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92 Cards in this Set

  • Front
  • Back
Life and Energy
-Every organism requires a constant supply of external energy to remain alive.

-Inability to obtain or use energy = DEATH
What is Energy?
-Definition = the capacity to do work
-Energy comes in many forms: some examples

Heat

Light

Moving Particles

Chemical bonds of molecules
Conservation of energy
• First law of thermodynamics (from physics)
• Energy can change from one form to another, but it cannot be created or destroyed.
Our source of energy
•Where does the energy needed to sustain life on Earth come from?

-The Sun (solar energy)
2 types of energy
-Potential Energy (Stored Energy)
-Kinetic Energy (Energy of Motion)
Potential Energy
-Can't be used by cells directly
-Chemical bonds that contain potential energy (chemical energy)
Kinetic Energy
-Useful energy cells used to do work
-Breaking chemical bonds releases kinetic energy
The relationship between kinetic and potential energy
• Potential energy is converted to kinetic energy which can then do work (eg. maintain homeostasis, reproduce)
Molecules
• 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)
Heat as a byproduct
• 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)
2 Types of chemical reactions
• 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
Chemical reactions in cells
• 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)
Exergonic Reaction of Life
• 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)
ATP
• 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
But why ATP?
• 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
There are other molecules besides ATP that can act as an energy source in cells
• 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
Regulating the RATES of Chemical Reactions
• 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
Things cells can do to regulate the activity of their own enzymes
• 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
An example of how a pharmaceutical agent targets enzyme activity to fix a medical problem
• 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
Cycle involving 2 important coupled reactions
• 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)
Overall summary of photosynthesis (PS) and respiration reactions
• 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
Why use glucose at all?
• 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)
Plants vs animals – who uses which of these coupled reactions
• 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
What types of organisms can undergo photosynthesis?
• Autotrophs
o Plants, algae, some prokaryotes
o Our focus will be on land plants
The anatomy of a plant LEAF – a primary site of photosynthesis
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
Note the real complexity of photosynthesis!
• 6CO2 + 6H2O + light energy → C6H12O6 + 6O2
• Simplifies reality substantially
• Dozens of reactions, each catalyzed by an enzyme
A “big picture” overview of photosynthesis
• 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)
Light-dependent pathway
• 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”
Plant pigments
• 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)
Role of pigments
• 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)
Light-independent reactions
• 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)
Relationship between the light-independent and light-dependent pathways
• “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
Thanks to Photosynthesis
• 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
Glucose vs other nutrients
• 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
Glycolysis & Cellular Respiration
• 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
Aerobic Cellular Respiration
• Starts with one molecule of glucose
• Results in recharge of 36-38 ATP molecules (and water)
• Requires constant influx of oxygen and glucose
Fermentation (anaerobic)
• 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
Heredity
• Concept that offspring resemble parents has been recognized for centuries
Science behind heredity
• 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?
Scientific method in action
• Discovery – chromosomes in the nucleus of cells were always copied before cell divided (reproduced)
• Did chromosomes contain genes? Seemed likely
Most Scientific Method in Action – Chromosomes
• 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
New question now that we know genes are on DNA
• 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!
The history of the search for DNA’s structure—Teamwork!
• 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
A bit more history—Rosalind Franklin
• Died of cancer in 1958
• Watson, Crick, and Wilkins given Nobel Prize in Medicine in 1962 for work on DNA
• No posthumous awards allowed
So what is DNA?
• 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)
Nucleotide Structure
• 3 parts:
• A phosphate group (PO4)
• A monosaccharide
o Ribose for RNA, deoxyribose for DNA
• A nitrogenous base
o (aka a base)
Bases
• 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
DNA – details
• 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
Backbone and rungs
• 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
Complimentary bonding
• 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
The DNA code
• 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
DNA must be replicated
• 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
DNA replication process
• 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
DNA replication process (cont)
• 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
DNA replication-summary
• 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
Semiconservative Replication
• DNA republication is called semiconservative
• The 2 new double helices are ½ old DNA, ½ new DNA
• Both should be identical
Some Details of Replication
• 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
Mistakes
• 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
Correcting mistakes
• 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
Mutations do occur
• 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
5 types of mutations
• 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
Nucleotide substitution
• A single base pair is altered
• Sickle Cell Anemia
Sickle Cell Anemia
• 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
Insertion
• One or a few base pairs are added into the sequence
Deletion
• One or a few base pairs are removed from the sequence
Inversion
• A piece of DNA is cut out and then replaced in the wrong direction
Translocation
• One or more pieces of DNA are removed and inserted into a different place (often another chromosome)
Mutations—good or bad?
• 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
Connection between genes and DNA
• 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.
New information, new rule
• 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)
What is RNA?
• 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)
There are 3 types of RNA
• Messenger RNA (mRNA)
• Ribosomal RNA (rRNA)
• Transfer RNA (tRNA)
RNA as the middle-man
• 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
DNA to Protein – 2 Major Steps
• 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”
Summary of Process
• 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)
The genetic code
• 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
Analogy for genetic code
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)
Codons use RNA bases
• 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)
Base pairing in nucleic acids
• 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
Transcription – Overview
• 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
Beginning and end of gene
• 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
Non-coding DNA
• 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
Final mRNA strand
• 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)
Translation—Overview
• 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
tRNA
• 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
Inside the ribosomes
• 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
Inside the ribosome
• 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
Translation – Summary
• 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
Mutations in DNA
• 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)
Frame shift
• 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)
Gene Regulation
• 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]
Gene Regulation lingo
• 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)