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92 Cards in this Set
- Front
- Back
Life and Energy
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-Every organism requires a constant supply of external energy to remain alive.
-Inability to obtain or use energy = DEATH |
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What is Energy?
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-Definition = the capacity to do work
-Energy comes in many forms: some examples Heat Light Moving Particles Chemical bonds of molecules |
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Conservation of energy
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• First law of thermodynamics (from physics)
• Energy can change from one form to another, but it cannot be created or destroyed. |
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Our source of energy
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•Where does the energy needed to sustain life on Earth come from?
-The Sun (solar energy) |
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2 types of energy
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-Potential Energy (Stored Energy)
-Kinetic Energy (Energy of Motion) |
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Potential Energy
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-Can't be used by cells directly
-Chemical bonds that contain potential energy (chemical energy) |
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Kinetic Energy
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-Useful energy cells used to do work
-Breaking chemical bonds releases kinetic energy |
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The relationship between kinetic and potential energy
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• Potential energy is converted to kinetic energy which can then do work (eg. maintain homeostasis, reproduce)
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Molecules
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• All molecules contain potential energy in their bonds (more bonds = more energy)
• Breaking these bonds releases energy for other uses (kinetic) • Some molecules broken down to obtain kinetic energy: o Living organisms (glucose & ATP) • E.g. A cell like a bacteria, or a person, 2 molecules which are really, really, really, the focus where living organisms get their energy from o Automation (gas, oil, coal, etc.) • E.g. o New technology (hydrogen, water, ethanol) |
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Heat as a byproduct
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• When PE in the bonds of molecules is converted to useful Kinetic Energy
• Conversion is not 100% efficient • Some energy is lost as a “waste product” – heat • PE -> KE + heat • 100 unites chemical energy -> (concentrated) 75 units heat energy + 25 units kinetic energy (motion) |
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2 Types of chemical reactions
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• Exergonic (energy out)
• Reactants contain more chemical energy than products, so when products form, excess energy is released • Endergonic (energy in) • Products contain more energy, so energy must be added to reactants to make products |
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Chemical reactions in cells
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• Exergonic reactions
• Used to break down molecules o Sucrose -> glucose and fructose • Energy released (kinetic) does work • Endergonic reactions (to make fat) • Used to build molecules o E.g. amino acids ->proteins • And store energy (putting it into potential energy, store as fat or ATP) |
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Exergonic Reaction of Life
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• Breakdown of ATP is the primary source of energy used by all living organisms
• Once ATP is broken down, it is changed quickly back to ATP and reused (recycled which is endergonic) |
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ATP
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• Adenosine triphosphate
o Adenine (a base, also found in DNA) o Ribose (5-carbon monosaccharide) o 3 phosphate group (PO4) attached in a chain to ribose • ATP is broken down to ADP by removing the last phosphate group o ADP = adenosine diphosphate |
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But why ATP?
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• Phosphate group bonds are VERY high energy
• When 3rd phosphate group is removed, lots of energy is released at once (good bang for your buck) • An ATP can be recycled 1000s of times per day o One muscle cell in your body uses ~10 million ATP molecules per second o You contain a few ounces of ATP, but break down ~200 lbs of ATP each day |
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There are other molecules besides ATP that can act as an energy source in cells
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• ATP is the primary, but not the only way cells store energy
• Energy can be transferred to electrons • Some molecules can hold these high energy electrons, then later donate the electrons (and the energy) to other molecules o -E.g. NADPH |
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Regulating the RATES of Chemical Reactions
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• All chemical reactions (exer- and ender- gonic) can occur spontaneously-but slowly
• All can be “jump started” and sped up by using enzymes (aka catalysts) • Spontaneous reactions occur too slowly to sustain life • Enzymes make chemical reactions occur fast enough to sustain life in cells/organisms |
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Things cells can do to regulate the activity of their own enzymes
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• Cells can control their own metabolism by controlling their enzymes:
o Make fewer or more from scratch o Inactivate them if not needed, activate if needed • Many drugs (pharmacy kind) are designed to block or mimic enzyme activity |
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An example of how a pharmaceutical agent targets enzyme activity to fix a medical problem
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• Parietal cells in stomach produce acid
o Too much acid = heartburn, ulcers, etc. • Drugs such as PrilosecTM and NexiumTM block enzymes in the acid production pathway o Less acid produced, problem solved |
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Cycle involving 2 important coupled reactions
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• One exergonic and one endergonic – they pair up and produce a cycle
• Photosynthesis (ender) • 6CO2 (6 Carbon Dioxide molecules) + 6H2O (6 water molecules) + light energy → C6H12O6 + 6O2 • Cellular respiration (exergonic) • C6H12O6 + 6O2 → 6CO2 + 6H2O + energy (to produce ATP and as heat) |
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Overall summary of photosynthesis (PS) and respiration reactions
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• Photosynthesis – uses energy from the sun (plus water and CO2) to make glucose
• Respiration – breakdown of glucose (to water and CO2) which releases energy used to make ATP • Energy IN – sunlight • Energy OUT – makes ATP • Glucose – middle man |
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Why use glucose at all?
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• Why not use energy from the sun to make ATP directly?
o More efficient, less loss of energy as heat (75% heat loss + 75% more heat loss) • This strategy never evolved, it doesn’t exist (yet) |
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Plants vs animals – who uses which of these coupled reactions
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• Autotrophs do BOTH Photosynthesis and respiratory – they make their own food and then use it (they need ATP!)
• Heterotrophs only do respiratory – rely on autotrophs, directly or indirectly for “food” • Chapter 7 is PS, Chapter 8 is respiratory |
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What types of organisms can undergo photosynthesis?
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• Autotrophs
o Plants, algae, some prokaryotes o Our focus will be on land plants |
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The anatomy of a plant LEAF – a primary site of photosynthesis
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Epidermis
• Layers of transparent cells that cover top and bottom surface of leaf Mesophyll • Layers of cells that make up the central portion of the leaf Chloroplasts • Photosynthetic organelle inside cells of mesophyll (40-200 per cell) Stomata (stoma –singular) • Openings (pores) in the leaf that allow gases to move in/out |
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Note the real complexity of photosynthesis!
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• 6CO2 + 6H2O + light energy → C6H12O6 + 6O2
• Simplifies reality substantially • Dozens of reactions, each catalyzed by an enzyme |
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A “big picture” overview of photosynthesis
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• Light-dependent reactions use sunlight and water to charge up 2 energy-storing molecules
o ATP and NADPH o O2 produced as a byproduct (waste) here • Light-independent (dark reactions) reactions use energy in ATP/NADPH, water and CO2 to make glucose o Energy depleted ADP/NADPH+ must be recharged again (cycle) |
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Light-dependent pathway
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• First step is to capture energy in sunlight
• Sun emits broad array of energy as an “electromagnetic spectrum” • Plants only absorb energy in the visible light (teeny tiny spectrum of light to tap into and use for energy) range -> “Roy Biv” |
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Plant pigments
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• Chloroplasts contain pigment molecules that absorb light with specific wavelengths, reflect others. (anything that isn’t in that wavelength bounces back)
• Primary plant pigment is chlorophyll • Absorbs violet/blue/red light, reflects green light (why leaves look green) • Chloroplasts contain pigment molecules that absorb light with specific wavelengths, reflect others • Primary plant pigment is chlorophyll • Absorbs violent/blue/red light, reflects green light (why leaves look green) |
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Role of pigments
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• Pigments capture energy from absorbed light, transfer that energy (via electrons) along a chain of molecules
• Energy released at the end of the chain recharges ADP to ATP and NADP+ to NADPH (know this area) |
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Light-independent reactions
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• Energy in charged up ATP and NADPH used to combine water and CO2 into glucose
• This step doesn’t require light, but does require lots of ATP/NADPH (which are made using light) |
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Relationship between the light-independent and light-dependent pathways
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• “photo” (light) deals w/ the light-dependent Pathway
• “synthesis” (of glucose) w/ the light-independent • Both are critical to survival and plants and thus, animals too |
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Thanks to Photosynthesis
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• Organisms have a source of energy (glucose) & O2
• Now cellular respiration can occur o C6H12O6O2 > 6CO2 + 6H20 + energy (to make ATP plus heat) • Note—Glucose breakdown can be done without O2 too- but much less efficient. o Fermentation-used by some yeast and bacteria and even our muscle cells when we can’t supply enough O2 |
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Glucose vs other nutrients
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• The most common monosaccharide, but not the only one
• Can other sugars or other types of organic molecules (lipids, proteins) be used to make ATP too? o YES! • All others are converted to glucose or a link in the respiration pathway first |
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Glycolysis & Cellular Respiration
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• 3 phases/steps
o Glycolysis (anaerobic –no O2) • Cytoplasm of cell o Krebs cycle (aerobic – w/O2) • Mitochondria (where ATP is made) o Electron Transport Chain (aerobic) • Mitochondria (Krebs & Electron Transport Chain = Cellular Respiration |
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Aerobic Cellular Respiration
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• Starts with one molecule of glucose
• Results in recharge of 36-38 ATP molecules (and water) • Requires constant influx of oxygen and glucose |
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Fermentation (anaerobic)
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• 1 molecule of glucose undergoes glycolysis
• Recharges 2 ATP per glucose • Then 1 of 2 sets of end products is formed: o 1 Lactic acid • Muscle burn, yogurt, cheese • Lactic acid be converted back to glucose (recycled) o 2 Ethanol and CO2 • How we make beer and wine! • Why champagne is bubbly and bread rises |
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Heredity
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• Concept that offspring resemble parents has been recognized for centuries
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Science behind heredity
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• Something must be passed on from parents to offspring, but what?
• Due to work of Mendel (and others), by mid 1800s we knew that the “something” were things called genes • Genes = discrete “units” of info passed on to offspring by parents (old definition) • But what is in a gene? Where is it in a cell? |
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Scientific method in action
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• Discovery – chromosomes in the nucleus of cells were always copied before cell divided (reproduced)
• Did chromosomes contain genes? Seemed likely |
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Most Scientific Method in Action – Chromosomes
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• By 1900, scientists knew chromosomes were composed of DNA and proteins
• Which one held genes? Both? Neither? • Work in 1940s-1950s confirmed that genes were found on DNA |
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New question now that we know genes are on DNA
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• OK, but, what does DNA look like?
• How does it carry and code for genes? • How is it replicated and passed on to offspring? • Lots of scientists worked on this! |
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The history of the search for DNA’s structure—Teamwork!
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• James Watson and Francis Crick were developing a #D model of DNA—but were missing critical information
• Maurice Wilkins and Rosalind Franklin had x-ray pictures of DNA • The combined information led to the discovery of DNA structures |
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A bit more history—Rosalind Franklin
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• Died of cancer in 1958
• Watson, Crick, and Wilkins given Nobel Prize in Medicine in 1962 for work on DNA • No posthumous awards allowed |
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So what is DNA?
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• DNA is a type of nucleic acid (organic)
o Deoxyribonucleic Acid • RNA (ribonucleic acid) is another type • Made up of chains of nucleotides (basic unit) |
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Nucleotide Structure
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• 3 parts:
• A phosphate group (PO4) • A monosaccharide o Ribose for RNA, deoxyribose for DNA • A nitrogenous base o (aka a base) |
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Bases
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• DNA’s nucleotides use 4 bases
o Adenine (A) o Guanine (G) o Thymine (T) o Cytosine (C) • The whole nucleotide is often just referred to by its base |
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DNA – details
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• DNA molecule is a double helix
• Double = two connected chains (strands) of nucleotides o Like a ladder • Helix-the 2 strands twist o Like a circular staircase |
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Backbone and rungs
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• Backbone of the strand is sugar-phosphate groups of nucleotides bonded to each other
o • Covalent bonds (strongest type of bond) • The two strands run in opposite directions • Anti-parallel (one goes up, the other goes down, interstate traffic one up one down) • Rungs of ladder are a pair of bases, one from each strand, bonded together o Hydrogen bonds (weak) • Bases pair in a precise combination (must find bonds or pairs and follow that pattern all the time) o Complimentary base pairs |
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Complimentary bonding
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• A always bonds to T (Ass to Titties)
o Via 2 hydrogen bonds • G always bonds to C (George Clooney) o VIA 3 hydrogens bonds • My goofy rule for remembering the pairing: o Curvy letters go together and straight line letters pair up |
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The DNA code
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• Now that we know what DNA looks like…
• How does a string of bases (ACGGTTAC…) result in genes? o Blue eyes, tall, allergic to eggs, etc…. o Focus of Chapter 12-stay tuned! • Hint: it relates to the SEQUENCE (order) of bases along the chain |
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DNA must be replicated
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• As cells divide, the DNA they contain must be accurately passed on to both daughter cells
• How is this done? • Before dividing, a cell produces two identical copies of all its DNA, one copy for each daughter cell |
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DNA replication process
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• Enzymes called DNA helicases break the hydrogen bonds and pull the two strands apart
o Unzip the double helix (splits the ladder lengthwise) • Each strand now has a backbone and half of each “rung” sticking out, unpaired |
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DNA replication process (cont)
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• Enzymes called DNA polymerases escort free nucleotides (free A,G, C, T) to each strand and match them to make new pairs
• The sugar/phosphate portions of the free nucleotides are also joined to make a new backbone |
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DNA replication-summary
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• Cell builds 2 new strands of DNA from scratch that pair up with each of the 2 new strands
• When complete the new double strands twist into a helix |
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Semiconservative Replication
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• DNA republication is called semiconservative
• The 2 new double helices are ½ old DNA, ½ new DNA • Both should be identical |
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Some Details of Replication
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• Actually requires 12 different enzymes
• Does replication start unzipping at one end and move to the other end? o No! Why not? Too slow! • In humans, the DNA in Chromosome 1 is 246 million bases long • DNA polymerases can chain new bases together at a rate of 50/second • It would take 57 days to copy DNA on Chromosome 1 • A better (faster) way • DNA helicases pull apart a section of DNA in the middle to create a bubble • DNA polymerases work to make new pairs inside bubbles • Multiple bubbles can be formed & replicated simultaneously-much faster! • Replication Bubbles |
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Mistakes
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• Changes in the sequence of DNA = mutations
• Can mistakes occur during DNA replication o (can mutations develop?) • but has DNA replications process has features that reduce mutations |
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Correcting mistakes
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• Newly replicated DNA is proofread for errors
• Repairs enzymes repair errors that are found • Uncorrected error rate for DNA replication is about 1 mistake per billion base pairs copied |
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Mutations do occur
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• 1 mistake per billion is good, but does generate mutations
• Environmental factors also damage DNA and create mutations o Chemicals (burning plants, industrial) o Low wavelength waves (x-rays, ultraviolent) • Damaged DNA is often, but not always repaired |
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5 types of mutations
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• 3 small scale mutations (one or few bases)
o Nucleotide substitution (point mutation) o Insertion o Deletion • 2 Large scale mutations (big chunks of DNA) o Inversion o Translocation |
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Nucleotide substitution
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• A single base pair is altered
• Sickle Cell Anemia |
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Sickle Cell Anemia
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• Mutation in the gene that makes hemoglobin, a blood protein
o Hemoglobin gene is 438 bases long o 1 substitution at the 17th base o T-----A becomes A-----T |
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Insertion
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• One or a few base pairs are added into the sequence
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Deletion
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• One or a few base pairs are removed from the sequence
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Inversion
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• A piece of DNA is cut out and then replaced in the wrong direction
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Translocation
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• One or more pieces of DNA are removed and inserted into a different place (often another chromosome)
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Mutations—good or bad?
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• Both and neither
• Some mutations have no effect (neutral) • Some mutations lead to new versions of genes that work better • Some mutations inactivate or change crucial genes—harmful or lethal effects |
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Connection between genes and DNA
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• DNA contains a huge amount of information but what do we do with it?
• Useful information on DNA is found in genes • Gene = a section of DNA that contains a set of instructions (new definition) • A single strand of DNA can contain 100s or 1000s of genes (in a row • Instructions to make what? o Research in late 1950s demonstrated that genes carry the code for making proteins • Original rule was: o 1 gene = 1 protein • One gene contain instructions to produce one protein o Enzyme, pump, channel, transport, etc. |
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New information, new rule
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• We now know that some genes code for the production of RNA (not proteins)
• Modify the rule: o 1-One gene = one protein (mostly) o 2-One gene = RNA (sometimes) |
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What is RNA?
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• Ribonucleic acid
• Ribose is the sugar (not deoxyribose) • Single stranded chain of nucleotides (not double) • Also has 4 different bases on nucleotides • G, C, A and U (Uracil replaces Thymine) |
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There are 3 types of RNA
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• Messenger RNA (mRNA)
• Ribosomal RNA (rRNA) • Transfer RNA (tRNA) |
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RNA as the middle-man
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• DNA (genes) are inside nucleus of cell
• Ribosomes (where proteins are made) are out in cytoplasm [manufacturing plants for proteins) • How do we get info on DNA out to ribosomes? o mRNA! • Intermediary molecule |
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DNA to Protein – 2 Major Steps
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• 1st step = transcription
o Copying information on DNA to RNA o In court, clerks transcribe spoken words to writing (same language) o DNA and RNA are both nucleic acids-“same language” • 2nd step = translation o Information on RNA used to make proteins o Translating is changing from one language to another o RNA (nucleic acid) and proteins are “different languages” |
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Summary of Process
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• DNA contains genes with instructions for making a protein
• DNA is too big to leave nucleus • A gene’s worth of information is copied onto mRNA • mRNA moves into cytoplasm to ribosomes • Information on MRNA is used to construct a protein (1 amino acid at a time) |
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The genetic code
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• We have: 4 DNA bases, 20 amino acids
• So can 1 base = code for 1 aa? o NO, not enough bases • Can 2 bases = code for 1aa? o 4 bases in groups of 2 make 16 unique combinations o Still not enough • 3 bases produce 64 unique combinations o That gives us enough combos. • Only need 20, what about the other 44? • There is redundancy, different 3 base combos code for same amino acids |
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Analogy for genetic code
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o Bases are “letters”
o DNA has a 4 letter alphabet (G,C,A,T) o Use this alphabet to make “words” o All DNA “words” have 4 letters • Codon o THE BIG RED DOG SAW THE CAT • CCC ATA GAC TTT GGA CTA Codons • A single codon “word” codes for: • 1 of the 20 amino acids, or • Signal for START (gene starts here), or • Signal for STOP (gene ends here) |
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Codons use RNA bases
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• Since RNA is actually involved in making proteins, codons written with RNA bases, not DNA
• When DNA is copied to RNA, A on DNA pairs with U on RNA (not T) |
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Base pairing in nucleic acids
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• DNA to DNA
G-C (George Clooney) C-G A-T (Ass and T****) T-A • RNA to RNA G-C (George Clooney) C-G A-U (Ass and underwear) U-A • DNA to RNA G-C (George Clooney C-G A-U (Ass and underwear) T-A (T*** and Ass) • Write a strand of DNA and then on the other side write RNA focus on red bolded section and get comfortable with it |
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Transcription – Overview
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• Goal is to accurately copy one gene’s worth of information from DNA to RNA
• Resulting RNA strand is mRNA • Book goes into lots of detail here • Basic Premise DNA helix is split near start of a gene • RNA polymerases (enzymes) find beginning of gene then pair RNA nucleotides with DNA until end of gene • Only one side of DNA is ever copied • RNA is released and DNA rezips |
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Beginning and end of gene
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• Short series of DNA bases called promoter region signals start of gene
• All DNA bases beyond promoter region are copied onto mRNA • Short series of DNA bases called termination signal signals end of gene o Copying stops |
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Non-coding DNA
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• In eukaryotic cells, a gene will contain bases that truly code for amino acids in the protein
o Exons • And, in between, will be bases that are not part of the code (non-coding) o Introns (doesn’t make sense) • Introns are junk and must be clipped out of mRNA after it is made |
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Final mRNA strand
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• The clipped mRNA carries only the code for the amino acid sequence of the protein
• mRNA leaves the nucleus and travels to a ribosome in the cytoplasm • Ribosome (dots in book) = bundle of proteins and rRNA that form 2 subunits (large & small) |
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Translation—Overview
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• Codons on mRNA are “read” in order and the appropriate amino acid assembled into a protein
• This occurs in ribosomes • Requires the use of tRNA |
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tRNA
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• Type of RNA folded and produce a binding site for 1 amino acid, and three exposed bases (anticodon) [twisty and bendy]
• Enzymes attach an amino acid to each tRNA so when anticodon (tRNA) binds to codon (mRNA) correct amino acid is delivered |
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Inside the ribosomes
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• Inside ribosome are 2 side-by-side sites where mRNA and tRNA can come together and bind
• 2 codons worth of mRNA sit in the sites, two matching tRNA bind to them and enzymes connect their 2 amino acids together • empty tRNA far and leaves |
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Inside the ribosome
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• mRNA slides over one codon
• Remaining tRNA slides with it • This codon/anticodon pair is now on far end and a new mRNA codon sits in the empty site • New tRNA binds to codon on empty site and aa chain on old tRNA is added to aa on new tRNA • Old tRNA leaves, mRNA slides over • Repeat until STOP codon arrives • AA chain released from ribosome |
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Translation – Summary
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• mRNA is pulled though the ribosome, codon by codon one at a time
• One new amino acid is added to the growing chain by tRNA molecules • When STOP codon arrives, amino acid chain is released from ribosome • Final touches placed on amino acid chain so it becomes a true, functional protein Polypeptide = protein Peptide = amino acid |
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Mutations in DNA
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• How do mutations in DNA affect proteins?
o Depends • Mutation may be neutral (e.g. new codon-but same aa, entire gene is moved) • Mutation may be beneficial – may cause a slightly different protein to be formed that may work better • Mutations may be harmful • Gene could be broken in the middle • Sometimes changing even one amino acid strong impacts the resulting protein o (Sickle cell anemia) • An insertion or deletion, affects EVERY codon after it occurs (causes a frame shift) |
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Frame shift
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• Deletions/additions of 1 or 2 bases
• The BIG RED DOG SAW THE CAT • THE BIR EDD OGS AWT HEC AT (Deletion) • CCC GGG AAAA UUU CC GGG AAA • CCC GGA AAU UUC CCG GGA AA (Addition) |
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Gene Regulation
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• Every cell in your body has a copy of every gene in your DNA
o Skin cells contain gene for hemoglobin o Liver cells contain genes for muscle proteins o Not all cells need or use all gene o Some needed only at certain times • Fetal development genes • Milk proteins (lactation) o Some genes are never used by a cell • Skin cells never need hemoglobin o On the other hand, some genes are needed by all cells all the time (e.g. respiration enzymes) o Gene regulation = concept that cells can control which genes are used and which are not [and when] |
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Gene Regulation lingo
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• Transcription and translation of a gene to protein or RNA
o Up-regulation of gene o Turning gene on o Expression of gene • Non-use of a gene o Down regulated, gene is turned off, not expressed o Gene regulation can occur at many levels o Transcription (yes/no, little/ lots) o Translation (yes/no, little/lots) o Cell can affect final modification of amino acid chain (active/inactive protein) |