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Biology 107- Intro to cell biology > Biology general > Flashcards

Biology general Flashcards

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1
Q

Living Organism Criteria

A
  • organized (system entropy decreases)
  • consist of cells
  • organize energy from environment
  • change/manipulate internal environment
  • have metabolism
  • respond to stimuli
  • interact with environment
  • capable of reproduction/growth
  • capable of evolution/change
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2
Q

Domains

A
  • Bacteria (prokaryotic)
  • Archaea (prokaryotic)
  • Eukarya (eukaryotic)
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3
Q

Kingdoms

A

Bacteria - Monera
Archaea - Monera
Eukarya - Protists/Animalia/Plantae/Fungi

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4
Q

Prokaryotic vs. Eukaryotic

A
  • Prokaryotic = “before nucleus”, no membrane-bound nucleus, DNA is in cytoplasm
  • Eukaryotic = “true nucleus”, membrane-bound nucleus that contains DNA
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5
Q

Cladogram Evolution

A
  • life started out as prokaryotic
  • archaea branched off of bacteria, eukarya branched off from archaea (more closely related)
  • bacteria and archaea look identical but are genetically different
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6
Q

Life Classification

A

Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species

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7
Q

Archaea Characteristics

A
  • prokaryotes
  • DNA-based genome
  • extremophiles
  • no peptidoglycan
  • circular and linear chromosomes
  • differs from bacteria in that it contains different phospholipids/cell walls/ribosomes
  • 1-10 micrometres
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8
Q

Bacteria Characteristics

A
  • prokaryotic
  • DNA-based genome (usually just a single cell of DNA)
  • circular chromosome
  • cell walls have peptidoglycan
  • 1-10 micrometres
  • metabolically diverse (can grow anywhere)
  • structurally limited
  • ex: E. coli
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9
Q

Eukarya Characteristics

A
  • membrane-bound organelles
  • uni or multi-cellular
  • structurally diverse
  • metabolically limited
  • linear chromosomes
  • ex: yeast
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10
Q

Elements of Life

A
  • carbon
  • hydrogen
  • oxygen
  • phosphorus
  • sulfur
  • nitrogen
  • some ions and trace elements
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11
Q

Water Characteristics

A
  • “solvent of life”
  • polar (unequal e- distribution)
  • O2 has high electronegativity
  • can associate with other H2O molecules since opposites attract (dipole-dipole)
  • can associate with any charged molecule
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12
Q

DNA Elements

A
  • carbon
  • hydrogen
  • oxygen
  • phosphorus
  • nitrogen
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13
Q

Protein Elements

A
  • carbon
  • hydrogen
  • sulfur
  • phosphorus
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14
Q

Covalent Bond

A
  • sharing of a pair of valence e- by 2 atoms
  • AKA molecular bond
  • stable balance of attractive/repulsive forces
    -ex: water
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15
Q

Ionic Bond

A
  • attraction between 2 opposite charges
  • one atom has all valence e-
  • forms ionic compounds
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16
Q

Hydrogen Bond

A
  • attraction between a hydrogen atom and another electronegative atom while also being covalently bonded to another electronegative atom
  • enabled by partial hydrogen positive charge
  • more electronegative = stronger bond
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17
Q

Van der Waals Interaction

A
  • molecules have ever-changing regions of positive & negative charge due to uneven e- distribution which enables atoms to possibly stick together
  • individually weak (strength in numbers)
  • only occurs when atoms are very close together
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18
Q

Macromolecule Characteristics

A
  • contains C-H bonds
  • carbon is backbone of organic molecules (since it has very low electronegativity and 4 valence e-)
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19
Q

Monomer

A
  • single building block of a macromolecule
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20
Q

Polymer

A
  • chain of monomers composed of similar but not identical subunits
  • linked by covalent bonds
  • allow for variation
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21
Q

Synthesis/Condensation/Dehydration Reaction

A
  • monomers are added to a growing chain
  • 1 water molecule is removed
  • covalent bonds are formed
  • when bonding, 1 monomer provides H and the other provides OH
  • requires energy
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22
Q

Breakdown/Hydrolysis Reaction

A
  • polymer covalent bonds are cleaved/broken down
  • water is added between 2 monomers (hydroxyl attaches to one and hydrogen to the other)
  • energy is released slowly
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23
Q

Carbohydrate/Polysaccharide/Sugar Characteristics

A
  • macromolecule
  • can serve as energy storage unit, rigid structural building material, cell-cell recognition and attachment
  • end in “ose”
  • covalent bonds
  • polar
  • can be 100-1000s units long
  • monomer = monosaccharides (3-7 carbons long)
  • multiple of “CH2O”
  • can be linear or ring-shaped
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24
Q

Glucose

A
  • C6H12O6
  • main cell energy source
  • monosaccharide
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25
Q

Sucrose

A
  • C12H22O11
  • disaccharide of fructose and glucose
  • connected by glycosidic (covalent) bond
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26
Q

Starch

A
  • nutritional polysaccharide
  • human glucose source
  • plant glucose storage
  • contains alpha 1-4 glycosidic bonds (glucose all pointed same way)
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27
Q

Cellulose

A
  • structural polysaccharide
  • provides plant cell wall rigidity
  • contains beta 1-4 glycosidic bonds (alternating glucose orientation) which can only be hydrolyzed by bacteria (into methane)
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28
Q

Lipid/Fat characteristics

A
  • hydrophobic/non-polar (more O2 = less hydrophobic)
  • no true polymers/monomers
  • have some O2/polar bonds but are mostly hydrocarbons
  • e - are equally shared, no dipoles, classified upon hydrophobicity
  • fats are made up of fatty acids and glycerol, serve as energy storage insulation
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29
Q

Fatty Acid

A
  • a component of fat
  • long hydrocarbon chain (usually 16-18) with a carboxylic acid (COOH) at one end which attaches to a glycerol backbone via esterification
  • non-polar
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30
Q

Glycerol (Backbone)

A
  • alcohol
  • each of its 3 carbons are attached to a hydroxyl group which can esterify with a fatty acid carboxyl group
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31
Q

Saturated Fats

A
  • whole carbon chain is ‘saturated’/filled with hydrogen
  • consists of solely single bonds
  • can pack more closely together and solidify easier
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32
Q

Unsaturated Fats

A
  • has one or more double bonds therefore fewer hydrogen atoms
  • the double bonds cause a ‘kink’ in the chain which causes the lipids to be further apart and liquefy easier
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33
Q

Phospholipid Characteristics

A
  • major cell membrane structural constituent
  • consists of 2 hydrocarbon fatty acids attached to a glycerol backbone (which has a phosphate head attached to its 3rd hydroxyl group)
  • fatty acids are non-polar/hydrophobic
  • phosphate head is negatively charged and hydrophilic
  • head + tails = amipathic (hydrophilic and phobic)
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34
Q

Steroid Characteristics

A
  • lipids characterized by a carbon skeleton of 4 fused rings
  • class of hormones
  • the backbone of cholesterol
  • mostly hydrocarbons with a bit of polar (OH) character at one end
  • are distinguished via by particular chemical groups attached to ring ensemble
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35
Q

Cholesterol

A
  • type of steroid
  • crucial molecule in animal cell membranes (sits in plasma membrane to maintain fluidity and increase stiffness)
  • precursor for other steroid synthesization
  • ex: testosterone, progesterone, estrogen
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36
Q

Protein Characteristics

A
  • polymer of amino acids
  • involved in every biological task
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37
Q

Amino Acid Characteristics

A
  • monomer of proteins
  • 20 biologically relevant aa
  • allow for extreme diversity
  • consist of an amino group (NH3+) on the left, an alpha carbon, a carboxylic acid (COO-) on the right, and a variable (R) group
  • R can be: non-polar (C and H), polar uncharged (OH or SH), polar charged acidic (-) (COO-), or polar charged basic (+) (NH3+)
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38
Q

Protein Structure Characteristics

A
  • function 3 dimensionally but are synthesized linearly (during translation at ribosome)
  • 3D shapes determine specific activities
  • amino acids determine 3D shapes
  • amino acids are covalently linked by peptide bonds which are formed via condensation rxn (links carboxyl group of 1 to amino group of another)
  • bonds are formed with directionality (one at a time, left to right)
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39
Q

Primary Protein Structure

A
  • sequence of linear amino acids determined by DNA, linked by peptide bonds
  • aa are written and translated with directionality
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40
Q

Secondary Protein Structure

A
  • coil and fold patterns that result from peptide chain backbone hydrogen bond interactions
  • contribute to overall protein shape
  • strength in numbers
  • amino acid subunits can be folded into an alpha helix (coil held together by hydrogen bonds) or a beta pleated sheet (segments of polypeptide laying side by side)
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41
Q

Tertiary Protein Structure

A
  • overall 3D shape/folding pattern of protein
  • driven by amino acid variable (R) groups interacting hydrophobically with water (CH group)
  • stabilized by disulfide (2 S-H groups) bridges, ionic bonds, hydrophobicity (van der Waals), and hydrogen bonds
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42
Q

Quaternary Protein Structure

A
  • the overall structure/formation of protein multimeric complexes
  • multiple peptides coming together to form a functional protein
  • held together by same forces as tertiary
  • ex: hemoglobin, collagen, ribosome
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43
Q

Chaperonin

A
  • protein that assists in the folding of other proteins
  • does not determine final structure, just provides ideal environment
  • “primary sequence dictates folding, folding dictates function”
  • many diseases exist due to incorrect protein folding
  • ex: Bacterial Chaperonin, “molecular changing room”
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44
Q

Nucleic Acid

A
  • polymer of nucleotide monomers
  • stores and transfers hereditary info (DNA = between cells, RNA = within)
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45
Q

DNA

A
  • deoxyribonucleic acid
  • polymer of deoxyribonucleotides (are deoxygenated at second carbon)
  • contains all life-essential info
  • 1 chromosome = 1 DNA molecule
  • provides directions for replication/gene expression
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46
Q

RNA

A
  • ribonucleic acid
  • polymer of ribonucleotides
  • has many forms/functions (ex: rRNA, mRNA, tRNA, snRNA)
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47
Q

Nucleotide

A
  • monomer of nucleic acid (connected by phosphodiester bonds)
  • composed of phosphate (-) + ribose (pentose) = sugar-phosphate backbone
  • also contains nitrogenous bases
  • connected with directionality along backbone (5’ to 3’)
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48
Q

Pyrimidines vs Purines

A
  • Pyrimidines: single 6-membered rings, includes Thyamine, Cytosine, Uracil
  • Purines: double rings (one 5-member + 1 6-member), includes Adenine and Guanine
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49
Q

(Deoxy)ribose Carbons

A
  • C1: attached to base
  • C2: attached to DNA hydrogen or RNA hydroxyl
  • C3: attached to hydroxyl
  • C4: nothing
  • C5: attached to phosphate
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50
Q

DNA Bonding

A
  • is double stranded, forms a double helix with bases pointing inward where they bond with their complementary base (A-T, 2 H bonds) (C-G, 3 H Bonds)
  • purines only bond with pyrimidines
  • the 2 helices run anti-parallel
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51
Q

RNA Bonding

A
  • single stranded helix (because the C2 OH group makes the helix more open/reactive)
  • free bases can pair with themselves/other RNA/DNA
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52
Q

Phospholipid Bilayer

A
  • is spontaneously formed when phospholipids are added to water
  • has 2 hydrophobic fatty acid tails and a hydrophilic phosphate head which form a cylindrical shape
  • phospholipids stack side-by-side due to shape
  • forms a boundary between cell and external environment
  • phospholipids are mobile, can freely move laterally within same membrane rapidly and frequently
  • only held together by hydrophobicity, no bonds
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53
Q

Micelle

A
  • forms with conical phospholipids with only 1 fatty acid tail
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54
Q

Flip-Flop Movement

A
  • phospholipid layers switch via the hydrophilic head passing through the hydrophobic core (not stable)
  • only happens rarely
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55
Q

Bilayer High Temperature

A
  • phospholipids will have more kinetic energy and will move faster
  • gap between them will increase which increases flexibility and permeability
  • adapts via increasing tail length (hydrophobicity), increasing saturation/decreasing double bonds, or increasing cholesterol content (acts as a pylon/movement barrier to decrease fluidity)
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56
Q

Bilayer Low Temperatures

A
  • gap between phospholipids decreases so flexibility/permeability decreases
  • adapts via decreasing saturation/increasing double bonds, decreasing tail length (decreasing hydrophobicity), or adding cholesterol (acts as a spacer between phospholipids)
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57
Q

Membrane Associated Proteins

A
  • Integral: penetrate hydrophobic bilayer interior, have non-polar aa’s which interact with hydrophobic core + hydrophilic regions which are exposed to outside
  • Peripheral: not embedded in bilayer, loosely bound to surface
  • protein-protein interactions are usually hydrophobic
  • proteins act as transporters, messengers, signalers, structure, etc.
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58
Q

Fluid Mosaic Model

A
  • “membrane is a fluid structure with a mosaic of different proteins embedded in/attached to the bilayer”
  • consists of proteins, cholesterol (only animal cells), bilayer, cytoplasm, glycolipids, and glycoproteins
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59
Q

Protein General Functions

A
  • transport, enzymes, signal transduction, cell-cell recognition, intercellular joining, and cytoskeleton/extracellular matrix attachment
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60
Q

Permeability

A
  • semi-permeable: only lets certain molecules pass through (ex: water)
  • permeable: allows free diffusion across bilayer (ex: non-polar/hydrophobic molecules, relatively small, like CO2 or O2)
  • impermeable: cannot cross hydrophobic core because they’re too large, charged, or polar
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61
Q

Osmosis

A
  • passive diffusion of water from low solute concentration to high
  • readily diffuses even though water is polar
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62
Q

Dipole Moment

A
  • unequal charge distribution of water temporarily disappears long enough for water to slowly diffuse across membrane, “following the solute”
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63
Q

Hydration Shell

A
  • sphere of water molecules around a dissolved ion
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64
Q

Tonicity

A
  • ability of a surrounding solution to cause a cell to gain or lose water
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65
Q

Diffusion

A
  • movement of molecules from an area of high concentration to low until equilibrium is reached
  • energy to do so comes from molecule thermal energy
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66
Q

Isotonic

A
  • solute concentrations inside and outside of cell are equal
  • no net water movement occurs
  • cell walls become flacid without movement
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67
Q

Hypertonic Solution

A
  • solute concentration of solution is greater than that of the cell’s
  • water will rush out of cell which risks cell shrinkage/death
  • plasmolysis can occur when the plasma membrane is pulled along with the water, possible wilting
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68
Q

Hypotonic Solution

A
  • solute concentration is greater in the cell than the solution
  • water rushes into the cell, swelling it and causing possible osmolysis (bursting of animal cell)
  • cell walls prevent osmolysis but can become turgid
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69
Q

Aquaporins

A
  • channel proteins/transmembrane channels that facilitate osmosis
  • greatly increase rate of water transport
  • ex: salmon will turn them off to adjust to water changes
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70
Q

Facilitated Diffusion

A
  • assistance of molecules (that are normally impeded by bilayer) while they passively diffuse down their concentration gradient via transport proteins
  • no energy needed
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71
Q

Channel Protein

A
  • hydrophilic “tunnel” that spans bilayer of allows specific solute transport without changing shape
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72
Q

Carrier Protein

A
  • “revolving door”, spans bilayer and transports specific solutes across membrane via changing shape
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73
Q

Active Transport

A
  • transport of molecules against/up their concentration gradient
  • requires energy
  • acts to concentrate cell nutrients, expel waste, and to maintain a voltage/chemical gradient
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74
Q

Sodium-Potassium Pump Role

A
  • generates and maintains a voltage difference/membrane potential = electrogenic
  • requires ATP
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75
Q

Sodium-Potassium Pump Steps

A
  • “SOPI PONI”
    -1) 3 Na+ bind to carrier protein
    -2) ATP provides energy for conformational change of protein
    -3) 3 Na+ are released extracellularly
    -4) 2 K+ bind to protein
    -5) ATP provides conformational change energy
    -6) 2 K+ are released intracellularly
    -7) resting membrane potential of -70mV is created
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76
Q

Electrochemical Gradient

A
  • difference in concentration of a charged molecule across a membrane
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77
Q

Cotransport

A

Cotransport
- transport of 2 molecules simultaneously
- chemical/electrical gradients are energy source

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78
Q

Sodium Cotransport System

A
  • via the Na/K pump, 3 Na+ are in the extracellular fluid where it then goes down the Na/Glucose co-transporter, bringing glucose into the cell
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79
Q

Coupled Transport

A
  • using one gradient to establish another (Na/K & Na/Glucose)
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80
Q

Symport

A

Symport

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81
Q

Anti-Port

A
  • cotransport of 2 molecules in opposite directions
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82
Q

Bulk Transport

A
  • molecules entering/exiting the cell that are too large for a transport protein
  • involves formation of vesicles (from the flexible membrane where it bends into different shapes and can pinch off)
  • requires energy
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83
Q

Exocytosis

A
  • bulk transport out of the cell
  • “secretion of biological molecules by the fusion of vesicles with the plasma membrane”
  • 1) a vesicle buds from the Golgi, moves along the cytoskeleton microtubules towards the plasma membrane
  • 2) the vesicle and plasma membrane come into contact and fuse
  • 3) vesicle contents spill out, vesicle membrane becomes part of PM
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84
Q

Endocytosis

A
  • bulk transport into cell
  • 1) the PM engulfs an external particle with pseudopodia and sinks inward to form a pocket
  • 2) the pocket deepends, pinches in, and forms a vesicle with the external material
  • 3) vesicle goes to the lysosome where contents are disgested
  • AKA phagocytosis
  • non-specific process, will bring anything in
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85
Q

Receptor-Mediated Endocytosis

A
  • specialized endocytosis of a specific ligand
  • receptors attach to ligands, form vesicle, and bring to lysosome
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86
Q

Lygand

A
  • anything that binds to a receptor
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87
Q

Receptor

A
  • integral membrane protein that recognizes and binds a specific ligand
  • congregate at clathrin-coated pit where it shapes vesicles and sorts cargo
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88
Q

Prokaryote Cell Characteristics

A
  • small (1-100 microns) due to its dilution problem (plasma membrane selective barrier only lets so much through at once)
  • is inhibitted by surface area/volume ratio (increase at different proportions, eukaryotes have internal membrane to solve this)
    -s.a. = membrane, volume = cytoplasm
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89
Q

Bacterial Cell Structure

A
  • no membrane-bound organelles
  • DNA is kept in a nucleoid region
  • perform all eukaryote functions, just without compartmentalization
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90
Q

Bacterial Flagellum

A
  • motile structure (differs greatly between eukaryotes and prokaryotes)
  • rotates like a corkscrew to enable movement
  • Hook: base of rotation
  • Basal Apparatus: anchors flagellum onto cell, contains gear system that drives hook rotation
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91
Q

Gram Positive Bacterial Cell Wall

A
  • required for cell defense, permeability, and structure
  • has 1 thick layer of peptidoglycan which contains peptide cross-bridges
  • stains violet
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92
Q

Peptidoglycan

A
  • bacterial structural polysaccharide
  • polymer of NAG and NAM sugars
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93
Q

Lypoteichoic Acid

A
  • links gram positive cell wall to membrane
  • is embedded in peptidoglycan and membrane
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94
Q

Teichoic Acid

A
  • molecule that links gram positive peptidoglycan layers together
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95
Q

Gram-Negative Cell Wall

A
  • thin layer of peptidoglycan + an outer membrane and cytoplasmic membrane
  • outer membrane/LPS layer contains lipopolysaccharides (negatively charged sugars)
  • Mg2+ associates with LPS to prevent repulsion
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96
Q

Antibiotic

A
  • substance that kills bacterial pathogens by targeting specific bacterial structures (ex: ribosomes, cell wall)
  • ex: penicillin: interrupts transpeptidation of peptidoglycan synthesis (inhibits cross linking), works best on gram positive
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97
Q

Fimbrae

A
  • small hair-like appendages that allow surface attachment of bacteria
  • not all bacteria have them but some pathogens do (ex: UPEC, E. coli that causes UTIs)
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98
Q

Biofilm

A
  • surface-coating colonies or “slime cities” of bacteria that can secrete a mucous that surrounds a cell (called a capsule)
  • can contain channels that allow for nutrient entry/waste expulsion
  • protects cell from dehydration and allows attachment
  • very difficult to remove
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99
Q

Microbiome

A
  • collection of organisms on human body
  • every skin inch is covered with trillions of microbes and many are essential to health
  • each body area has unique microbe collections
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100
Q

Colonization

A
  • establishment of microbial growth in host tissue, begins at birth
  • life begins in sterile womb environment
  • all bacteria comes from environment
  • many systems exist to encourage microbial growth
  • early exposure comes from mouth via feeding/exploring
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101
Q

Colonizing Bacteria Sources

A
  • birth canal: skin bacteria grow here only during pregnancy
  • feeding: ~600 bacteria species in breast milk, many are involved in milk digestion, can contain prebiotics
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102
Q

‘Normal’ Flora Purposes

A
  • pathogen protection: compete with pathogens for space and nutrients, can produce inhibitory compounds (toxins, organic acids) that prevent growth
  • killing off beneficial bacteria (from stress, diet, antibiotics) can allow pathogens to occur
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103
Q

Prebiotic

A
  • food and growth factors for bacteria
  • can be found in breast milk
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104
Q

C. difficile treatment

A
  • fecal transplants (more benificial (90% effective) than antibiotics (25%))
  • infections are persistent and resistant
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105
Q

Flora in Development

A
  • microflora are involved in gut development as well as triggering gene expression involved in nutrient metabolism
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106
Q

Flora in Nutrients

A
  • E. coli is our only source of vitamin K
  • bacteria gives us most of our vitamin B
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107
Q

Flora in Digestion

A
  • bacteria can digest complex carbs (ex: fiber)
  • babies receive aid in digesting lactose
  • species compositions change with diet
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108
Q

Flora in Immune System

A

Flora in Immune System

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109
Q

Hygiene Hypothesis

A
  • exposure to microbes helps maintain healthy immune system
  • lack of exposure to healthy microbes leads to hyperactive immune system
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110
Q

Eukaryote SA/Volume

A
  • managed to evolve to increase size and surface area while keeping constant volume
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111
Q

Endosymbiont Hypothesis

A
  • most common eukaryotic ancestor (~2 billion years ago)
  • O2 was accumulating in atmosphere, and since it is toxic to all cells, organisms had to adapt
  • eukaryotes evolved O2 neutralizing enzymes
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112
Q

Endomembrane System

A

subset of membrane-bound organelles that arise from infolding of membrane and are interconnected via vesicles
- consists of outer-nuclear membrane, endoplasmic reticulum, Golgi apparatus, and lysosomes

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113
Q

Endosymbiotic Organelles

A
  • mitochondria (mt) and chloroplasts (cp)
  • arose from a primitive prokaryote living inside a primitive eukarya (archaea)
  • both have circular chromosomes/their own DNA with bacteria-like gene organization
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114
Q

“Good Roommate Hypothesis”

A
  • mitochondria have very efficient metabolism whileas archaeal cell has space/protection from O2
  • ingested but not digested bacteria has been observed within
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115
Q

Nucleus

A
  • DNA storage site/site of gene expression (arranged in multiple linear chromosomes)
  • is double membrane-bound (outer one is continuous with ER)
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116
Q

Nuclear Pore Complex

A
  • transmembrane complex/intricate protein structure (~60) that spans both bilayers and allows for non-selective transport
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117
Q

Nucleolus

A
  • site of ribosomal subunit assembly (originate from cytoplasm)
  • subunits independently enter it via the NPC and then complex with rRNAs
  • then leave nucleus and come together for translation
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118
Q

Nuclear Envelope

A
  • both nuclear membranes
  • separates nucleoplasm from cytoplasm
  • consists of 2 lipid bilayers
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119
Q

Nuclear Lamina

A
  • netlike array of protein filaments that maintain nucleus shape, provide structural protection, and lines inner membrane
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120
Q

Chromatin Packaging

A
  • chromatin = DNA/protein complex that makes up chromosomes
  • packages DNA as to organize and protect it
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121
Q

Nucleosomes

A
  • DNA coiled around histone octomer
  • resembles a “bead on a string”
  • basic unit of DNA packaging
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122
Q

Histones

A
  • positively charged proteins
    -2 of each
  • 4 types: H2A, H2B, H3, H4
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123
Q

Solenoid/30nm Fibre

A
  • nucleosomes stack with help of H1 histone
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124
Q

Looped Domains

A
  • 30nm fibre forms loop off of a non-histone protein scaffold
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125
Q

Mitotic Chromosome

A
  • looped domains coil/fold into a fully condensed chromosome (only during cell division)
  • unknown mechanisms
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126
Q

Endoplasmic Reticulum

A
  • Rough: covered in ribosomes (translation enzymes that carry out protein synthesis), associated with proteins designated for within EMS = bound ribosomes (vs. cytoplasmic free ribosomes)
  • Smooth: no ribosomes, involved in Ca2+ ion storage, phospholipid synthesis, steroid synthesis, steroid synthesis, and detoxification
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127
Q

Chromatin Orders of Packaging

A
  • 1) nuclesomes
  • 2) solenoid/30nm fibe
  • 3) looped domainds
  • 4) mitotic chromosome
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128
Q

Golgi Apparatus

A
  • set of flattened membrane-bound compartments called cisternae that are not interconnected
  • “warehouse/FedEx” of cell, packs into vesicles
  • receives cargo from ER and sorts it according to destination (lysosome, PM, or back to ER)
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129
Q

Golgi Cisternae Classification

A
  • cis side = closest to ER, receives cargo
  • trans side = closest to PM, sends it
  • medial = middle
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130
Q

Golgi Trafficking

A
  • Vesicle Trafficking: cargo travels between cisternae via multiple vesicles
  • Cisternal Maturation: cis cisternae “mature” into trans ones, bringing the cargo with them where the trans cisternae eventually vesiculates
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131
Q

Lysosomes

A
  • membranous-sac of hydrolytic enzymes
  • “cell stomach”
  • digests endocytotic macromolecules
  • enzymes function best at pH of 5 (actively pump in protons to maintain)
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132
Q

Autophagy

A
  • “self eating”
  • breaking down or recycling of old organelles
  • cell suicide can occur if lysosome(s) rupture
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133
Q

Tay Sachs Disease

A
  • lysosomes lack the enzyme to digest a particular lipid, so it accumulates and can cause neuronal cell death
  • is heritable
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134
Q

Vacuole

A
  • large vesicles derived from ER and Golgi
  • funtion depends of type (food, contractile - pumps out excess water, or central - plant cell storage)
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135
Q

Path of Protein Within Cell

A
  • nucleus (transcription, mRNA synthesis from DNA)
  • nucleolus (subunit/rRNA
    assembly)
  • then in a vacuole to the rough ER to be translated into a protein
  • then in a vacuole to the Golgi, where it is either sent to a lysosome, plasma membrane, or back to ER
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136
Q

Cytoskeleton

A
  • network of fibres extending throughout cytoplasm
  • not part of EMS
  • functions as support, motility, and cell shape
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137
Q

Microtubules

A
  • hollow rods constructed from tubulin dimers (monomer consisting of protein and 2 subunits)
  • tubulin dimers polymerize into protofilaments (quaternary structure), 13 protofilaments bundle into a tube
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138
Q

Motor Protein

A
  • protein that changes shape with ATP hydrolysis and generates force
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139
Q

Microtubule Motor Proteins

A
  • Kinesin: uses “monkey bar movement” to move towards the “+” end of the MT
  • Dynein: uses unknown movement mechanisms to move toward the “-“ end
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140
Q

Eukaryotic Flagellum

A
  • works for cell movement via whip-like movements, dynein ‘walking’ to (-) MT end
    -ex: sperm tail
  • powered by ATP hydrolysis
  • is membrane bound/embedded in the cytoplasm
  • single/long = flagellum
  • multiple/short = cilia
  • has 10x width of prokaryotic flagella
  • covered by plasma membrane
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141
Q

Microfilaments

A
  • thin solid rods composed of actin (a globular protein) monomers
  • are a twisted double chain of actin subunits
  • function as tension resistance + movement (cytokinesis, muscle contraction)
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142
Q

Microfilament Motor Protein

A
  • Myosin (many forms exist, ex: myosin II)
  • muscle myosin forms bipolar filaments through tail-tail dimerization
  • muscle contracts when myosin shortens (within Sarcomere)
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143
Q

Intermediate Filament

A
  • tension-bearer
  • many different structural subunits that form rope-like filaments
  • not very dynamic, no known associated motor proteins
  • low turnover (very stable)
  • ex: laminin (forms nuclear lamina)
  • ex: keratin (hair & nails)
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144
Q

Plant Cell Wall

A
  • extracellular plant structure that distinguishes them from animal cells
  • maintains cell shape and prevents excess water uptake
  • main component is cellulose (structural supportive polysaccharide)
  • much thicker than plasma membrane
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145
Q

Animal Extracellular Matrix (ECM)

A
  • maintains cell attachments across long distances
  • allows communication
  • maintains tissue integrity
  • stores growth factors
  • main component is glycoproteins
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146
Q

Glycoproteins

A
  • Membrane carbohydrates that are covalently bonded to proteins
  • hydrate the ECM
  • ex: collagen and fibronectin
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147
Q

Collagen

A
  • a glycoprotein
  • forms strong fibres outside of cells
  • a long protein that acts to link cells
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148
Q

Fibronectin

A
  • An extracellular glycoprotein secreted by animal cells that helps them attach to the extracellular matrix
  • links collagen to integrins
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149
Q

Integrin

A
  • In animal cells, a transmembrane receptor protein with two subunits that interconnects the extracellular matrix and the cytoskeleton.
  • cell surface receptor proteins
  • integral membrane proteins that link ECM to CSK
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150
Q

Epithelial Cells

A
  • skin cells that cover the outside of the body and line the internal surfaces of organs
  • layers between body and environment
  • have an apical (facing environment) and basal (facing collagen, integrins, etc.) side
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151
Q

Epithelial Cancer

A
  • ~90% of all cancers are epithelial in original
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152
Q

Tumour

A
  • a mass of cells that arose from uncontrolled cell division (since mitosis should ideally be heavily regulated)
  • one major step in tumour progression is detachment from the ECM (potential cancer cells must detach to find room to grow)
  • cancer = cells dividing uncontrollably
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153
Q

Animal Cell-Cell Attachments

A
  • happen over long distances (like the ECM) but cells can also be directly attached to one another via 3 different attachments types/set of intercellular junctions in epithelial layers that maintain integrity
  • tight junctions, desmosomes, and gap junctions
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154
Q

Tight Junctions

A
  • Membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid
  • function as rivets to seal cells together (establish barriers across epithelial layers)
  • prevent passage of molecules between cells from environment into body or vice versa
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155
Q

Desmosomes

A
  • Anchoring junctions that prevent cells from being pulled apart
  • distribute stretching forces across a tissue
  • connect cytoskeletons (intermediate filaments) of adjacent cells
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156
Q

Gap Junctions

A
  • Points that provide cytoplasmic channels from one cell to another with special membrane proteins. Also called communicating junctions.
  • provide non-selective transport of small molecules between adjacent cells
  • large cytoplasmic channels that allow sharing of nutrients and signals between cells
  • ex: heart muscle cells (are mononucleate but each cell is connected via gap junctions - allow spread of Ca2+ for muscular contractile signals)
157
Q

Metabolism

A
  • totality of a cell’s chemical exns
  • managing the materials and energy resources in a cell
  • ATP made in catabolism drives anabolism, then that ADP is recycled for catabolism
158
Q

Anabolism

A
  • Metabolic pathways that construct molecules, requiring energy
  • organize the cell
  • ex: DNA replication, transcription, translation
159
Q

Catabolism

A
  • Metabolic pathways that break down molecules/nutrients, releasing energy.
  • ex: cell resp
160
Q

Energy

A
  • the capacity to cause change or to do work/move something
161
Q

Work

A
  • a force acting on an object over a distance
162
Q

Kinetic Energy

A
  • energy due to movement/associated with relative motion of objects
163
Q

Potential Energy

A
  • stored energy due to composition or position
164
Q

The cell is a(n) ___ system

A

open

165
Q

1st Law of Thermodynamics

A
  • energy cannot be created or destroyed, only converted from one type to another
  • ATP is not ‘created’
166
Q

2nd Law of Thermodynamics

A
  • every energy transfer increases the entropy of the universe- heat is the most disordered form of energy, therefore rxns will be spontaneous if system disorder is increased - an “offering of energy”
  • the system becomes more stable
167
Q

Entropy

A
  • A measure of disorder or randomness.
168
Q

Free Energy

A
  • portion of a system’s energy that is available to perform work
  • systems with high free energy are complexed/organized and have low entropy
  • systems with low free energy are disordered/random and have high entropy, have less energy available to do work
169
Q

Gibb’s Free Energy

A
  • The energy in a system that can be used to drive chemical reactions. If the change in free energy of a reaction (Delta G, the free energy of the products minus the free energy of the energy of the reactants) is negative, the reaction will occur spontaneously.
  • G = H - TΔS
  • G = free energy
  • H = total system energy
  • T = temp
  • S = entropy
  • ΔG = energy difference between beginning and end of a biological rxn
  • magnitude of change indicates amount of energy available for work
170
Q

Exergonic Rxn

A
  • net release of free energy
  • -ΔG
  • spontaneous (energetically favourable)
  • ex: cell resp or forming of bonds (E released)
  • the greater decrease in free energy = greater work amount can be done
171
Q

Endergonic Rxn

A
  • absorbs free energy from surroundings
  • +ΔG
  • non-spontaneous
  • ex: photosynthesis, bond breaking, DNA replication
172
Q

Energy Coupling

A
  • The use of an exergonic process to drive an endergonic one.
  • ex: sodium/potassium pump + sodium/glucose pump
173
Q

ATP

A
  • adenosine triphosphate
  • cellular energy currency
  • contains ribose sugar + nitrogenous base and a 3-phosphate chain
  • the bonds joining the phosphates onto adenosine are high energy bonds that store energy
  • hydrolysis of these bonds releases that energy (exergonic)
  • the terminal phosphate is removed to create ADP
  • major cell energy source
  • not a storage form of energy like glucose, rather just temporarily holds it to transfer it between rxns
  • contains potential energy due to position and composition
  • the ‘farthest’/3rd PO4 has a high energy bond (due to charge repulsion and steric hinderance), everyone ‘hates’ the 3rd PO4 and wants to get rid of it
174
Q

ATP to ADP

A
  • ATP + H2O —> ADP + Pi (inorganic phosphate)
  • hydrolysis of ATP to ADP can do 13kcal of work
  • ΔG = -13kcal/mol under ideal conditions
175
Q

ATP Hydrolysis Glutamic Acid Coupling

A
  • ATP Hydrolysis can be coupled to power endergonic rxns
  • glutamic acid is converted to glutamine (= non-spontaneous/endergonic/+ΔG)
  • 1) glutamic acid is phosphorylated by ATP, becoming less stable
  • 2) glutamine is formed via displaying the PO4 with ammonia (‘glu-P’ is more reactive and therefore the rxn is more spontaneous)
  • often the 3rd ATP PO4 is transferred to a reactant because the addition of it makes the reactant more reactive and spontaneous
176
Q

ATP Regeneration

A
  • can be regenerated during cell resp
  • ATP is formed from ADP + Pi using energy from catabolism (not spontaneous)
  • ATP Hydrolysis provides energy for anabolic rxns
177
Q

AMP

A
  • adenosine monophosphate
  • ATP ⇋ ADP + Pi ⇋ AMP + Pi
178
Q

Enzymes

A
  • biological catalysts that provide an alternate energy path for a rxn to proceed with a lower activation energy without being consumed itself
  • catalytic protein
  • names end in ‘-ase’
  • can function in both exer and endergonic rns
  • catalyzed rxns = more spontaneous
  • do not change overall ΔG
  • lower Ea barrier necessary for rxns to occur without changing ΔG
  • bind and act on substrates (reactants)
  • are very specific to certain substrates
  • have an active(binding) site
  • bind with non-covalent interactions which provides specificity
179
Q

Activation Energy

A
  • energy required to contort reactant molecules so bonds can break
180
Q

Active Site

A
  • a region on an enzyme that binds to a protein or other substance during a reaction.
  • typically a pocket or groove on enzyme surface
  • this catalytic site has geometrical and chemical compatibility with substrate
181
Q

Catalysis

A
  • substrate conversion into products
  • often proceeds by induced fit (ex: handshake)
  • enzyme is unchanged and can be used
182
Q

Induced Fit

A
  • Brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction.
  • a slight shape shift to accommodate substrate
183
Q

Lowering Activation Energy

A
  • bringing reactants closer together, forming non-transient covalent bonds with ‘R’ groups
  • active sites contain unique chemical environments that are favourable for rxns
  • physically stressing bonds to be broken
  • covalently stabilize rxn intermediate (Ea peak/transition state)
  • placing substrates in correct orientation
184
Q

Enzyme Inhibition

A
  • means by which cells regulate enzyme activity; may be competitive or noncompetitive inhibition
  • certain chemicals selectively inhibit specific enzyme actions
185
Q

Competitive Inhibition

A
  • substance that resembles the normal substrate competes with the substrate for the active site
  • binds active site but does not participate in rxn
  • ‘mimics’
  • can be outcompeted by higher substrate concentration
186
Q

Non-Competitive Inhibition

A
  • a molecule that binds to an enzyme at a location outside the active site and inhibits the enzyme’s function.
  • binds other enzyme site (not active) to block activity
187
Q

Autotrophs

A
  • self-feeders
  • use inorganic carbon (CO2) as their carbon source
  • sustain themselves via production of their own organic molecules
  • ‘producers’ of the biosphere
  • include photoautotrophs and chemoautotrophs
188
Q

Photoautotroph

A
  • organism that uses energy from sunlight to convert carbon dioxide and water to carbon compounds
  • uses light energy source to ‘fix’ carbon (photosynthesis)
  • plants and bacteria
189
Q

Chemoautotroph

A
  • organism that makes organic carbon molecules from carbon dioxide using energy from chemical reactions
  • uses chemical energy (redox rxns) to drive carbon fixation
  • prokaryotes only
190
Q

Heterotrophs

A
  • use organic carbon as their carbon source
  • live on compounds produced by other organisms
  • ‘consumers’
  • include Chemoheterotrophs and Photoheterotrophs
191
Q

Chemoheterotroph

A
  • organism that must take in organic molecules for both energy and carbon
  • uses organic carbon as both sources
  • ex: humans
192
Q

Photoheterotroph

A
  • organism that is photosynthetic but needs organic compounds as a carbon source
  • uses organic carbon as their carbon source but light as energy
  • prokaryotes only, rare
193
Q

‘-Troph’ Naming

A
  • 1st prefix is their energy source
  • 2nd prefix is their carbon source
194
Q

Chloroplast

A
  • organelle found in cells of plants and some other organisms that captures the energy from sunlight and converts it into chemical energy
  • uses light energy to drive organic compound synthesis
  • arose from Endosymbiont Theory
  • double-membrane bound with stacks of internal membraes (thylakoids)
  • provide ‘host’ cell with organic carbon
  • ‘host’ provides protection from O2
  • thylakoid space pH ≈ 5 (3x more protons)
  • stroma pH ≈ 8
195
Q

Light Reactions

A
  • The first of two major stages in photosynthesis (preceding the Calvin cycle). These reactions, which occur on the thylakoid membranes of the chloroplast or on membranes of certain prokaryotes, convert solar energy to the chemical energy of ATP and NADPH, releasing oxygen in the process.
  • use energy stored in light and convert/transform it into chemical energy in the form of ATP and NADPH which are then used by Calvin Cycle to drive carbon fixation
  • atmospheric —> organic
196
Q

Light

A
  • form of energy/electromagnetic waves
  • composed of a range of wavelengths (visible = 380-750nm)
  • energy is inversely related to wavelength (purple = highest energy)
  • generates ATP/NADPH to power carbon fixation
197
Q

Pigments

A
  • chemicals that absorb light
  • the colour that it appears as is the wavelength that it reflects
  • absorbed energy can be captured by photosynthetic pigments and used to excite an e- from H2O
  • include chlorophyll (green), xanthophyll (blue-green), and carotenoids (orange)
198
Q

Photosystem

A
  • cluster of chlorophyll and proteins found in thylakoids
  • composed of a protein complex called the reaction centre
  • surrounded by light harvesting complexes (each of which contain a special pair of chlorophyll ‘a’ pigment molecules)
  • a complex of integral membrane proteins and pigment molecules in a thylakoid membrane + an antenna
  • light strikes photosystem pigments, the absorbed energy is transferred to a rxn centre (chlorophyll a), then photolysis occurs
199
Q

Accessory Pigments

A
  • pigments that indirectly enhance photosynthesis by absorbing specific wavelengths of light and transferring this energy to chlorophyll molecules that are directly involved
  • ex: xanthophyll/carotenoids that allow a broader range of light to be absorbed
200
Q

Photolysis

A
  • In the thylakoid membranes of a chloroplast during light-dependant reactions, two molecules of water are split to form oxygen, hydrogen ions, and electrons.
  • energy is used to split water, energy excites an e- from H2O
201
Q

Photosystem II

A
  • One of two light-harvesting units of a chloroplast’s thylakoid membrane; it uses the P680 reaction-center chlorophyll.
  • site of photolysis
  • AKA P680 or PSII
  • optimally uses light at 680nm
  • is the first to function but the second one that was discovered/evolved
202
Q

Photosystem I

A
  • One of two light-harvesting units of a chloroplast’s thylakoid membrane; it uses the P700 reaction-center chlorophyll
  • no photolysis occurs here, the excited e- comes from PSII
  • AKA P700 or PSI
  • is the second to function but the first to evolve
  • associated with receiving e- from plastocyanin and passing e- to ferredoxin
203
Q

Photosynthesis Electron Transport Chain

A
  • A sequence of electron carrier molecules (membrane proteins) that shuttle electrons during the redox reactions that release energy used to make ATP.
  • set of increasing strength (low to high EN) of e- acceptors = cytosomes
  • allows energy to be released in small usable amounts, with every successive stronger acceptor - the e- becomes more stable and releases free energy
  • exists between PSII/PSI across the thylakoid membrane
  • e- is transferred to NADP+ for reducing power to promote Calvin Cycle rxns
204
Q

Light Reaction Process

A
  • 1) light photon strikes a pigment molecule in PSII/P680
  • 2) an e- is boosted to a higher energy level where it then falls back down to its ground state and releases energy to another e
  • 3) the cycle is repeated until the energy reaches a PSII/P680 chlorophyll ‘a’ pair, exciting an e- (light energy —> chemical energy)
  • 4) the chlorophyll ‘a’ e- is transferred to the primary e- acceptor
  • 5) a water molecule is split (via enzyme catalysis) into 2 e-/1 oxygen/2 H+.
  • 6) the e- are supplied to P680 1 by 1, the H+ are released into thylakoid space, and the O combines with another O (from another H2O) to form O2
  • 7) the excited e- passes along the ETC, from the primary e- acceptor of PSII to PSI (energy loss via heat is prevented by thylakoid membrane structure)
  • 8) the ‘fall’ of an e- along the ETC to lower energy levels is exergonic and provides energy for ATP synthesis
  • 9) while e- go through the chain, H+ are still being pumped into thylakoid space, creating a gradient which is used in chemiosmosis
  • 10) light energy excites PSI reaction centre e-, P700 acts as an e- acceptor, accepting e- from PSII/ETC
  • 11) the excited e- goes through a series of redox rxns from PSI down a 2nd ETC
  • 12) e- are transferred to NADP+, 2e- are used to reduce NADP+ into NADPH (with NADP+ reductase)
  • 13) NADPH is now at a higher energy state than water, and thus more readily available for Calvin Cycle
205
Q

Photosynthesis Chemiosmosis

A
  • use of a proton gradient to make ATP with ATP Synthase
  • occurs across thylakoid membrane where ATP is made in stroma
  • uses ATP Synthase (large protein complex) to couple an endergonic rxn (ADP + Pi —> ATP) with an exergonic one (H+ gradient)
  • 1) during the ETC, H+ is pumped from the stroma across the thylakoid membrane into the thylakoid space via ETC proteins
  • 2) the H+ gradient that was established by the ETC then diffuses through the ATP Synthase ‘F0 stalk’ and exits through the catalytic ‘F1 head-piece’ back into the stroma
  • 3) the flow of H+ through the channel releases energy, allowing for ATP to be formed from an ADP+Pi, where it can then be used for the Calvin Cycle
  • ATP formed by the ETC is exclusively used in the Calvin Cycle
206
Q

NADPH

A
  • e- shuttle/carrier for photosynthesis
  • prevents loss of e- energy by storing them until they’re ready to do work
  • e- are sources of energy (have reducing potential - reduced molecules have more energy than oxidized ones)
  • carry e- between redox rxns
  • “reducing power”
207
Q

Dark Reactions/Calvin Cycle

A
  • uses energy from light rxns (ATP/NADPH) to convert CO2 (oxidized) into glucose sugar (reduced)
  • uses carbon fixation to convert atmospheric nutrients into organic form within the stroma
  • is highly endergonic
  • CO2/ATP/NADPH enter the cycle, ADP/G3P/NADP+ leave
  • direct product = glyceraldehyde-3-phosphate (G3P) = 3 carbon sugar
  • cycle takes place 3x for 1 G3P
  • 2 G3P = 1 glucose
  • other products include ADP/Pi/NADP+/CH2O
  • 1) carbon fixation 2) reduction 3) regeneration
  • 3CO2 + 9ATP + 6NADPH —> 1G3P + 9ADP + 9Pi + 6NADP+ + 6H+
208
Q

Carbon Fixation

A
  • first step of Calvin Cycle
  • 1) 3 CO2 molecules are added per turn of the cycle (needing 3 turns total per product)
  • 2) 3 CO2 attach to the enzyme Rubisco (most important/numerous enzyme on the planet, 5 carbon) via its substrate RuBP
  • 3) 3 temporary/unstable 6-carbon intermediates are created
  • 4) the intermediate immediately splits in half into six 3-phosphoglycerate molecules (3 carbon)
209
Q

Reduction

A
  • 2nd step of Calvin Cycle
  • 1) each of the six 3-phosphoglycerates from Carbon Fixation receives a PO4 from ATP (is phosphorylated, 6 total, leaving behind 6 ADP) and becomes six 1, 3-biphosphoglycerates
  • 2) NADPH donate an e- pair to each (reduces 6 total), making it lose a PO4 and become G3P (6 total)
210
Q

Regeneration

A
  • 3rd step of Calvin Cycle
  • 1) 1 G3P leaves the cycle, to later become 1 glucose molecule when combined with another (2 G3P needed)
  • 2) the carbon skeletons of the 5 remaining G3Ps are rearranged into 3 molecules of RuBP (ribulose biphosphate = Rubisco substrate, 5 carbons)
  • 3) RuBP is regenerated using 3 ATP
  • 4) set of complex rxns is carried out, and RuBP is now prepared to receive CO2 again
211
Q

Rubisco

A
  • most important/numerous enzyme on planet
  • 5 carbons
  • attaches to a CO2 molecule to create an unstable 6-carbon intermediate that immediately splits into two 3-phosphoglycerates (3 carbons)
212
Q

Ribulose Biphosphate

A
  • substrate for Rubisco
  • is regenerated in Regeneration step of Calvin Cycle
  • regeneration of it takes 3 ATP
  • ‘RuBP’
  • is what Rubisco attaches on to (therefore is what CO2 attaches onto as well)
  • 5 carbons
  • RuBP (5C) + CO2 (1C) —> unstable 6C molecule (breaks down into two 3C molecules during carbon fixation)
213
Q

Net Requirements per G3P

A
  • 3 CO2
  • 6 NADPH
  • 9 ATP (more needed than NADPH)
214
Q

Cyclic Electron Flow

A
  • A route of electron flow during the light reactions of photosynthesis that involves only photosystem I and that produces ATP but not NADPH or oxygen
  • makes ATP without making NADPH in order to meet demand of Calvin Cycle
  • excited e- gets recycled back to the ETC instead of reducing NADP+, thereby pumping more H+ for chemiosmosis
  • the stimulus for cyclic flow = higher ADP concentration
  • the ATP generated by the ETC is exclusively used in the Calvin Cycle
215
Q

Cellular Metabolism

A
  • the sum of all chemical reactions in the cell
216
Q

Cellular Respiration

A
  • catabolic process to release energy from glucose
  • includes both aerobic and anaerobic processes
  • converts energy stored in glucose into ATP
  • requires complete oxidation of glucose
  • 3 phases = glycolysis (cytoplasm), Citric Acid/Kreb’s Cycle (mitochondrial matrix, and Oxidative Phosphorylation (across inner mitochondrial membrane)
  • ATP is generated at all 3 steps (but majority is from ox-phos)
217
Q

Oxygen Requirements

A
  • O2 is a very toxic molecule even though it’s essential for life in many organisms
  • can react with/damage DNA
  • organisms can be either anaerobic or aerobic
218
Q

Obligate Anaerobe

A
  • O2 = toxic
219
Q

Aerotolerant/Facultative Anaerobe

A
  • do not utilize oxygen but can survive and grow in its presence
  • O2 = not used
220
Q

Obligate Aerobe

A
  • organism that requires a constant supply of oxygen in order to live
221
Q

Facultative Aerobe

A
  • organism that can live with or without oxygen
  • O2 = used when available
222
Q

Cell Resp Redox Reactions

A
  • A chemical reaction involving the transfer of one or more electrons from one reactant to another; also called oxidation-reduction reaction
  • cell resp. relies heavily on energy released from redox rxns
  • oxidation of glucose released energy
  • “LEO GER”
  • organic carbon acts as an e- donor (C-H = reduced carbon)
  • O2 is the strongest e- acceptor/oxidizing agent
  • when organic carbon (C-H) is oxidized, energy is released, then O2 is used as the best/terminal e- acceptor (TEA)
223
Q

Glycolysis

A
  • the breakdown of glucose by enzymes, releasing energy and pyruvic acid
  • converts glucose into 2 pyruvate molecules
  • in cytoplasm
  • occurs whether or not O2 is present
  • occurs in all 3 domains which suggests ancient origins
  • begins the oxidation of glucose
  • extracts e- and reduces NAD+ into NADH
  • consists of energy investment phase and energy payoff phase
224
Q

NADH

A
  • the reduced form of NAD+; an electron-carrying molecule that functions in cellular respiration
  • NAD+ is reduced into NADH
  • is higher in energy than NAD+, carries 2 high energy e- from glucose to the ETC
225
Q

Net Products per Glucose Molecule

A
  • 2 pyruvate (3 carbon), which are then fully oxidized in mitochondria if O2 is present
  • 2 ATP (via substrate-level phosphorylation)
  • 2 NADH
226
Q

Substrate-Level Phosphorylation (SLP)

A
  • a phosphate group is directly transferred from an organic molecule/substrate/phosphorylated sugar to ADP
  • occurs in both glycolysis and the Kreb’s cycle
  • doesn’t involve O2
  • used by cell to power endergonic rxns
  • produces 2 ATP used in glycolysis
227
Q

Energy Investment Phase

A
  • first phase of glycolysis, net 2 ATP used
  • 1) glucose is relatively stable
  • 2) hexokinase transfers a PO4 from ATP to glucose, making it more chemically reactive
  • 3) phosphofructokinase (PFK) transfers another ATP to phosphorylate the sugar
  • 4) 2 Pi (PO4-) attach to the sugar
  • 5) the 6-carbon sugar molecule is split into two 3-carbon compounds (G3P)
228
Q

‘-kinase’ ending

A

= an enzyme that phosphorylates

229
Q

Phosphofructokinase (PFK)

A
  • a key rate-limiting enzyme of the anaerobic glycolytic energy system
  • transfers a 2nd ATP to glucose during the energy investment phase of glycolysis
230
Q

Energy Payoff Phase

A
  • 2nd phase of glycolysis
  • consists of 5 rxns that end in producing 4 ATP per glucose
  • every rxn occurs twice per glucose
  • 1) the two 3-carbon molecules (G3P) are oxidized by NAD+, forming 2 NADH
  • 2) 4 ATP are produced during energy payoff, although 2 were already used in energy investment, so net = 2 ATP
  • 3) end product of glycolysis = 2 pyruvate/2 ATP/2 NADH/2 H+
231
Q

Net Glycolysis Products

A
  • 2 pyruvate (still contains lots of reduced carbon, 3C each)
  • 2 ATP
  • 2 NADH
  • 2 H+
232
Q

Mitochondria

A
  • site of cell resp
  • arise from the Endosymbiont Hypothesis
  • completes oxidation of glucose
  • the energy released is used to make ATP
  • has outer membrane + inner membrane (site of the ETC), intermembrane space (pH ~ 5), and a matrix (site of Kreb’s cycle)
233
Q

Transition/Bridge Reaction

A
  • oxidation of pyruvic acid (3C) to Acetyl CoA
  • pyruvate (2 per glucose) enters the mitochondria in the presence of O2
  • occurs across both the mitochondrial inner and outer membrane, into the matrix
  • catalyzed by pyruvate dehydrogenase complex (PDH)
  • 1) 2 pyruvate begin in the cytoplasm, then cross the outer/inner membrane into the matrix
  • 2) pyruvate is acted upon by PDH, releasing a CO2
  • 3) pyruvate is oxidized, releasing an e- that reduces NAD+ into NADH
  • 4) coenzyme A enters, catalyzing the conversion of pyruvate into an Acetyl CoA (2C) and facilitates the entrance into the Kreb’s Cycle also in the matrix
234
Q

Pyruvate Dehydrogenase Complex (PDH)

A
  • converts (oxidizes) pyruvate to acetyl-CoA
  • catalyzes the transition/bridge rxn
  • O2-dependent pyruvate transport
  • pyruvate will not enter the mitochondria without O2 present
235
Q

Coenzyme A

A
  • catalyzes the production of Acetyl CoA from pyruvate
  • facilitates entrance into the Kreb’s Cycle from within mitochondrial matrix
236
Q

Kreb’s/Citric Acid Cycle Description

A
  • completes the oxidation of glucose (CH becomes CO2)
  • CO2 is released (exhaled)
  • occurs in mitochondrial matrix
  • produces 2 ATP per glucose via SLP
  • 2 organic C (C-H) enter, 2 inorganic (CO2) leave
237
Q

Kreb’s/Citric Acid Cycle Process

A
  • 1) an Acetyl CoA (2 per glucose) adds its acetyl group (2C) to oxaloacetate to produce citrate (6C)
  • 2) citrate is converted to isocitrate via the removal of H2O and addition of another
  • 3) isocitrate gets oxidized, its e- reduces an NAD+ into an NADH resulting in the loss of a CO2 = remaining 5C compound
  • 4) another CO2 is lost, the resulting compound is oxidized, and other NAD+ is reduced to NADH = 4 remaining C
  • 5) ADP + Pi are combined, making 1 ATP (via SLP) that then leaves the cycle
  • 6) 2 H+ are added to a FAD, forming FADH2 (a 2nd e- carrier like NADH, but carries lower energy e-)
  • 7) H2O is added to the carbon compound, which changes the bond configuration
  • 8) the compound is then again oxidized, reducing another NAD+ into NADH, forming oxaloacetate (4C)
  • 9) oxaloacete is now reformed, ready to receive another acetyl group from Acetyl CoA (2C)
  • the cycle is turned twice per glucose (since each glucose results in 2 pyruvate = 2 Acetyl CoA)
238
Q

Net Reaction per Glucose of Cell Resp

A
  • glycolysis = 2 ATP + 2 NADH
  • transition/bridge rxn = 2 NADH + 2 CO2
  • kreb’s = 2 ATP + 6 NADH + 2 FADH2 + 4 CO2
  • total = 4 ATP + 10 NADH + 2 FADH2 + 6 CO2
  • there is a possible 32 ATP per glucose, all the remaining energy is in the form e-, glucose is now fully oxidized (in form of CO2)
239
Q

Cell Resp Electron Transport Chain

A
  • set of increasing strength e- acceptors (low to high EN)
  • couples the energy released from falling e- with the pumping of p+
  • functions similarly to the ETC between photosystems
  • the strongest oxidizing agent is O2, therefore it is the terminal e- acceptor (TEA) for aerobic respiration
  • e- source = glucose
  • sits across the mitochondrial inner membrane
  • e- get transferred between complexes via redox rxns (which power pumping of H+ active transport, the energy released is available to do work)
  • at Complex I (NADH Dehydrogenase Complex), NADH gets oxidized into an NAD+ and H+, releasing an e- that travels through Complex ‘C’, Complex III, then Complex IV, to arrive at the TEA (O2)
  • at Complex II, FADH2 is oxidized into FADH+ and H+, releasing an e- into Complex II (donates e- at a lower energy level than NADH, pumps fewer protons = contributes less to the gradient because its e- don’t pass through the NADH Dehydrogenase Complex), the e- then flows through Complexes C, III, and IV to arrive at O2
  • once e- have arrived at O2, the TEA receives them (gets reduced) and combines with H+ to form H2O
  • the O2 TEA allows e- to leave the ETC
  • the H+ released from NADH/FADH2 flow ‘up’ the complexes, through the inner membrane and into the intermembrane space
240
Q

Cell Resp Chemiosmosis

A
  • synthesis of ATP using a proton gradient
  • uses similar mechanism of ATP formation to photosynthesis, the only difference is the direction of p+ flow
  • in photosynthesis, H+ flow through ATP Synthase and out of the thylakoid space = innermost compartment
  • in cell resp, the H+ flow through ATP Synthase into the matrix (innermost)
  • utilises oxidative phosphorylation (vs photosynthesis’ photophosphorylation)
  • 1) H+ from the intermembrane space (flowed up during the ETC) flows ‘down’ into the ‘Fo stalk’ of ATP Synthase (inner membrane) and into the ‘F1 headpiece’ (matrix)
  • 2) the flow of H+ down the channel provides energy for oxidative phosphorylation, ADP + Pi forms ATP
  • ~2.5 ATP formed per NADH, ~1.5 ATP/FADH2
  • 28 ATP (from oxphos)+ 4 ATP (from SLP in Kreb’s/Glycolysis) = total 32 ATP per glucose
241
Q

Photophosphorylation

A
  • The process of generating ATP from ADP and phosphate by means of a proton-motive force generated by the thylakoid membrane of the chloroplast during the light reactions of photosynthesis
  • energy for H+ gradient comes from light
242
Q

Oxidative Phosphorylation

A
  • The production of ATP using energy derived from the redox reactions of an electron transport chain; the third major stage of cellular respiration.
  • energy for H+ comes from oxidation of organic nutrients
243
Q

Differences between Cell Resp/Photosynthesis

A
  • chloroplast innermost compartment = thylakoid space
  • mitochondria innermost = matrix
  • both have different number of membranes
  • photosynthesis ATP is made in stroma via photophosphorylation
  • cell resp ATP is made in matrix via oxidative phosphorylation
244
Q

Similarity between Cell Resp/Photosynthesis

A
  • both types of cells (mitochondria/chloroplast) have prokaryotic-like ribosomes that contain circular DNA, have no DNA centromere, and replicate via binary fission
245
Q

Fermentation

A
  • A catabolic process that makes a limited amount of ATP from glucose without an electron transport chain and that produces a characteristic end product, such as ethyl alcohol or lactic acid
  • recycles NAD+ in the cytosol for continued glycolysis in the absence of a TEA
  • harvests chemical energy without using O2 or an ETC
  • an extension of glycolysis that allows continuous ATP generation via SLP
  • requires a sufficient NAD+ supply to accept e- during glycolysis oxidation (without it, NADH would pool and shut the cell down)
  • consists of glycolysis + rxns that regenerate NAD+ via transferring e- from NADH to pyruvate
  • when O2 is depleted from the environment, organisms can either die or utilize a secondary metabolic pathway (fermentation or anaerobic respiration (prokaryotes only))
246
Q

Eukaryotic Fermentation

A
  • eukaryotes have 2 possible fermentation pathways
  • lactic acid (human muscle/liver cells)
  • ethanol (yeasts)
247
Q

Ethanolic Fermentation

A
  • when O2 is unavailable, some cells have the capacity for it
  • 1) glucose goes through glycolysis, with 1 glucose producing 2 pyruvate (3C each) + 2 NADH + 2 ATP (via SLP)
  • 2) 2 CO2 are released from the pyruvates, converting it to 2 acetaldehydes (2C)
  • 3) acetaldehydes accept e- from 2 NADH (are reduced), forming 2 ethanol = waste
  • 3) NAD+ supply is now regenerated for glycolysis
  • pyruvate acts as an e- acceptor to free up NAD+ and is also the “decision point”. It only decides to enter the mitochondria and complete respiration if O2 is present (Pyruvate Dehydrogenase Complex is O2-dependent pyruvate transport)
248
Q

Metabolism of Other Macromolecules

A
  • primary source for catabolic rxns = sugars
  • secondary = fats (take up more energy to break down but store more energy. Fatty acids enter as 2C molecules (Acetyl CoA), glycerol enters glycolysis)
  • tertiary = proteins
249
Q

Regulation of Cellular Respiration

A
  • negative feedback inhibition (product of rxn inhibiting its own production) is used
  • ATP inhibits Phosphofructokinase as an allosteric regulator, changing its shape
  • ATP = high energy form of adenosine, AMP = low. If [AMP] is high, then [ATP] is low. AMP activates PFK
  • citrate inhibits PFK to coordinate flux through glycolysis and Kreb’s
250
Q

Allosteric Regulator

A
  • A substance that binds to site on a protein and causes a conformational change in the protein, but neither activates nor prevents activation of the protein
  • ex: ATP causing shape change in PFK
251
Q

Cell Division Key Roles

A
  • reprodution (unicellular organisms dividing to produce more organisms)
  • growth & development (multicellular eukaryotes are composed of many cells which arose from a single fertilized cell)
252
Q

Prokaryotic Cell Division/Binary Fission

A
  • prok. cells are unicellular organisms with a single circular chromosome and no nucleus, therefore cell division is much simpler than euk. mitosis
  • divide via binary fission (“division in half”), not mitosis
253
Q

E. coli Binary Fission

A
  • 1) singular circular chromosome is attached to the membrane where it then replicates = origin of replication. Replication proceeds bidirectionally
  • 2) each genome (origin copy) moves rapidly to opposite cell sides and attaches
  • 3) cell elongates/grows its membrane at the middle to separate its chromosomes
  • 4) plasma membrane pinches inward and a new cell wall is deposited
  • 5) division occurs (fission separates cells)
  • 6) result = 2 genetically identical daughter cells
254
Q

Prokaryotic Origin of Replication

A
  • a specific ntd sequence/short DNA stretch
  • is A=T rich which is weaker than C(triple bond)G base pairs due to base stacking interactions
255
Q

Prokaryotic Growth Curve

A
  • growth is exponential
  • continued growth depends upon sufficient resources/space/nutrients from the environment
  • phases of population growth in lab bacterial culture =
  • 1) Lag Phase (cells preparing to divide)
  • 2) Log/Exponential Phase (cells dividing)
  • 3) Stationary Phase (cell division ≈ cell death, nutrients/space become limiting)
  • 4) Death Phase (cells die, nutrients are depleted and toxic waste builds up)
256
Q

Eukaryotic Chromosomes

A
  • multiple and linear
  • made of DNA and proteins
  • replicated during S-Phase of eukaryote cell cycle
  • 23 pairs per human body cell
257
Q

Sister Chromatids

A
  • Identical copies of a chromosome; full sets of these are created during the S subphase of interphase.
  • products of DNA replication
  • joined copies of original chromosome
  • are still connected so still counted as 1 chromosome
258
Q

Chromatin

A
  • Substance found in eukaryotic chromosomes that consists of DNA tightly coiled around histones
  • entire DNA/protein complex that is the building material of chromosomes
259
Q

Chromosome

A
  • a threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes.
  • 1 DNA molecule
  • packaged structure
260
Q

Centromere

A
  • site where the chromatids of a chromosome are attached
  • allows formation of kinetochore
261
Q

Kinetochore

A
  • a complex of proteins associated with the centromere of a chromosome during cell division, to which the microtubules of the spindle attach
  • assembles on specific DNA centromere sections
  • 2 per chromosome facing opposite directions
262
Q

Eukaryotic Cell Cycle

A
  • series of events that cells go through as they grow and divide
  • consists of 4 distinct phases
  • ~24 hours in human cell
263
Q

Gap 1 (G1) Phase)

A
  • the first part of interphase where the cell grows
  • normal cell activity
  • cell is “deciding” to divide
  • only 1 genome copy (no replication yet)
  • is the most variable in length in different cell types
264
Q

Synthesis (S) Phase

A
  • The phase of the cell cycle during which DNA is synthesized and chromosomes are replicated
  • 1 genome copy becomes 2
  • 2nd part of interphase
265
Q

Gap 2 (G2) Phase

A
  • the third part of interphase where the cell finishes growing and prepares for cell division
  • normal cell activity
  • cell is now committed to eventual division because there’s 2x amount of DNA which is not sustainable
266
Q

Mitotic (M) Phase)

A
  • The part of the cell cycle when the nucleus is divided (via mitosis), its chromosomes are distributed to the daughter nuclei, and the cytoplasm divided (via cytokinesis), producing two daughter cells
  • not part of interphase
  • separation of sister chromatids
267
Q

Mitosis

A
  • unique cell cycle phase where DNA is equally separated into daughter cells
  • nuclear division process within eukaryotic cells conventionally divided into 6 phases
  • conserves chromosome number by allocating replicated chromosomes equally to each daughter nuclei
268
Q

Prophase

A
  • 1st phase of mitosis
  • chromosomal condensation occurs (packaging into mitotic chr’s to facilitate movement later on, become visible)
  • mitotic spindle begins to form (composed of centrosomes and the microtubules that extent from them)
  • centrosomes/MTOCs move away from eachother (partly propelled by MT)
  • a cell with 2 chromosomes = 4 centromeres
269
Q

Chromosomal Condensation

A
  • packaging into mitotic chromosomes during prophase
  • occurs as to facilitate chromosomal movements later on in mitosis (necessary to be moveable structures, if they weren’t then it would be like ‘separating a bowl of spaghetti’
  • chromosomes become more tightly coiled and are now visible with a light microscope
  • accomplished by histones + other DNA scaffolding proteins
  • nucleoli (site of RNA subunit assembly) disappear
  • each duplicated chromosome appears as 2 identical sister chromatids joined at centromeres
270
Q

Microtubule Organizing Centre (MTOC)

A
  • AKA centrosome (in animal cells)
  • replicated in S-phase and moves away from nucleus during prophase
  • the (-) ends (not charge, just labelling) of microtubules are anchored in the MTOC
  • MTs move the chromosomes during mitosis
  • located in the cytosole and can’t access the DNA until the nuclear envelope breaks down
271
Q

Prometaphase

A
  • 2nd phase of mitosis
  • nuclear envelope breakdown occurs (disassembles/forms smaller chunks) so that the MTOC’s microtubules can invade the nuclear area and bind to kinetochore/centromeres (can’t access DNA until NE breaks down)
  • chromosomes have become more condensed
  • microtubules polymerize in all directions = a ‘search and capture’ of kinetochores
  • if they attach, then the MT is stabilized (stable attachments include kinetochore, other MTs, and membrane)
  • kinetochore MTs will ‘jerk’ the chromosome back and forth whileas non-kinetochore MTs will interact with those from the opposite spindle/MTOC
272
Q

Metaphase

A
  • 3rd phase of mitosis
  • lining up of chromosomes/sister chromatids at the metaphase plate (‘imaginary line’)
  • movements require MT motor action and are accomplished by kinetochore MT (via MT polymerization/depolymerization which is the dominant force, as well as kinesin and dynein - ‘pull’ the MT)
  • centrosomes are at opposite cell poles
  • metaphase plate is equidistant between poles, in line with each chromosome’s centromere
  • Astral MTs are connected to the cell membrane
273
Q

Anaphase

A
  • 4th mitosis phase
  • separation of chromatids, becoming chromosomes
  • involves pulling apart of chromatids to opposite cell poles via kinetochore MTs (depolymerization + dynein)
  • chromosomes are no longer attached to the same centromere
  • the shortest stage
  • the cell currently now have 4 chromosomes
  • cell is elongated using kinesin on Polar MTs (‘walks’ to + end)
  • MTOC is anchored by Astral MTs
274
Q

Overlapping/Polar Microtubules

A
  • elongate the cell using kinesin during Anaphase
  • kinesin ‘walks’ to the + end of the MT = away from the MTOC its originating from
275
Q

Astral Microtubules

A
  • anchor the MTOC near the membrane so that the chromosomes move towards the poles (via kinetochore MTs/ dynein)
  • “seatbelt”
276
Q

Kinetochore Microtubules

A
  • MTs originating from either cell MTOC that attach to the kinetochore/centromere of a chromosome
  • can depolymerize or polymerize
  • dominant force in lining up chromosomes at Metaphase Plate (assisted by kinesin/dynein)
  • depolymerizes to pull chromatids to opposite cell poles (assisted by dynein)
277
Q

Telophase

A
  • 5th mitosis phase
  • nuclear envelope reformation + chromosomal decondensation
  • for mitosis completion, daughter cell NE reformation is required
  • the envelopes arise from fragments of the parent NE and/or other endomembrane system components
  • 2 genetically identical nuclei now officially exist
  • microtubules are no longer attached
278
Q

Cytokinesis

A
  • 6th phase of mitosis
  • splitting/separation of the cytoplasm
  • begins during late anaphase and continues through telophase until complete separation of the daughter cells into distinct compartments
  • microfilaments form a cyotkinetic furrow/contractile ring
  • myosin ‘walks’ along the MFs to constrict the furrow
279
Q

Cell Cycle Control

A
  • A cyclically operating set of proteins that triggers and coordinates events in the eukaryotic cell cycle
  • several checkpoints exist to ensure that the cell is prepared to move onto the next phase
  • coordinates/regulates cell division rates and timing
  • includes Restriction/G1 Point, G2 Point, and Metaphase/Anaphase Point
280
Q

Restriction Point

A
  • A point of no return in the cell cycle; once this point passes, a cell is committed to a full round of the cell cycle.
  • most important point
  • AKA G1 Point
  • “are there signals to divide?”, “is there enough space to divide?”, “are there enough nutrients?”
  • if ‘yes’ to all, then S-phase proceeds
281
Q

G2 Point

A
  • “is DNA replication complete?”
  • “are there still primers?”
  • 2nd point following the Restriction Point, preceding Metaphase/Anaphase Point
282
Q

Metaphase/Anaphase Point

A
  • “are all kinetochores attached by MTs?”
  • 3rd point following the Restriction/G1 Point then the G2 Point
283
Q

Cancer

A
  • uncontrolled cell division
  • signals controlling division are lost or ignored due to accumulation of both spontaneous and induced mutations
  • mutations allow progress through a cell cycle checkpoint
  • 2 main classes of cancer-causing genes: Tumor-Suppressors and Proto-oncogenes
  • many random mutations are required to get full-blown cancers
284
Q

Mutation

A
  • permanent change to DNA sequence
285
Q

Tumor-Suppressor Genes (TSG)

A
  • their normal function is to be the product of genes/proteins
  • prevent cell division
  • acts as a ‘brake pedal’ to cell cycle
  • when mutated, the protein fxn changes such that it causes loss of fxn
  • ex: BRCA1 - normally slows the cell cycle but if dysfunctional gene copies are inherited, one can be predisposed to breast cancer
286
Q

Proto-oncogenes

A
  • normal fxn is to promote the cell cycle
  • ‘gas pedal’
  • mutation causes the mutant protein to say ‘yes’ to checkpoints without control
  • ex: EGFR - a growth factor receptor (normally receives signals but the mutant lacks a signal domain)
287
Q

DNA = Genetic Material

A
  • for only about 60 years, DNA has been accepted as the transforming principle
  • proteins have more monomers and therefore could be more diverse
  • DNA was originally believed to be incapable of being genetic material because it only has 4 monomers
  • little was known about nucleotides
  • “4 ntds couldn’t specify 20 different amino acids”
  • proteins were then assumed to carry hereditary info
288
Q

Properties of Hereditary Material

A
  • carry info
  • replicate faithfully/transmit info
  • have variation
289
Q

Griffith’s Transforming Experiment Concept (1928)

A
  • “is there a transforming principle?”
  • Frederick Griffith showed that there’s a non-living cell component that was able to transform other cells
  • used virulence (disease-causing) and non-virulence (not disease-causing) to ask if something in the cell was able to confer a new property to another cell, able to transform it
290
Q

Transforming Principle

A
  • abiotic factor that carries hereditary info
291
Q

Griffith’s Transforming Experiment Procedure

A
  • took 2 bacteria strains (same species, different properties) and injected them into mice
  • R(ough) strain = non-virulent
  • S(mooth) strain = virulent
  • live R-strain was ‘transformed’ by taking up a transforming principle, therefore an abiotic principle exists
  • virulent S-strain = mouse dies
  • non-virulent R-strain = mouse lives
  • heat-killed S-strain = mouse lives
  • heat-killed S-strain + living R-strain = mouse dies
  • inherited trait of pathogenicity was passed onto descendants of transformed bacteria
  • identity of substance was unknown but Griffith called the phenomenon “transformation” (now defined as a change in geno/phenotype due to assimilation of external DNA by a cell)
292
Q

Avery/MacLeod/McCarty Experiment (1944) Concept

A
  • took Griffith’s experiment further to ask “what is the transforming principle?”
  • added different enzymes to specifically degrade different cellular components/macromolecules (DNA vs proteins)
  • determined DNA as transforming substance instead of proteins
293
Q

Avery/MacLeod/McCarty Experiment (1944) Procedure

A
  • added different enzymes to specifically degrade different cellular components/macromolecules (DNA vs proteins)
  • determined DNA as transforming substance instead of proteins
  • heat-killed S-strain + living R-strain + lipases/sucrases = mouse died
  • heat-killed S-strain + living R-strain + RNAse = mouse died
  • heat-killed S-strain + living R-strain = mouse died
  • heat-killed S-strain + living R-strain + protease = mouse died
  • heat-killed S-strain + living R-strain + DNAse = mouse lived
294
Q

Hershey-Chase “Phage in a Blender” Experiment (1952) Concept

A
  • “is DNA the universal transforming principle for a non-cellular life form?”
  • several things were known about viruses = weren’t like normal cells (now know that they’re little more than DNA or RNA enclosed by a protective coat (often protein)), can infect bacteria, can transform it
  • phage infections transform bacteria into little ‘phage factories’, hijacking the bacterial cell to create more and more phages
  • used radioactivity to trace proteins and DNA via differentially labeling them with different radioactive isotopes
  • DNA has phosphorus but no sulfur
  • proteins have sulfur but no phosphorus
  • DNA used 32P, proteins used 35S = both isotopes emitted energy
295
Q

(Bacterio)phage

A
  • A virus that infects bacteria
  • exclusively 2 macromolecules = hexagonal ‘head’ + tail made of protein, DNA inside head
  • phage infections transform bacteria into little ‘phage factories’, hijacking the bacterial cell to create more and more phages
296
Q

Hershey-Chase “Phage in a Blender” Experiment (1952) Procedure

A
  • 1) radioactively-labeled phages were mixed with bacteria where they then infected them
  • 2) mixture was agitated in blender to free phage parts from the outer bacterial cell
  • 3) mixture was centrifuged so bacteria formed a pellet at bottom of tube
  • 4) supernatant consisted of free phages + phage parts = lighter
  • 5) radioactivity of pellet and liquid were compared
  • 35S - phages with radioactive protein injected their non-radioactive DNA into the bacteria. Tube was centrifuged, the free radioactive phage parts ended up in the supernatant while the pellet had non-radioactive phage DNA
  • 32P - phages with radioactive DNA injected it into bacteria. Tube was centrifuged, the non-radioactive phage parts were in supernatant, the radioactive phage DNA in pellet
  • conclusion = DNA is universal transforming principle
297
Q

“DNA is a Double Helix”

A
  • “what is the structure of DNA?”
  • proposed by James Watson and Francis Crick in 1953 for which they won the Nobel Prize
  • used others’ work
  • discovered that DNA is a double helix with a sugar-phosphate backbone + complementary base pairing which satisfied Chargaff’s Rule as well as Rosalind Franklin’s x-ray crystallography data/image of DNA (which confirmed helical shape)
298
Q

Chargaff’s Rule

A
  • DNA base composition varies between species
  • %A = %T
  • %C = %G
299
Q

Double Helix Characteristics

A
  • anti parallel (5’—>3’, 3’<—5’)
  • complementary pairing (Chargaff’s rule)
  • double-stranded
  • bases point inwards
  • purines always pair with a pyrimidine as to maintain helix diameter
300
Q

DNA Chemical Composition

A
  • 1 phosphate group (off 5’ C of sugar)
  • 1 deoxyribose sugar
  • 1 of 4 nitrogenous bases (Adenine, Guanine, Cytosine, Thymine) off of 2’ C
301
Q

DNA Stabilizing Forces

A
  • 1) backbone phosphodiester bonds (strong covalents between 3’ and 5’ carbons of ntds)
  • 2) base pairing hydrogen bonds
  • 3) hydrophobic base stacking (as to minimize base/water contact, combined with van der Waals forces = stronger than H-bonds)
302
Q

Watson-Crick DNA Replication

A
  • “it has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material” - Watson/Crick (1953)
  • if DNA is transforming principle + hereditary material, then it must be stably replicated and passed onto daughter cells
  • happens in S-phase
  • strands are complementary
  • they proposed semi-conservative replication and asked if this model is true
303
Q

Meselson-Stahl Experiment (1958) Concept

A
  • “what is the mechanism of replication?”
  • attempted to determine which hypothetical process of DNA replication is correct
  • after the double helix model was discovered by Watson/Crick in 1954, 3 different models were proposed = semi-conservative, conservative, dispersive
  • attempted to differentiate between 3 models using 2 rounds of replication in different nitrogen isotopes (14N and 15N)
  • used radioactivity to change molecular mass of parent vs daughter strand
304
Q

Semi-Conservative Replication

A
  • 2 parental strands separate and each functions as a template for synthesis of a new complementary strand
  • parent replicates then pairs with daughter = identical
305
Q

Conservative Replication

A
  • 2 parental strands reassociate after acting as templates for daughters
  • parent double helix is restored while daughters pair together
306
Q

Dispersive Replication

A
  • each daughter strand contains a mixture of old/newly synthesized DNA
  • ‘cut and paste’ model where resulting strands are a mix of parent/daughter down the DNA backbone
307
Q

Meselson-Stahl Experiment (1958) Procedure

A
  • conservative: DNA in 15N “heavy parent” was replicated in “light” 14N. Expected results were that a heavy 15N band would appear lower in the tube after being centrifuged with a lighter 14N band above it. Observed results were a “14.5” band (= hybrid isotope) in between the 2 expected bands. Conservative disproved.
  • semi-conservative: DNA in 15N “heavy parent” was replicated in “light” 14N. Both expected and observed results were a 14.5 band. A daughter DNA sample (1 parent strand, 1 new) was then replicated again in 14N, resulting in an expected/observed 14.5N and 14N band. This second round proved semi-conservative.
  • dispersive: DNA in 15N “heavy parent” was replicated in “light” 14N. Both expected/observed = 14.5N band. A second round of replication expected a “14.25”N hybrid, but observed = 14N + 14.5N. Dispersive disproved.
308
Q

Replication Mechanics

A
  • how DNA moves
  • DNA is polymerized 5’–>3’ (all nucleid acids polymerized by adding ntds to 3’ OH)
309
Q

DNA Polymerase

A
  • Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule
  • enzyme of synthesis
  • catalyzes phosphodiester bond formation (dehydration rxn)
  • joins together dNTPs
  • addition of ntds to a 3’ OH requires energy (provided by hydrolysis of a 2 pay-off ntd = pyrophosphate, hydrolyzed into 2 Pi molecules)
  • the nucleoside triphosphate originally has 3 phosphates, but 2 of them are removed to form pyrophosphate (leaving 1 PO4 on the nucleotide).
310
Q

Deoxynucleoside triphosphates (dNTPs)

A
  • reactants of DNA Polymerase
  • joined to form a growing DNA chain
  • a deoxyribose sugar with 3 attached phosphates + a nitrogenous base
311
Q

Nucleotide vs Nucleoside

A

A nucleoside consists of a nitrogenous base covalently attached to a sugar (ribose or deoxyribose) but without the phosphate group. A nucleotide consists of a nitrogenous base, a sugar (ribose or deoxyribose) and one to three phosphate groups.

312
Q

DNA Replication Rules

A
  • 1) DNA runs anti-parallel (5’—>3’, 3’<—5’)
  • 2) DNA Polymerase only extents 5’—>3’
  • 3) DNA Polymerase requires an existing 3’ OH
313
Q

Replication Fork

A
  • Y-shaped region where DNA parental strands are unwound
314
Q

Leading Strand

A
  • The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5’ to 3’ direction
  • synthesizes in the same direction as fork opening
315
Q

Origin of Replication

A
  • Site where the replication of a DNA molecule begins, consisting of a specific sequence of nucleotides
  • forms a replication bubble (unwound area) with a replication fork on each side, the parental strand opens in the direction of the fork
316
Q

Lagging Strand

A
  • A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5’ to 3’ direction away from the replication fork.
  • synthesized in opposite direction of fork opening
317
Q

Okazaki Fragments

A
  • Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.
  • short/discontinuous DNA sequence segments made on lagging strand
  • are facing away from the fork opening
318
Q

DNA Replication Initiation

A
  • 1) double helix begins unwinding at the origin of replication, accomplished by DNA Helicase after it’s attracted by an initiation protein (it breaks base pair H-bonds), unwinds at the Replication Bubble, forming a Y-shaped Replication Fork
  • 2) single-strand binding proteins stabilize the unwound template strands, keeping the fork open
  • 3) Primase synthesizes RNA ntds into an RNA Primer (is attracted to original template strand via base pairing interactions), allowing for DNA Pol III to begin synthesizing the leading strand in the 5’—>3’ direction
319
Q

DNA Helicase

A
  • enzyme that unwinds double-stranded DNA via breaking base pair hydrogen bonds
  • acts after being attracted by an initiation protein
320
Q

Replication Bubble

A
  • a region of DNA, in front of the replication fork, where helicase has unwound the double helix
321
Q

Single-Strand Binding Proteins

A
  • molecules that stabilize the unwound parent template strands
  • keep the Replication Bubble unwound via staying in the Replication Fork
  • there’s 1 of them on the ‘top’ strand while the bottom one has 3 (due to replication delay, needs to hold it open longer)
322
Q

Primase

A
  • an enzyme that synthesizes RNA nucleotides into an RNA Primer
323
Q

RNA Primer

A
  • short segment of RNA used to initiate synthesis of a new strand of DNA during replication
  • initial nucleotide chain to which DNA Polymerase III can begin adding ntds in the 5’—>3’ direction
  • involved in both leading and lagging strand
324
Q

DNA Replication Elongation

A
  • 1) complementary base pairing occurs, DNA Pol III catalyzes joining of DNA ntds
  • 2) Polymerization occurs, adjacent ntds are linked with phosphodiester bonds (occurs with ease with the leading strand with 5’—>3’ but encounters an issue with lagging strand - is synthesized discontinuously in small Okazaki fragments)
  • 3) Prime creates an RNA Primer for each segment, moving in the direction of the opening (‘left’)
  • 4) DNA Pol III adds DNA ntds to fragment 1’s primer (moving ‘right’) until reaching origin of replication
  • 5) DNA Pol III detaches and moves onto the next primed fragment (to the left), synthesizing fragment 2 (in the right direction) until reaching fragment 1’s primer
  • 6) this sequence repeats for all fragments, physically synthesizing fragments ‘right’ (5’—>3’), but overall creating new ones in the ‘left’ direction (direction of fork opening) until all are complete and DNA Pol III dissociates (because it can’t remove primers)
  • 7) DNA Polymerase I replaces RNA with DNA (removes Primers via adding DNA ntds to the 3’ end of each fragment as it finishes synthesizing)
  • 8) DNA Ligase joins the Okazaki Fragment sugar-phosphate backbones (forms phosphodiester bonds between DNA ntds), ‘seals nick’
325
Q

DNA Polymerase III

A
  • responsible for adding DNA nucleotides off of an RNA Primer
  • synthesizes both leading and lagging strand
  • catalyzes joining of ntds
326
Q

Polymerization

A
  • a chemical process that combines several monomers to form a polymer or polymeric compound
327
Q

DNA Polymerase I

A
  • replaces RNA Primers with DNA
  • adds DNA dntds to the 3’ end of each fragment as it finishes synthesizing
  • requires an existing 3’ OH
  • can polymerize DNA
  • has 5’—>3’ exonuclease activity (can break phosphodiester bonds = between Primers and DNA)
  • acts on lagging and leading strand
328
Q

Exonuclease Activity

A
  • ability to break phosphodiester bonds
  • ex: DNA Pol I breaks bonds between Primers and DNA as to remove the Primers
329
Q

DNA Ligase

A
  • A linking enzyme essential for DNA replication; catalyzes the covalent bonding of the 3’ end of a new DNA fragment to the 5’ end of a growing chain.
  • ‘seals the nick’
  • joins Okazaki fragment sugar-phosphate backbones
  • forms phosphodiester bonds between adjacent DNA ntds
  • does not add or remove ntds
  • ‘fills in’ empty space left by RNA Primer (which was removed by DNA Pol I)
  • acts on leading and lagging strand
330
Q

Genes

A
  • DNA segments that serve as the key functional units in hereditary transmission
  • DNA sequence within a chromosome, region of DNA that directs synthesis of an RNA molecule
  • a unit of heredity
  • can code for many things but we’re focusing on proteins
  • genes in our DNA define everything about us
  • subtle sequence changes account for diverse ranges in populations
  • DNA contains genes that direct protein synthesis (proteins do cell work)
  • info stored in DNA must be stored and communicated to the cytoplasm (where it directs protein synthesis)
  • primary protein structure dictates folding, folding dictates function
  • DNA dictates what primary structure will look like
  • multiple genes exist per chr (separated by start and stop sites, can be on same strand)
331
Q

Genetic Expression

A
  • process by which DNA directs synthesis of proteins (or sometimes just RNA)
  • in eukaryotes, DNA info is stored in nucleus but most cell activity happens in cytoplasm
  • therefore, info must be transmitted to the cytoplasm
  • info is transmitted according to Central Dogma of molecular biology (flow of info in cell is unidirectional)
332
Q

Central Dogma

A
  • theory that states that, in cells, information only flows from DNA to RNA to proteins
333
Q

Prokaryotic Promoter

A
  • a DNA sequence that directs transcription
  • site of RNA Polymerase assembly (attaches and initiates transcription)
  • includes start site
  • ‘-10’ = ~6 base pairs that are A=T rich, recruits RNA Pol
  • ‘-35’ = ~6 base pairs that orient RNA Pol (both these specific sequences are common to most prok promoters)
  • ‘upstream’ of the start site (‘left’)
334
Q

Start Site

A
  • The location on a chromosome where transcription begins
  • the first transcription ntd
335
Q

Transcription Factors

A
  • Collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription.
  • control trxn
  • recognize and bind RNA Pol
  • helps recruit a gene
336
Q

Transcription

A
  • synthesis of RNA using info in DNA within the nucleus (eukaryotes) or cytoplasm (prokaryotes)
  • DNA is double-stranded, RNA is single-stranded, therefore only 1 strand is needed to be transcribed
337
Q

Template Strand

A
  • The DNA strand that provides the template for ordering the sequence of nucleotides in an mRNA transcript.
  • the strand used in transcription
  • runs 3’—>5’ away from the promoter
  • strand used is determined by transcription enzyme orientation
  • DNA is read 3’—>5’
  • RNA is made 5’—>3’
338
Q

Coding Strand

A
  • the strand of DNA that is not used for transcription and is identical in sequence to mRNA, except it contains uracil instead of thymine
  • complementary and anti-parallel to template strand
  • runs 5’—>3’ from promoter
339
Q

Transcript

A
  • RNA product of transcription
340
Q

RNA Polymerase

A
  • Enzyme similar to DNA polymerase that binds to DNA and separates the DNA strands during transcription
  • enzyme of transcription
  • ‘pries’ 2 strands of DNA apart and joins together RNA ntds complementary to the DNA template strand
  • elongates the RNA polynucleotide
  • catalyzes phosphodiester bond formation between RNA ntds based on base pairing with template (pairing between RNA/DNA gives transcript specificity)
  • is part of transcription initiation complex that assembles at promoter
  • does not require a primer or helicase because it performs both fxns
  • ‘knows’ where a gene is because it’s located via transcription factors
  • drawn as a ‘guitar pick’ shape around the trxn bubble
341
Q

Transcription Initiation Complex

A
  • The completed assembly of transcription factors and RNA polymerase bound to a promoter.
  • includes RNA Pol, transcription bubble, both DNA strands, sigma factor
342
Q

Prokaryotic Transcription Initiation

A
  • 1) RNA Pol binds to the dsDNA at the promoter sequence (at the 5’ end of the non-template strand to be transcribed = opposite to 3’ end of template)
  • 2) RNA Pol unwinds the double helix to expose the unpaired bases, then identifies the template strand (has transcription factors and -10/-35 sequences)
  • 3) template strand is read 3’—>5’ from the promoter (non-template runs 5’—>3’ but is not read)
  • 4) RNA Pol aligns the first 2 ribonucleotides (which becomes the 5’ end of the mRNA molecule, is polymerizes 5’—>3’)
343
Q

Sigma Factor

A
  • controls the binding of RNA polymerase to the promoter
  • DNA-binding protein that binds promoter and recruits RNA Pol
  • located at/near promoter
344
Q

Prokaryotic Transcription Elongation

A
  • catalysis of phosphodiester bonds between RNA ntds
  • 1) as RNA Pol moves along DNA, it untwists the double helix to expose ~10-20 DNA ntds at a time = unwinding the transcription bubble
  • 2) RNA Pol adds RNA ntds to the 3’ end of the RNA molecule (after sigma factor is released = end of initiation = polymerization can begin)
  • 3) after RNA has been synthesized/transcribed, the dsDNA helix reforms and the new ssRNA molecule hangs out of/peels away from DNA template strand
  • 4) once RNA Pol has moved off the promoter, another one can begin - therefore a gene can undergo trxn times simultaneously
345
Q

Prokaryotic Transcription Termination

A
  • RNA Pol reaches a termination sequence/synthesizes a terminator sequence
  • RNA Pol and the mRNA chain are released
346
Q

Transcription Terminators

A
  • RNA sequences that signal the end of transcription
  • transcribed from specific DNA sequences
  • often form ‘hairpin loops’ which help release RNA Pol/mRNA chain
347
Q

Post-Transcriptional Processing

A
  • enzymes in eukaryotic nuclei modify pre-mRNA before the genetic message is dispatched to the cytoplasm
  • occurs after transcription
  • only in eukaryotic nuclei
  • produces mature messenger RNA
  • required to increase stability of transcript in cytosol before translation (aqueous cytoplasm component)
  • 3 total modifications = methyl-guanosine cap, poly-A-tail, and RNA Splicing
  • both ends of primary transcript are altered
  • modifications may also promote mRNA export + facilitate ribosome attachment
  • modifications are not translated themselves
348
Q

Methyl-guanosine Cap

A
  • since the 5’ end of mRNA is synthesizes, a methyl-guanosine cap (modified form of guanine ntd) is added to the 5’ end = a methylated (CH3) guanine meG cap
  • adding a single meG creates a 5’-5’ linkage which ‘hides’ the 5’ end from exonuclease digestion
  • evolved as an anti-viral response to degrade only viral RNA
349
Q

poly-A-tail

A
  • a poly-A-tail which is ~200 adenine ntds, is added to the 3’ OH of an mRNA via the actions of poly-A-polymerase
  • prevents or delays exonuclease digestion
  • aids in translation initiation
350
Q

RNA Splicing

A
  • removal of introns (large portions of initially synthesized RNA in eukaryotes)
  • 1) an intron is looped out via cutting it at its 5’ and 3’ end with a spliceosome
  • 2) the 5’ end covalently links to ‘branchpoint A’, creating a lariat (with 5’-2’ linkage)
  • process of splicing initially evolved ‘because it had to’
  • provided opportunity for alternative splicing
351
Q

Introns

A
  • non-amino acid coding regions which contain intervening sequences found in a gene’s DNA but not in mature mRNA
  • removed during RNA splicing
352
Q

Exons

A
  • amino acid coding regions which contain expressed sequences found in both DNA and RNA
353
Q

Lariat

A
  • shape of excised/cut intron after first step of RNA Splicing
  • is shaped like an RNA ntd
  • 5’ end has a CH2 + a PO4 attached
  • 2’ end has an O + a PO4 attached = branchpoint A
  • the 2 PO4s covalently link
354
Q

Spliceosome

A
  • A large complex made up of proteins, small RNA molecules, and small nuclear ribonucleoproteins (ssRNPs) that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joining the two adjacent exons.
  • splicing enzyme/large complex that recognizes and binds to exon/intron boundaries
355
Q

Alternative Splicing

A
  • Splicing of introns in a pre-mRNA that occurs in different ways, leading to different mRNAs that code for different proteins or protein isoforms. Increases the diversity of proteins.
  • mix and matching exons that can result in genes giving rise to multiple polypeptides
  • splicing patterns differ resulting in different proteins
  • euks only
356
Q

Translation

A
  • process in which genetic code carried by mRNA directs the synthesis of polypeptides or proteins from amino acids in the cytoplasm
357
Q

‘The Genetic Code’

A
  • collection of codons of mRNA, each of which directs the incorporation of a particular amino acid into a protein during protein synthesis
  • the relationship between mRNA sequence and aa’s
  • proteins were originally thought to be the transforming principle because it had greater diversity than DNA (20 vs 4 monomers)
  • “how can 4 ntds encode for 20 aa?” = because DNA ntds are read as 3-letter ‘words’ = codons = 1 aa = triplet code = allows 4 ntds to have 64 possible different combinations (4^3)
  • largely contributed to by Francis Crick
  • is (almost) universal
  • contributed to by Nirenberg Experiment (1961)
358
Q

Codon

A
  • A specific sequence of three adjacent bases on a strand of DNA or RNA that provides genetic code information for a particular amino acid
  • 3 DNA ntds = codon = 1 aa = triplet code = allows 4 ntds to have 64 possible different combinations (4^3)
359
Q

Nirenberg Experiment (1961)

A
  • knew that DNA was read in triplet code but didn’t know which codon encoded for aa’s
  • synthesized an artifical mRNA with repeating UUU codons using in-vitro translation (test tube)
  • determined that UUU = phenylalanine
  • then continuted on with GGG (glycine, AAA, etc.
360
Q

Codon Table

A
  • 64 codon possibilities with triplet codes for 4 ntds
  • 61 encode for aa’s
  • 3 have no associated aa’s = stop codons (UAA, UAG, UGA)
  • genetic code is universal and non-overlapping
  • displays Mutational Tolerance
361
Q

Mutational Tolerance

A
  • redundant aa coding
  • multiple codons encode for same aa, therefore reducing chance of mutation
  • different codons for same aa = 3rd ntd has variability
362
Q

(t)ransfer RNA

A
  • type of RNA molecule that transfers amino acids frpm cytoplasmic aa pool to a growing polypeptide in a ribosome
  • adaptor molecules that mediate the transfer of info from nucleid acid to protein
  • some recognize more than 1 codon for the aa they carry
  • functional RNA molecule with 2 regions = aa binding region and anticodon
  • consists of single RNA strand (~80 strands)
  • ntd bases can H–bond to eachother, so the strand can fold in on itself to form a 3D structure
363
Q

Amino Acid Binding Region

A
  • 1 of 2 regions on a tRNA molecule
  • at the 3’ end of the single RNA strand
  • depicted at the ‘top’ of a solid tRNA
364
Q

Anticodon

A
  • group of three bases on a tRNA molecule that are complementary to an mRNA codon
  • ntd triplet that base-pairs to a specific mRNA codon
  • anti-parallel to mRNA codon
  • conventionally written 3’—>5’ to align with the codons written 5’—>3’
  • not at the end of the RNA strand, in the ‘middle’
  • depicted at the ‘bottom’ of a solid tRNA
365
Q

Aminoacyl-tRNA Synthetase

A
  • family of related enzymes that carry out correct matching of tRNA + its associated aa
  • each synthetase fits only a specific combination
  • “the translator”
  • 20 different synthetases for 20 different aa’s
  • a synthetase can bind to all the different tRNAs that code for its particular aa
  • pairs correct aa based on sequence of anti-codon (covalently links aa to tRNA)
  • ATP dependent rxn
  • 1) the aa/appropriate tRNA enter the specific synthetase active site
  • 2) using ATP, synthetase catalyzes the covalent bonding of the 2
  • 3) ATP Hydrolysis causes a slight shape change in the enzyme to faciliate catalysis
  • 4) the tRNA charged with its aa, is released by the synthetase
366
Q

Ribosomes

A
  • facilitate specific coupling of tRNA anti-codons with mRNA codons during protein synthesis
  • large protein complexes with associated r(ibosomal)RNAs
  • catalyze formation of peptide bonds
  • have 2 major subunits = large and small
  • have 3 important sites = “P(olymerization)” site, “A(pproach)” site, and Exit site
  • prokaryotic ribosome: 70s = 50s (large subunit) + 30s (small)
  • eukaryotic: 80s = 60s + 40s
  • ’s’ = density measurement
367
Q

Ribosomal Large Subunit

A
  • catalytic subunit (provided by rRNAs)
  • prok = 50s (out of 70s, + small 30s)
  • euk = 60s (out of 80s, + small 40s)
368
Q

Ribosomal Small Subunit

A
  • mRNA base-pair recognition subunit (provided by rRNAs)
  • binds to mRNA ribosomal binding site (proks only)
369
Q

Ribosomal Binding Site

A
  • a sequence in bacterial mRNA that is needed to bind to the ribosome and initiate translation
  • rRNA in small subunit can bind to this mRNA sequence (proks only)
370
Q

Ribosomal P-site

A
  • Site that holds tRNA carrying the growing polypeptide chain
  • “polymerization” site
371
Q

Ribosomal A-Site

A
  • Site that holds the tRNA carrying the next amino acid to be added to the chain.
  • “approach” site
372
Q

Exit Site

A
  • briefly binds empty/discharged tRNA before it leaves ribosome
373
Q

Prokaryotic Translation Initiation

A
  • brings together mRNA + tRNA bearing first polypeptide aa + 2 ribosomal subunits
  • 1) rbs is recognized by complementary sequences (purine-rich) in the 16s rRNA of the 30s (small) subunit
  • 2) small subunit binds to mRNA and a specific initiator tRNA (carrying aa methionine)
  • 3) at the AUG start codon, the small subunit associates such that tRNA^f-met sits in the middle at the P-site (tRNA associates by codon-anticodon base pairing = specificity)
  • 4) union of mRNA/initiator tRNA/small subunit is followed by attachment of large subunit which completes the translation initiation complex (requires initiation factor proteins to bring it together, expends energy obtained by GTP molecule hydrolysis)
  • 5) initiator tRNA is now in P-site
  • 6) vacant A-site is now ready for next aminoacyl tRNA
  • 7) polypeptides are always synthesized in 1 direction, from initial methionine at the amino/N-terminus toward the final aa at the carboxyl/C-terminus
374
Q

Translation Initiation Complex

A
  • the union of mRNA, initiator tRNA, a small ribosomal subunit, and a large ribosomal subunit
375
Q

Prokaryotic Translation Elongation Phase

A
  • aa’s are added 1 by 1 to the previous aa at the C-terminus of the growing chain = BIND, BOND, SHIFT
  • 1) anti-codon of incoming tRNA^aa base pair binds with its complementary mRNA codon in the A-site (is a GTP-dependent process which increases accurary/efficiency = anabolic/endergonic, escorting of tRNA into A-site is done by various elongation factors)
  • 2) peptide bond forms between the A-site amino groups and the P-site’s growing polypeptide carboxyl end (removes polypeptide from tRNA in P-site and attaches it to the aa on tRNA in A-site. Formation of peptide bond is catalyzed by peptidyl-transferase between formylmethionine and 2nd aa)
  • 3) ribosome shifts down the mRNA (towards the 3’ end) in 1 codon step (is translated N—>C, tRNA/polypeptide in A-site is translocated to P-site while at the same time, the empty P-site tRNA moves to the E-site where it’s released into the cytoplasm to be reloaded with another aa. mRNA moves along with its bound tRNAs, bringing the next codon to be translated into A-site)
376
Q

Peptidyl Transferase

A
  • catalyzes the formation of a peptide bond between formylmethionine (of the growing polypeptide in the P-site that is moved to the A-site) and the 2nd aa in the A-site
377
Q

Prokaryotic Translation Termination Phase

A
  • elongation continues until an mRNA stop codon reaches the A-site
  • 1) when an mRNA stop codon is read, the A-site accepts a release factor
  • 2) the peptide chain/tRNA are cleaved/hydrolyzed and the ribosome is dismantled (GTP dependent) via the release factor
  • 3) the 2 ribosomal subunits and other assembly components dissociate
378
Q

Release Factor

A
  • a protein that is shaped like tRNA that recognizes a stop codon
  • is accepted by the A-site when a stop-codon is read
  • causes cleavage of the peptide chain off the P-site tRNA via promoting hydrolysis = frees the chain from ribosome
  • causes dismantling of ribosome (requires 2 GTP)
  • ribosomes stall after A-site encounters a stop codon unless a release factor enters
  • stop codons = UAA, UAG, UGA (no associated tRNAs)
379
Q

Prokaryotic Transcription/Translation Coupling

A
  • in proks, transcription/translation both occur in the cytoplasm and can therefore occur at the same place and time
  • the translation of mRNA can begin as soon as the leading 5’ end of it peels away from the DNA strand
  • attached to each RNA Pol is a growing mRNA strand (which is already being translated by ribosomes)
  • ribosome moves 5’—>3’/N—>C
380
Q

Mutations

A
  • heritable changes in base sequences that modify info content of DNA
  • if DNA is modified then it MAY affect primary protein structure
  • if primary structure is altered then it MAY have consequences on protein folding and thus function
  • ‘wild-type’ alleles generally dominate in a wild population
  • different mutation types can occur, protein coding changes are 1 of many
381
Q

Base-Pair Substitution Mutation

A
  • the replacement of 1 ntd base pair with another pair
  • a mutation at a DNA level which can result in changes at protein level
382
Q

Silent Mutation

A
  • A mutation that changes a single nucleotide, but does not change the amino acid created.
  • because of redundance in genetic code, there is no change in primary protein sequence
383
Q

Missense Mutation

A
  • A base-pair substitution that results in a codon that codes for a different amino acid.
  • encodes for the wrong aa and changes the primary sequence
  • may or may not affect protein function
  • ex: sickle cell anemia
384
Q

Nonsense Mutation

A
  • A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.
  • causes a premature stop codon/a shortened protein
  • may or may not affect protein function
385
Q

Insertion/Deletion Mutation

A
  • addition or deletion of base pairs in a gene
386
Q

Frameshift Mutation

A
  • mutation that shifts the “reading” frame of the genetic message by inserting or deleting a nucleotide
  • causes improper codon grouping
387
Q

Sickle Cell Anemia

A
  • a genetic disorder that causes abnormal hemoglobin, resulting in some red blood cells assuming an abnormal sickle shape
  • most common form is caused by a single base pair substitution = missense
  • causes folding and aggregation of hemoglobin (can’t carry O2)
388
Q

Spontaneous Mutation

A
  • a random change in the DNA arising from errors in replication that occur randomly
  • is estimated that every 1 in 10^10 base pairs is altered/not repaired and results in mutation
389
Q

Induced Mutation

A
  • caused by mutagens
  • ex: x-rays, gamma rays, base analogs (mimic bases but don’t pair correctly), oxidizing agents (cause base damage so they pair incorrectly), benzene, carcinogens (cancer-causing)

Biology 107- Intro to cell biology (4 decks)

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