basic biology i

7/25/2019 Basic Biology I

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Basic Biology I: Cells

How organisms work


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Outline

Chemistry (pp. 8-1!: atoms" molecules an# $on#" polar $on#s" water

Biochemistry (pp. 11-1%!: &our $asic macromolecules

Cells (pp. '-'!: mem$rane" osmotic pressure" organelles"

en#osym$iosis" cell #i)ision" gene e*pression

+n,ymes an# energy generation (pp. %-8 an# /-!


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Chemistry

Name the components of atoms andtheir role in determining the atoms

identity and in forming chemical bonds. Distinguish between the 3 main types of

chemical bond

Understand the relationship betweenwater, polar and non-polar, andhydrophilic and hydrophobic


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Chemistry

0t the $ottom" $iology is nothing $ut applie# chemistry

0ll matter is compose# o& atoms

+lements such as car$on an# o*ygen are a group o& atoms o&the same type. or instance" a nail ma#e o& iron is 2ust a largegroup o& iron atoms.

3here are ' naturally occurring elements" plus a$out 'arti&icially-create# elements.

4i)ing things are mainly compose# o& the elements car$on"hy#rogen" o*ygen" an# nitrogen. 0nother #o,en or soelements are also use#: phosphorus" iron" magnesium" so#ium"

potassium" chlorine" to name a &ew.


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0toms 0toms ha)e 5 components: protons" neutrons" an#electrons

6 3he type o& element (car$on" iron" etc. ! is entirely

#etermine# $y how many protons are in the nucleus.

protons an# neutrons are in the nucleus6 7rotons ha)e a 1 charge

6 9eutrons ha)e no charge

+lectrons circle aroun# the nucleus" in a series o&

shells.

6 +lectrons ha)e a -1 charge6 Chemical $on#s are create# $y mo)ements o& the

electrons $etween atoms

3he num$er o& protons #etermines which

element the atom is.

6 Hy#rogen: 1 proton" car$on protons" o*ygen 8

protons.

6 Biological an# chemical processesneverchange the

num$er o& protons in any atom.

9ormally" the num$er o& electrons is e;ual to the

num$er o& protons" so the atom has no electrical

charge: it is neutral.


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Chemical Bon#s

0toms can com$ine with each other to &orm molecules.

0 molecule is a #e&ine# num$er o& atoms groupe# into a #e&ine# spatialrelationship. or e*ample" water" H'O" is ' hy#rogen atoms connecte# toan o*ygen atom. 3he o*ygen is in the mi##le" an# the hy#rogens areattache# at an angle to it.

0 large group o& the same molecule is calle# a compoun# (2ust as a largegroup o& the same atom is calle# an element!.


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Ionic Bon#s

In an ionic $on#" one atom gi)es an electronto another atom. 3his makes $oth atomsions" an# they are hel# together $ecause theiropposite charges attract each other.

> In so#ium chlori#e (ta$le salt!" so#ium startsout with 1 electron in its outer shell. 3hene*t shell #own has 8 electrons" so $y gi)ing1 electron away" the so#ium atom gets a &ullouter shell. It then has a 1 charge.

Chlorine starts out with % electrons in itsouter shell. By gaining one more electron" itgets 8 in the outer shell" an# a -1 charge.

> 3he charge# so#ium an# the 6 charge#chlorine attract each other" an# they packtogether in salt crystals.


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Co)alent Bon#s Co)alent $on#s occur when ' atoms

share a pair o& electrons. 3he

electrons spen# part o& their time with$oth atoms" so the octet rule issatis&ie# su&&iciently.

0 molecule o& hy#rogen gas" H'" has' hy#rogen atoms. +ach atompro)i#es 1 electron" so in the $on#

each atom shares '" a complete shell&or hy#rogen.

3he $on# is sym$oli,e# as a lineconnecting the ' H?s: H-H

> In water (H'O!" the o*ygen has electrons in its outer shell" an# itshares one with each o& the 'hy#rogens" gi)ing 8 share# electrons&or o*ygen an# ' &or each hy#rogen.

Co)alent $on#s are the most commontype in $iological molecules.


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7olar Co)alent Bon#s

@ometimes the electrons in a co)alent $on# aren?tshare# e;ually" $ecause one atom attracts electrons

more strongly than the other. Ahen this happens" theelectrons spen# more time with one atom" an# thatatom $ecomes slightly negati)ely charge#. 3he otheratom $ecomes slightly positi)ely charge#. 3his is apolar co)alent $on#" $ecause the atoms &orm positi)ean# negati)e poles.

Aater is a polar compoun#" $ecause the o*ygen isslightly negati)e an# the hy#rogens slightly positi)e.6 O*ygen attracts electrons more than hy#rogen

9ote that the total charge on the molecule is $alance#"same num$er o& electrons as protons" $ut within themolecule the charges are slightly separate#.

(Bon#s where the electrons are share# e;ually are calle#non-polar.!

7olar molecules attract each other: the oppositecharges attract.


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Hy#rogen Bon#s

3he slight an# 6 charges in polar

$on#s attract each other. In $iologicalmolecules" it is common &or thepartial charge on a hy#rogen toattract the partial 6 charge on anear$y o*ygen or nitrogen. 3hisattraction is calle# a hy#rogen $on#.0 hy#rogen $on# is the attraction

$etween a hy#rogen atom an# thesmall negati)e charge on anotheratom.

> Hy#rogen $on#s are )ery weakcompare# to co)alent $on#s" $ut largenum$ers o& them can a## up to a

strong $on#. 3he stran#s o& 90 arehel# together $y hy#rogen $on#s.

Hy#rogen $on#s also &orm $etween#i&&erent parts o& the same molecule"an# $etween water an# othermolecules.


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Aater

0ll li&e occurs in water.


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Aater 7olar su$stances #issol)e in

water" $ecause water &ormshy#rogen $on#s with the polarmolecules. 3hus" polarsu$stances are calle#hy#rophilic" or water-lo)ingD.

9on-polar su$stances #on?t#issol)e in water $ecause theycan?t &orm hy#rogen $on#s" sothey are calle# hy#ropho$ic" orEwater-&earingD. Oils an# &ats aree*amples o& non-polarsu$stances.

Cells are surroun#e# $y ahy#ropho$ic mem$rane. Feepsthe cell?s contents separate# &romthe outsi#e worl#.

Hy#rophilic coating re#uces &riction $y

trapping a thin layer o& water ne*t to the $oat?s

hull.


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Biochemistry

Name the 4 types of macromolecule,their subunits, and their functions in the

cell. Distinguish between dierent sub-types

of carbohydrate, lipid, and nucleic acidin terms of their structure and role in the

cell. Understand how protein folding is

related to en!yme acti"ity.


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Organic Compoun#s

It use# to $e thought that only li)ing

things coul# synthesi,e thecomplicate# car$on compoun#s&oun# in cells

German chemists in the 18?slearne# how to #o this in the la$"

showing that organicD compoun#scan $e create# $y non-organicmeans.6 aw materials: coal an# oil

3o#ay" organic compoun#s are thosethat contain car$on. (with a &ewe*ceptions such as car$on #io*i#ean# #iamon#s!


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our Basic 3ypes o&


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Car$ohy#rates

@ugars an# starches: sacchari#esD.

3he name car$ohy#rateD comes &romthe appro*imate composition: a ratio o&1 car$on to ' hy#rogens to one o*ygen

(CH'O!. or instance the sugar glucoseis C.H1'O..

Car$ohy#rates are compose# o& rings o& or car$ons" with 6OH groupsattache#. 3his makes mostcar$ohy#rates water-solu$le.

Car$ohy#rates are use# &or energypro#uction an# storage (sugar an#starch!" an# &or structure (cellulose!.


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@ugars


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Comple* Car$ohy#rates

polysacchari#es (many sugars linke#

together!.6 Can $e linear chains or $ranche#.

@ome polysacchari#es are use# &or &oo#storage: starch.6 @tarch is a glucose polymer" we ha)e

en,ymes that easily #igest starch.

6 @tarch is a con)enient way to storeglucose in $oth plants an# animals.

@ome polysacchari#es are structural: thecellulose o& plant cell walls an# &i$ers isa polysacchari#e compose# o& manyglucose molecules" $ut linke# together

#i&&erently than starch.6 Ae #on?t ha)e en,ymes that can #igestthese polymers. Cows an# termites#epen# on $acteria in their guts to #igestcellulose" pro#ucing methane as a$ypro#uct.


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4ipi#s

4ipi#s are the main non-polar component

(hy#ropho$ic! o& cells.


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3riglyceri#es an# 7hospholipi#s

3riglyceri#es are the main type o& &at.

0 triglyceri#e is compose# o& 5 &attyaci#s attache# to a molecule o&glycerol.6 atty aci#s are long hy#rocar$on

chains with an aci# group at one en#.

ats store a$out twice as much energyper weight as car$ohy#rates like

starch.

7hospholipi#s are the maincomponent o& cell mem$ranes.6 they ha)e a glycerol with ' &atty aci#s

attache#" plus a phosphate-containing

hea#D group instea# o& a thir# &atty aci#. 3he hea# group is hy#rophilic" while

the &atty aci#s are hy#ropho$ic.

Cell mem$ranes are ' layers" with thehea# groups &acing out an# the &attyaci#s &orming the interior o& themem$rane.


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7roteins

3he most important type o&macromolecule. oles:6 +n,ymes: all chemical reactions in the

cellsare cataly,e# $y en,ymes" which areproteins: $uil#ing up" rearranging" an#$reaking #own o& organic compoun#s""generating energy

6 @tructure: collagen in skin" keratin in hair"crystallin in eye. 0lso" mo)ement o&

materials insi#e the cell.6 3ransport: e)erything that goes in or out o& acell (e*cept water an# a &ew gasses! iscarrie# $y proteins.

0ll organisms contain protein" $utanimals ha)e much more protein than

plants: most o& the animal $o#y is

compose# o& protein" while most o& theplant $o#y is car$ohy#rate.6 7roteins are 1J5 nitrogen. 0c;uiring

this nitrogen an# getting ri# o&nitrogenous waste is a $ig pro$lemanimals &ace.


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0mino 0ci#s

0mino 0ci#s are the su$units o&proteins.

+ach amino aci# contains an aminogroup (-9H'! an# an aci# group(COOH!. 7roteins consist o& longchains o& amino aci#s" with the aci#

group o& one $on#e# to the aminogroup o& the ne*t.

3here are ' #i&&erent kin#s o& aminoaci#s in proteins. +ach one has a&unctional group (the groupD!attache# to it.

i&&erent groups gi)e the ' amino

aci#s #i&&erent properties" such ascharge# ( or -!" polar" hy#ropho$ic"etc.

3he #i&&erent properties o& a proteincome &rom the arrangement o& theamino aci#s.

7 t i @t t


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7rotein @tructure 0 polypepti#e is one linear chain o&

amino aci#s. 0 protein consists o& one ormore polypepti#es" an# they sometimescontain small helper molecules such asheme.

0&ter the polypepti#es are synthesi,e# $ythe cell" they spontaneously &ol# up into acharacteristic con&ormation which allowsthem to $e acti)e. 3he proper shape is

essential &or acti)e proteins. or mostproteins" the amino aci#s se;uence itsel&is all that is nee#e# to get proper &ol#ing.6 3he 2oining o& polypepti#e su$units into a

single protein also happensspontaneously" &or the same reasons.

enaturation is the #estruction o& the 5-#imensional shape o& the protein. 3hisinacti)ates the protein" an# makes iteasier to #estroy. Heat is the easiest wayto #enature proteins: this is the e&&ect o&cooking &oo#s.


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9ucleic 0ci#s

9ucleoti#es are the su$units o& nucleic

aci#s. 9ucleic aci#s store an# transmit geneticin&ormation in the cell.

3he two types o& nucleic aci# are 90(ri$onucleic aci#! an# 90(#eo*yri$onucleic aci#!.

+ach nucleoti#e has 5 parts: a sugar" a

phosphate" an# a $ase. 3he sugar" ri$ose in 90 an#

#eo*yri$ose in 90" contain car$ons.3hey #i&&er only in that an 6OH group inri$ose is replace# $y a 6H in 90.

3he main energy-carrying molecule inthe cell is 037. 037 is an 90nucleoti#e with 5 phosphate groupsattache# to it in a chain. 3he energy isstore# $ecause the phosphates each ha)ea negati)e charge. 3hese charges repeleach other" $ut they are &orce# to staytogether $y the co)alent $on#s.

0 # 0


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90 an# 90 90 uses / #i&&erent $ases: a#enine

(0!" guanine (G!" thymine (3!" an#

cytosine (C!. 3he or#er o& these $asesin a chain o& 90 #etermines thegenetic in&ormation.

90 consists o& ' complementarychains twiste# into a #ou$le heli* an#hel# together $y hy#rogen $on#s.90 is a sta$le molecule which cansur)i)e thousan#s o& years un#erproper con#itions

6 3he 90 $ases pair with each other: 0with 3" an# G with C.

90 consists o& a single chain that also

uses / $ases: howe)er" the thymine in90 is replace# $y uracil (K! in 90.90 is much less sta$le than 90: itis use# to con)ey in&ormation &orimme#iate use $y the cell.


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Cells

#ist the tenets of the cell theory.

$now the essential dierence between pro%aryotes andeu%aryotes, and which types of organism belong to which group.

Understand how the cell membrane allows only certain moleculesin and out of the cell.

&'plain what osmotic pressure is, and describe the function of thecell wall in resisting osmotic pressure.

&'plain the endosymbiotic theory for the origin of mitochondriaand chloroplasts.

$now the functions of these organelles( nucleus, mitochondria,chloroplast, endoplasmic reticulum, )olgi body, lysosome

Understand the relationship between chromosomes, DN*, andgenes.

Understand the purpose of mitosis +but not the steps in"ol"ed.

#ist the steps of gene e'pression and the molecules in"ol"ed ineach step.

$now the purpose of the genetic code and transfer N*


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3he Cell 3heory

Kse o& the microscope &or 1 years or so le# to these $asic

$elie&s a$out cells:

1. 0ll li)ing things are compose# o& cells.

'. 3he cell is the smallest unit o& li&e.

5. 0ll cells arise &rom pre-e*isting cells.

i ll i i


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Basic Cell Organi,ation

0ll cells contain:6 1. cell mem$rane that keeps the

insi#e an# outsi#e separate.

6 '. 90-containing region thathol#s the instructions to run the

processes o& li&e.

6 5. Cytoplasm: a semi-&lui# regioncontaining the rest o& the cell?smachinery.

7rokaryotes: ($acteria!: simplecells with 90 loose in thecytoplasm. 9o nucleus or other

internal mem$rane-$oun#organelles.

+ukaryotes (plants" animals" &ungi"protists!: comple* cells with 90in a nucleus separate# &rom thecytoplasm $y a mem$rane.

C ll $


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Cell


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3ransport 0cross the Cell


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7assi)e an# 0cti)e 3ransport

7assi)e transport uses protein channelsthrough the mem$rane that allow aparticular molecule to go through it"#own the concentration gra#ient.Glucose is a goo# e*ample: since cells$urn glucose &or energy" theconcentration insi#e is less than theconcentration outsi#e.

0cti)e transport uses proteins aspumps to concentrate moleculesagainst the concentration gra#ient.3he pumps use 037 &or energy. Onee*ample is the calcium pump" whichkeeps the le)el o& calcium ions in the

cell 1 times lower than outsi#e" $yconstantly pumping calcium ions out.3he $alance o& so#ium an# potassiumions is maintaine# with potassium highinsi#e an# so#ium low insi#e" using apump. Kp to 1J5 o& all energy use# $ythe cell goes into maintaining the

so#iumJpotassium $alance.


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Aater in the Cell Aater also mo)es #own the concentration

gra#ient. @ince the cell is &ull o& other

molcules" water wants to mo)es into the cellto #ilute them. 3his process is calle# osmosis"an# it e*erts a pressure that can cause cells toswell up an# $urst.

Ae say that pure water is hypotonic relati)e tothe insi#e o& a cell: pure water has &ewerparticles in it" so the water mo)es into the cell.

0 plant cell in pure water swells up against thecell wall: a nice crisp )egeta$le" &or e*ample.

Con)ersely" i& cells are put into a concentrate#salt solution" water will lea)e the cells" mo)ingto #ilute the water outsi#e. 3he concentrate#salt solution is hypertonic: has more particlesin it than the insi#e o& the cell. 3he cell shrinks

away &rom the cell wall: the plant wilts. 9ormal $o#y &lui#s are isotonic" ha)ing the

same concentration o& particles as the insi#e o&the cell.

3he most important &unction o& the plant cellwall is to #e&en# against osmotic pressure.


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+n#osym$iont Hypothesis

9 l


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9ucleus 3he main components o& the nucleus are

the chromosomes. 0 chromosome is

compose# o& a single )ery long 90molecule plus the proteins that support itan# control it.

3he 90 carries the genes" which areinstructions nee#e# to $uil# an# maintainthe cell" respon# to changes in theen)ironment" an# to #i)i#e into ' cells.

+ach gene is a short region o& thechromosome?s 90. 3here are se)eralthousan# genes on each chromosome.

Ahat genes #o: the nucleoti#e se;uence o&each gene co#es &or a single polypepti#e"the chain o& amino aci#s that make up

proteins.


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Cell i)ision an# Genes Cells #i)i#e to make more cells. 3he

chromosomes must $e precisely

#i)i#e# so that each #aughter cell getse*actly the same 90.6 0ll the other organelles are 2ust

ran#omly separate# into the #aughtercells"

Fey points a$out genes:

60ll cells within an organism ha)e thesame genes.

6 Ahat makes cells #i&&erent &rom eachother is that #i&&erent genes are turne#on an# turne# o&& in #i&&erent cells.

Be&ore a cell can #i)i#e" it mustreplicate its 90" so there are 'copies o& each chromosome (' 90molecules!" attache# at thecentromere.

Once the 90 has $een replicate#"

the cell is rea#y to #i)i#e" using theprocess o& mitosis.

@ &


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@ummary o&


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Gene +*pression

+ach gene is a short section o& achromosome?s 90 that co#es &or a

polypepti#e. i&&erent genes are acti)e (e*presse#! in

#i&&erent cells

Genes are e*presse# $y &irst making an90 copy o& the gene calle# messenger90"(transcription! an# then using the

in&ormation on the 90 copy to make aprotein (translation!.

3ranscription occurs in the nucleus" $uttranslation occurs in the cytoplasm. 3hemessenger 90 nee#s to $e transporte#out o& the nucleus.


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3ranscription

3ranscription is the process o& making an90 copy o& a single 90 gene.

6 3he 90 copy is messenger 90

3he copying is #one $y an en,yme: 90polymerase.

3he $ases o& 90 pair with the $ases o&90: 0 with 3 (or K in 90!" an# G withC. 3he 90 copy o& a gene is 2ust acomplementary copy o& the 90 stran#.

90 polymerase attaches to a signal at the$eginning o& the gene" then it mo)es #own

the gene" a##ing new $ases to the 90copy" until it reaches a termination signal atthe en# o& the gene.

Genetic Co#e


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Genetic Co#e

3here are only / $ases in 90 an#90" $ut there are ' #i&&erent amino

aci#s that go into proteins. How can90 co#e &or the amino aci#se;uence o& a proteinL

+ach amino aci# is co#e# &or $y agroup o& 5 $ases" a co#on. 5 $ases o&90 or 90 1 co#on.

@ince there are / $ases an# 5

positions in each co#on" there are / */ * / / possi$le co#ons.

3his is &ar more than is necessary" somost amino aci#s use more than 1co#on.

5 o& the / co#ons are use# as @3O7signals= they are &oun# at the en# o&e)ery gene an# mark the en# o& theprotein.

One co#on (0KG! is use# as a@303 signal: it is at the start o&e)ery protein.

3 & 90


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3rans&er 90

3rans&er 90 molecules act as a#apters$etween the co#ons on messenger 90 an# theamino aci#s. 3rans&er 90 is the physicalmani&estation o& the genetic co#e.

+ach trans&er 90 molecule is twiste# into aknot that has ' en#s.

0t one en# is the antico#onD" 5 90 $asesthat matches the 5 $ases o& the co#on. 3his isthe en# that attaches to messenger 90.

0t the other en# is an attachment site &or theproper amino aci#.

0 special group o& en,ymes pairs up the propertrans&er 90 molecules with theircorrespon#ing amino aci#s.

3rans&er 90 $rings the amino aci#s to theri$osomes" which are 90Jprotein hy$ri#s thatmo)e along the messenger 90" translatingthe co#ons into the amino aci# se;uence o& the

polypepti#e.

3ranslation


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3ranslation irst step: initiation. 3he messenger 90 $in#s to a

ri$osome" an# the trans&er 90 correspon#ing to the@303 co#on $in#s to this comple*

6 3he ri$osome has ' sites &or $in#ing trans&er 90.3he &irst t90 with its attache# amino aci# $in#sto the &irst site" an# then the trans&er 90correspon#ing to the secon# co#on $in# to thesecon# site.

6 3he ri$osome then 2oins the two amino aci#stogether.

@tep ' is elongation: the ri$osome mo)es #own themessenger 90 a #istance o& one co#on.

6 3he ol#" empty t90 is remo)e#.

6 0 new trans&er 90" matching the new co#on"$in#s

6 3he ri$osome attaches the new amino aci# to the

growing polypepti#e6 3he process repeats: the ri$osome mo)es #own themessenger 90" a##ing new amino aci#s to thegrowing polypepti#e chain.

3he &inal step in translation is termination. Ahen theri$osome reaches a @3O7 co#on" there is nocorrespon#ing trans&er 90. Instea#" the whole

comple* &alls apart" releasing the new polypepti#e.


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Internal


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+n#oplasmic eticulum

eticulumD means network= the +

is a network o& tu$ules in thecytoplasm" compose# o& mem$ranes2ust like the cell mem$rane. Itpro)i#es a mem$rane channel &romthe nucleus to the cell mem$rane.

3wo types" connecte# together: rough+ an# smooth +

ough + looks rough $ecause it isstu##e# with ri$osomes" the cellularmachines that synthesi,e proteins.i$osomes on the rough + make theproteins that are inserte# into themem$rane" using the instructions&rom messenger 90. Other

ri$osomes" not attache# to the +"make the non-mem$rane-$oun#proteins.

@mooth + has no ri$osomes. It isuse# to synthesi,e the lipi#s o& themem$rane.


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Golgi Bo#y an# @ecretion

7roteins that are going to $e secrete#out o& the cell are synthesi,e# in therough +. 3hey get &inishe# in theGolgi $o#y: sugar molecules areattache# to some o& the amino aci#s.3he sugars help protect the e*porte#

proteins &rom #egra#ation.

Golgi looks like a series o& stacke#plates.

Mesicles are small" mem$rane-$oun#organelles. Mesicles carry proteins&rom the + to the Golgi" an# then&rom the Golgi $o#y to the cellmem$rane. @ecretion to the outsi#eworl# occurs $y e*ocytosis: the)esicle &uses with the cell mem$rane"releasing its contents.

7roteins synthesi,e# into themem$rane o& the + en# up in the cell

mem$rane $y the same mechanism

4ysosomes an# 7ero*isomes


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4ysosomes an# 7ero*isomes

4ysosomes are intracellular stomachs: they

are &ull o& #igesti)e en,ymes that operate atlow pH. Nou can think o& them as little aci#)ats. Mesicles transport materials to thelysosomes" an# the lysosomes #igest them.

7ero*isomes are mem$rane-$oun# sacs

use# to $reak #own &atty aci#s an# someother molecules. 3hey generate hy#rogenpero*i#e" a poisonous molecule" in theprocess" which is the source o& the namepero*isome.


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+n,ymes an# +nergy

tate the two laws of thermodynamics.

Understand how en!ymes cataly!e chemicalreactions.

Diagram the relationship between glucose,carbon dio'ide, electrons, o'ygen, and waterin the generation of energy.

Distinguish between glycolysis, the $rebs

cycle, and electron transport( what the startingand ending molecules are, where they occur,under what conditions do they occur

+nerg in the Cell


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+nergy in the Cell

0ll li&e nee#s energy. Cells con)ertthe chemical $on# energy in &oo#molecules to chemical $on# energystore# in 037 molecules.6 037 energy is then use# to run

meta$olism an# all other $o#ilyprocesses.

oo# molecules contain potential

energy in their chemical $on#s. Aeare going to e*amine how this energyis trans&erre# to 037.

caloriesD are a measure o& energy.6 Ae are ignoring the #i&&erence $etween

calorieD an# :DCalorieD

@ome &oo#s contain more energy pergram than others" $ecause theirchemical $on#s store more energy.or instance" car$ohy#rates an#proteins store / calories per gram"while &ats store calories per gram.

3hermo#ynamics


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3hermo#ynamics

irst 4aw: the total mount o& energy in theKni)erse is constant. +nergy is neither

create# not #estroye#" it 2ust changes &orm.6 Ahen energy is e*pen#e#" part o& it goes to#o use&ul work" an# the rest en#s up as wasteheat. 9one o& it is lost" $ut it changes &orms.

@econ# 4aw: #isor#er (entropy! increases.+nergy goes &rom use&ul &orms to uselessheat.6

+)ery energy trans&ormation step isine&&icient (as a conse;uence o& the @econ#4aw!" meaning that some o& the energy iscon)erte# to waste heat at e)ery step" an# theamount o& use&ul work #ecreases with e)erystep.

4i&e is )ery or#erly compare# to non-li)ingthings. 4i)ing things are a$le to locally

re)erse the o)erall #irection o& entropy $yusing a lot o& energy.

3he energy o& li)ing cells comes &rom the@un" an# it en#s up as waste heat.

In general" only a$out 1 o& the totalenergy in &oo# gets use# to #o somethinguse&ul. 3he other is lost as heat.

037


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037

In li)ing cells" energy is carrie# inmolecules o& 037" a#enosine

triphosphate.6 Ahen the energy is use#" one o& the

phosphates attache# to 037 isrelease#" gi)ing 07" a#enosine#iphosphate.

6 037 is ma#e $y a##ing a phosphate

to 07.

6 037 is constantly $eing generate#"an# it is use# almost as soon as it isma#e.

How energy is store# in the 037molecule: 3he 5 phosphates eachha)e a negati)e charge" an# so theyrepel each other. Ahen the $on#hol#ing them together is $roken" the

phosphates &ly apart" like a spring$eing release#.


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+n,ymes +n,ymes are proteins that cause

speci&ic chemical reactions to occur.

+n,ymes act as catalysts: they helpthe reaction occur" $ut they aren?tuse# up in the reaction.

0ll reactions re;uire an input o&energy to get them starte#: theacti)ation energy. 3hink o& touchinga match to a piece o& paper to start a

&ire: the match is supplying theacti)ation energy.

+n,ymes work $y lowering theacti)ation energy &or a reaction. 3hereaction occurs thousan#s or millionso& times &aster than without theen,yme. 3he little $it o& acti)ation

energy nee#e# is supplie# $y thecollision o& the molecules in)ol)e#.

+n,ymes are )ery speci&ic &or theirsu$strates: they work on only a )erylimite# num$er o& similar molecules.

O*i#ation o& Glucose


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O*i#ation o& Glucose 3he $asic &oo# molecule is glucose" a simple sugar that has car$on atoms.

+nergy &rom chemical $on#s is trans&erre# in the &orm o& electrons. O*i#ationmeans remo)ing electrons. Its opposite is re#uction" which is gaining electrons.

4+O 4ose +lectrons O*i#ation= G+ Gain +lectrons e#uction. Cells o*i#i,e glucose to &orm car$on #io*i#e an# water. 3he cell remo)es high

energy electrons &rom glucose (in a series o& steps!" which con)erts it to car$on#io*i#e. 3he energy store# in the electrons is use# to make 037. 3he electrons(now low energy! are gi)en to o*ygen molecules" con)erting them to water.

By passing the electrons through a series o& steps $e&ore their &inal #estination inwater" the cell can har)est the energy e&&iciently. In contrast" $urning releases the

energy all at once" so it can?t $e capture# easily.6 @ome common &orms o& o*i#ation: $urning an# rusting.

espiration: 3hree @teps


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espiration: 3hree @teps

espiration is generating energy $y $reaking #own &oo# molecules"con)erting the energy in their chemical $on#s to 037 energy.

6 0ll cells respire" inclu#ing plants.1. Glycolysis: 3he anaero$ic $reak#own o& glucose into the 5-car$on sugar

pyru)ate.6 4ong ago" $e&ore o*ygen was present in the atmosphere" all cells use#

anaero$ic respiration" which means generating energy in the a$sence o&o*ygen.

6


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Glycolysis Occurs in the cytoplasm" not in mitochon#ria

oes not use o*ygen.

0lmost all li)ing things use this pathway.

Basic process: a## phosphates (&rom 037! toeach en# o& the glucose" then split it in hal&"using that chemical $on# energy to generate /037s.6 inal 5-car$on pro#ucts pyru)ate.

6 9et yiel#: ' 037s per glucose

Glycolysis also releases ' electrons. 3heseelectrons can $e con)erte# to energy i& o*ygenis present" $ut they cause pro$lems i& not.

Ahat to #o with e*cess electronsL Gi)e them$ack to pyru)ate in some way:

6 In yeast" the pyru)ate gets con)erte# to ethanol

when the electrons are a##e# $ack. +thanol isthe alcohol in alcoholic $e)erages like $eer"wine" an# )o#ka.

6 In humans an# many $acteria" pyru)ate getscon)erte# to lactic aci#. Causes muscle pain#uring intense e*ercise when not enougho*ygen gets to the muscle cells.

Fre$s Cycle


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Fre$s Cycle

e;uires o*ygen" occurs in themitochon#ria

Con)ersion o& pyru)ate (&romglycolysis! to car$on #io*i#e" withgeneration o& high energy electronsan# 037.6 7yru)ate an# pyru)ic aci# are the

same thing.

7reliminary steps $e&ore startingthe Fre$s cycle: 5 car$on pyru)ateto ' car$on acetyl Co0= thir#car$on lost as car$on #io*i#e.Generates high energy electronscarrie# $y 90H an# 0H'

Fre$s cycle: a## ' car$on acetyl

Co0 to / car$on sugar" pro#ucingcitric aci#. 3hen remo)e the ' e*tracar$ons one at a time as car$on#io*i#e" generate se)eral highenergy electrons (90H in the#iagram! plus some 037.

+lectron 3ransport


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+lectron 3ransport

3he &inal stage in aero$ic respiration

3he Fre$s cycle generates many high

energy electrons. 0lso some &romglycolysis. 3hese nee# to $econ)erte# to 037 so the cell can usethem.

+lectron transport pumps H ions&rom the inner compartment to theouter compartment o& the

mitochon#ria.6 3his is uphill pumping" against theconcentration gra#ient.

6 Kses energy &rom high energyelectrons to run the pumps.

3he &inal protein pump a##s theelectrons (plus hy#rogen! to o*ygen"

pro#ucing water. 3he H le)el $uil#s up $etween themem$ranes. It &lows $ack into theinsi#e through a special proteinchannel calle# 037 synthase" whichuses the energy o& their &low tocom$ine 07 an# 7i into 037. 3his

basic biology i

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