in the cytoplasm
- Protein factories: make primary protein structures by stringing amino
acids together
Endoplasmic Reticulum:
- Twisting network of canals and sacs extending through the cytoplasm and connecting
the cell membrane to the nuclear membrane
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Rough Endoplasmic Reticulum:
- Has ribosomes attached to it
- Produces, modifies, and transports proteins
- Smooth Endoplasmic Reticulum:
- No ribosomes on it
- Produces lipids (cholesterol and phospholipids) and steroid
hormones
Golgi Apparatus:
- Sacs of membranous plate-like bags which produce vesicles (sacs)
- Produce and store cellular secretions (eg. fighting off infections)
- Many proteins and lipids undergo final processing in the golgi
complex
- Apparatus helps to fold molecules into final shape
completing tertiary and quaternary structures (eg. attaching
cofactors to enzymes)
Lysosomes:
- Membrane-bound sacs that are used for digestion of various structures within the cell
- Have acidic environment and hydrolytic enzymes to help digest foreign cells,
damaged organelles, macromolecules
Mitochondria:
- Site of aerobic cellular respiration (converts sugar energy
into adenosine triphosphate, ATP)
- Sugar + O​2​ → CO​2​ + H​2​O + ATP
- ATP is used by other organelles and cell processes for
energy
- Mitochondrial Structures:
- Cristae: site of chemical reactions using embedded
proteins
- Matrix: mitochondria cytosol (liquid portion of cytoplasm)
- Mitochondrial DNA: self replicating organelle, producing its own unique
proteins
Chloroplasts:
- Found only in green and photosynthetic organisms
- Convert sunlight to energy via photosynthesis
- CO​2​ + H​2​O → C​6​H​12​O​6​ + O​2
- Chloroplast Structures:
- Stroma: chloroplast cytosol
- Lamella: membrane that attaches inner chloroplast
structures
- Thylakoid disc: have a specialized membrane for photosynthesis
- Grana: stack of thylakoid discs (connected by lamella)
- Chloroplast DNA: self-replicating organelle
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Cilia and Flagella:
- Made of protein fibres
- Used for locomotion
- Cilia: short and numerous on cell surface
- Flagella: long and usually few in numbers on cell surface
Cytoskeleton:
- Structures that give the cell its shape and help organize its parts
- Provide a basis for movement and cell division (allows
for organelles to move along them)
- Made of filamentous proteins
- Microtubules: anchor organelles
- Actin filaments: contract muscle cells
Vacuoles:
- Fluid-filled sac
- In protozoa, vacuoles perform functions such as storage,
ingestion, digestion, excretion, and expulsion of excess water
- In plants, the large central vacuole help regulate water: turgor pressure is controlled
by vacuole
Theory of Endosymbiosis:
-
Explains the origin of eukaryotic cell organelles like mitochondria and chloroplasts
Works were advanced by Lynn Margulis in the 1960s
Passive Transport:
-
The movement of molecules through the cell membrane without the use of cellular
energy
Diffusion:
- Process by which particle move naturally from areas of high concentration to areas of
low concentration until the dynamic equilibrium is reached
- Moving with the concentration gradient
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Molecules are in constant motion (until equilibrium)
Small molecules are capable of passing through the phospholipids in the cell
membrane (eg. O​2​, CO​2​, H​2​O, alcohol, small lipids)
- Rate of diffusion
- Concentration of particles (increased concentration increases the rate of
diffusion)
- Temperature of particles (increased temperature increases the rate of diffusion)
- Pressure (increase in pressure increases the rate of diffusion)
- Agitation (increase in agitation increases the rate of diffusion)
Osmosis:
- The diffusion of water through a semipermeable membrane
- Solute: dissolved substance (eg. sugar)
- Solvent: able to dissolve things (eg. water)
- Solution: mixture of solvent and solute
- Types of membranes:
- Impermeable: nothing can move across it
- Semi-permeable: only some molecules can cross it (eg. cell membrane)
- Permeable: any molecules can pass through it
Types of Solutions:
- Hypertonic Solution: The solution surrounding the cell
has a higher concentration of solute than the cell’s
cytoplasm, causing water to leave the cell
- Hypotonic Solution: The solution surrounding the cell
has a lower concentration of solute than the cell’s
cytoplasm, causing water to enter the cell
- Isotonic Solution: The concentration of the solute is the same on the inside and the
outside of the cell
Turgor Pressure:
- The rigid cell wall of the plant prevents it from bursting
when it’s filled with water, causing outward water
pressure called turgor pressure
- Plant cells full with water are called turgid
Plasmolysis:
- When plant cells are placed in a salt solution, the cells
shrink, resulting in plasmolysis
Facilitated Diffusion:
- Some molecules are too large or are hydrophilic so they
cannot pass through the phospholipid bilayer (eg. glucose)
- Transport proteins assist in getting these molecules
through the cell membrane
- Transport occurs within the concentration gradient (no
energy is required)
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Active Transport:
-
The movement of molecules through the cell membrane against the concentration
gradient using transport ions
- Movement from low concentration to high concentration
- Requires the use of cellular energy (ATP)
- Transport proteins are highly selective (eg. Na​+​ and
K​+​ pump)
Endocytosis:
- Transports materials into the cells by the means of
vesicles
- Energy is required
- Cell engulfs the materials by folding a portion of
its membrane around it
- Types of endocytosis:
1. Phagocytosis: movement of large and whole molecules into the cell’s interior
2. Pinocytosis: transport of liquids into vesicles inside the cell
3. Receptor-mediated endocytosis: molecules bind to receptors on the cell’s
surface and are folded into vesicles within the cell
Exocytosis:
- Transport of macromolecules (eg. hormones) out of a cell
by means of vesicles made by the Golgi complex
- Energy is required
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