EVERY BODY'S MADE FROM CELLS by Arthur W. Siebens, Ph.D., Copyright 1995

Every body's made from cellsGot to be small to do their job wellYour body's made of millions, a Euglena's made of oneSome cells eat others, others just lie in the sun.
The cell membrane covers the outside like a skinIt keeps the bad out, lets the good stuff inInside the cell membrane's the cytoplasmFull of organelles--if you're a eukaryote, you has 'em.
The nucleus commands and controlsThe lysosome digests cell parts when they're oldBut the cell wouldn't work, it just couldn't runWithout the power released by the MIGHTY MITOCHONDRION!
Yes, the mitochondrion's got that peanut lookThe energy it releases makes the rest of the cell "cook"It takes the energy from glucose*, makes ATPSo that muscle cells contract and white cells can fight disease.
Digestive enzymes are made in the pancreas on ribosomesThen they're transported through the endoplasmic reticulumTo the Golgi where they're packed in a bubble (secretory vesicle), To keep them out of troubleBut when you eat, they're released on the double To turn your food into monomer rubble!
Now plant cells have structures animal cells lackCell walls, large vacuoles and chloroplastsStarch is stored in leucoplasts in a potatoThe red comes from chromoplasts in a tomatoWith all those organelles hummin', a cell runs like an organized tornado.
Every body's made from cellsGot to be small to do their job wellYour body's made of millions, a Euglena's made of oneSome cells eat others, others just lie in the sun.But the cell wouldn't work, it just couldn't runWithout the power released by the MIGHTY MITOCHONDRION!
* The glucose (6 carbons) is first broken down to 2 pyruvic acid molecules (3 carbons) in the cytoplasm in glycolysis. The pyruvic acid then enters the mitochondrion and its energy is used to make ATP in cellular respiration.




A SINGING SUMMARY OF BIOTECHNOLOGYby Arthur W. Siebens, Ph.D., Copyright 1995(to the tune of "She'll Be Comin' 'Round the Mountain")

Here's a song 'bout biotechnology There's a lot to know in reality But it's really not that hard If you just let down your guard So here's an instant singing summary.
In the central dogma, start with DNAThis codes for messenger RNAOn the message triplet codonsCode which amino acids load onSo codes for proteins come from DNA.
Let's say you want to isolate some DNAUse detergent plus enzymes like proteaseAdd alcohol that's coolNow the DNA will spoolWrap it 'round a glass rod and walk away.
To separate DNA fragments by sizeUse agarose electrophoresis if you're wiseDriven by their chargeThey migrate slower if they're largeNow the lengths of DNA are undisguised.
To amplify DNA use PCRPolymerase Chain Reaction's best by farTake Taq (Thermus aquaticus) polymerase, two primersNTP's (deoxyriboNucleoside TriPhosphates), a thermocycler30 cycles later you're a star!
Restriction enzymes are used to cutAt specific sites, no "ifs", "ands" or "buts"At the recognition sequence of the enzymeDNA is cut in no timeThey're essential -- without them we'd go nuts!
Like in analysis of RFLP's (Restriction Fragment Length Polymorphisms)Restriction fragments are made with easeSpread the fragments on a gelThey identify you wellTo decide paternity becomes a breeze.
Now cloning is another tool you use Cut genes out, insert in vectors that you chooseWith plasmids, phage or YAC's (Yeast Artificial Chromosomes)Host cells express genes they lackSo human protein from bacteria's no longer news.
Half the story's been omitted as you know By tomorrow what we know today will grow Just stay tuned and keep on learning There are always questions burning Biotech will ease us down the road.

CHAINS by Arthur W. Siebens, Ph.D., Copyright 1995(Chorus to the tune of "Chains," by Gerald Goffin and Carole King, as sung by the Beatles)

CHORUSChains -- biology is all full of chainsBut they ain't the kind, that you can seeNo, to see these chains takes electron microscopy.
Chains -- polymers are what we call chemical chainsChains made of monomers -- chemical linksIf your brain weren't made with polymers you couldn't think.
Starch -- starch is just a chemical chainChain made of glucose, a thousand links longRepeat the same old bond (alpha-1,4 glycosidic linkage), never get it wrong.
Now plants store glucose as starch -- think they're coolYou eat the starch, digest it -- your small intestine ain't no fool.Now you're back to glucose, you burn it (oxidize it) if you pleaseIf not your liver stores it as glycogen, for your future needs'Course glycogen's a chain ...CHORUS
Protein, protein's another chemical chainMade of amino acids, a thousand links longRepeat that peptide bond, never get it wrong.
Now when you eat protein from meat or baked beansYour small intestine digests it to amino acids -- the building blocks you needThen your muscle cells use them to make you strong like ArnoldSo remember next time you flex, that bulge that makes your shirt rip is made of chains ...CHORUS
DNA and other nucleic acids are just giant chainsChains of nucleotides, a thousand links longRepeat the same old bond (phosphodiester linkage), never get it wrong.
Now like the others DNA's digested in your G.I. (gastrointestinal) tract, oh yeahThen your cells can make what used to code for peanutsCode for you, in fact.With similar nucleotides you could also make RNAIts flexible, there's no waste, your cells make what they need that day.But they usually make chains ...CHORUS
Lipids, lipids are usually short kinds of chainsChains of fatty acids, just three links longAttached to glycerol (ester linkage), never get it wrong.
Now, distinguishing triglycerides don't take much toil, no, noIf it's a solid at room temp its a fat, if it's a liquid it's an oilIn any case lipids don't dissolve in H2O'Course waxes and steroids are also lipids, but they're harder to know'Cause they're not chains ...CHORUSYes, to see these chains takes electron microscopy!

THOSE MAGIC MEMBRANES(Short version - the one recorded)by Arthur W. Siebens, Ph.D., Copyright 1995(to the tune of "La Bamba" by Richie Valens and "Twist and Shout," by Medley and Russell)

How do things get into cells?How do things get out?Transport across cell membranesIs what this song's about.
Diffusion, osmosisActive transport, too.To make your cells and organs work rightThe right solutes must get through.
CHORUSOh, those magic membranesIn each and every cellDifferences between solutes may be smallBut membrane transporters can tell.
Oh those magic membranes!
They let the good stuff in Get the bad stuff outThrough transporters made of proteinThere's lots of different routes.
Membranes are mainly made of lipidMost solutes can't penetrateProteins transport specific solutesMany change their shape (conformational state).
Facilitated diffusion(From) high concentration to low.In cotransport a solute going "downhill"Moves another "uphill" as it goes (secondary active transport).
There's also (primary) active transportAnd that takes energySolutes are moved uphillEnergy from ATP.
CHORUS
If solutes can't cross a membraneBut water can diffuseIt will cross 'til equilibrium (the water concentration is the same)Osmosis is when water moves (across cell membranes).
CHORUS
Oh those magic membranes! Yeah!
GLUCOSE (Plants make it so you can shake it, you've got to burn it to boogie)by Arthur W. Siebens, Ph.D., Copyright 1995

You've heard of glucose, it's in your blood.If you've got diabetes, you've got too much.Let me tell you where it comes from (I'll keep it clean)You can't make it yourself, cause you ain't green.Plants make it so you can shake it,You've got to burn it to boogie.
What this is all about, is energy,It's stored in chemical bonds, like in ATP.Now, "photo" means light, "synthesis" means make.It's 'cause of photosynthesis that you can shake.Take CO2 and water, and a little light,That chloroplast will make glucose, it's out of sight.
Now photosynthesis takes two steps, can't do it in one.And you start with the energy from the sun, Son-or Daughter.In the light reaction (light -dependent reaction), you take the energy,Store it in the bonds of ATP.In the dark reaction (light -independent reaction), the energy's transferred,From ATP to glucose, for you to burn.Plants make it so you can shake it,You've got to burn it to boogie.
Now plants can burn glucose, and so can you,To get energy and water, and CO2.But you've got to burn it slowly, so you won't fry,It's called respiration--it keeps you alive.You've got whole body respiration, That's what breathing's about.Oxygen comes in, CO2 goes out.But respiration takes place, in nearly every cell,In the mitochondrion, that mighty organelle.The energy in glucose has to be transferred, Back to ATP, which the cell prefers.Then when you want to move your muscles, go where you please, You break the ATP, the energy's released.
So that's how it is, that's how it's done.The energy you use in muscles, comes from the sun, Son-or Daughter.Through photosynthesis, the energy is stored.In the glucose you eat, that's what you're eatin' for.In respiration, you break the glucose down,To get the energy, to move your bod' around.And in the cycle of making glucose and breaking it down, CO2 and water, go 'round and 'round.
So when you're feeling hungry, or want to move, Glucose is the secret, keeps you in the groove.Plants make it so you can shake it,You've got to burn it to boogie.

CHRISTMAS AND BIOLOGYby Arthur W. Siebens, Ph.D., Copyright 1995(to the tune of [You picked a fine time to leave me] "Lucille," by Hal Bynum and Roger Bowling, as sung by Kenny Rogers)

'Bout 2000 years ago an event took place That would change the evolution of man (and woman). A child was born to a virgin mother And the government couldn't understand. So they started a science, called it "biology," Set up funding to study all things Pertaining to Christmas, the name that they called it, To see what adaptations this event would bring. CHORUS The repercussions went so far and wide, But by far the most important was biology's rise. Once we were all lost, but now we're all found, We can't explain virgin birth, but at least we're around.
It wasn't long after that small child was bornPeople rejoiced with a Christmas feast.But it soon `came apparent, you couldn't eat muchWithout a GI (gastrointestinal) motility increase.So the secretions got turned up, the food moved much faster'Til today you can eat like a horse.But if you look through phylogeny to find the reason,You'll be all wrong, it was Christmas, of course!
Soon people gave presents, went shopping around,The capitalists invented the store (thus starting the field of economics).Before long, the pulmonary system was exhausted,The poor heart just didn't have no more.Fifteen stores an hour, five aisles a minute,It's a wonder we made it at all.But the body's adaptive, it adjusts to the stress,'Til today you can race through the biggest shopping mall.
CHORUS
Now being able to shop for large numbers of packagesMade problems they never foresaw.Standing in line in one spot for an hour, All the blood rushing down to the floor,So like a smart plumber, we got some small valves,Keeping the blood off our feet.So just 'cause there's Christmas, you can wait hours for buses,And cops can all stand on their beat.Now the vomit reflex is something of interest To lovers of the finest music. 'Cause every year another disgusting Christmas song Makes those with low thresholds* sick. Maybe someday, with more adaptation, We'll withstand bad songs one and all But in the meantime, for those with low thresholds The bathroom is right down the hall.

ENZYMES by Arthur W. Siebens, Ph.D., Copyright 1999(to the tune of "Blue Moon," by Lorenz Hart and Richard Rogers)

Make ma make ma make, break ba break ba break, cut cu cut cu cut, bind ba bind Enzymes, enzymes, enzymes
They speed reactions--they catalyze Without them life would stop on a dimeBecause of them cells work just fineThey're blinding fast-they're so sublime
Enzymes-proteins with active sitesThat bind their substrates just rightInduce their fit to bind tight, Oh...
Some (anabolic) enzymes make-they make the protein in steakSome (catabolic) enzymes break-cut up the steak you intake.* Oh...
Lock la lock la lock, key ka key, enzymes/substrates like lock and keyEnzymes, enzymes, enzymes
They're regulated under controlSome work in groups--each has a roleMake up pathways with a final goalFinal product can feed back to slow the whole.**
Enzymes have allosteric sites,Inhibitor bound from the backStops the enzyme in its tracks. Alternatively...
The active site can be knocked out of commissionIn competitive inhibition-fights for the substrate's position. Whoa…
Make ma make ma make, break ba break ba break, cut cu cut cu cut, bind ba bind Enzymes, enzymes, enzymes
Lower the energy it takes (the activation energy)To get reactants through the transition stateTo make products 'fore it's too lateSo your life depends upon those great... ENZYMES!
  • In small quantities if a healthy heart is considered desirable. For example, the nine-enzyme pathway of glycolysis is inhibited by allosteric inhibition of the third enzyme, phosphofructokinase by one of the final products, ATP.





REPLICATION by Arthur W. Siebens, Ph.D., Copyright 1999 (to the tune of "Oklahoma," by Oscar Hammerstein II, and Richard Rogers)

Re-plication when DNA's copied in S-phaseInitiator proteins start, the strands are pushed apart At the origin of replication, yeah!
Now, helicase- opens the fork, for (RNA) primase to prime with RNAThen replication starts, (DNA) polymerase does its partBuilds from 5' to 3' all the way.
Now the leading strand's a piece of cakeThousands of base pairs without a break.
Topoisomerases-nickSingle strands don't-stick Single-strand binding proteins keep things stableReplication's got tricks!
The lagging strand- is harder-how it works was found by OkazakiIt's built from 5(') to 3('), in short pieces, you seeFrom RNA (primers) then DNA-it's wacky!
The RNA-'s then cut out and replaced with DNAEnds are joined by ligase, RNA's erasedAnd you're left with double-stranded DNA.
Now, replication's got other stepsGot to copy it right-can't be inept!
(DNA) polymerase- proofsRepair enzymes replace- goofsYou're not mutated? Just thank replicationReplication made you!
AMINO ACIDS ARE SURRENDEREDby Arthur W. Siebens, Ph.D., Copyright 1999(to the tune of "No Retreat, No Surrender," by Bruce Springsteen)
Pa-pa, pa, pa, pa-pa, pa, pa, pa-pa proteinsRibosomes are protein-making machines
Now, transcription's the process of reading genes The DNA with the protein's codeAnd making messenger RNA (by RNA polymerase) with its genetic payloadThe message goes to the ribosome where it initiatesIt binds to the small subunit and uses AUG as baitThe anticodon on transfer RNA carrying fMetBinds to the initiator codon, the large subunit is next.
The central dogma is the name of the gameTranscribe the DNA into messenger RNAWith the message at the ribosome amino acids are surrenderedIn translation* -is that too hard to remember?
With initiation now complete, the protein must elongateAmino acids are added by tRNA's at a staggering rate
Codons set the sequence, there's making of peptide bonds (by peptidyl transferase)tRNA's released, recycled, as the ribosome moves alongtRNA's keep landing at the "A" (aminoacyl) site,Keep releasing from the "P" (peptide)'Til the transcript is read, and elongation is complete.
Now, transfer RNA is the great translatorDrags an amino acid to the ribosome like a molecular freighterIts anticodon reads the codon, its amino acid is surrenderedIn translation-is that too hard to remember?
When a stop codon is reached, the protein is releasedThe "A" site binds a release factor, the two (ribosomal) subunits leaveSo that's termination-this song's almost through tooExcept aminoacyl tRNA synthetases have not received their just dueThey load tRNA's with amino acids, allow them to translateIf you're a molecular freighter, you've got to carry the right freight.
The central dogma is the name of the gameTranscribe the DNA into messenger RNAWith the message at the ribosome amino acids are surrenderedIn translation--is that too hard to remember?No, ribosomal work is easy to remember!Yes, protein synthesis is EASY to remember!
* An easy way to remember transcription versus translation is to relate them to a written record of a meeting: a transcript is in the same language as the speakers (i.e., nucleotides, DNA to RNA) whereas a translation is in a different language (i.e., nucleotides to amino acids).** About 17 amino acids per second (N.A. Campbell, Biology, 1993, p.330).









THE CELL CYCLE RAP by Arthur W. Siebens, Ph.D., Copyright 1999

You began as one cell, called a zygoteSo how'd you get to be so big? Just take noteThat first cell divided, so then there were twoThose two became four, then eight as you grewTo help you understand that process is our mission'Cause you've got to have a vision of cell division.
Before we get too far we need to thinkAbout the genes on chromosomes that control everythingYour cells have DNA, DNA makes your genesAnd through transcription and translation genes code for proteinsBut keeping track of those genes (about 100,000 in humans) is one of natures tricksCells use chromosomes - humans have 46Now, when the cell's not dividing, chromosomes are unwoundIt's called chromatin, DNA's spread all around*But when a cell divides, DNA will condenseInto rods called chromosomes - it makes lots of senseThat way you get all your genes - and not any moreToo many, too few - you've got problems in storeThere's some birth defects you can detect right away (e.g. Down's syndrome)In a karyotype, an ordered chromosome display.Each chromosome has two halves, exactly the sameThey're sister chromatids - remember that nameThey're held together at the centromereBut not for long as you soon shall hear.
Now, chromosomes come in pairs - you've got 23One per pair from each parent, most cells are diploid (2N) you see'Course eggs and sperm have only one from each pairSo fertilization results in chromosome "re-pair"23 from Mom, 23 from DadA zygote's back to 46, then it divides like madNow, in all but gametes (eggs, sperm) the nucleus divides through mitosisThere are four stages on which we need to focus:
In prophase through a 'scope you can see chromosomesThe nuclear membrane breaks down, so they can find a new homeIn metaphase the chromosomes form a lineIt's like they're doin' a dance and they're lookin' real fineIn anaphase the centromere dividesAnd the chromatids move towards opposite sidesIn telophase chromatids (now chromosomes) are at opposite endsNew nuclei form - that's how mitosis happensThen cytokinesis takes place, the cytoplasm splitsNow you've got two cells - that's just about it.
Except the cell's got to grow, and DNA replicate (in S phase)Made of G1, S, G2 - it's called interphaseThough mitosis and cytokinesis are more excitingThrough most of the cell cycle the cell's not dividingSo that's the cell cycle and all of its parts Hope this little rap helps you to learn it by heart!

MEIOSIS ALL RAPPED UP by Arthur W. Siebens, Ph.D., Copyright 1999

Keeping track of genes is one of nature's wondersThat's why you've got chromosomes-to avoid major blundersCell duplication's impressive, it's called mitosisBut you ain't seen nothin' 'til you've seen meiosisRemember eggs and sperm are called gametesWant to know how they're made? You're in for a treat!
Now meiosis takes eight steps instead of just four'Cause there's two cell divisions1 we're about to exploreIn prophase I a unique event happensHomologous chromosomes join-its called synapsis2Yes, when tetrads form, DNA can be swappedSo genes from Mom's chromosome are now on Pop'sThis crossing over increases recombinationSo there's no one like you in all the United Nations!Chromosomes then line up in metaphase IBut what's important in anaphase (I) is what's not undoneThat's the centromere, which remains unbrokenHomologous chromosomes move apart3-the products will be 1N (haploid).
So the chromosome number's down to 23'Course that assumes you're a human like meBut each chromosome's got two chromatids Which just won't work when making kidsSo after telophase I and interphase IIThe cell divides again--similar phase names are usedSo there's prophase (II) and metaphase (II) and anaphase (II)In anaphase II the centromere finally breaks4,*So each sperm or egg gets only one copyOf 23 chromosomes 5-can't afford to be sloppySo after telophase II and cytokinesis Meiosis is through and this little rap ceases.
1,2,3,4,5 Key differences between meiosis and mitosis.* Chromatids are called chromosomes after the centromere breaks.







RESPIRATION: WHAT GOES IN, WHAT COMES OUT by Arthur W. Siebens, Ph.D., Copyright 1999(to the tune of Ob-la-Di Ob-la-Da by John Lennon and Paul McCartney)

Glúcose oxidátion has a lót1 of stéps, móst of which you dó not need to knówFive májor parts are crítical so hóld on tíght and listen clósely because thís is how it góes:
1. Glycólysis tákes 6 carbon glúcose, bréaks it to 2 pýruvates with 3 (C's)Makes 2 NADH's then through súbstrate lével phosphórylation mákes 2 ATP's
CHORUSWhat goes ín/what comes óut-don't get bógged dówn, all those stéps will make your héad spín 'róund!
2. The pýruvate énters mitochóndriá (the matrix), from the cýtosol whére it just got mádeThe múltienzyme cómplex chops off CO2, yields NADH and Acétyl CoÁ3. Acétyl CoA énters the Krebs cýcle, adds 2 carbons to 4 (oxaloacetic acid) now you've got 6 (citric acid)As it lóses 2 CO2's, 3 NADH's fórm, 1 FADH2 and an ÁTP 2 for kícks
CHORUSWhat goes ín/what comes óut-don't get bógged dówn, all those stéps will make your héad spín 'róund!
4. The NADH (and FADH2) with 2 high énergy eléctrons, gíves them to the eléctron tránsport cháinAs they móve to oxygén making H2O 3, protons are púmped across the ínner mémbráne5. Now you've gót a gradiént of prótons (chemical and electrical)-they wánt to go back tó the matríxATP sýnthase lets them ín, converts their énergý, makes ATP-its one of náture's gréatest trícks.
So oxidátion of NADH is cóupled to phósphorylátion of 3 ATP'sAnd suppórt for chemiosmósis cómes from uncóuplers like DNP (dinitrophenol) Yés, ít dóes!
They máke the inner membrane léaky-there's no (proton) grádient, phosphórylation's blóckedBut glúcose oxidátion keeps húmming stróng, and the sécret to the cóupling ís unlócked! Óxidative phósphorylátion's óne of evolútion's biggest cóups4It mákes 90 percént of your ÁTP- so withóut it, in a féw minutes you're thróugh!
CHORUSWhat goes ín/what comes óut-don't get bógged dówn, all those stéps will make your héad spín 'róund!So breathe ín, then breathe óut-got that áll dówn? Réspirátion5 kéeps yóu 'róund!So you gót thát áll dówn? Réspirátion5 kéeps you 'róund!
1 Accent marks (as in "lót") indicate accented syllables.2 Through substrate level phosphorylation. "For kicks" reinforces the concept that this accounts for only 1 of the 12 ATP's ultimately resulting from each turn of the Kreb's cycle.3 2 e - + 1/2O2 + 2H+ = H2O4 The evolution of eukaryotes (with their mitochondria) from prokaryotes took roughly twice as long as the evolution of prokaryotes from non-living matter.5Whole-body respiration in breathing provides oxygen for cellular respiration in mitochondria.



PHOTOSYNTHESIS by Arthur W. Siebens, Ph.D., Copyright 1999(to the tunes of "Parigi, o cara" from LaTraviata by Giuseppe Verdi and "La donna e mobile" from Rigoletto by Giuseppe Verdi)(to the tune of Parigi, o cara)

Chloroplasts can take some light, transform its energyThrough the light (-dependent) and dark reactions (light-independent), make glucose for you and meIt starts with photosystem II, 2 electrons get a boostChlorophyll steals two more from water, oxygen's produced.
The electrons then pump protons as to photosystem I they flow onThrough photophosphorylationThere's ATP formation.
This ATP is synthesized through chemiosmotic proton flowFrom the electron transport chainAcross the thylakoid membraneBy ATP synthase, you know.
Much of the energy remains, now the electrons are boosted highBy photosystem I to an electron acceptor, then they backslide (down a second electron transport chain)The final carrier of electrons two, is NADPHThe light reaction's through-but we've got glucose to create.
(to the tune of La donna e mobile)The Calvin cycle takes a CO2 (in the stroma) Adds it to 5 carbons1 (ribulose bisphosphate) then splits in two (phosphoglycerate, 3C's) With energy from 3 ATP's2 NADPH's complete the deed (donating 2 high energy electrons), Glyceraldyhde phosphate (P-Gal) will emerge (after 3 turns of the Calvin cycle)Glucose (6 C's) results when two (P-Gals) converge That's the dark reactionBut O2 can cause a detraction.
Rubisco likes CO2, but it also accepts O2If CO2 is low and O2 is high (e.g., within the leaf with stomata closed on a hot, dry day)Carbon fixed is kissed good-bye (up to 50%) In photorespiration there's fixed carbon eliminationCO2 's released, the chloroplast is fleeced!
(To the tune of Parigi, o cara)Certain plants avoid this fate-they use isolationCarbon's fixed in 4-carbon acids2 away from the Calvin cycle's exploitationC4 plants use space3, CAM plants use time4, they control CO2 releaseThe Calvin cycle's still used, but fixed carbon's increased.
(to the tune of the end of La donna e mobile)Pho-to-syn-the-sis is increased!Pho-to-syn-the-sis is increased!
1 By the enzyme ribulose bisphosphate carboxylase (rubisco), probably the most abundant protein on earth.2 C4 plants use mainly oxaloacetate and malate, CAM plants mainly malate and isocitrate.3 C4 plants (e.g. corn) fix carbon into organic acids in cells lacking the Calvin cycle (mesophyll cells), then transport the acids to other cells containing the Calvin cycle (bundle sheath cells).4 CAM plants (e.g., cacti) fix carbon into organic acids in their mesophyll cells at night with their stomata open. The next day CO2 is released and incorporated into sugars (with stomata closed and the light reactions supplying ATP and NADPH).