BIOL1000 MIDTERM 1
LECTURE TWO SEPT 5 :
WAVELENGTHS
Higher the energy the lower the wave length becomes, lower the energy higher the wave length is – higher energy: gamma rays, X-rays, ultra-violet – lower energy: infrared, micro-waves, radio waves
How do we know they exist? How they affect the environment
Light behaves as particles called photons
Pigment molecules have a molecular structure that allows them to absorb light energy
How we know pigments have something in common is to do with their structure – they have alternating double and single bonds
STRUCTURE/INFO OF EYEBALL - NOT IN TESTING
retina - the structure of the vertebrate eye - in the back, has a layer coating the back of the eyeball – retina is used to process (receive) light and colours. (SLIDE 7)
Cone - have its own nucleus, and is an almond nail shaped structure and is used to see colour
Rod - have a squareish nail shape - have its own nucleus, used to see in dim light (dark settings)
Photoreceptors are the only cells in the retina that contain pigments
Conformational change occurs after photon is absorbed - the retinal molecule inside the rhodopsin changed shape when retinal absorbs light - (SLIDE 9) leads to vision once light hits the layers in the retinal – depends on which pigments is involved - creates a domino effect when the light hits
Cis - inactive, trans - active
colour (chromatic) vision: CONE cells - cone cells allow light of the different wavelengths to see which colour in the brain – someone that is colour blind (like ba) cant see certain colours and will determine them as different colour or cant see the colour entirely.
Trichromatic (can see all colours) vision is the result of three different opsin proteins
Do all cells have the COLOUR opsin gene? Are in all cells in the body but are only present in cells that are being expressed such as the cone cell since they are expressed to see colour
What is the role of opsins: short wave sensitive (SWS), medium wave sensitive (MWS), long wave sensitive (LWS) – those who have SWS and MWS opsins will have dichromatic vision (has one out of the three cones missing or nonfunctional, limited colours – colourblind (ba)) those who have SWS,MWS,LWS have trichromatic vision (have 3/3 cone cells and can see all the colours and distinguish them easier
FUNDAMENTAL CHARACTERISTICS OF LIFE IN ALL ORGANISMS
Cells (membrane)
Evolution
Information (outside factors)
Energy (all cells need energy)
Replication
TWO MAJOR UNIFYING CONCEPTS OF BIOLOGY
Theory of evolution by natural selection - a characteristic of a population change over time (pattern) - individuals with certain heritable traits produce more offspring than those without those traits (mechanism)
All species are related by descent from a common ancestor and all species come from a descend from another pre-existing species.
Cell theory - all organisms are made up of cells (pattern) - all cells come from preexisting cells. (mechanism)
All single-cell organisms in a population related to a common ancestor and all cells in a multicellular organism descend from an ancestral cell.
Diversity: species change over time as a result of natural selection
Unity: all organisms alive today descended from a common ancestor
SUMMARY:
Vision and Light
Light is the visible part of the electromagnetic spectrum that humans can detect, behaving as particles called photons. Pigment molecules in our eyes are able to absorb this light energy due to their unique molecular structure, which includes alternating single and double bonds.
Vision begins in the retina, a layer of cells at the back of the eye that processes light and colours. Within the retina are photoreceptors (rods and cones), which are the only cells containing these light-absorbing pigments.
Cone cells are responsible for colour vision.
Rod cells are used for seeing in dim light. When a photon is absorbed by a pigment, a conformational change occurs, triggering a "domino effect" that leads to vision.
Colour Vision Mechanisms
Colour vision depends on opsin proteins.
Trichromatic vision allows an individual to see all colours and is the result of having three different opsin proteins: Opsin S (for blue/short wavelength light), Opsin M (for green/medium wavelength light), and Opsin L (for red/long wavelength light).
Dichromatic vision occurs when an individual possesses only two types of opsin proteins, specifically SWS and MWS opsins, leading to limited colour perception.
Fundamental Biological Concepts
All organisms share fundamental characteristics of life: cells (with membranes), evolution, information, energy, and replication. These characteristics are explained by two major unifying concepts in biology:
Cell Theory:
All organisms are made up of cells.
All cells come from pre-existing cells. This means all cells, whether in single-celled or multicellular organisms, are related by common ancestry.
Theory of Evolution by Natural Selection:
Characteristics of a population change over time.
Individuals with certain heritable traits produce more offspring. This theory explains both the unity of life (all organisms descended from a common ancestor) and the diversity of life (species change over time due to natural selection). A scientific "theory" is a broad explanation based on many lines of evidence that has been rigorously tested. Phylogenetic trees visually represent these evolutionary relationships, illustrating shared ancestry and diversity.
LECTURE THREE SEPT 8:
WHAT IS EVOLUTION AND HOW DOES IT WORK:
Variation in a population → variation is heritable – where does this variation come from: mutation, selection process, meiosis → differential survival & reproduction → frequency of selected traits increases in next generation → a change in the traits of a population over time = EVOLUTION
THE GENE OF COLOUR VISION
The section of DNA on a chromosome that codes for an opsin protein is called an opsin gene.
GENE > PROTEIN > FUNCTIONAL UNIT (PHOTORECEPTOR) > CELL > ORGANISM} this creates the domino effect
THINGS TO REMEMBER ABOUT SELECTION
Survive to pass on genes to next generation
Must successfully reproduce
Individual survive or don't survive – populations evolve
Selection is directed by circumstances (environment) – as circumstances changes, so may direction of selection
SUMMARY:
What All Living Cells Share
All living cells, whether from bacteria, archaea, or eukaryotes, have some fundamental things in common. They all share basic building blocks (the chemical molecules needed to make a functional cell). They also all have a plasma membrane (the outer boundary of the cell), use energy for their activities, and follow a specific genetic information flow.
How Genetic Information Works
Genetic information in cells flows in a specific pathway: DNA → RNA → proteins.
DNA contains all the genetic instructions.
RNA acts as an intermediary, carrying a copy of these instructions.
Proteins are the final product, carrying out most of the cell's functions.
This process involves two main steps:
Transcription: Making RNA from a DNA template. This step involves an enzyme called RNA Polymerase.
Translation: Making proteins from the RNA instructions. This happens using structures called Ribosomes.
The Importance of Proteins
Proteins are incredibly important for life; they are the most abundant and versatile macromolecules in living things. They carry out many critical functions.
Proteins are made up of smaller units called amino acids. Each amino acid has a unique "side chain" (R group) which gives it specific chemical and physical properties. These amino acids are linked together by peptide bonds.
Proteins have different levels of structure, which are crucial for their function:
Primary structure: This is the unique, linear sequence of amino acids in the protein.
Secondary structure: This refers to local folded patterns formed by hydrogen bonds in the protein's backbone, like the alpha-helix (a spiral shape) and the beta-pleated sheet (a folded sheet-like shape).
Tertiary structure: This is the distinct three-dimensional (3D) shape of a single protein chain, determined by interactions between the amino acid side chains. This 3D shape is what determines the protein's function.
Quaternary structure: If a protein is made of more than one protein chain (polypeptide), the way these chains fit together is its quaternary structure.
Proper folding is absolutely critical for a protein to function correctly.
LECTURE FOUR SEPT 10
CHARACTERISTICS CELLS IN ALL THREE DOMAINS SHARE
Common building blocks ( the chemical molecule to make functional cells)
Genetic information flow (DNA → RNA → proteins)
Plasma membrane
Uses energy
PROTEINS
Proteins are the most abundant and versatile macromolecules in life
Protein structure:
PRIMARY – SECODARY – TERTIARY – QUATERNARY
Each amino acid has a different side chain (R), which determines its chemical & physical properties
Amino acids in proteins are linked by peptide bonds – peptide bonds formation – electron sharing here gives the peptide bond the characteristics of double bond
The primary structure of a protein is the unique amino acid sequence of a protein – a line of amino acids with makes them unique protein
Secondary structure is due to hydrogen bonding between backbone atoms – alpha - helix is cylinder and beta-pleated sheet is folded
tertiary structure; distinct 3D shape that determine protein function – when they are are curly they are mostly of alpha-helices, when they are straight and only alittle curly is mostly beta-pleated sheets
Proteins are critical for life's functions
Composed of amino acids with unique side chains
Protein structure levels:
Primary: unique amino acid sequence
Secondary: hydrogen bonding structures (α-helix & β-sheet)
Tertiary: 3D shape determining function
Quaternary: multiple polypeptide interactions
MOLECULAR DIVERSITY
- Proteins are the most diverse molecular class
- Other key molecules include:
- Carbohydrates (structural support, cell identity)
- Lipids (predominantly hydrophobic)
- Nucleic acids (DNA, RNA)
GENETIC INFORMATION FLOW
- All cells contain DNA as genetic information
- DNA codes for RNA
- RNA codes for proteins
- Key processes: Transcription and Translation
Transcription
- Process of making RNA from DNA
- Involves RNA Polymerase
Translation:
- Process of making protein from RNA
- Occurs using Ribosomes
Key Pathway
• Information flows: DNA → RNA → Protein
- DNA contains genetic information
- RNA acts as an intermediary
- Protein is the final product
SUMMARY:
Cell Theory
All organisms are composed of cells
Cells are the smallest units with life properties
Cells arise only through growth and division of pre-existing cells
Common Cellular Characteristics Across Domains
- Shared fundamental building blocks include:
- Proteins
- Genetic information flow (DNA → RNA → proteins)
- Plasma membrane
- Energy metabolism
Protein Structure and Importance
- Proteins are the most diverse class of molecules
- Protein function depends on proper folding
- Protein structures include:
- Primary structure (amino acid sequence)
- Secondary structure (α-helix & β-sheet)
- Tertiary structure (3D shape)
- Quaternary structure (multiple polypeptides)
Molecular Information Flow
- All cells contain DNA as genetic information
- DNA codes for RNA
- RNA codes for proteins
- Information pathway: Transcription → Translation
LECTURE FIVE SEPT 12
CELLULAR CHARACTERISTICS ACROSS DOMAINS -
Basic Building Blocks: Chemical molecules essential for functional cells
Genetic Information Flow: Follows DNA -> RNA -> proteins pathway
Plasma Membrane: fundamental feature shared in all three domains of life: bacteria, archaea and eukaryotes
Energy Metabolism: All cells require energy and use ATP as primary energy carrier
MODES OF NUTRITION/METABOLISM
ENERGY
SOURCE
CARBON SOURCE
OXIDATION OF MOLECULES
(CHEMO-)
LIGHT
(PHOTO-)
CO2 (AUTO-)
CHEMOAUTOTROPH
Some bacteria and archaea; no eukaryotes
PHOTOAUTOTROPH
Some bacteria, some protist (eukaryotic microorganisms); and most plants
ORGANIC MOLECULES
(HETERO-)
CHEMOHETEROTROPH
Some bacteria, archaea and protists; also fungi, animals and even some plants
PHOTOHETEROTROPH
Some bacteria
BACTERIA AND ARCHAEA (PROKARYOTES); CELL STRUCTURE AND FUNCTION
smaller/ simpler in structure vs eukaryotic cells – less genetic info, no nucleus, no organelles
Has genetic and biochemical diversity - uses a lot of different substances as energy and carbon sources (light +oxidation of molecules)
Can live everywhere on earth's surface (antarctic to the hot springs)
Has millions of different species – outnumber all other types of organisms – REPRODUCTION.
Most prokaryotic cells share several common cell structures:
(bacteria is a type of prokaryotic cell but not all prokaryotic cells are bacteria.)
No nucleus –DNA located in nucleoid
Contains ribosomes, cytoplasm, cell membrane, cell wall, glycocalyx
MANY (not all) have flagella and/or pili
Most are ~ 1 micrometer in diameter, 1/10 the size of a eukaryotic cell
BACTERIAL DNA COMPONENTS
Bacterial genomic DNA
Most bacteria is a single circular DNA molecule (1 chomosome)
Contained in a nucleoid (no membrane)
Bacteria needs genes to survive
(Humans have a linear DNA)
Bacterial plasmids
Extra-chromosomal piece of DNA that carry non- essential genes
Small circular DNA molecules
Non-essential genes can have beneficial functions (antibiotic resistance, metabolism, toxins etc.)
Replicate independently of the chromosomal DNA
Bacterial DNA is involved with metabolism by the fundamental genetic information flow mechanism - DNA – RNA — PROTEINS
Also supports ATP production because of genes for the necessary proteins – without the instructions of the bacterial DNA the cells would not be able to to produce the proteins required for the process of the metabolism that generates ATP = unable to to perform essential life processes.
BACTERIAL CELLS
Contain cytoplasm, ribosomes, cytoskeleton and some organelles
Ribosomes: RNA and protein, macromolecules machines for protein synthesis
Cytopskeleton: proteins (FtsZ(dividing) and MreB(shape)) involved in support, shape and cell division
Organelles: membrane enclosed, store calcium, enzymes, etc..
The cell wall can either be positive Garm ( PURPLE); single, thick peptidoglycan layer
negative Garm (PINK); thin peptidoglycan layer surrounded by outer membrane
FUNCTIONS
Boundary of cell
Metabolism (ATP production)
Photosynthetic bacteria often ahas internal membrane which e=derives from the plasma membrane
ARCHAEAL CELL CHARACTERISTICS
Unique Attributes:
Found in extreme environments
Diverse metabolism
Shares similarities with bacteria and eukaryotes
Distinct molecular structures
Cellular Diversity and Adaptation
- Organisms possess varied modes of nutrition
- Different energy and carbon source strategies
- Incredible genetic and biochemical diversity
SUMMARY:
The sources detail the fundamental characteristics of life, modes of energy metabolism, and the structure of prokaryotic cells (Bacteria and Archaea).
Core Characteristics of Life
Cells across all three domains (Bacteria, Archaea, Eukarya) share fundamental traits: they use chemical molecules as basic building blocks, maintain a plasma membrane, utilize and require energy for metabolism, and follow the genetic information flow from DNA to RNA to proteins.
Energy and Metabolism
All cells need both a source of carbon and a source of energy. They use ATP as the major energy carrier to build macromolecules and sustain life processes. Modes of nutrition are categorized by their energy source (Chemo-/Photo-) and carbon source (Auto-/Hetero-). Bacteria possess the most diverse modes of nutrition.
Mode
Energy Source
Carbon Source
Key Observation
Autotrophs
Chemo- or Photo-
CO2
Chemoautotrophs include some bacteria and archaea, but no eukaryotes.
Heterotrophs
Chemo- or Photo-
Organic Molecules
Chemoheterotrophs include bacteria, archaea, protists, fungi, animals, and some plants.
Prokaryotes (Bacteria and Archaea)
Prokaryotes are generally smaller and simpler than eukaryotic cells, exhibiting immense genetic and biochemical diversity. They successfully inhabit almost all regions of Earth and vastly outnumber other organisms.
Common Prokaryotic Structures:
No nucleus; DNA is located in a nucleoid (which lacks a membrane).
Presence of ribosomes, cytoplasm, cell membrane, and cell wall.
Many possess a Glycocalyx, Flagella, and/or Pili.
Bacteria Structure
Most bacteria are about~ 1 micrometer in diameter. They typically have a single, circular DNA chromosome. They frequently contain plasmids—small, circular, extra-chromosomal DNA molecules carrying non-essential genes (e.g., antibiotic resistance) that replicate independently.
Cell Envelope: The bacterial cell membrane is the cell boundary and is vital for metabolism, including ATP production. The cell wall is made of peptidoglycan (peptide cross-bridge and carbohydrate backbone).
Gram-Positive Bacteria have a single, thick peptidoglycan layer.
Gram-Negative Bacteria have a thin peptidoglycan layer surrounded by an outer membrane.
The cell wall can be targeted by antibiotics or lysozyme, leading to cell rupture and death.
External Features: The Glycocalyx (capsule or slime layer) surrounds the cell wall and protects bacteria from environmental stressors like extreme temperatures, desiccation, viruses, and antibiotics. Flagella provide motility. Fimbriae and Pili are used primarily for attachment, with Pili facilitating the initial contact to bring bacteria together.
Archaea Structure and Uniqueness
Archaea are prokaryotic cells that share structural similarities with both bacteria and eukaryotes.
Similarity to Eukaryotes: Their information system (ribosomal structure and aspects of transcription/translation) is more similar to eukaryotes than to bacteria.
Molecular Distinction: Archaea are structurally distinct from both other domains at the molecular level, possessing unique cell walls (which are not peptidoglycan), unique flagella, unique glycocalyx, and unique membrane lipids.
Habitat: Many Archaea are found in extreme environments and have diverse metabolisms. No identified human pathogens belong to Archaea.
LECTURE SIX
SUMMARY:
Eukaryotic Cell Structure and the Endomembrane System, highlighting the key differences between eukaryotes and prokaryotes and outlining the function of essential internal components.
Eukaryotic Cell Fundamentals
Eukaryotic cells are characterized by being larger than prokaryotes and possessing a distinct nucleus surrounded by a nuclear envelope. They contain membrane-bound organelles, which divide the cell into functional and structural compartments.
Major eukaryotic cell structures include:
Nuclear membrane
Endoplasmic Reticulum (Smooth ER, Rough ER)
Golgi Apparatus
Lysosomes
Vacuoles
Peroxisomes
Mitochondria
Chloroplasts
Cytoskeleton
Plasma membrane (and cell wall in plants)
An organelle is generally defined as a membrane-bound compartment inside a cell that contains enzymes or structures specialized for a particular function.
The Nucleus and Genetic Material
The nucleus physically separates the hereditary material from the rest of the cell. It holds the nuclear genome and is surrounded by a double membrane (two lipid bilayers) that form the nuclear envelope.
Nuclear DNA exists as chromatin:
Euchromatin: Represents lighter regions containing loosely packed DNA where genes are active and transcription is occurring.
Heterochromatin: Represents darker regions associated with inactive genes.
The nucleus is also supported internally by the Nuclear lamina, found inside the nucleus under the double membrane. The Nucleolus is a non-membrane bound structure composed of proteins and nucleic acids, and is the site of ribosomal RNA (rRNA) synthesis and ribosomal subunit assembly.
The Endomembrane System
The Endomembrane System is a collection of interrelated internal membranous sacs. Membranes within this system are highly similar, suggesting they are either directly connected or otherwise related. One hypothesis suggests that these related membranes were derived from the plasma membrane.
Organelles included in the Endomembrane System are:
Nuclear membrane
Endoplasmic Reticulum (SER, RER)
Golgi Apparatus
Vesicles
Lysosomes
Vacuoles
The system carries out several crucial functions:
Synthesis, modification, transport, and secretion of proteins.
Synthesis of lipids and detoxification of toxins.
Transportation and breakdown (digesting) of large biomolecule-containing particles.
Nuclear Transport
The cell must rigorously control what moves into and out of the nucleus. This traffic control is managed by Nuclear Pore Complexes (NPCs), which are multiprotein complexes embedded in the Nuclear Envelope.
Movement through the NPC is regulated by specific signal sequences:
A Nuclear Localization Signal (NLS) is required for nuclear import.
A Nuclear Export Signal (NES) is required for nuclear export.
These signals ultimately facilitate interaction with the NPC, enabling the entry or export of the cargo.
LECTURE SEVEN
SUMMARY:
This summary simplifies the structural components of bacteria and the processing pathway for proteins within the eukaryotic endomembrane system.
I. Simple Cells (Bacteria)
Bacterial cells contain cytoplasm, ribosomes (macromolecular machines made of RNA and protein for protein synthesis), and a cytoskeleton (proteins like FtsZ and MreB) used for support, shape, and cell division. Importantly, bacteria have no enclosed organelles, though they may store things like calcium or enzymes.
II. The Eukaryotic Control Center (Nucleus)
The nucleus holds the nuclear genome. Its main function is to physically separate the hereditary material from the rest of the cell. It is surrounded by a double membrane called the nuclear envelope and contains nuclear lamina (made of lamins) for structural support.
III. Protein Synthesis and Targeting
Ribosomes are the major site of protein synthesis. After a gene is transcribed into mRNA, the cell must determine where the resulting protein needs to go.
Rough ER (RER): The RER is involved in protein production and export. It is a network of membrane tubules that has ribosomes attached to its surface and is connected to the nuclear outer membrane. Proteins destined for export or other parts of the endomembrane system are synthesized, folded, and processed on the RER.
ER Signal: For a protein like Insulin to be made on the RER, the ribosome synthesizes an ER Signal sequence (a 20-30 amino acid sequence).
SRP Detection: A Signal-recognition particle (SRP) detects this sequence. The SRP directs the entire ribosomal unit to the SRP receptor on the ER membrane.
Synthesis: Protein synthesis then continues through a translocon channel. The growing protein is fed into the ER lumen (for secreted proteins) or inserted into the membrane (for membrane proteins).
IV. Protein Delivery (Vesicles and Golgi)
Vesicles are the "delivery guys". These are membrane-enclosed structures that allow proteins to move between organelles. Vesicles connect the ER with the Golgi, the Golgi with the plasma membrane, and the plasma membrane with lysosomes and peroxisomes.
Golgi Function: The Golgi is a system of flattened sacs called cisternae. Proteins coming from the RER enter at the cis face and leave via the trans face.
Modification and Sorting: The Golgi processes proteins by performing further modification, which can include adding sugars or lipids or removing amino acids. The modified products are then sorted to the plasma membrane or other parts of the endomembrane system.
Secretion: For exported proteins (like insulin), the protein leaves the ER via a vesicle, fuses with the Golgi, leaves the Golgi in another vesicle, and finally fuses with the plasma membrane where the protein is released.
ER, cis-Golgi, trans-Golgi, vesicles
LECTURE EIGHT
SUMMARY:
1. Universal Life Functions
All cells, whether simple (prokaryotes) or complex (eukaryotes), share essential functions: they follow the DNA →RNA → protein information flow, require a plasma membrane, and need energy, using ATP as the primary carrier.
2. The Endomembrane System: Synthesis and Cleanup
This system handles the creation, modification, storage, and breakdown of cellular material.
A. The Nucleus and ER
The Nucleus is the control center, holding the cell's genetic material (genome).
Rough ER (RER): Has ribosomes attached. Its main job is to synthesize and process proteins destined for export or for use in other membrane organelles [Summary provided in conversation history].
Smooth ER (SER): Has no ribosomes. It performs specialized tasks like synthesizing lipids for cell membranes, storing calcium for cell signaling, and, in organs like the liver, breaking down drugs, poisons, and toxic by-products. It also makes steroid sex hormones in reproductive organs.
Tracking Proteins: Scientists can follow proteins as they move through the system using a method called "Pulse" (labeling amino acids) followed by a "Chase" (washing away the label).
B. Transport, Modification, and Waste Management
Vesicles (The Delivery Trucks): These are membrane-enclosed structures that move material between organelles (e.g., from ER to Golgi) [Summary provided in conversation history]. Vesicles are also formed when the cell takes in outside material (endocytosis).
Golgi Apparatus: Processes and sorts products received from the ER. It modifies proteins (e.g., by adding sugars) and then sorts them for their final destination [Summary provided in conversation history].
Lysosomes (The Recycling Centers): Only present in animal cells. They contain enzymes and maintain a low pH (due to proton pumps) to break down macromolecules. They can break down material ingested by the cell (like Amoeba taking in food or Macrophages engulfing bacteria) or digest old, unnecessary organelles (autophagy).
Vacuoles: Large, membrane-bound sacs used for various functions like storing food or performing digestion (in plants/fungi).
3. Energy Transformers: Mitochondria and Chloroplasts
These organelles are responsible for energy conversion.
The Theory of Endosymbiosis explains their origin:
Mitochondria came from ingested aerobic prokaryotes (bacteria).
Chloroplasts came from ingested cyanobacteria.
The host and the bacteria formed a relationship where both benefited, eventually becoming inseparable.
Evidence for this theory includes:
They are the same shape and size as bacteria.
They contain their own circular DNA.
They have their own machinery for making RNA and proteins.
They multiply independently via binary fission.
4. The Cytoskeleton: Support and Movement
The cytoskeleton is a dynamic network of protein fibers and tubules that is constantly changing (not static).
Functions: It provides strength and cell shape, facilitates intracellular transport, and enables whole cell movement.
A. Three Types of Filaments
Microfilaments (Actin): These are dynamic and polar (meaning they have a '+' and '-' end). They polymerize (grow) along the leading edge to help cells crawl (Amoeboid Movement) and are crucial for dividing animal cells. They work with the motor molecule Myosin to cause muscle contraction and cytokinesis.
Intermediate Filaments: These are less dynamic and have no polarity. Their main role is to provide mechanical strength and maintain the position and shape of the cell and nucleus (e.g., lamins and keratin).
Microtubules: These are also dynamic and polar. They are involved in intracellular transport, organelle location, cell division (mitosis), and cell movement.
B. Motor Molecules
Movement along microtubules depends on ATP-hydrolyzing motor molecules:
Kinesin: Moves towards the fast growing or "plus" end of the microtubule, carrying organelles and vesicles.
Dynein: Moves towards the slow growing or "minus" end. It transports vesicles and is essential for the movement of cilia and flagella.
C. Flagella and Cilia
Eukaryotic Flagella and Cilia are used for locomotion and fluid movement. They use microtubules and Dynein in a characteristic 9+2 complex structure. Note that Bacterial and Eukaryotic flagella have the same function but evolved independently (they are analogous, not homologous).
LECTURE NINE
Flagella and eukaryotic cells are analogous structures (they have the same function) but ARE NOT evolutionary related.
Important of cell size; the cell size - larger organism just have more cells
SURFACE AREA TO VOLUME RATIO
Surface area (length^2) important for transporting oxygen and nutrients into the cell and waste products out
Volume (length^3) represents the size of the cell which contains the total body mass of the cell.
As the cells grows bigger its diameter increases – the volume increases more than the surface area. A high surface area and less volume enable the transport of material across the cell membrane, ensuring everything gets where it needs to go quickly.
6:1 ratio being the surface area to volume ratio
EUKARYOTIC CELLS:
How they compensate for higher surface area to volume ratio:
Compartmentalization: they have a large area of internal membranes: endomembrane system (helps maintain efficient transport and chemical processes – adding surface area internally)
Being thin: being thin allows the SKINNY LONG “arms” (thin projections) to maximise the surface area but also keeping the total volume about the same. the dendrites and an axon in neurons (nerve cells), helps the cell maximize its balance of surface area versus volume.
Using folds: microvilli increases surface area while minimising volume – the wrinkles of the eukaryotic cell helps create more surface area into a small space – the volume inside the eukaryotic cell stays the same as the surface area increases due to the WRINKLES
Specialized structure: has specialised functions – mitochondria – makes energy ATP
WHAT IS ENERGY:
To do work or the ability to move or bring out change in matter (anything that has mass)
ENTHALPY (H) - INTERNAL ENERGY (total stored energy in the system)
Potential energy: stored energy due to location/chemical structures (chemical bonds – specific arrangement of atoms)
Kinetic energy: energy associated with motion
First law of thermodynamics: ENERGY CANNOT BE CREATED OR DESTROYED BUT ONLY CONVERTED FROM ONE FORM TO ANOTHER
CONCERVATION OF ENERGY
CHEMICAL ENERGY
Energy resulting from chemical reactions (burning of fossil fuels)
potential energy in the bonds of the molecules
Chemical reactions in the body provide energy
BREAKS BONDS → ENERGY CAN BE RELEASED
BUILD BONDS → ENERGY STORED (POTENTIAL ENERGY)
Energy stirred in chemical bonds of molecules as a form of potential energy
METABOLISM - the SUM of ALL CHEMICAL REACTIONS in the BODY.
ANABOLIC (CHEMICAL REACTIONS): use simple molecules to build more complex ones. Eg. protein synthesis
USE energy (endergonic reaction)
CATABOLIC (CHEMICAL REACTIONS): breakdown complex molecules into simpler compounds. Eg. scratch broke down into glucose molecules
RELEASES energy (exergonic reaction)
ENERGY released by CATABOLIC reactions is used to power ANABOLIC reactions
Food energy is converted into ATP through a series of catabolic and anabolic chemical reactions
DIGESTION → GLUCOSE (enters the blood and is absorbed by body cells) →
CELLULAR RESIRATION
Not all energy is used – some energy becomes UNUSEABLE
SECOND LAW OF THERMODYNAMICS: THE ENTROPY OF A SYSTEM AND THE SURROUNDINGS WILL INCREASE – ENERGY WILL ALWAYS BECOME MORE SPREAD OUT
HEAT THERMAL ENERGY:
Homeotherms (an animal) who use heat to maintain their internal temperature (typw of kinetic energy
METABOLISM helps maintain internal temperature
GIBBS FREE ENERGY (G):
Portion of a system’s energy that is available to do work (convertible energy)
ᅀG = ᅀH - TᅀS
ᅀ(DETLA) = CHANGE
ᅀG = CHANGE IN FREE ENERGY
ᅀH= CHANGE IN THE ENTHALPY (INTERNAL ENERGY)
T= ABSOLUTE TEMPERATURE (DEGREE KELVIN)
ᅀS= CHANGE IN ENTROPY
ENTROPY(S) - MEASURE OF ENERGY DISPERSAL
Of a system and its surroundings always INCREASES → energy tends to disperse from being localized to becoming spread out
ANABOLIC REACTION:
ENTHALPY (H) INCREASES
ENTROPY (S) DECREASES
CATHOLIC REACTION:
ENTHALPY (H) DECREASES
ENTROPY (S) INCREASES
EQUATION:
ᅀG = ᅀG final state - ᅀG initial state
OR
ᅀG = FREE ENERGY IN PEODUCTS - FREE ENERGY IN REACTANTS
SUMMARY:
Cell Structure & Size
Flagella in prokaryotes and eukaryotes have the same function but are not evolutionarily related.
Larger organisms have more cells, not bigger cells.
Surface Area to Volume Ratio (SA:V):
Surface area → exchange of materials (nutrients, oxygen, waste).
Volume → amount of cell mass.
As cells grow, volume increases faster than surface area, lowering efficiency.
Optimal ratio: 6:1 (high SA, lower volume).
Eukaryotic Cell Adaptations to SA:V Limitations
Compartmentalization: Endomembrane system increases internal surface area.
Thin projections: e.g., dendrites and axons maximize SA with minimal volume.
Folds: e.g., microvilli increase SA without much volume change.
Specialized organelles: e.g., mitochondria produce ATP.
Energy Concepts
Energy = ability to do work or cause change in matter.
Forms of energy:
Potential → stored (chemical bonds).
Kinetic → motion.
First Law of Thermodynamics: Energy cannot be created or destroyed, only converted (conservation of energy).
Second Law of Thermodynamics: Entropy (disorder/energy dispersal) always increases.
Metabolism
Sum of all chemical reactions in the body.
Anabolic reactions: Build complex molecules (protein synthesis). Require energy (endergonic).
Catabolic reactions: Break down molecules (digestion, cellular respiration). Release energy (exergonic).
Catabolic energy powers anabolic reactions.
Energy in Cells
Food → glucose → ATP (via catabolic + anabolic reactions).
Not all energy is usable; some lost as heat.
Homeotherms use metabolic heat to maintain body temperature.
Thermodynamics in Biology
Enthalpy (H): Internal energy (total stored energy).
Entropy (S): Energy dispersal (always increases).
Gibbs Free Energy (G): Energy available to do work.
ΔG = ΔH – TΔS
ΔG = free energy of products – free energy of reactants.
Reaction types:
Anabolic: ↑H, ↓S - positive - enderogonic
Catabolic: ↓H, ↑S - negative - exergonic
LECTURE 10:
Positive G:
less reactants →(energy)→ more products
(amount of energy required (G>0))
MORE free energy in products than reactants
ENERGY USED (PUT INTO THE SYSTEM)
ENDERGONIC (ANABOLIC)
Moves from low to high Enthalpy (H>0)
Energy moves from dispersed to localized (S<0)
G=H - TS > 0
Systems are more stable at a starting point. NOT SPONTANEOUS.
NEGATIVE G:
More reactants →ENERGY↗→ less products
(amount of energy released (G<0))
Products have LESS free energy than reactants
ENERGY IS RELEASED
EXERGONIC (CATABOLIC)
Energy moves from higher to low Enthalpy (H<0)
Energy moves from localized to dispersed (S>0)
G=H - TS < 0
systems begin in LESS stable state. SPONTANEOUS
Can have a positive G - but overall negative – what is the overall is how you define it
USE ENERGY (ENDERGONIC REACTION) G>0 – ANABOLIC REACTION
→→→→
Enthalpy (H) increases
Entropy (S) decrease
←←←←
RELEASED ENERGY (EXERGONIC REACTION) G<0 – CATABOLIC REACTION
Enthalpy (H) decreases
Entropy (S) increases
ATP ( ADENOSINE TRIPHOSPHATE)
A “high” energy molecule
Energy released through ATP creates a HYDROLYSIS REACTION
-30.5 kJ/mol – energy
-7.3 kcal/mol – energy
—
A catabolic reaction doesn't need the extra energy (HYDROLYSIS REACTION) - already a spontaneous reaction
ATP
Energy released during ATP hydrolysis is often transferred to a substrate by phosphorylation
Phosphorylation is adding a phosphate group
Usually causes a change in shape
Exergonic phosphorylation reactions are coupled to endergonic reactions
ACTIVATION ENERGY (EA)
Activation energy, EA : initial energy investment required to start a reaction – the is a push to start something (reaction)
Ex. Lighting a Candle:
A candle wants to burn (it has wax and air!), but it needs a match (your "push"!) to start the fire. Once lit, it keeps burning on its own!
🔥 The match = activation energy!
Molecules that gain necessary activation energy occupy the transition state. – transition state is when it is at the highest energy-state (PEAK STATE)
activation energy: energy required to get a reactant t the transition state to start a reaction
ENZYMES
Catalyze - to increase the rate of a chemical reaction – a shortcut for reactions – helps it happen faster and easier - is reusable, lowers activation energy, speeds things up. ARE NOT DESTROYED DURING CHEMICAL REACTION - can be used multiple times
Enzymes bring substrates together – Enzymes bring substrates together to hold them close and twist them into the perfect position—like a puzzle master snapping the last piece into place!
Lowers the activation energy – by grabbing the substrates for the activation energy – without it it takes a lot of energy to find each substrate to find the perfect fit for the active site.
Substrate– is the ingredient that enzyme grabs and creates something new
3 MAJOR MECHANISMS FOR LOWERING (EA)
Bringing reactants together to react – Enzymes bring substrates together
Creating a environment that promotes the reaction – they create a tiny space in the active site that is different from the surrounding cell, this helps because it makes the reactions faster, easier, and more precise
WHAT HAPPENS TO THE ENZYME IN THE ACTIVE SITE:
What Happens
Why It Matters
Enzyme changes shape temporarily
Allows precise substrate binding ("induced fit").
Enzyme stabilizes the transition state
Lowers activation energy (makes reactions faster).
Enzyme releases products
It’s reusable—one enzyme can catalyze millions of reactions!
Enzyme is never consumed
Cells don’t need to constantly make new enzymes.
SUMMARY:
Free Energy (ΔG)
Positive ΔG (Endergonic / Anabolic)
Requires energy input (non-spontaneous).
Products have more free energy than reactants.
H (enthalpy) increases, S (entropy) decreases.
Example: building molecules.
Negative ΔG (Exergonic / Catabolic)
Releases energy (spontaneous).
Products have less free energy than reactants.
H decreases, S increases.
Example: breaking down molecules.
Overall ΔG determines spontaneity—even if a step has +ΔG, the reaction can proceed if coupled with a larger -ΔG.
ATP (Adenosine Triphosphate)
“High-energy” molecule.
Hydrolysis of ATP releases energy: –30.5 kJ/mol (–7.3 kcal/mol).
Energy is transferred by phosphorylation (adding a phosphate group), often changing substrate shape.
Exergonic phosphorylation reactions can be coupled with endergonic reactions to drive cellular processes.
Activation Energy (Ea)
Initial energy required to start a reaction (the “push”).
Example: A match is needed to light a candle.
Transition state = highest energy peak before reaction proceeds.
Enzymes
Biological catalysts that:
Speed up reactions by lowering activation energy.
Bring substrates together and position them correctly.
Are reusable (not consumed in reactions).
Mechanisms to lower Ea:
Bringing substrates together.
Creating a favorable microenvironment.
Stabilizing the transition state.
At the active site:
Enzyme temporarily changes shape (induced fit) → precise binding.
Stabilizes transition state → faster reaction.
Releases products → enzyme remains unchanged.
LECTURE 11
CONCENTRATION
Rate of reaction is based on the substrate and the enzyme concentration
The rate of reaction depends on both the substrate and enzyme concentration
Linear reaction when increasing enzyme concentration with excess substrate – meaning when there is extra enzyme it can make more products due to the extra enzymes forming a linear reaction.
The maximum rate of reaction is when there is an increase of substrate concentration with a FIXED amount of enzymes – meaning there is a lot of substrate but a fix (certain amount of) enzymes.
COMPETITIVE INHIBITION:
When an inhibiting molecule ( a random molecule not a substrate) binds with an active site – making the substrate not bond with the active site – they compete with a substrate for the active site
This happens because if the regular molecule has a higher concentration than the substrate its active site wants to bind with the higher one.
NON-COMPETITIVE INHIBITION:
Inhibiting molecules will bind to the enzyme but NOT the active site – this will change the shape of the enzyme making the substrate NOT bind with the enzyme.
This makes the enzyme inactive
Many poisons work this way.
ALLOSTERIC ENZYMES
Composed of two or more polypeptides
ALTERNATE between inactive and active form
ALLOSTERIC ACTIVATION
Without the regulatory molecule in the enzyme the substrate cant go into the active site, with the regulatory molecule it changes the shape of the enzyme
Starts off as an in inactive state
Noncompetitive binding of molecules to an enzyme to increase affinity (the attracted force between two molecules) of the enzyme for the substrate to help with the binding of the subtract binding site
Site of binding: allosteric site
ALLOSTERIC INHIBITION
Doesn't need a regulatory molecule to help blind the substrate to the enzyme
With the regulatory of the molecule it changes the shape of the active site so nothing can bind with the enzyme – this usually happens when there is too much product coming out of the enzyme
REVERSIBLE VS IRREVERSIBLE INHIBITION
TEMPPERATURE ; enzyme activity increases with temperature – can go up to 100c
pH: each enzyme works differently (better) at specific pH
Some enzymes require cofactors — molecules other than proteins
Inorganic metal ions – iron, copper, zinc
Organic – NAD+, NADP+, vitamin C
METABOLIC PATHWAYS
They are regulated by feedback
When there is low in product (active) the enzyme makes more products till there is enough
The feedback inhibition is when there is too much product, it becomes an allosteric inhibition so there is a regulatory molecule to stop the the making of the product when there is not enough product it removes the allosteric inhibition to create more product
Little recap:
Temp affects humans Metabolic rate
Temp INCREASES = INCREASE of metabolic rate – UP TO A LIMIT
Enzyme catalyzed catabolic and anabolic chemical reactions
Enzyme activity INCREASES with temperature
ENEZYMES begin denature ( conditions that compromise their structure and function) at temps above 40c
↓
Enzymes do not function properly
↓
Rate of chemical reaction decrease & metabolic rate decreases
THE STRUCTURE IS IMPORTANT FOR THE FUNCTION – this is due to extreme temp, pH and salinity
SUMMARY:
Enzyme concentration: With excess substrate, increasing enzyme concentration leads to a linear increase in reaction rate (more enzymes = more product).
Substrate concentration: With fixed enzyme concentration, increasing substrate raises the rate until it reaches a maximum velocity (Vmax), where enzymes are fully saturated.
Enzyme Inhibition
Competitive inhibition:
An inhibitor binds to the active site, preventing substrate binding.
Inhibitor and substrate compete; whichever has higher concentration dominates.
Non-competitive inhibition:
Inhibitor binds to a site other than the active site.
Changes enzyme shape → substrate cannot bind.
Enzyme becomes inactive (many poisons act this way).
Allosteric Enzymes and Regulation
Made of two or more polypeptides.
Alternate between active and inactive forms.
Allosteric activation:
A regulatory molecule binds at the allosteric site (not active site).
Changes enzyme shape to increase substrate binding affinity.
Allosteric inhibition:
A regulatory molecule binds at the allosteric site.
Changes active site shape so substrate cannot bind.
Often occurs during feedback inhibition when product levels are high.
Reversible vs Irreversible Inhibition
Temperature:
Activity increases with temperature (faster reactions) up to ~40°C in humans.
Above 40°C → enzymes denature → decreased reaction rate & metabolism.
pH:
Each enzyme has an optimal pH; too high/low disrupts activity.
Cofactors
Some enzymes need non-protein helpers:
Inorganic ions: Fe²⁺, Cu²⁺, Zn²⁺.
Organic molecules: NAD⁺, NADP⁺, Vitamin C.
Metabolic Pathways & Feedback
Enzyme activity is regulated by feedback inhibition:
Low product → enzymes stay active → more product is made.
High product → product binds as an allosteric inhibitor → shuts down pathway until levels drop.
Key Recap
Temperature increases metabolic rate up to a limit.
Above ~40°C, enzymes denature (lose structure & function).
Enzyme structure is critical; extreme pH, temperature, or salinity disrupt function.
Enzymes regulate both catabolic (breaking down) and anabolic (building up) reactions.