Molecules
Molecules and Carbon
Every part of an organism has a form and function that are directly related.
The form of a molecule refers to its shape and underlying structure.
Biological molecules are based on carbon.
Carbon Characteristics:
Can form four bonds
Can form single, double, and triple bonds
Can form covalent and polar bonds
Can form rings and chains
Living things depend on the structural diversity of molecules built from carbon backbones.
Carbon is the 15th most abundant element on Earth; however, without carbon, life could not exist.
Its chemical properties allow it to have a wide range of combinations and functions with nearly limitless possibilities, due to the ability to form stable, covalent bonds (electron sharing) between two adjacent atoms.
Covalent bonds are the strongest type of bond between atoms, allowing for the production of stable carbon-based molecules.
An example in biology includes titan, the largest protein in the body, which consists of 100,000 carbon atoms.
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Condensation and Hydrolysis Processes
Condensation reaction:
Works by removing water molecules from monomers, creating bonds and forming a polymer.
Hydrolysis reaction:
Breaks down a polymer into monomers by adding water and breaking bonds.
Monosaccharides
Monosaccharides have between three and seven carbon atoms.
Pentoses: 5 carbon atoms
Hexoses: 6 carbon atoms
Both pentoses and hexoses normally have structures comprising a ring of atoms, including one oxygen atom and four or five carbon atoms.
Monosaccharides possess properties allowing them to be utilized in various ways by living organisms.
Glucose is a widely used monosaccharide.
Glucose
Like all monosaccharides, glucose is soluble and a relatively small molecule, facilitating easy transport.
It circulates in blood and is dissolved in plasma.
Like most carbohydrates, glucose is chemically very stable, a property useful for food storage.
However, storing large quantities of glucose in cells may cause osmotic problems, thus it is usually converted into glycogen or starch.
Glucose yields energy when oxidized, serving as a substrate for respiration.
Polysaccharides
Starch and glycogen serve as energy stores.
Starch is utilized in plants, whereas glycogen is used in animals.
Both substances comprise large numbers of glucose molecules, which can function as substrates for both aerobic and anaerobic cellular respiration.
Types of starch molecules:
Amylose:
Unbranched chain of glucose linked by 1 → 4 glycosidic bonds.
Due to bond angles, the chain is helical rather than straight.
Amylopectin:
Similar structure to amylose but includes some 1 → 6 glycosidic bonds, making the molecule branched.
Amylopectin vs Amylose
Glucose can be removed from starch and glycogen molecules when required.
Adding or removing glucose occurs more rapidly with amylopectin than with amylose, due to amylopectin's branched structure which provides more ends of chains to break.
Glycogen
Glycogen has a structure similar to amylopectin, consisting of α-glucose linked by 1 → 4 glycosidic bonds and branched by 1 → 6 bonding.
About 1 in 10 glucose molecules in glycogen have a 1 → 6 bond, as opposed to about 1 in 20 in amylopectin, indicating that glycogen is more branched.
Cellulose
Cellulose, like starch and glycogen, is composed of glucose; however, its properties differ significantly as it is a polymer of β-glucose rather than α-glucose.
Condensation reactions link the C1 and C4 molecules in β-glucose.
A cellulose molecule consists of 10,000 β-glucose molecules.
In β-glucose, the -OH group on C1 is angled upwards, while the -OH group on C4 is angled downwards.
To facilitate condensation, each β-glucose added to the chain must be inverted concerning the preceding one, resulting in alternating upwards and downwards orientations of the glucose subunits in the chain.
Glycoproteins
Glycoproteins consist of polypeptides with carbohydrates attached.
They play a role in cell-to-cell recognition, aiding in tissue organization, and enabling identification and destruction of foreign or infected cells.
An example is the ABO antigens in red blood cells, which provide a medium for cell-to-cell recognition.
Glycoproteins act as signals for cells to produce the correct antibodies to combat pathogens.
ABO Blood Groups
Antigen: A substance or molecule, often found on a cell or virus surface that triggers antibody formation, characteristic to the surface of a cell or cell type.
Antibody: A globular protein that recognizes and binds to a specific antigen as part of an immune response; antibodies are specific to certain antigens.
Lipids
Lipids are a diverse group of substances in living organisms that dissolve in non-polar solvents.
Examples of non-polar solvents include ethanol, toluene, and propane (acetone).
Lipids are sparingly soluble in aqueous (water-based) solvents and are described as hydrophobic.
The term "hydrophobic" is somewhat misleading because lipids are not repelled by water but are attracted more to non-polar substances.
Ester bonds are formed between triglyceride lipids.
Common types of lipids include:
Fats: Melting point between 20°C and 37°C, solid at room temperature.
Oils: Melting point above 37°C, solidify at low temperatures.
Waxes: Melting point above 37°C, liquefy at high temperatures.
Steroids: Characterized by a four-ring structure.
Phospholipids: Similar to triglycerides, but consist of two fatty acids linked to a glycerol and have a phosphate group instead of a third fatty acid.
The phosphate in phospholipids is hydrophilic, resulting in phospholipid molecules being partly hydrophilic and partly hydrophobic.
Monounsaturated vs Polyunsaturated Fatty Acids
A fatty acid with single bonds between all carbon atoms is saturated (containing maximum hydrogen).
A fatty acid with one double bond is called mono-unsaturated.
A fatty acid with more than one double bond is termed poly-unsaturated.
Phospholipid Bilayer
Phospholipids have two distinct parts: the phosphate head and hydrocarbon tails.
Phosphate head: Hydrophilic (water-attracting)
Hydrocarbon tails: Hydrophobic (water-repelling)
When phospholipids are mixed with water, the phosphate heads are attracted to water while the hydrocarbon tails are more attracted to each other than to water.
This results in the arrangement of phospholipids into double layers, known as phospholipid bilayers, with hydrophobic hydrocarbon tails facing inwards and hydrophilic heads facing outwards towards water on either side.
These bilayers are stable structures and form the basis of all cell membranes.
Steroids
Steroids are a category of lipids with structures similar to sterol.
Identification features:
Four fused rings of carbon atoms
Three cyclohexane rings and one cyclopentene ring
Total of 16 carbon atoms
Testosterone
Testosterone and oestradiol share similar molecular structures despite having markedly different effects on the body.
Proteins
Proteins are crucial as they constitute our muscles and enable movement.
Composed of amino acids held together by peptide bonds.
Each amino acid contains a central carbon atom called the "alpha carbon," which has single covalent bonds to four other atoms.
Attached to the alpha carbon are:
Carboxyl group
Hydrogen atom
R group (side chain, variable with 20 possibilities)
Amine group
Types of Amino Acids
With 20 different amino acids available, an infinite number of proteins can be created and varied.
All protein sequences are found in the human genome.
Amino acids are divided into two categories:
Essential amino acids: Cannot be synthesized by the body; must be obtained through food.
Non-essential amino acids: Can be synthesized naturally by the body.
Amino acid composition varies in foods based on their chemical makeup.
Types of Polypeptides
Examples include:
Beta-endorphin: A natural painkiller consisting of 31 amino acids.
Titin: The largest polypeptide, made up of 34,350 amino acids.
Alpha amylase: An enzyme in saliva initiating starch digestion; consists of 496 amino acids, associated with one chloride ion and one calcium ion.
Insulin: A small protein containing two short polypeptides, one with 21 amino acids and the other with 30.
Denaturation
The 3D conformation of proteins is stabilized by bonds between R-groups of amino acids.
Many of these bonds are relatively weak and can be disrupted, leading to a change in protein structure termed denaturation.
A denatured protein typically does not return to its original structure (the process is generally permanent).
Heat can induce denaturation by causing molecular vibrations that break R-group bonds.
Some proteins, like Thermus aquaticus, can withstand extreme temperatures (nearly 80°C) without denaturing, while most proteins denature at much lower temperatures.
pH and Denaturation
Extremities in pH (both acidic and basic) can also induce denaturation by altering the charges on R-groups, thereby breaking ionic bonds or causing new ionic bonds to form.
Levels of Protein Structure
Primary Structure:
Refers to the unique sequence of amino acids in a protein, determined by the nucleotide base sequence in the organism's DNA.
The primary structure is merely a chain of amino acids linked by peptide bonds, potentially encompassing hundreds of amino acids.
Secondary Structure
Formed by hydrogen bonds between the oxygen from the carboxyl group of one amino acid and the hydrogen from another.
The secondary structure does not involve side chains (R-groups).
Two common configurations are:
Alpha-helix (α-helix)
Beta-pleated sheet (β-pleated sheet)
Tertiary Structure
Involves bending and folding of the polypeptide chain due to R-group interactions and the peptide backbone, resulting in a defined 3D structure.
Forces contributing to tertiary structure include:
Covalent bonds (disulfide bridges) between sulfur atoms.
Hydrogen bonds between polar side chains.
Van der Waals interactions between hydrophobic side chains.
Quaternary Structure
This structure arises from the combination of multiple polypeptide chains into a single functional unit.
Not all proteins possess a quaternary structure.
Involves all bonds identified in the first three levels of protein organization.
Examples include hemoglobin, a conjugated protein containing four polypeptide chains each housing a non-polypeptide group called a haem, which has an iron atom that binds oxygen.
Membranes
A membrane acts as a semi-permeable boundary within a cell, regulating the transport of materials in and out of the cell.
Phospholipid Structure
Phospholipid molecules consist of a polar (charged) phosphate head and long non-polar lipid tails.
The head is hydrophilic (water-attracting).
The tails are hydrophobic (water-repelling).
Phospholipids arrange themselves into bilayers in water due to their amphiphilic nature.
Membrane Proteins
Two types of proteins are found in the phospholipid membrane:
Integral Proteins:
Permanently embedded in the membrane, hydrophobic and situated in the hydrocarbon chains within the membrane.
Transmembrane, extending across the membrane with hydrophilic portions interacting with the phosphate heads on either side.
Peripheral Proteins:
Hydrophilic on their surface; not embedded within the membrane.
Generally attached to the surfaces of integral proteins, with this attachment often being reversible.
Some may have a single hydrocarbon chain anchoring them to the membrane surface.
Fluid Mosaic Model
The current model of the cell membrane is known as the Singer-Nicolson Fluid Mosaic Model.
Key features:
Phospholipid bilayer: Phospholipids are fluid and capable of lateral movement.
Peripheral proteins bound to inner or outer membrane surfaces.
Integral proteins that permeate the membrane.
The membrane is a dynamic fluid mosaic of phospholipids and proteins.
Endocytosis vs Exocytosis
Endocytosis:
Process of forming a vesicle by pulling a small region of the membrane inward and pinching it off.
Mediated by proteins using ATP.
Vesicles formed will contain material that was originally outside the cell.
- Examples include:
Phagocytosis (white blood cells engulfing pathogens).
Transfer of antibodies from a mother to a fetus.
Feeding mechanisms in organisms such as Amoeba and Paramecium.
Exocytosis:
Expulsion of waste products or unwanted materials from the cell.
An example includes removing excess water using a contractile vacuole that moves to the plasma membrane for expulsion.
Other examples:
Exocytosis of packaged proteins from the Golgi apparatus.
Secretion of digestive enzymes.
Gated Ion Channels in Neurons
Ion channels facilitate specific ions passing through the membrane in either direction, enabling the movement from a higher to lower ion concentration.
This is a form of membrane transport termed facilitated diffusion.
Gated ion channels can open and close reversibly, allowing the switching on and off of diffusion, crucial for neurons.
Neurons have voltage-gated sodium and potassium channels and transmitter-gated channels at synapses.
Facilitated Diffusion
Larger and polar molecules cannot pass through the membrane via simple diffusion.
Transmembrane proteins identify particular molecules, assisting their movement across the membrane.
The transport direction aligns with the concentration gradient (from higher to lower concentration).
No ATP is utilized in this mechanism.
Active Transport
Active transport requires ATP to occur.
Integral protein pumps harness energy from ATP hydrolysis to transport ions or large molecules against the concentration gradient across the cell membrane.
ATP (Adenosine Triphosphate):
Breaks down to ADP (Adenosine Diphosphate) during hydrolysis, releasing energy via phosphate release.
Cells respire to recombine ADP and a phosphate for further processes.
Sodium-Potassium Pump
The sodium-potassium pump is a cyclical process: Moving three sodium ions out of the axon and two potassium ions into it, consuming one ATP per cycle.
Sequence in the cycle:
Three sodium ions enter the axon, attaching to the binding site.
The phosphate ion detaches from ATP, releasing energy, and causing the pump to open and expel sodium ions.
As sodium exits, two potassium ions attach to the binding site into the axon.
The phosphate ion releases from the pump allowing potassium ions entry into the cell.
Gating Mechanism in Sodium and Potassium Channels
The gating mechanism involves reversible conformational changes in the subunits.
Subunits can be in two states:
Open position: Narrow pore present, allowing ions to pass through.
Closed position: No pore present, blocking ion passage.
The potassium channel has four subunits and an additional globular protein resembling a ball, attached via a flexible amino acid chain.
The ball can fit inside the open pore, stalling ion movement immediately after the pore opens until the channel reverts to its original configuration.
Ball movement is regulated by minor voltage changes.
Sodium-dependent Glucose Transport
Sodium-glucose cotransporter proteins facilitate the transfer of sodium ions along with glucose molecules across the plasma membrane into a cell.
The glucose molecule is pulled in as sodium ions are channeled out, driven by the concentration gradient.
Glucose absorption relies on a higher Na⁺ ion concentration outside than inside the cell, maintained by active transport of Na⁺ out.
Sodium-potassium pumps on the inner (basal) side of the cellular membrane facilitate the transfer of Na⁺ toward nearby blood capillaries.
This transport mechanism is categorized as indirect or secondary active transport, as energy from ATP fuels it, but not directly through the cotransporter.
Cell Adhesion Molecules (CAMs)
Cells in a tissue link via cell-to-cell junctions relying on cell-adhesion molecules (CAMs) found in adjacent cells’ plasma membranes.
CAMs are typically proteins, half embedded in the phospholipid bilayer with the other half extending toward the extracellular environment.
Junctions form as CAMs in adjacent cells push them together.
Double Membrane of the Nucleus
The nucleus has a double membrane (nuclear envelope) encasing DNA, creating an isolated area for DNA to function without interference from other cellular processes.
The nuclear membrane includes numerous pores extending through both layers, allowing ions and small molecules to diffuse between the nucleoplasm (fluid within the nucleus) and the cytoplasm.
Larger molecules, such as mRNA, require transport proteins for transference across the nuclear membrane.
The nucleus contains the nucleolus, which produces ribosomes.
Compartmentalization of the Cytoplasm
Compartmentalization divides the cytoplasm into different organelles tasked with specialized functions.
Advantages include:
Isolation of enzymes
Process separation
Enhanced control over cellular processes.
Lysosomes and Phagocytosis
Lysosomes are constrained to prevent cell destruction.
Phagocytosis occurs surrounding lysosomal enzymes to avert cell destruction.
Steps in phagocytosis:
The cell engulfs the lysosome.
A vacuole forms around it.
The vacuole merges with the lysosome.
The vacuole can breakdown materials using lysosomal enzymes.
Mitochondria
Mitochondria are known as the site of cellular respiration, facilitating energy production within cells.