lOMoARcPSD|53469771 BIOL 111 Notes- full Introduction To Modern Biology (The University of British Columbia) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes What is Life? Living VS Non-living things Living Things Non Living Things Try to maintain a stable internal environment Do not maintain a stable internal environment Respond to Changes in the environment Do not respond to changes in the environment Will age No aging Reproduce No reproduction Have some level of internal organization No internal organization, random Require energy Do not require energy Metabolize No metabolism Produce waste No waste production *Exceptions exist for all the conditions above *There is no definitive “list” of properties of living things Generalized List of Properties of Living things that most Biologists Agree upon: 1. Living things are Organized: Organisms are highly orderly or organized in contract to the nonliving environment. Eg: Organs, cells, atoms, molecules, etc. 2. Living things maintain a stable internal environment: Homeostasis; the inside is different from the outside 3. Living things respond to external stimuli: Eg- Pyrocystis lunula (single-celled bioluminescent organism). When there is light, plastids extend out. When there is no light, plastids retract 4. Living things Grow and Develop 5. Living things Reproduce 6. Living things Use and Process Energy: takes energy to make sure the inside is different from the outside and to grow and reproduce. Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes ● Law of conservation of energy- energy is converted from one form to another ● Ultimate source of abiotic energy is the Sun ● How is energy stored in Living Things? ○ As chemical energy, i.e., energy stored in the bonds between atoms of molecules ○ In plants and other photosynthetic animals, light energy is used to put sugars (like glucose) together ○ Bonds can be broken apart, and the energy can be converted to another form Autotrophs VS Heterotrophs Autotrophs Heterotrophs Use Abiotic (non-biological) sources of energy (light) to produce complex organic molecules Must use the complex organic molecules produced by autotrophs as an energy source These molecules store energy to be used for other processes in the organism Ingests organic molecules (no production) “Producers” because they can make their own food/ energy “Consumers” because they cannot make their own food; rely on the environment Viruses ● Need an appropriate host to reproduce ● Neither grow nor use energy while outside a host ● Most biologists say viruses are not living Building Blocks of Life ● “Organic” molecules contain carbon bonded to other carbons or Hydrogen ● Carbon monoxide, carbon dioxide = inorganic ○ Consumes energy to break these bonds and turn them into something that’s biologically relevant Carbon fixation: The process of converting inorganic bonds to organic molecules Hydrogen Bonds ● Water behaves uniquely due to how the atoms are bonded together ● These behaviors are crucial to the earth’s biochemistry Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes ● When Hydrogen is bonded with oxygen- Slight -ve charge on the oxygen and slight +ve charge on the hydrogen ● Strong enough to be biologically relevant ● 4 Major Biological Molecules 1. Lipids ○ ○ ○ ○ ○ Long chains of carbon and hydrogen, neutral in charge Important source of energy Sometimes can form rinds (as in sterols) Don’t interact well with water- Hydrophobic Lipids placed in water= “shield” the hydrophobic portions away from water ■ Potential points of interaction are where there is Oxygen and Nitrogen ■ The parts that can interact with water are forced to be on the outside, while the hydrophobic tails are shielded away ■ MOST past do not interact well with water (only small portion does) ■ *The shape of molecules plays a huge role in how they behave Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes Phospholipids ● Very important to life ● Their shape allows them to form sheets in water ● 2. Carbohydrates ○ ○ ○ ○ They have lots of oxygen in their structures Water can readily interact with carbohydrates. They are NOT hydrophobic Energy rich compounds Can be chained together for storage or for structural purposes 3. Nucleic Acid ○ When chained together, they form important structures for information storage in cells ○ Chains of nucleotides ■ Used to store genetic sequence information Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes Base: determines the identity of the nucleotide Nucleoside: the ribose sugar + base Nucleotide: Sugar + Base + 1-3 phosphates (the entire molecule is called a nucleotide) ● On their own, nucleotides can be: ○ Temporary high-energy molecules in cells ○ Signaling molecules ○ As energy “currency” ■ Energy from breaking down sugars and lipids are usually NOT directly used for a cell function that needs it ■ Energy is stored in individual nucleotides (ATP or GTP) that can be used universally throughout the cell in a variety of functions ■ Thus, nucleotides are like energy “currency”, supplying energy to whatever cellular function needs it. ATP (Adenosine Triphosphate) ● Has extra phosphates ● Transfers energy from broken down sugars and fats TO VARIOUS CELLULAR FUNCTIONS ● ● Energy from breaking down sugars and lipids= fuel ATP production ● Energy stored in the bonds of sugars and lipids are transferred to ATP Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes Base Pairing: Each nucleotide specifically pairs with another ● A pairs with T (or U in RNA) ● G pairs with C ● Number of bonds affect the strength of interaction Base Pairing and DNA Structure ● Chains of nucleotides have directionality ● End with PHOSPHATE= 5’ ● End with HYDROXYL= 3’ ○ New nucleotides are added at the 3’ end ● One chain or “strand” interacts with a complementary strand ● The complementary strand runs in the opposite direction– the strands are “antiparallel” DNA ● Composed of 4 different nucleotides ● The 4 bases have different structures that confer identity. ● Chromosome= a single long chain of DNA RNA DNA Uses ribose Uses deoxyribose ^This difference makes it more unstable than DNA ^This difference makes it more stable overall than RNA Uses Uracil (U). Uracil (U) still base pairs with adenine Uses Thymine (T) Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes 4. Protein ○ ○ ○ ○ ○ Chains of various amino acids Each amino acid has a unique “side chain” There are 20 kinds of amino acids relevant to life Proteins do all sorts of things in the cell- most diverse in function All living things and viruses have proteins. Viruses must have at least some sort of protein to keep their genetic material safe Amino Acids: the fundamental units that make up proteins (at least 20 different ones exist) ● The types of amino acids the chain contains determines its properties Peptides: Short chains of amino acids (less than 30 amino acids) ● Eg: “Beefy meaty peptide” has 8 amino acids ● Proteins: Long chains of amino acids (more than 30, no clear definition) ● Some common proteins: ○ Albumen (egg whites) ○ Keratin ○ Insulin ○ Collagen ○ Spike protein ○ Gluten ○ Immunoglobulin (antibodies) ○ Various enzymes ● Proteins have many functions inside and outside of the cell like: ○ Structural proteins Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes ○ Enzymes (proteins that help reactions proceed) ■ While enzyme names usually end in “-ase,” other proteins often end in “-in,” “-en,” or “-ein.” ○ Transporter proteins ○ Binding proteins ○ Cofactors (helps other proteins out) ○ Molecular switches (turns other proteins on and off) ○ Tags, etc. RNA World Hypothesis ● Precursors for these kinds of molecules needed to spontaneously form in early earth ● According to this, RNA (ribonucleic acid) existed first, capable of replicating themselves exactly ● RNA is capable of self-replicating and it can fold into structures that can possibly speed up (or catalyze) chemical reactions like its own replication ● Eventually, proteins replaced the role of RNA in speeding up chemical reactions as the earliest enzymes Other ways chemical reactions can be made to be more efficient? 1. LUCA ● We now have something that might resemble cells- LUCA- Last Universal Common Ancestor 2. Enclose everything in a phospholipid vesicle ● The environment inside can be controlled ● Eventually DNA took over as the information storage molecule Hypotheses VS Theories Hypothesis Theory Testable When there is overwhelming evidence supporting a hypothesis, it’s called a theory Falsifiable statements that attempt to explain an observation/ phenomenon Strongly supported explanations We look for evidence (through experiments/ observations) that either support or refute the hypothesis Can still be refuted if evidence is found otherwise Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes The Cell Theory ● Says that life is dominated by cellular organisms ● The cell theory states that: ○ All organisms are composed of one or more cells ○ Cells are the basic structural and functional unit of all living organisms ○ Cells only arise from preexisting cells The “Typical” Cell At the minimum, cells have the following: ● Cell membrane (plasma membrane) ● DNA (information storage) ● Cytoplasm (cell body/ fluid) ● Ribosomes (way to make proteins) Cells ● There are 2 very distinct kinds of cells on earth. This makes one DOMAIN of life different from the other ● Three domains of life ○ Bacteria ○ Archaea ○ Eukarya (or Eukaryota or Eukaryotes) Prokaryotes VS Eukaryotes Prokaryotes Eukaryotes Less complex More complex Make up the overwhelming majority of organisms on this planet Eukaryotic cells are not more successful. Less in number Have less ORGANELLES than eukaryotes with lesser functions Have a large variety of ORGANELLES within their cells. ● These further compartmentalize different functions No nucleus Major defining intracellular structureNucleus Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes LUCA- probably a prokaryote. Early cells are more likely to be less complex LUCA was probably not a Eukaryote NO cytoskeleton Have a cytoskeleton ● Allows cells to change shape among other things No membranes (usually) Membrane-bound organelles Eg: archaea, bacteria Eg; plant and animal cells Biological Membranes ● All life makes use of biological membranes ● Very important in separating the outside world from the inside ● But things still need to get across membranes, hence all biological membranes are selectively permeable Plasma Membrane ● Semi-permeable, selective barrier encasing the cell ● Mostly made of phospholipids and proteins with highly specialized functions ● We consider biological membranes a “fluid mosaic” ○ Mosaic= variety of different components ○ Fluid= because things can slide around the membrane ○ ○ Experiment: imagine the membrane below with labeled phospholipids. What if we use a laser to inactivate the fluorescent label and bleach a part of this membrane? Predict what happens to the bleached spot Answer: The bleached spot FADES because non-lasered phospholipids move into the bleached area Passive Transport (crossing the membrane) ● Does not require energy, but may require a protein to serve as a channel or pore (small, neutral things with no charge) Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes ● Movement is with the concentration gradient ● Diffusion: dissolved materials moving from areas of higher concentration to lower concentration ○ Molecules (if they are capable of crossing the membrane) will naturally want to cross from the left (where their concentration is higher) to the right (where their concentration is lower) ○ ● Osmosis: water moving from an area of lower solute concentration to a higher solute concentration ○ Net water movement across a selectively permeable membrane toward area with higher solute concentration ○ Real environments have more than one kind of solute, and they all contribute to solute concentration. Each solute will have their own concentration gradients. ○ Cells have high solute concentration, so they have developed different strategies to handle osmosis ○ Note: ● Na+ is charged= can’t cross without proteins ● O2 is equal in concentration on both sides ● CO has a concentration gradient- there are more outside the cell. Hence, it would show a net movement from outside to inside of the cell without any transporter proteins ● Sugar is too big to cross Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes Active Transport (crossing the membrane) ● For substances either too big or has an electrical charge so it can’t just pass through the plasma membrane ● Or when moving things against a concentration gradient ● A transport protein must consume energy to move that substance across the membrane ● Eg: Protons (H+) are pumped AGAINST a concentration gradient; Hydrolysis of ATP to ADP provides the energy required Organelles (for non-science friends) ● “A component within a cell which serves a specific role and/ or participates in certain organismal processes” ● “A part of a cell that has a unique function” ● “An organelle is to the cell as an organ is to the human body” ● “Organelles are a cell’s organs” Endomembrane System: expansive network of internal membranes that process proteins Exo/ Endocytosis Eukaryotes have a cytoskeleton that allows cells to change shape (among other things) that allows for endo and exocytosis. ● Endocytosis ○ Things that are too large (like prey bacteria) for membrane proteins must be endocytosed ○ A groove forms in the plasma membrane around the target ○ The membrane pinches inward and forms a vesicle and joins the endomembrane system ● Exocytosis ○ Essentially the reverse of endocytosis Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes ○ Vesicles fuse with the plasma membrane and release (secrete) its contents Endosymbiotic Theory (Dr. Lynn Margulis): the cytoskeleton and endocytosis allowed for the acquisition of 2 very important eukaryotic organelles: mitochondria and plastids (of which chloroplasts is one) which descended from the undigested food (see below) Evidence: 1. Mitochondria and chloroplasts really look like bacteria with their two membranes. 2. These organelles still maintain a genome (their own DNA) 3. Mitochondria and chloroplasts divide like bacteria (by fission). They also divide independently of its host cell *The establishment of mitochondria and chloroplasts opened up new lifestyles for eukaryotes and brought photosynthesis into this domain Carbon Fixation & Photosynthesis ● It takes a lot of energy to convert carbon dioxide into something biologically relevant ● Waste product of photosynthesis= Oxygen ● Photosynthesis sets off the establishment of the carbon cycle. Autotrophs fix carbon, heterotrophs eat autotrophs containing the fixed carbon Molecular Basis of Genetics ● Genome: all the genetic material in an organism passed from parent to offspring ○ Approximately 3 billion base pairs of nucleotides comprise the nuclear genome ○ Genome length does not necessarily correlate with organismal complexity or success in the environment ○ Multicellular organisms descend from a single cell, so all cells should have the same genome Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes ○ Organellar genomes are part of an organism’s overall genome ■ Eg: in a kiwifruit consist of nuclear, mitochondrial and chloroplast DNA ■ How an organism functions is also related to environmental conditions, not just gene-dependant Prokaryotes and Eukaryotes organize their genomes very differently– Eukaryotic genomes Comprised of multiple linear chromosomes inside the nucleus Prokaryotic genomes (includes the ones inside mitochondria and chloroplasts) - usually are in single CIRCULAR chromosomes ● Gene: a hereditary unit passed from parent to offspring ○ Segment of a genome (DNA) ○ Transcribed into functional RNA (mRNA, tRNA, rRNA) ○ mRNA is used to guide protein production The Central Dogma of Molecular Biology: flow of genetic information in all of life flows only in one direction= DNA → RNA → Protein / RNA → Protein ● Links together DNA, RNA and proteins as well as the flow of all genetic information in life ● There are differences, but the order and direction of information flow is the same for bacteria and eukaryotes Transcription 1. Initiation of Transcription: The ribosome attaches to the 5’ end of the mRNA. Then it slides along the mRNA from 5’ to 3’ until the first start codon. The first amino acid, Met, is brought by the tRNA with an anticodon that base pairs with the start codon a. In Eukaryotes, translation initiation starts with tRNA and SMALL ribosomal subunit recruitment by initiation factors at the 5’ cap Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes b. Once the start codon is detected, the LARGE ribosomal unit attaches with the first tRNA in the P (peptidyl) site c. Beginning synthesis at the start codon establishes the reading frame i. The reading frame is critical for correct protein synthesis 2. Extension/ elongation of RNA by RNA polymerase: tRNAs bring amino acids to the ribosome in the correct sequence via complementary base pairing between codons and anticodons, and peptide bonds are formed.. The ribosome moves along the mRNA in the 5’ to 3’ direction. a. The entire complex moves toward the 3’ end of the mRNA by exactly 1 codon b. Codons do not overlap !! c. The first tRNA moves into the E (exit) site and is ejected d. The second tRNA moves into the P site and the next tRNA enters the A site (process repeats) 3. Termination: The ribosome encounters a stop codon and the amino acid chain is released. The ribosome then disassembles. a. Eventually a stop codon is reached b. Amino acid chain gets cut off the tRNA in the P site and everything disassembles A gene consists of regulatory sequences and coding sequence: ● Promoters= regions where RNA polymerases bind before initiating transcription ● Coding sequences= regions that determine the amino acid sequence in a protein ● Terminators= regions where RNA polymerases fall off to end transcription Eukaryotic transcription complex: RNA polymerase binds to the promoter region → forms giant complex with other proteins that bind to regulatory regions (enhancers) ● Eukaryotic promoters have a “TATA box” that orients the RNA polymerase complex ○ Sequence containing TATA ○ Eg: 5’-TATAAA-3’ ● Transcription starts at transcription start (initiation) site ○ This is where the first nucleotide of the RNA strand is recruited ● Other upstream sequences called enhancers may be present ○ Increase frequency of transcription of that gene Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes Transcript functions There are 3 major types of RNA in all cells: 1. mRNA (messenger RNA) a. Eukaryotic mRNA usually represents a single gene and codes for a single product b. Prokaryotic mRNA carries a series of functionally-related genes (an “operon”) that code for multiple products 2. rRNA (ribosomal RNA) 3. tRNA (transfer RNA) Transcript Processing ● Eukaryotic RNA transcripts are processed further ● mRNA is processed by: ○ RNA splicing ○ 5’ capping ○ Poly-adenylating 3’ tails ● Following processing, the mature mRNA is exported out of the nucleus into the cytosol for translation into protein Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes mRNA Splicing ● Eukaryotic mRNA transcripts are interrupted by non-coding sequences= Introns ○ Why do they exist as extra bits that get transcribed only to be removed? Process allows for multiple products to result from the same gene. ● The pieces of coding sequence= Exons. Coding sequence usually begins and ends with an exon (exons are expressed) ● All this happens in the nucleus and requires special enzymes called spliceosomes (RNA + protein) Translation RNA → Protein ● This is the process by which mRNA are translated into functional proteins ● The sequence information represented in the mRNA transcript is now “decoded” to represent all possible amino acids ● 4 different nucleotides in RNA. 20(ish) different amino acids in proteins ● Major components of translation: ○ mRNA ■ mRNA acts as a template for chaining together amino acids in a specific sequence ■ The information within the coding sequence is divided into codons, which are “words” made of 3 nucleotides each. ■ Eg: AUG, CCC, UAA, CCG ○ Ribosomes, rRNA ■ Ribosomes= protein synthesis machines ■ Made of proteins and ribosomal RNAs (rRNAs) ■ rRNA acts like an enzyme ■ Physically links amino acids together ■ 2 components- (1) Small subunit (2) Large subunit ■ Large subunit contains binding sites for tRNAs ○ tRNA ■ RNA molecules that carry amino acids to the ribosome ■ tRNAs fold to form a specific structure ■ tRNAs have specific anticodons and hold specific amino acids ● Anticodon= 3 nucleotide sequence on a tRNA molecule that base pairs with the codons in mRNA ● Directionality of the codon and anticodon = important ■ Each amino acid corresponds with a specific codon via its anticodon Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes Note: Proteins have directionality too. By convention, amino acids in proteins are ordered from the N- terminus (amino-terminus) to the C-terminus (carboxy-terminus). This relates to the order in which amino acids are added The Universal Genetic Code: summarizes all 64 possible codons and their meaning in protein synthesis. ● All 3 domains of life + viruses use this code. (it has significant implications) ● More than 1 codon can code for the same amino acid. ○ This is why the genetic code is termed “degenerate” or “redundant” ○ Also means that translation cannot occur in reverse. Sequence information can only flow from RNA to protein Cell Cycle: The name of the process through which cells REPLICATE and make new cells. (How do we grow up? Ans: Our cells divide) ● Cell cycle has 4 different stages: ○ G1 (interphase) ○ S (interphase) ○ G2 (interphase) ○ M (Mitosis and cytokinesis) ● Interphase ○ Cell spends most of its time in interphase where: ■ It grows ■ Replicates its chromosomes ■ Prepares for cell division ● G1= Gap 1= Cell growth= the main DECISION point. ○ Once the cell passes the G1 checkpoint it becomes irreversibly committed to division ○ G1 Checkpoint ensures that everything is ready for DNA synthesis Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes ○ Decision to commit to entering the cell cycle ○ Cell checks internal and external conditions: ■ Size- is it big enough to divide? ■ Nutrients: Does the cell have enough energy or available nutrients to divide? ■ Molecular signals: Is the cell receiving positive cues (like growth factors) from neighbors? ■ DNA integrity: Is any DNA damaged? ○ NOTE: If a cell doesn’t get the go-ahead cues it needs at the G1 checkpoint, it may leave the cell cycle and enter a resting state called G0 phase. Some cells stay permanently in G0, while others resume dividing if conditions improve. ● S= Synthesis= DNA Replication ○ Each of the 46 chromosomes is replicated by the call ● G2= Gap 2= Growth + preparation for Mitosis ○ G2 Checkpoint ensures that everything is ready for the Mitosis 9M) phase ○ Check for any DNA damage ■ DNA integrity ■ DNA Replication: Was the DNA completely copied during S phase? ○ If errors or damage are detected, the cell will pause at the G2 checkpoint to allow for repairs. If the damage is irreparable, the cell may undergo apoptosis (programmed cell death) ● CDKs= Cyclin-dependant Kinases= Main mechanism of the cell cycle checkpoints’ regulation DNA Damage and Cell Cycle: ● DNA Repair and cell cycle checkpoints have been intimately linked with cancera mutation in an important gene can lead to a tumorigenesis process. Proto Oncogenes ● Normal gene- regulates cell growth positively ● 1 mutation– Gain of function– accelerates cell growth and division ● Rarely inherited because they don't often result in embryonic lethality. 2 known exceptions to this= RET and CDK4 oncogenes. Tumor Suppressor gene ● TP53 (p53)= guardian of the genome ● Normal gene– negatively regulates cell growth ● 2 mutations– loss of function of cell cycle regulation and DNA repair ● More common and responsible for the familial cancers Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes DNA Damage Repair ● P53 familial syndrome- Li-Fraumeni Syndrome ● Hereditary cancer predisposition syndrome ○ 90% chance of developing one or more types of cancer in their lifetimes and a 50% chance of developing cancer before age 30. ● The inherited risk of developing cancer across several generations ● Eg: Brazilian germline TP53 mutation ○ High frequency in Southern and Southeastern Brazil ○ Founder mutation during colonization Mitosis ● Chromosomes are condensed (composed of 2 sister chromatids) ● At the end of prophase, the membrane around the nucleus in the cell dissolves ● Chromosomes line up neatly end-to-end along the center of the cell (Metaphase plate) ● The centrioles are now at opposite poles of the cell with the mitotic spindle fibers extending from them ● The mitotic spindle fibers attach to each of the sister chromatids ● M checkpoint= ensures all the sister chromatids are correctly positioned at the metaphase ● The sister chromatids are then pulled apart by the mitotic spindle which pulls one chromatid to one pole and the other chromatid to the opposite pole ● At each pole of the cell a full set of chromosomes exists ● A membrane forms around each set of chromosomes to create 2 new nuclei ● The single cell then pinches the middle to form 2 separate daughter cells. Each containing a full set of chromosomes within a nucleus. This process is called cytokinesis. Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes ○ Telophase VS Cytokinesis ■ Mitosis ends with telophase. The stage at which the chromosomes reach the poles. ■ The nuclear membrane then reforms and the chromosomes begin to decondense into their interphase conformations ■ Telophase is followed by cytokinesis, the division of the cytoplasm into 2 daughter cells Plant reproduction ● Asexual reproduction ○ Process that does not involve changes in chromosome NUMBER ○ Progeny genetically identical to parents ○ Results in new individuals that are CLONES ○ New individuals form from part of a parent plant ○ Advantages: faster generation of new individuals (faster reproduction) because there is no need to necessarily grow a new individual or find a different individual of the same species ○ Disadvantages: Lack of variation. If the environment changes, or some disadvantageous mutation arises, this would affect all clonal offspring. ● Sexual reproduction Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes ○ Involves production of cells where chromosome number change (formation of GAMETE cells– Individuals that have a different no. of chromosomes than others of the same species) ○ These then fuse back together to “restore” the correct no. of chromosomes (always requires more than 1 individual of the same species) ○ Results in genetic variation in progeny ○ (in flowering plants), flowers have male and female parts, which are sometimes not in the same flower of the same individual. ■ Produces 2 different types of gametes: ● Pollen- male gamete ● Ovule- female gamete ● Humans have 23 pairs of chromosomes (46 total). Because of this our nuclear genomes are considered diploid ○ As humans we spend our entire lives as diploids– our chromosomes always exist paired. Only gametes (sperm and egg cells) are haploid. ○ Haploid human gametes have 23 unpaired chromosomes, half as many as all other cells ○ All 46 chromosomes are replicated in the S Phase of Cell Cycle ○ The phase when chromosomes are pulled apart– Anaphase Gametes ● Cells involved in sexual reproduction ○ Does not have the same no. of chromosomes as parent ● Frequently in organisms that undergo sexual reproduction gametes are differently sized ○ FEMALE gametes are much larger (and often fewer) ○ MALE gametes are much smaller (and more numerous) Classical Genetics ● Throughout history, humans have proposed many ideas on how TRAITS are passed from parent to progeny ○ It was well understood long ago that offspring inherited aspects/ characteristics of their parents ○ TRAITS= characteristics that can vary among individuals in a population ○ Heredity or biological inheritance= passing of traits from parents to progeny ● We NOW understand that passing of genetic material (DNA) forms the basis of heredity ○ Genes provide instructions to make a product (proteins) (Central Dogma) Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes ○ Proteins confer function ○ Variations in genes vary the protein’s function, which effects some sort of trait ● Gregor Mendel ○ Monk at the Augustinian Abbey of St. Thoman in Brno ○ Performed experiments to elucidate mechanisms of heredity ○ Chose the garden pea (pisum sativum) as the main model organism for his studies. Why?-■ Continuously variable ● Eg: Human height ● Varies across a variety of values not just tall and short ■ Discrete or discontinuous ● Eg: Pea flowers are either purple or white ● Nothing in b/w What makes for good model organisms in general? Ans: Easy to grow/ maintain, short generation times Mendel’s Experiments/ Punnett Squares Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes ● These ratios turned out to apply for all these characteristics ● One trait is vanished in F1 hybrids ● Self-pollinated in F1 hybrids always resulted in a 3:1 ratio of these traits in the F2 plants ● Vanished trait= recessive. Other= dominant Mendel surmised these traits were carried in some sort of hereditary unit (gene):Each individual would have two of these units for each characteristic– one inherited from each parent ● Traits for each characteristic were carried by different versions or forms (alleles) of these units ● These units would separate randomly into gametes ● These would also join back together randomly ● Heritable material= DNA ● “units”= genes and there are different versions or alleles of genes ● Meiosis segregates alleles into gametes randomly Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes ● The connection b’w genes and an individual’s characteristics turns out to be MUCH more complex Mendel was accurate to conclude that most organisms would have a pair of alleles for each trait. ● One originating from each parent ● Homozygous: an individual is a homozygote for a particular trait if both alleles are the same (BB, bb) ● Heterozygous: an individual is a heterozygote for a particular trait is they possess one of each allele (Bb) Phenotype: Represents all the observable traits of an individual. (sometimes we talk about them w.r.t. a single trait) Genotype: represents the total of an individual’s genetic material, or the complement of alleles an individual has. (sometimes we talk about them w.r.t. a single trait) Law of Mendelian Genetics 1. Law of dominance a. In a heterozygous individual, the recessive trait is masked or hidden by the dominant trait b. The gene product (a protein, for eg.) from a single dominant allele is enough to cause a trait 2. Law of Segregation a. For a 3:1 ratio of dominant to recessive traits, both alleles are equally likely to be passed on. This is the law of (random) segregation 3. Law of Independent Assortment Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes a. When Mendel looked at 2 characteristics at a time, he found specific ratios that showed the characteristics does not influence each other in gametes b. The alleles assort independently in gametes c. In other words, having a particular allele for one characteristic does not mean a gamete is more likely to have a specific allele for a different characteristic Other Patterns of inheritance– The characteristics Mendel observed show clear patterns and gave us a lot of insight as to how these are passed from parent to offspring. But there are many other patterns that we see: ● Incomplete dominance: Some characteristics may have intermediate phenotypes in the heterozygote. ○ These characteristics would definitely support any hypotheses about blending. ○ In snapdragons, a cross b/w plants with red flowers and plants with white flowers results in pink flowers ● Codominance: Some characteristics may have BOTH TRAITS show up in the phenotypes of the heterozygote. ○ Eg: White and roan (red) cattle parents result in spotted progeny– Both white and red hairs are present in the offspring. ● Multiple “codominant” alleles: ○ Some characteristics may have 3 or more traits, with unique patterns of phenotypes in heterozygotes Meiosis (m!) ● Haploid gamete cells require nuclear division that cuts the no. of chromosomes in half ● Meiosis= mitosis happening twice in succession Errors in meiosis ● Errors in meiosis typically result in an incorrect no. of chromosomes in gametes– becomes more frequent with age ● Inability to perform meiosis correctly is responsible for seedless fruits ○ Major cultivars of seedless bananas are triploid, meaning they have 3 copies of each chromosome Other Life Cycle Types: ● Most fungi exist as haploids– gametes form from mitosis and not meiosis ● Mating results in a diploid, and meiosis returns the organism to being haploid Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes Meiosis and Mendel’s Laws ● Meiosis readily explains the laws of segregation and independent assortment– alleles of particular traits have equal chances of segregation into gametes, independently of each other ● Mendel might have gotten lucky with the traits he picked. Some combinations of alleles may not necessarily separate independently. We call this LINKAGE ○ Linkage depends on physical distance b/w genes Variation in a population ● Expected amongst individuals within a population ● The phenotype of an individual affects how it functions in and interacts with its environment Sexual Reproduction introduces genetic variation ● The ultimate source of genetic variation= MUTATIONS or nucleotide changes. ○ Usually not in a good way as protein function is affected ○ It takes a population of the same species to make meaningful comparisons of phenotypic variation. Hence, we should think about genetic and phenotypic variation at the level of a population of the same species. Fitness ● Quantification of an individual’s genetic contribution to the next generation ● DOES NOT consider the survival or ability to “thrive” of an organism Toward evolutionary theory ● Throughout history, people had various ideas about the types (species) of living things around them and in different environments ○ Did they change? ○ Where they immutable/ unchanging? ○ Do new species arise? ○ Do species ever disappear (go extinct)? ● Jean-Baptiste Lamarck proposed inheritance of acquired characteristics as a mechanism for species to change over time. ○ Use it or lose it repeated use of a trait change and strengthens it and (vice versa) ○ These strengths and advantageous (acquired) characteristics are passed onto offspring ● Charles Darwin and Alfred Wallace independently devised a different mechanism that ultimately became current evolutionary theory. Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes ○ On darwin’s voyage on the HMS Beagle, he visited the Galapagos Islands ■ These islands were physically close together, yet the variety of environments presented diverse species. ■ Most notably, in Darwin’s Finches, he notes a “gradient of variation” in their appearances, which continued with species he encountered on the South American continent. ● He notes how each species appeared specialize to their niche environments 1. There exists variations in heritable traits within populations 2. Some variants are more successful (and more able to reproduce) than others in a given environment 3. The population thus changes over time with respect to this trait– this trait becomes more common => What’s different in this mechanism compared to Lamarck’s ideas? Peppered Moths ● The peppered moth (Biston Betularia) is found all over the Northern Hemisphere. ● Carbonaria was initially very rare. By the mid 1800s, more could be found in urban centers, and by late 1800s, almost all moths in urban centers were carbonaria. ● A single gene is responsible for this trait, and the allele for the dark trait is dominant ● Kettlewell in the 1950s attempted to test this by releasing marked typica and carbonaria into the polluted woods around Birmingham and “pristine” forests in Dorset. ○ After 2 days, he recaptured marked typica than carbonaria less frequently in the polluted woods around Birmingham ○ After 2 days, he recaptured marked typica than carbonaria more frequently in the pristine woods in Dorset. ● The results of Kettlewell’s experiment and earlier observations all appear to support the ideas of evolutionary theory by natural selection: ○ THere exists variations in heritable traits within populations ○ Some variants are more successful and more able to reproduce than others in a given environment ○ The population changes over time with respect to this trait Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes Selection: Some variants are more successful (and more able to reproduce) thanothers in a given environment ● These more successful variants are thought of as being “selected” by its environment ● Selective pressures can act on population in different ways Population changes not by selection ● Genetic Drift ○ Evolution can occur by chance ○ By chance certain individuals in a population cannot reproduce; thus, the proportion of variants change ● Genetic bottleneck ○ Drift to the extreme ○ A sudden loss of population can dramatically change the traits and variation of a population ○ The survivors are the only contributes to the gene pool ○ Usually the result of a disaster ● Founder Effect ○ Similar to a bottleneck ○ Small population that moves to a new place is just a sample of the old population’s diversity Evolutionary theory: Given that evolution by natural selection can help explain the diversity of species on Earth, there are some profound implications from this: ● The diversity of life share a common ancestor ○ This common ancestor no longer exists (is extinct) ● Evolution is continuous and shapes future life ● As living things on Earth, humans are also part of this ○ Humans and extant (still living) great apes share a common ancestor, but we did not descend from them Allopatric Speciation ● Geographic separation physically prevents species from interbreeding ● Allo= other, patric= country, land ● (1) For eg: anoles that descended from a common ancestor, but ended up on a different island evolved into different species ○ This is an example of dispersal ○ The populations move on their own accord to new areas ● (2) For Eg: Darwin’s Finches Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes ○ Combines concepts of the founder effect , dispersal and adaptive radiation as the finches colonized the islands ● Sometimes the geographic separation is not caused by individuals migrating ● Geological and hydrological changes can split populations ○ This is called vicariance Adaptive Radiation ● When found population colonizes a new area, new species can rapidly emerge as the offspring begin settling into their own unique microenvironments (niches) Sympatric Speciation ● Sym= same; patric= country, land ● Populations not physically isolated can also result in speciation ● As populations diverge, they may eventually no longer be able to mate and reproduce! A reproductive barrier has formed Reproductive isolation and speciation ● As populations diverge, they may eventually no longer be able to mate and reproduce. A reproductive barrier has formed ○ This can occur through– ■ Temporal isolation (mating at different times) ■ Habitat isolation (already covered in allopatric speciation) ■ Hybrids not viable ● We can also split into the following categories instead: ○ Prezygotic isolation (“before zygote”-- zygote= fertilized egg) ■ Individuals cannot/ do not physically mate ■ Sperm doesn't fertilize egg ○ Postzygotic isolation (“after zygote”) ■ Individuals can mate, but offspring are inviable (do not survive) or infertile (cannot reproduce) Temporal isolation ● Species do not interbreed because reproduction happens at different times ● Particularly common in plants and insects ● Eg: Periodic cicadas (able to produce viable offspring but hardly ever meet) Habitat isolation ● Species do not interbreed because they occupy different habitats ● Eg: apple maggot fly; 200 years ago they only laid eggs in hawthorn fruit (no apples in North America). Now lay eggs in both apples and Hawthorns. Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes ● Little gene flow b/w the 2 populations even though they can occur in the same areas Hybrid inviability ● Species can interbreed but hybrid offspring do not survive or offspring are infertile ○ Embryonic development failure ○ Failure to survive to sexual maturity ● Eg: Enstina eschoscholtzii ○ Subspecies eschscholtzii and klauberi can interbreed but their offs[ring are more visible to predators ● Hybrid inviability often the result of meiotic errors ○ If offspring survive, they often cannot perform meiosis properly.. No preproduction Hybridization ● Formation of NEW species through hybridization ● Hybrids often end up reproductively isolated from their parent species What’s a species? ● We actually discussed the concept of biological species. This concept still has its disadvantages ○ Recognized separate species can form hybrids ○ Not everything reproduces sexually ○ Extinct groups are impossible to verify ○ Separate populations may still be able to interbreed ● Definition– A species is a group of organisms that are capable of interbreeding, and can produce viable offspring that can also reproduce Morphological species ● Use physical similarity or difference to delineate species ● Used by botanists and zoologists in the field ● Paleontologists must rely on this ● Example: Environmental influence on sea star phenotypes Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes ● Binomial species names: each species has 2 names, composed of a genus and a specific epithet. Ef: Corn= Zea Mays Linnaean classification system: Carl Linnaeus was prolific in categorizing the natural world into three categories: ● Animals ● Plants or vegetables ● Minerals– no longer in use => this field of study of classification is called taxonomy => These were then further subdivided hierarchically into various levels of categories Phylogeny– Visualizing evolutionary relationships Phylogenetic trees– diagrams that depict the hypothesized evolutionary relationships b/w taxa (groups of organisms) ● Phylogenetic trees can be constructed based on: ○ Morphological changes ○ Developmental changes ■ Works best on multicellular organisms (plants, animals) ○ Molecular changes ■ DNA, protein sequences ● Phylogenetic trees represent hypotheses, not unassailable facts Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes ○ Hard to test empirically– we were not there to see speciation happen ● We cannot know evolutionary relationships with 100% certainty ● It is normal to revise and update phylogenetic trees as new information becomes available. ● The same tree can be oriented in different ways. All of these trees have the same topology ● Evolutionary change happens continually along branches, not instantaneously at nodes. Nodes represent speciation events Monophyletic group ● “Clade” ● It is an ancestral taxon and all of its descendants and only those descendants ● Use the snip test to determine if a group is monophyletic Paraphyletic group ● Consists of the group’s last common ancestor and all its descendants except a few ○ Aves (bird) is excluded from Reptilia (reptiles) Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes Polyphyletic group ● Includes organisms that arise from multiple common ancestors and excludes most descendants ● Mammalia and Aves share a common ancestor but it and most of its descendants are not included ● Typically used to identify species that have undergone convergent evolution Parallel Evolution Convergent Evolution Trait results from shared ancestry Trait results from shared ancestry HOMOLOGOUS traits ANALOGOUS traits NOTE: Taxa appearing at branch tips are not equivalent to ancestral taxa. Ecology: The study of the interactions of living things with their environment => Living things do not exist in isolation but are part of a larger population and community Selection and adaptations ● Driven by natural selection from their environment, species possess features (adaptations) that allow them to succeed in their environmental interactions ● Each finch species have unique bills that are adapted to their food ● Driven by natural selection from their environment, species possess features (adaptations) that allow them to succeed in their environmental interactions Ecological Niches ● In a given ecosystem, each species settles into their unique ecological niches ● Niches represent the range of resources a species can use, within the range of environmental conditions it can tolerate within an ecosystem Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes Life histories ● The ● life history of a species can determine its place in its environment and niche ● Aspects of life history: ○ Size of mature individual ■ Large or small? ○ Timing of maturity ■ Early or late? ○ Longevity ■ Long or short lives? ○ Parental care? ■ Extensive or not? ○ Offspring number (fecundity) ■ Lots or few? ○ Number of reproduction events ■ Once per lifetime or more? => Energy is not unlimited. There are benefits and tradeoffs for specific values of each aspect. Population Ecology ● Concerns how populations (no. of individuals of a species) change over time in a given environment ● Population ecologists measure changes in a population over time and in response to various biotic and abiotic factors ● Data are used to build models to study changes in population size ● Involves a lot of mathematical modeling. ○ Main parameters to describe a population as it changes are the following: ■ N= no. of individuals in a populations ■ t= time span (researcher defined) ■ r(max)= the maximum growth rate of the population (combines birth and death rates; a species’ life history determines these) ■ K= carrying capacity, the max. Population size that a given environment can sustain Population size (N)= How many individuals of a species in a given environment? Density= How many individuals within a specific area Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes Distribution= How are they spread within an area Models of Population growth ● Exponential growth ○ Can describe how a population changes if resources are essentially unlimited ○ A population will increase consistently and indefinitely by a constant factor ○ ○ Eg: when bacteria first colonize a nutrient rich environment, their populations grow exponentially ● Logistic Growth ○ Resources are not infinite. Population size will hit some sort of ceiling that depends on the species and on a given environment ○ Logistic growth models add in this limit to exponential growth models ○ The limits’ impact increases as the population size (N_ approaches the environment's carrying capacity (K) ○ Many populations follow this model ○ Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes What else regulates population growth? => A population’s given environment likely changes over time; thus, carrying capacity does not remain constant ● Density-dependent regulation; at high population densities: ○ There is more competition among individuals for limited resources ○ Individuals are more easily preyed upon ○ Disease spreads faster (all of the above are BIOTIC factors) ● Density-independent regulation ○ Usually abiotic factors: seasonal changes, disasters, etc. ○ Seasonal changes are a density independent regulator of population growth in Australian thrips r- and K- selected species => connecting concepts of maximum growth rate (r) and carrying capacity (K) leads to a classic model that attempts to explain why species evolved specific life histories Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes K-selected species ● When environmental conditions are stable (as would carrying capacity K), species appear to favor expending energy to being as competitive as possible.. And exist close to carrying capacity of the environment r-selected species ● When environmental conditions are not stable or prone to disturbance (carrying capacity changes), species appear to favor maximizing reproductive rate (r) Community ecology ● Concerns how species interact with each other and may include aspects of population ecology ● Species interact w each other through– ○ Competition ■ When 2 species in a community can use the same resources (their niches overlap) there is competition ■ Neither species benefit from this interaction ■ Under the competitive exclusion principle, species cannot occupy same niche ■ One outcome is resource partitioning; each species evolves to modify their niches until they no longer compete for the same resources Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes ■ If niches completely overlap, one species could be forces out of the community or driven to extinction ■ If niches completely overlap, one species could be forces out of the community or driven to extinction ○ Consumption ■ Heterotrophic species consume other species ■ Predation and herbivory can drive some very interesting population dynamics and evolutionary adaptations => can drive evolutionary arms races => predation drives evolution of adaptations such as camouflage and warning colouration => plants have also evolved adaptations to avoid or discourage herbivory => caffeine and nicotine are alkaloids which discourage insect herbivory ■ The consumer species benefits but the food species definitely does not ○ Symbiosis ■ Sym= together; biosis= living ■ There are many different named modes of symbioses: ● Parasitism, where the parasite species benefits but the host species does not ● Commensalism, where one species benefits while the relationships remains neutral for the other ● Mutualism where both species benefit Interactions drive co-evolution ● When all the living things are evolving against each other at the time, perhaps all that can be done is merely survive ● This is the premise for the Red Queen hypothesis of evolution Biodiversity ● Biodiversity loss affects: ○ Genetic diversity ○ Community interactions ○ Biological productivity Viruses ● Very small Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes ● Variety of shapes ● Can be classified based on whether they contain a small lipid membrane or not. ○ NAKED viruses do not contain a lipid membrane– the Virion usually consists of just a protein capsid protecting the genome within ○ ENVELOPED viruses contain a small envelope of lipid membrane derived from the host. This envelope encloses the capsid within ● Can also be classified based on how their genome is arranged: ○ Whether their genome is made of DNA or RNA ○ Whether their genome is single or double stranded ○ Whether their genome is directly readable by a ribosome ● Viruses reproduce by exploiting their host cell’s normal functions to generate more copies of themselves ○ Since viruses exploit and therefore disrupt cellular processes, they are agents of DISEASE. ■ Disease: a condition that impairs normal cellular or tissue function; may cause death ■ Pathogen: an entity that causes disease in a host ● Viruses are examples of pathogens ● Viruses generally infect their host and reproduce in these steps: ○ Attach to the host ○ Enter the host ○ Make virus parts (viral proteins/ genome) ○ Assemble new virions ○ Leave the host Eg: Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes Introduction to the immune system => Pathogens (like viruses) drove the evolution of immune systems in animals but also in plants => in animals,, 2 main kinds: ● Innate immunity: recognized general signs of pathogens, always present, indiscriminate, not specific, fast ● Adaptive Immunity: triggered by infections, specific to a pathogen, slow, generates immunological memory Antibodies ● Adaptive immunity is extremely complex ○ Depends on antibody interactions with the pathogen ● Key part of the adaptive immune system Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com) lOMoARcPSD|53469771 BIOL 111 Notes ● Bind to things that are not “self” ○ Triggers an immune response ○ If antibodies bind to harmless things, allergies and autoimmune disease ● SARS-CoV-2 with antibodies bound to spike protein can’t interact with ACE2 ○ White Blood Cells are triggered to eat them ● Antibodies are SPECIFIC– they only interact with antigens (eg: the part of a pathogen with the matching shape) ○ Encounters with antigens result in the matching antibodies being made ○ These antibodies and the cells that made them remain in our blood= immunological memory Vaccines ● Variolation= old technique that used scabs from an infected individual to hopefully indice a milder form of smallpox and result in future immunity ● Edward Jenner= inducing someone to have cowpox (vaccination, from “vacca”= cow) rendered them immune to smallpox ● Further developments led to these types of vaccines: ○ Attenuated vaccines ■ Uses weakened (but still alive) pathogens ○ Inactivated vaccines ■ Uses killed or no longer virulent (disease-causing) pathogens ○ Subunit vaccines ■ Only a part of the pathogen is used Downloaded by Jason Zhai (zsyjasonzhai2005@gmail.com)
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