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BIO1090
Intro to Molecular and Cellular Biology
| Term | Definition |
|---|---|
| Nucleolus | largest structure in the nucleus, performs biosynthesis of ribosomes, transcribes ribosomal RNA |
| Nuclear Pores | gateways between cytoplasm and nucleus, 3000-4000/nucleus |
| Nuclear Lamina | thin meshwork of filamentous proteins, lamins in animal cells |
| Nuclear envelope | 2 phospholipid bilayers serperated by 10 - 50 nm of space |
| Outer Nuclear Membran (ONM) | binds ribosomes- is continuous with rough ER, allowing translation to occur |
| Chromatin | DNA wrapped around histone proteins |
| Euchromatin structures | looser, more gene activity |
| Heterochromatin structures | tighter, less gene activity |
| Nucleoplasm | gel-like internal fluid |
| Tubulin dimers | cell shape/support, cell movement by cilia/flagella, cell division/chromosome segregation, vesicle transport, organelle arrangement |
| Actin monomers | cell shape/support, cell movement by crawling, cell division/cytokineses, vesicle transport, muscle contraction |
| Myosin | motor proteins associated with microfilaments |
| Conventional Myosins | Type II, primarily for muscle contraction |
| Unconventional Myosins | Type I and III-XVIII, generate force, contribute to motility in non-muscle cells |
| ARP2/3 Complex | helps in the creation of branch points for polymerization of new actin fibres |
| Microfilaments | double helix of actin monomers, enable cell movement (muscle contracting), 7 - 9 nm |
| Actin | an enzyme that binds and slowly hydrolyzes ATP |
| Intermediate Filaments | stable compared to MTs, exclusive to multicellular animal cells, non-polar, anchor nucleus/organelles (resist force), 10 nm |
| Microtubule-Organizing Center (MTOC) | central site of MT assembly, only found in eukaryotic cells |
| Basal Bodies | associated with cilia and flagella |
| Centrosome | associated with spindle formation |
| Microtubule-Associated Proteins (MAPs) | several different proteins that bind MTs, stabilize/stimulate assembly |
| Non-Motor MAPs | control MT organization in cytosol |
| Motor MAPs | use ATP to generate force, move materials along MT track, generate sliding force between MTs |
| Kinesin | +end direction, transports cargo away from cell center, slower |
| Dyenin | -end direction, transports cargo towards cell center, faster |
| Axonemal MT | highly organized, stable |
| Cytoplasmic MT | loosely organized, dynamic, located in cytosol |
| Microtubule (MT) | maintain cell shape (resist compression), α-tubulin and β-tubulin, 25 nm |
| Microvilli | maintian cell polarity and junction |
| Cytoskeleton | network of interconnected filaments and tubes that extends through cytosol and organelles |
| Vacuoles | fluid-filled, membrane-bound, regulate cytoplasmic pH and cell rigidity, remove toxic ions, store amino acids, sugars, and CO2 in the form of malate |
| Tonoplast | Vacuolar membrane that contains active transport systems that allow ion and molecule transport |
| Autophagy | process of disassembling unnecessary or dysfunctional cellular components - organelle turnover (golgi vesicle engulfs target organelles -> release contents to cytosol) |
| Lysosomes | digestive organelles, 25 nm - 1 μm |
| COPII | anterograde transport of proteins from the ER to the Golgi |
| COPI | retrograde transport of proteins from the Golgi to the ER |
| Clathrin | post-Golgi trafficking, forms the structural scaffold of vesicles |
| Clathrin Adaptor Proteins (AP) | proteins that link membrane-bound cargo to clathrin |
| Endocytic Pathways | retained in the ER lumen or transported to Golgi for further modification/delivery |
| Transmembrane Protein | single-anchor sequences thread through channel until sequence is encountered |
| Peroxisomes | "microbody", involved in enzymatic reactions |
| Post-Translation Import | proteins are made in the cytosol, then transported (targeted to mitochondria/chloroplats |
| Cotranslational Import | protein enters the ER as it is being made, not after |
| Rough ER | contains ribosomes, membrane phospholipids synthesis |
| Smooth ER | does not contain ribosomes, lipid synthesis, production of steroid hormones, detoxification |
| Transport Vesicles | ~50 - 75 nm, small, spherical, membrane-enclosed organelles, bud off donor compartments to fuse with acceptor/recipient compartments |
| Green Fluorescent Protein (GFP) | fusion protein fluoresces can be visualized under a microscope |
| Caspaces | disrupt cell adhesion, destroys lamins, breaks down cytoskeleton, activates DNase |
| Apoptosis | death of cells in a coordinated sequence of events, part of growth/development, initiated by the an intracellular stimuli (usually the release of cytochrome c) |
| Bone Morphogenetic Protein (BMP) | a secreted protein that binds to BMP receptors (BMPRs) |
| Light-Independent Reactions | dark reactions/calvin cycle, occurs in stroma, ATP and NADPH made in light is used to make carbohydrate energy reserve, low supply of O2 = disfunction |
| Light-Dependent Reactions | occurs in thylakoid membrane, electron enters ETC (thylakoid membrane), H+ pumped into thylakoid lumen |
| Photosynthesis | building carbohydrates using energy from sunlight and CO2, leads to cellular respiration, neither aerobic nor anaerobic |
| Oxidization Phosphorylation | chemical energy of organic molecules is transferred first to electron carriers to create an electrochemical gradient that can power ATP synthesis |
| Substrate-Level Phosphorylation | hydrolysis reaction releases enough energy to drive phosphorylation of ADP to ATP |
| Cellular Respiration | process by which glucose is transformed into energy within cells |
| Aerobic Respiration Stages | Glycolysis, Acetyl Coenzyme A, Kreb's Cycle, Electron Transfer |
| Glycolysis | glucose molecules are broken down to create GATP, pyruvate, and NADH in the cytoplasm |
| Acetyl Coenzyme A | pyruvate is used to create acetyl coenzyme A and carbon dioxide in the mitochondria |
| Kreb's Cycle | acetyl coenzyme A is used to create more NADH, FADH2, carbon dioxide, and additional ATP |
| Electron Transfer | NADH, FADH2, and oxygen create ATP and water through electron transfer |
| Outer Mitochondria Membrane (OMM) | contains many enzymes with diverse metabolic functions |
| Porins | large channels permeable to many molecules when opened (OMM) |
| Inner Mitochondria Membrane (IMM) | 3:1 protein/lipid ratio, rich in phospholipids called cardiolipins, contains electron transport chains (ETC) |
| Cristae | double-layered folds, increase membrane surface area and contain machinery for aerobic respiration and ATP formation (IMM) |
| Cardiolipins | characteristic of bacterial membranes, needed for optimal function of many enzymes |
| Aerobic Respiration | in the presence of oxygen, converts energy stored in food into chemical energy stored in ATP |
| Symbiosis | close and long-term biological interactions |
| The Endosymbiotic Theory | an evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms |
| Cytosol - function | protein synthesis, many metabolic pathways |
| Nucleus - function | contains genome, DNA, RNA synthesis, ribosome assembly |
| Endoplasmic Reticulum (ER) - function | synthesis of lipids, synthesis of ribosomes |
| Golgi Apparatus - function | protein modification, packaging of proteins and lipids |
| Lysosomes - function | degration of cellular material |
| Endosomes - function | sorting, recycling |
| Mitochondria - function | ATP synthesis, apoptosis |
| Chloroplasts - function | photosynthesis, ATP synthesis |
| Peroxisomes - function | oxidation of toxic materials |
| Anchor Membrane Proteins | interact with components of the ECM, connect the cytoskeleton to ECM components (ex. collagen and fibronectin) |
| Extracellular Matrix (ECM) | organized network of materials produced and secreted by cells, compartments: glycoproteins, collagen, proteoglycans |
| ECM - functions | cell adherence, communication between cells, cell shape/mechanical support/structural integrity, serves as a barrier (filters out particles) |
| Signal Transduction | membrane proteins convert an extracellular signal into intracellular signal(s) |
| Ligand | small molecule that binds to a receptor, changes conformation of the receptor protein, activates other proteins |
| Signal Transduction Stages | binding of ligand receptor, signal transduction via second messenger, cellular response |
| Movement Across Cell Membrane Mechanisms | simple diffusion, diffusion through a channel, facilitated diffusion, active transport |
| Simple Diffusion | small, uncharged molecules flow from an area of high concentration to one of low concentration |
| Diffusion through a Channel | small, charged molecules (ions) flow from an area of high concentration to one of low concentration through a specific channel |
| Facilitated Diffusion | large, charged molecules flow from an area of high concentration to one of low concentration with the help of carrier proteins |
| Active Transport | flow from an area of low concentration to one of higher concentration, require energy (ATP) |
| α Helices | spiral shapes that help stabilize transmembrane protein |
| Transmembrane Protein Domain | a peptide sequence that is largely hydrophobic and spans across the PM, permanently attatches protein to PM |
| Transmembrane Proteins | Transporter, Receptor, Enzyme, Anchor |
| Transporter | allows ions, glucose, and water to move across the membrane |
| Receptors | detect signals and trigger a response within the cell |
| Enzymes | catalyze chemical reactions |
| Anchors | anchor different types of structural components |
| Affects fluidity | Temperature (warming -> increases, cooling -> decreases) Membrane fluidity (unsaturated -> increases, saturated -> decreases) |
| Lipid Composition can be changed by | desaturation of lipids, exchange of lipid chains |
| Cholesterol | modulates membrane fluidity (liquid crystal membrane fluidity will decrease, crystalline gel membrane fluidity will increase) |
| Membrane Proteins | Integral, Peripheral, Lipid-Anchored |
| Integral Protein | span the lipid bilayer |
| Integral Protein - function | transport of nutrients and ions, cell-cell communication, attatchement |
| Peripheral | associate with the surfaces of the lipid bilayer |
| Lipid-Anchored | attach to a lipid in the bilayer |
| Myelin | modified plasma membrane made from specialized glial cells (oligodendrocytes in the central nervous system) |
| Lipid Rafts | organize membrane proteins to facilitate signal transduction, regulate protein interactions, play a role in immune responses, virus entry, and neurotransmission |
| Biological Membranes - structure | ~6 nm thick (with water), stable, flexible, capable of self-assembly, contains glycoproteins, integral membrane proteins, peripheral membrane proteins |
| Lipids | move easily, laterally, within leaflet |
| Plasma Membrane (PM) | two-dimensional liquid that restricts the diffusion of membrane components |
| Phospholipids Synthesis | occurs at the interface of the cytosol and outer endoplasmic reticulum membrane |
| Phosphotidyl- | -ethanolamine, -choline, -serine, -inositol |
| Phospholipids | amphipathic molecules, hydrophilic head, hydrophobic tale |
| Hydrophilic | attracted to water |
| Hydrophobic | repelled by water |
| Lipid molecules | spontaneously aggregate to expose their hydrophilic heads to water |
| Micelle | solid ball |
| Liposome | hollow sphere with a fluid-filled centre |
| Plasma Membrane (PM) - structure | trilaminar structure made of phospholipid bilayer, ~6 nm |
| Replicase | make a lot of copies of the RNA template for antigens |
| RNA Vaccines | trick the body's cells into producing antigens |
| Microcephaly | major consequence of congenital Zika, lifelong neurological complications |
| Zika Virus | disrupts brain development by infecting neural progenitor cells during neurogenesis |
| Viral Life Cycle Stages | Attachment and Entry, Endocytosis, Encoding and Replication, Synthesis, Exocytosis |
| Attachment and Entry | enveloped virus releases nucleic acid inside |
| Endocytosis | cell internalizes the virus, becomes endosome |
| Encoding and Replication | capsid breakdown, viral genome release |
| Synthesis | viral nucleic acid syntesizes viral components by hijacking the cell's machinery |
| Exocytosis | progeny viruses are released out of the cell |
| Lytic Infection | production of virus particles ruptures and kills cell (ex. influenze) |
| Non-Lytic Infection | viral DNA is inserted into host genome, infected cell can survive, often with impaired function (ex. chicken pox) |
| Host Range | the ability to bind to a cell's surface |
| Narrow Host Range | infect epithelia (ex. cold and influenza) |
| Wide Host Range | infect several animals (ex. rabies) |
| Bacteriophage | infects and replicates within bacteria and archaea |
| Adenoviruses | cause respiratory illnesses |
| Ebola Virus | filovirus, encodes their genome in single-stranded, negative-nonsense RNA, cause hemorrhagic fever |
| Hepatitus-B | hepadnavirus (DNA type), affects the liver causing infection |
| HIV | retrovirus, RNA virus that inserts a copy of its genome into the DNA of a host cell |
| Baltimore Classification | categorizes viruses based on type of genome and their method of replication |
| Virion | inanimate particle that viruses exist in (outside of cells), made of a small amount of DNA or RNA that encodes genes and a protein called capsid |
| Viruses | macromolecular packages that can function and reproduce only within living cells |
| Eukaryotic Cells | multicellular organisms, 10 - 100 μm, nucleus and organelles, ribosomes are large, genetic material found in nuclear compartment |
| Prokaryotic Cells | single-celled organism, 1 - 10 μm, no nucleus or organelles, ribosomes are small, reproduce asexually, genetic material found in nucleoid |
| The Cell Theory | all living organisms are composed of one or more cells, the cell is the basic unit of life, all cells arise from pre-existing cells |
| Amino Acids | generated in conditions that mimic the Earth |
| Abiogenesis | chemical origin of life (inorganic chemicals + energy = organic chemicals) |
| Enucleation | mechanism where mature red blood cells, "erythrocytes", eject their nucleus |
| Red Blood Cells | lack nuclei and organelles, mature cells cannot synthesize RNA and therefore cannot divide |
| Differentiation | process by which cells become specialized |
| The Central Dogma of Molecular Biology | DNA to RNA (transcription) and RNA to Protein (translation) |
| Cells | possess DNA which provides the information to build proteins, the cell's primary machinery |
| Steps in Translation | Initiation, Elongation, Termination |
| Initiation | AUG is recognized (initiator codon) |
| Elongation | successive amino acids are added one by one |
| Termination | stop codon is recognized (UAA, UAG, UGA) |
| Transfer RNA Subunits | A site, P side, E site |
| A site (Aminoacyl-tRNA site) | incoming aminoacyl-tRNA molecule binds |
| P site (Peptidyl-tRNA site) | holds tRNA that is linked to the growing polypeptide chain, ribosome catalyzes the formation of a peptide bond between the amino acid in the P site and the new amino acid in the A site |
| E site (Exit-tRNA site) | "empty" or deacylated tRNA from the P site moves to the E site, the final holding place before the deacylated tRNA is released from the ribosome to be reused |
| Properties of Genetic Code | no spaces between codons, non-overlapping, degenerate, nearly universal |
| Requirements to Translate RNA Transcription | start codon, genetic code to specify amino acids, stop codon |
| Factors of Translation | mRna, initiation factors, elongation factors, release factors, aminoacyl tRNA synthetases, tRNA, ribosome |
| Lac Operon | lactose is metabolized into allolactose which acts as a ligand to bind to the repressor, relieving the repressor of its function and allowing for the transcription of LacZ, LacY, and LacA |
| Negative Inducible Operon | transcription is normally off and must be turned on, repressor must be removed for transcription to proceed |
| Negative Regulator Proteins | inhibit transcription |
| Positive Regulator Proteins | activate transcription |
| Inducible Operons | transcription operon is normally off and something happens that turns it on |
| Repressible Operons | transcription operon is normally on and something happens that turns it off |
| RNA Polymerase II | enzyme responsible for generating the majority of mRNA making proteins |
| Template Strand | 3' -> 5' orientation, transcribed |
| RNA Strand | 5' -> 3' direction, similar to non-template (U replaces T) |
| Terminator | a sequence of nucleotides that signals where transcription ends, incorporated into RNA |
| Transcription Unit | a promoter, RNA-coding sequence, terminator |
| Forward Mutation | wild type -> mutant type |
| Reverse Mutation | mutant type -> wild type |
| Missense Mutation | amino acid -> different amino acid, results in an amino acid substitution |
| Silent Mutation | codon -> synonymous codon, has no affect on the protein sequence |
| Neutral Mutation | no change in function |
| Somatic Mutations | arise during a person's lifetime, not inherited by off-spring |
| Germ-Line Mutations | present in all the body's cells, can be passed on to off-spring |
| Expanding Nucleotide Repeats | increase in the number of copies of a nucleotides set |
| Frameshift Mutation | results from insertion/deletion of nucleotides, may change many codons |
| Nonsense Mutation | substitutes a stop codon for an amino acid |
| Mutations | inherited alterations in DNA sequence |
| Codons | mRNA read three nucleotides at a time, the genetic code |
| Telomeres - function | stability and integrity of the chromosomes, resist degradation by DNases, prevent fusion of chromosomal ends, DNA replication |
| 5' end | has a free phosphate group |
| 3' end | has a free hydroxide group |
| Histones | proteins that provide structural support for chromosomes, allow various levels of DNA packaging |
| Ribonucleic Acid (RNA) | the genetic material (genome) of some viruses (ex. HIV and SARS-CoV-2) |
| Deoxyribonucleic Acid (DNA) | a polymer with each subunit being a nucleotide containing a phosphate group, a five carbon sugar, one of four cyclic nitrogenous bases |
| Temperature Sensitive Alleles | product is functional only at certain temperatures |
| Expressivity | the degree to which a character is expressed (phenotype is present but varies among individuals) |
| Penetrance | % of individuals having a particular genotype that express the expected phenotype (#phenotype/#genotype *100) |
| Characteristics of Dominance | a result of the interactions between genes on the same locus, does not alter the way genes are inherited, only how they're expressed, type of dominance depends on the level at which the phenotype is examined |
| Incomplete Dominance | the phenotype of the heterozygote falls between the two homozygotes |
| Codominance | heterozygotes expressed the phenotype of both homozygotes simultaneously |
| Complete Dominance | the phenotype of the heterozygote is the same as one of the homozygotes |
| Polymorphism | any allele found in at least 1% of the population |
| Genetic Mosaicism | different cells of the body have different genetic constitutions |
| Y-Linked Trait | only males are affected, passed from father to sons, does not skip generations |
| X-Linked Dominant Trait | both sexes affect (f>m), does not skip generations, affected fathers->daughters, affected mothers->1/2 sons, 1/2 daughters |
| X-Linked Recessive Trait | both sexes (m>f), skips generations, carrier mother->1/2 sons, affecter fathers -> carrier daughters |
| Autosomal Dominant Trait | appear in both sexes, does not skip generations, heterozygous parent -> 1/2 off-spring |
| Autosomal Recessive Trait | appear in both sexes, skips generations, both heterozygous parents -> 1/4 off-spring |
| Pedigree | a pictorial representation of a family history that outlines the inheritance of characteristics |
| Binomial Equation | [n!/s!t!]p^s*q^t |
| Binomial Probability | probability for s = p, and t = q |
| Multiplication Rule | ___ and ___ |
| Addition Rule | ___ or ___ |
| Dihybrid Crosses | crosses between parents that differed in 2 characteristics |
| Monohybrid Crosses | crosses between parents that differed in a single characteristic |
| Concept of Dominance | when two different alleles are present in a genotype, only the dominant trait is observed in the phenotype |
| Dominant (R) | traits that appear unchanged in the F1 heterozygous off-spring |
| Recessive (r) | traits that disappeared in the F1 heterozygous off-spring |
| Principle of Segregation | each individual organism possesses two alleles encoding a trait, alleles separate when gametes form, alleles separate in equal proportions |
| Principle of Independent Assortment | alleles at different loci separate independently |
| Gene | an inherited factor (encoded in the DNA) that helps determine a characteristic |
| Allele | one or two of more alternative forms of genes |
| Locus | a specific place on a chromosome occupied by an allele |
| Genotype | a set of alleles possessed by an individual organism |
| Homozygote | an individual organism possessing two of the same alleles at a locus |
| Heterozygote | an individual organism possessing two different alleles at a locus |
| Characteristics | an attribute or feature possessed by an organism |
| Phenotype | the appearance or manifestation of a characteristic |
| Mitosis | occurs in somatic cells, results in 2 diploid daughter cells, daughter cells are genetically identical, continues for many cycles |
| Meiosis | occurs is germ(sex) cells, results in 4 haploid daughter cells, daughter cells are genetically unique, terminal event |
| Stem Cells | cells that have the ability to differentiate into any specialized cell |
| Tumor Suppressors | encode proteins that inhibit cell division |
| Proto-oncogenes | control cell division (growth factors, G proteins, kinsases) |
| Oncogenes | mutated, cancer causing genes |
| p53 | binds to DNA and arrests cell at G1 checkpoint |
| Cyclins | proteins that rise and fall with each turn of the cell cycle |
| Kinases | proteins that promote cell division |
| Cyclin-Dependent Kinases (CDKs) | trigger cell cycle events when bound to cyclins |
| M Cyclin CDK | prepares the cell for mitosis |
| S Cyclin CDK | initiates DNA synthesis |
| G1/S Cyclin CDK | prepares cell for DNA replication |
| Kinetochores | associate with the centromere and form an attachment to the microtubules |
| Centromere | holds sister chromatid together |
| Sister Chromatid | identical DNA copies |
| Karyotype | the general appearance of an individual's complete set of chromosomes |
| Chromosomes | single DNA molecule and proteins |
| Cell Division | how cells make more cells, continues even after cell is fully grown |
| Bacteria Cells | DNA is arranged in a circular fashion (plasmid) |
| Sequence of Key Steps in the Rabies Virus Replication Cycle | absorption -> endocytosis -> fusion -> replication -> transcription -> glycoprotein synthesis -> budding |
| Simple Diffusion - Ex. Molecule | NO |
| Membrane Transition Temperature | the temperature at which the membrane transitions from a crystal-like to a fluid-like state |
| Glycoproteins | involved in cell signalling and interactions |
| Endomembrane Movement of Secreted Hormone Sequence | RER -> COPII-coated vesicles -> plasma membrane -> bloodstream |
| Thylakoid Membrane | contains electron transport chains (ETC) of chloroplasts |
| SNARES | proteins that are required to facilitate docking and fusion of vesicles to their target membrane |
| Materials Move from ER to Golgi and beyond in a ____ to ____ direction | proximal to distal |
| Insulin (secretary protein) | is synthesized on ribosomes of the rough ER and its release is regulated |
| Stroma | the fluid-filled space within a chloroplast that surrounds the grana (stacks of thylakoids) |
| Na-glucose sympoter | A carrier - causes a conformational change allowing glucose molecules to move against it's concentration gradient |
| Zellweger Syndrome | caused by a defect in the import of enzymes to the peroxisome |
| Signal-Anchor Sequence Enters the ER Translocon | growing polypeptide stops entering the ER lumen and becomes positioned in the membrane |
| Clathrin Adaptor Proteins Lose Function | excess AMPA receptors remain on the membrane -> increased synaptic strength |
| Dynamic Instability | microtubule behaviour where they rapidly grow and shrink |
| cAMP | "second messenger", carries the signal inside the cell after the hormone binds outside |
| O2 | final electron acceptor in the ETC |
| Free Ribosomes | where all protein synthesis begins |
| Signal Recognition Particle | directs protein synthesis during co-translational import |
| Curare | acts as a competitive antagonist to the nicotinic acetyl choline receptor |
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