Eukaryotic Cell Structures

Eukaryotic Cell Structures

• Eukaryotic cells, both plant and animal, contain various structures with specific functions.
• The nucleus houses chromosomes made of DNA and controls the cell's activity.
• The nucleolus within the nucleus is responsible for ribosome production.
• A double membrane called the nuclear envelope encloses the nucleus.
• The cell surface membrane, composed of lipids and proteins, regulates the movement of substances in and out of the cell.
• Mitochondria, with their double membrane and folded inner membrane, are the sites of respiration and ATP production.
• Ribosomes, small structures found on the rough endoplasmic reticulum or in the cytoplasm, are involved in protein synthesis.
• The Golgi apparatus, a fluid-filled membrane, processes and packages new lipids and proteins.
• Golgi vesicles bud off from the Golgi apparatus to transport these lipids and proteins.
• Chloroplasts, found only in plant cells, are the location of photosynthesis and have a double membrane with thylakoid membranes inside.
• The rough endoplasmic reticulum (RER), covered in ribosomes, processes proteins made within the ribosomes.
• The smooth endoplasmic reticulum (SER) synthesizes and processes lipids.
• Lysosomes contain digestive enzymes, kept separate from the cytoplasm by the lysosome membrane.
• The cytoplasm is where most cellular reactions occur
• Plant cells have a cell wall that maintains cell structure.
• Plant cells also have a vacuole containing sap, which helps maintain cell shape through pressure.

Adaptations of Eukaryotic Cells

• Physical adaptations, such as microvilli and biconcave shapes, maximize diffusion rates in cells needing efficient substance exchange.
• Cells adapted for storage, like fat cells, have large lipid stores often within vacuoles.
• Red blood cells lack a nucleus to maximize space for hemoglobin, increasing oxygen-carrying capacity.
• Cells adapted for secretion, like goblet cells, have a large Golgi apparatus for producing many vesicles to secrete mucus.
• Cells with high energy requirements, such as muscle cells and nerve cells, have numerous mitochondria for ATP production
• Cells involved in active transport have many channel and carrier proteins in their cell membranes and increased ribosomes for protein production.

Prokaryotic Cell Structure

• Prokaryotic cells have cytoplasm without membrane-bound organelles.
• Ribosomes are present for protein production.
• A cell surface membrane controls substance entry and exit.
• A cell wall maintains structure and contains glycoproteins.
• Flagella are long structures used for motility.
• DNA is located in the cytoplasm as a coiled strand, not within a nucleus.
• Plasmids, small DNA bits, can be transferred between bacteria, spreading genes like antibiotic resistance.
• Some prokaryotic cells have capsules of secreted slime to protect against attack.

Units of Measurement in Biology

• Biological measurements range from millimeters to nanometers.
• 1 millimeter (mm) = diameter of a grain of sand.
• 100 micrometers (µm) = diameter of a grain of pollen.
• 10 micrometers (µm) = size of a red blood cell.
• 1 micrometer (µm) = approximate size of bacteria.
• 100 nanometers (nm) = approximate size of viruses.
• 10 nanometers (nm) = approximate size of proteins.
• 2 nanometers (nm) = diameter of a DNA helix.
• 1 nanometer (nm) = size of a buckyball (carbon 60).
• 0.1 nanometers (nm) = size of an atom.
• Conversions:
  • Millimeters to micrometers: multiply by 1,000.
  • Micrometers to nanometers: multiply by 1,000.
  • Nanometers to micrometers: divide by 1,000.
  • Micrometers to millimeters: divide by 1,000.

Types of Microscopes

• Optical microscopes use light to form an image, while electron microscopes use electrons.
• Optical microscopes can view objects larger than 0.2 micrometers, while electron microscopes can view much smaller objects.
• Optical microscopes provide color images and can be used to view living specimens, while electron microscopes produce black and white images (sometimes pseudocolored) of dead, fixed samples.
• Optical microscopes have a maximum magnification of around 1,500x, while electron microscopes can magnify up to 1.5 million times.

Optical Microscope Parts & Function

• Key components of an optical microscope include the eyepiece, base, light source, coarse and fine focus knobs, objective lenses, and stage.
• Optical microscopes use convex glass lenses.
• The resolution differentiates two close spots, distinguishing two objects instead of one; a light microscope resolution is roughly 0.2 micrometers.

Electron Microscope Types

• Transmission Electron Microscopes (TEM):
  • Have a very high resolution.
  • Require extremely thin specimens.
  • Used for imaging fixed (dead) samples in a vacuum.
  • May produce artifacts.
• Scanning Electron Microscopes (SEM):
  • Have a lower resolution compared to TEM.
  • Produce 3D images by reflecting electrons from the surface of the sample.
  • Require fixed samples.

Electron Microscope

• Electron microscopes are large and require dedicated rooms with controlled environments.
• Electromagnets focus the electron beam instead of lenses.
• Images are computer-generated from electrons interacting with the specimen.

Magnification Calculations

• Magnification = Image Size / Actual Size.
• Convert all measurements to the same scale before calculation.
• Eyepiece graticules are calibrated for each lens magnification to measure image size.

Biological Drawings

• Must be accurate and scaled.
• Use a sharp pencil and clear, continuous lines.
• Avoid shading.
• Include a title, labels, and fill the given space.

Chemical Bonds in Biological Molecules

• Covalent bonds: sharing of electrons between non-metals.
• Ionic bonds: transfer of electrons from a metal to a non-metal, forming oppositely charged ions with an attraction between them.
• Hydrogen bonds: weak attraction between opposite dipoles.

Water Molecule

• Water (H2O) is a bent, polar molecule with slightly positive hydrogens and a slightly negative oxygen.
• Hydrogen bonds form between water molecules due to these partial charges.
• Individual hydrogen bonds are weak, but collectively, they have a significant impact.

Properties of Water

• High latent heat of vaporization provides a cooling effect (e.g., sweating).
• Surface tension & Cohesion allows unbroken water columns in xylem
• High specific heat capacity stabilizes temperatures in organisms and environments.
• Water is a good solvent, dissolving ionic and polar compounds for transport and reactions.
• Water is an important metabolite, taking part in metabolic reactions like condensation and hydrolysis.

Inorganic Ions

• Atoms gain/lose electrons and become ions.
• Sodium ions (Na+): involved in co-transport across membranes.
• Phosphate ions (PO43-): essential for DNA, RNA, and ATP.
• Hydrogen ions (H+): determine pH ([H+]).
• Iron ions (Fe2+/Fe3+): involved in respiration and hemoglobin.

Monomers and Polymers

• Monomer: one "bit" (mono = one, mer = bit).
• Polymer: many "bits" (poly = many, mer = bit).
• Examples:
  • Amino acids (monomer) polymerize into proteins.
  • Nucleotides (monomer) polymerize into DNA/nucleic acids.
  • Glucose (monomer) polymerize into polysaccharides/carbohydrates.
• Polymers are macromolecules (large molecules).

Hydrolysis and Condensation Reactions

• Hydrolysis: breaks a chemical bond using water (hydrate = water, lysis = break).
• Condensation: joins two molecules, forming a chemical bond and eliminating a molecule (usually water).
• Examples of hydrolysis:
  • Polypeptides break down to amino acids.
  • Lipids break down to glycerol and fatty acids.
  • Nucleic acids (DNA) break down to nucleotides.
• Condensation is the reverse process.

Monosaccharides

• Single sugars, monomers of carbohydrates (mono = one, saccharide = sugar).
• General formula: (CH2O)n.
• Examples: glucose, galactose, fructose, with the same ratio of carbons, hydrogens, and oxygens, but different structures.

Glucose

• Exists in two forms: alpha glucose and beta glucose (C6H12O6).
• The difference lies in the position of the hydrogen and hydroxyl (-OH) group on carbon 1.

Alpha and Beta Glucose

• Alpha and beta glucose are non-superimposable
• Their spatial arrangement makes them react and behave very differently

Fructose and Galactose

• Structural formulas need to be known
• The are differences in the positioning of H and OH

Disaccharides

• Two monosaccharides joined together (di = two, saccharide = sugar).
• Join through the -OH groups via a glycosidic bond; water molecule is eliminated (condensation reaction).
• Examples:
  • Maltose: two alpha glucose molecules.
  • Sucrose: glucose and fructose.
  • Lactose: glucose and galactose.

Polysaccharides

• Many sugars joined together (poly = many, saccharide = sugar).
• Long chains of monosaccharides joined by glycosidic bonds (condensation reactions).
• Starch: a polymer of alpha glucose.
• Coil into an alpha helix shape.
• Insoluble --> do not affect osmosis.
• Branched --> large surface area.
• Composed of amylose (coiling) and amylopectin (branching).

Glycogen

• Polymer of alpha glucose
• Similar structure to starch.
• Shorter chains with more branches.
• Found ONLY in animal cells (liver and muscle)
• Quickly broken down when needed.

Cellulose

• Polymer of beta glucose.
• Forms long, straight, unbranched chains running parallel.
• Cross-linked by hydrogen bonds.
• Structural material --> plant cell walls.

Reducing Sugars Test

• Benedict's Test
• Add Benedict's solution to a sugar solution.
• Heat for 5 minutes, looking for a color change to brick red (positive result) due to the insoluble precipitate of copper(I) oxide formed.
• Quantitative test that detects amount, and not just presence of reducing sugars

Non-Reducing Sugars Test

• Treat the non-reducing sugar to break the glycosidic bonds.
• Add the solution to diluted hydrochloric acid to break the glycosidic bonds by hydrolysis
• Heat it for
• Neutralize the hydrochloric acid with sodium hydrocarbonate
• Preform the conventional Benedict's test

Quantitative Tests

• Measuring the change in color - use a color emitter to assess a change.
• Insoluble precipitate - filter, dry then re-weigh.
• More sugar = more precipitate forming.

Lipids

• Lipids, or fats, are insoluble in water but soluble in organic solvents.
• Triglycerides (fats and oils) and phospholipids are great stores of energy.
• Waxy lipid cuticles in plants and oily glands in skin are used for water conservation
• Lipids can be mixed with a test of ethanol, and with the introduction of water a positive result can be found when the solution goes cloudy

Triglycerides

• Triglycerides are made up of glycerol and three fatty acids joined by ester bonds (condensation reaction).
• Variations occur due to the wide range of fatty acids (over 70 different types).
• Saturated fatty acids have only single carbon-carbon bonds.
• Unsaturated fatty acids have some double carbon-carbon bonds, and polyunsaturated have many.

Phospholipids

• Phospholipids contain a phosphate group, glycerol, two fatty acids, and are all attached through ester bonds.
• The phosphate group head is hydrophilic (attracted to water), while the fatty acid tail is hydrophobic (repels water).
• In water, phospholipids:
  • Form emulsions of oil and water.
  • Form bilayers, which are double layers with heads facing outwards and tails facing inwards.
  • bilayers create hydrophobic middles that is what repels water and prevents water-soluble molecules from passing through the bilayer (special channel proteins allow its passage)

Amino Acids

• Amino acids have:
  • A central carbon atom.
  • A carboxylic acid group (COOH).
  • A hydrogen atom.
  • An amino group (NH2).
  • An "R" group (side chain) that varies and determines the amino acid's structure and properties.
• R groups can be small/large, acidic/basic, and determine bonding.

Peptide Bond

• Amino acids join by condensation reactions, forming a peptide bond.
• Two amino acids joined = dipeptide; many = polypeptide.

Protein Structure and Roles

• Proteins serve multiple roles in biology:
  • Enzymes: break down/build molecules by forming/breaking chemical bonds.
  • structural proteins: Parallel polypeptide chains that are strong and stable
  • Antibodies: immune response.
  • Membrane proteins: hydrophobic and hydrophilic.

Testing For Proteins

• Burt Test
• Mix equal volumes of test solution and sodium hydroxide.
• Add a few drops of dilute copper(II) sulfate.
• Change in color from blue to purple indicates a positive results

Protein Primary Structure

• Amino acid composition
• Is coded via DNA.
• Impacts r group that dictate properties.
• Interaction between strands can be impacted by r group arrangement/order.

Protein Secondary Structure

• Alpha Helix:
  • Bonds forming between polypeptide chains.
  • Creates a pleated shape.
• Beta Pleat structures:
  • Can be seen under microscopic resolution as layers of structure.

Protein Tertiary Structure

• Large amount of polypeptide bonding.
• Bonding can be broken by environmental shifts (pH).
• Can be the end point for a proteins 3D structure

Protein Quaternary Structure

• Many 3D chains that all interact cohesively
• Divided into two types:
  • Fibrous.
  • Globular.
• Fibrous Proteins - Insoluble
  • Collagen - Structural support.
  • Keratin - Water proofing.
  • Elastin - Stretch or elasticity
• Globular Proteins - Soluble.
  • Hemoglobin - Prosthetic helium group which allows it to bind oxygen
• Insulin - Hydrophilic r groups
• Pepsin - Acidic groups, allows stability in acidic conditions.

Separating Mixtures - Chromatography

• TLC plate - silica layer where substances interact
• Pencil line at bottom is the measured point
• Solvent is introduced, moving up the line in relation ot polarity
• More similar to the solvent will allow the substance to move up the plate
• Less similar will cause more of the substance to hold on the plate
• Mobile phase - solvent or water.
• Stationary phase - paper or TLC plate.

RF Value Measurement

• If the substance is colorless, will need UV light to identify
• Calculation is distance travel / solvent front
• Works from substance polarity (how long the substances go up the paper):
• UV light can show the line.
• Ninhydrin (amino acid) can show purple or brown.
• Practical uses:
  • Detect drugs in urine.
  • Analysis the purity of medication.
  • Analyze food.

DNA/RNA - Nucleotides and structure

• RNA and DNA components contain nucleotides
• The nucleotides contain a phosphate group, a pentose sugar and an organic base (joined together):
  • AGCT
• These bases form bonds with other nucleotides:
  • Bonding with A and T (double bond).
  • Bonding with C and G (triple bond).

DNA structure

• Strands are joined by phosphodiester bonds in a row.
• RNA has "ribose" sugar.
• MRNA - RNA coding structure.
• TRNA - RNA ribosome transporter.

DNA Replication

• Starts with DNA Helicase breaking hydrogen bonds in paired bases.
• Ends with one long coiled strand.

Messenger RNA

• Manufactured in nucleotides during transcription.
• Contains RNA polymerase as the DNA structure.
• Can be created in eukaryotic cells.

Splicing (Eukaryotes)

• The RNA undergoes slicing to remove introns.
• Coding sections are called extrons

TRNA

• Translations occur in cytoplasm and in ribosomes with enzymes.
• Active process that requires ATP.
• There is an anti-codon.
• Amino chains get formed while it is a constant process of the codon and anti-codon coming together

Genes

• A loci is the position in the DNA of that section.
• An allele is a different variation of the same kind.
• A triplet is a three based pair.
• Non-overlapping code means only read once.
• A genome is all the genes in a cell.
• A portome are all the proteins that a cell can make.

ATP

• Adenosine Triphosphate
• Adenosine diphosphate
• Bonds are unstable that exist in the structures, easily broken
• Breaking the bond -> releases energy
• ATP Hydrolase breaks down ATP to ADP, and can be rapidly reformed.
• Process is needed to phosphorylate molecules that require ATP

Reaction Energy with Enzymes

• Enzymes lower amount of reaction energy required.
• Enzymes are very specific.
• There is a narrow window of enzyme and other biological interactions for substrates

Lock and Key Method

• Now superseded method.
• Only works if there is exact matches but is too rigid.
• Juice method, current - Active site changes after bonding, more accurate
• Reactions can affect the rate of an enzyme, measured through measuring the product mass and loss

Factors that change Rate of reactions

• Substrates collide rapidly, bonding between 2 different substrates at a fast rate
• Change in temperature can affect the reaction.

Enzyme Graphs

• Rate of reactions with enzyme activity are important
• Reactions bonds start to dissolve, the tertiary structure shifts, and the active site changes
• Optimum temperature can vary between enzymes
• Human temperatures usually are around 37 degrees.

Temperature Coefficient

• Reaction increase factor by 10 degrees
• Formula can be use to calculate this based on temperature shift
• If shifts above optimum temperature - drops quickly, but usually doubles on each shift

PH Impact on Enzymes

• PH is concentration of hydrogen ions - impact enzyme
• Can change tertiary structure - change active site.
• Either side can denature the process.
• Active sites only work on narrow ph areas
• Higher amounts of ions means bonding stops function

Enzyme and Substrate Concentration Relationship

• More active site = more substrate
• Enzyme concentration is the primary variable and key
• Low enzyme, there is more substrates
• High enzyme , more area than active ingredients (reversely limiting)
• Reaction rate is dependent on both of these, both enzyme and substrate have a positive relationship if increased

Testing Substrate

• Uses indicators to detect PH
• Changes are good indicators.

Urease Enzyme

• Turns urea into ammonia, which increases alkaline
• Phenol turns red
• Filter on colorimetre needs green filtration.

Inhibitors

• Types of Inhibitors:
  • Competitive (biding same area).
  • NON-Competitive (changes shape of active site, which stops the binding)
• Competitive bonds take longer.
• NON can not work to that point because of its effect.

Cofactors

• Types of Groups:
  • Prosthetic (Metallic Ions).
• Temporary: Change charge distribution.

Coenzymes

• Organic molecules, temporary bind active side, needs to be recycled to original state at the end through other process.

Cell Membranes, Phospholipids and other Proteins

• Key components of all cell membranes need to be understood
• Phospholipids main part: hydrophilic heads point outwards from the outer part of the membrane - Hydrophobic tails are internal.
• Allows for lipid to move through membranes easily - entering easy.
• Stops water from moving through this path
• Constantly moving, flexible, self healing
• Proteins are inside that membrane :
  • Carrier Protein
  • Channel Protein
• Glycoproteins: Act as cell surface receptors.

Key Structure: Cholesterol

• Give strength and stability
• Hydrophobic prevents water
• Prevents the movement, keeps the cell regid

Breaking Down the Structure: Glycolipids

• Glyco means sugars in greek.
• Important for Signal recognition and create attachments

Fluid Mosaic

• Movement
• Mosaic is the shape and sizes

Membrane Permeability

• Increase in heat means phospholipids move and increase permeability
• Solvents: Detergent increase.
• Beetroot: measure osmosis
• Beetroot practical: If membrane damaged = release
• More damage = increase the leak of colour

Osmosis

• Definite use of word is important. Can write down as an answer
• Use of the correct terms are importance to show level
• The rate in which something diffused impacts water potential.
• dynamic equilibrium if reach - not saying all movement stops, saying net movement stops

Red blood Cells

• The membrane structure is thin, and is affected
• If there is more potential OUTSIDE of the cell: Water leaves the cell and shrinks.
• In ISOTONIC solutions, where there equal balance of solutions, there is an equal dynamic equation

Osmosis in Plant Cells

• Different structures and functions with different needs.
• Higher water potential than water enters.
• Lower potential than water exits.

Factors - Simple Diffusion

• Easy and correct understanding of world.
• Definitions are important.
• All things are distributed with enough kinetic energy.
• Non-polar molecules tend to pass through phases to reach equal balance.

Facilitated Diffusion

• Channel proteins allow the passage while avoiding lipid barrier
• Transmembrane carrier protein can allow the protein to pass in or out.
• No ATP is needed for the process.

Active Transport, molecules and Ions

• Move into cell, from low concentration to high

Explore the structures within eukaryotic cells, including the nucleus, mitochondria, ribosomes, and Golgi apparatus. Understand their roles in DNA storage, respiration, protein synthesis, and material processing. Focus on both plant and animal cells.