New User Special Price Expires in

Let's log you in.

Sign in with Facebook


Don't have a StudySoup account? Create one here!


Create a StudySoup account

Be part of our community, it's free to join!

Sign up with Facebook


Create your account
By creating an account you agree to StudySoup's terms and conditions and privacy policy

Already have a StudySoup account? Login here


by: Brady Spinka


Marketplace > University of Texas at Austin > Chemistry > CH 369 > FUNDAMENTALS OF BIOCHEMISTRY
Brady Spinka
GPA 3.98


Almost Ready


These notes were just uploaded, and will be ready to view shortly.

Purchase these notes here, or revisit this page.

Either way, we'll remind you when they're ready :)

Preview These Notes for FREE

Get a free preview of these Notes, just enter your email below.

Unlock Preview
Unlock Preview

Preview these materials now for free

Why put in your email? Get access to more of this material and other relevant free materials for your school

View Preview

About this Document

Class Notes
25 ?




Popular in Course

Popular in Chemistry

This 73 page Class Notes was uploaded by Brady Spinka on Monday September 7, 2015. The Class Notes belongs to CH 369 at University of Texas at Austin taught by Staff in Fall. Since its upload, it has received 25 views. For similar materials see /class/181881/ch-369-university-of-texas-at-austin in Chemistry at University of Texas at Austin.




Report this Material


What is Karma?


Karma is the currency of StudySoup.

You can buy or earn more Karma at anytime and redeem it for class notes, study guides, flashcards, and more!

Date Created: 09/07/15
Today s plan A Few minu res wi rh amino acids and pro reins Then all of chap rer 3 From Genes ro Pro reins Pro reins are polymers of amino acids linked roge rher by pep ride bondsquot Single amino acid H 0 II R group is diFFeren r depending on aa rype HgN C c O R 20 diFFeren r amino acid rypes commonly occur in pro reins Examples of amino acids H O II HaN C C O CH 3 alanine HO II HsN C C O O H serine phenylalanine Amino acids are linked by pep ride bonds lo Form proleins Ala Ser Phe I f f CH3 CH2 CH2 pep ride bond I O Alanine serine phenylalanine Linked loge rher by pep ride bonds Pro reins lypically con rain hundreds of aa linked Jroge rher Examples 0F Promins Keratin is a brous protein Found in hair nger nails tortoise shells etc Myoglobin is involved in oxygen transport r Heme group binds oxygen mum um Protein Function depends on its structure Structure depends on the amino acid sequence Amino acids I like 0 draw Tex rbook likes rhis rhem like rhis COO H I H3N Cl COO39 H CR R NH Ei rher way is OK Structures and abbreviations of the 20 standard amino acids Hydrophobic amino acids or non polar 00 00 u f cu u c Mn N I Alanine Ala A Vallne Val V coo cu coo 39 in n cm l n c cn cn NH H NH Leucine Leu L Isoleucine lle I 00 C00 quot i 0 NH rm in Phenylalanine lPhe F Tvyptophan Trp W 00 C100 M f G C S C H f CQ O NH mu gt 39 Methionine Met M Praline the P Polar amino acids or hydrophilic 3900 3900 n cl u c NH H N Serine SH 5 Ihreonine ThrT CIOO loo u g M NH NH Tyrosine Tyr Y Cysteine Cys C 0039 390039 3900 H Cl nl HCl H CI H NH NH Asparagine Asn N Glutamine Gln Q Charged amino acids C00 0 C00 0 H m 039 H cCM CHc039 plan 39 NH Aspartate Asp D Glutamate Glu E NH NH Histidine His H Glycine Gly G foo NH u f curcm og og m u cl H CNN NH d mm NH NH Lysine Lys K Arginina Arg R Become Familiar wi rh rhe 20 amino acids rha r commonly occur in pro reins 3 le r rer abbrevia rions proper ries Wednesday amp Thursday class rhis week will be on pro rein s rruc rure Chap rer 4 Chapfer 3 of rex rbook From Genes ro Profeinsquot Central dogma oF molecular biology n oquot Lo rep I t I t39 DNA mRNA Prote39quot messenger RNA A Few words about DNA amp RNA These are polymers of nucleic acids Componenfs of DNA amp RNA DNA adenine A guanine G cyfosine C fhymine T RNA adenine A guanine G cytosine C uracil U A amp 6 have a similar purine ring structure NH2 0 N21 N N I KN HZNkN l H H Adenine Guanine C T 84 U have a similar pyrimidine ring sfrucfure NH2 0 H I I N I H l Cytosine Thymine Uracil U is a componenf of RNA Looks like fhymine bu1L wifh mefhyl group O Uracil Nucleosides A base attached to a ribose sugar ring OH OH Ribose RNA 2deoxyri bose in DNA Examples of nucleosides adenosine deoxyadenosine Found in RNA Found in DNA Nucleo rides have one or more phosphafe groups affached on OH OH OH Adenosine monophosphale Guanosine diphospha e AMP mop NH 0 o o 0AM II II II o O P O T O T D uxt Jr 039 o H n H n on on Cytidinetriphosphale CT Some nucleofides of DNA dGDP deoxyguanosine diphosphate deoxyadenosine monophosphafe deoxycyfosi e friphosphate Vocabulary NTPs means nucleo rides of RNA all roge rher NTPs ATP CTP GTP UTP dNTPs means nucleo rides of DNA all roge rher dNTPs dATP dCTP dGTP dTTP S rruc rure of a single oo I NH s rrand of DNA polymer 5quot o 1 3 an H Phosphodiester bond 0 Ilgt o o o I NH a cquot O lt L Guanine N quotN quot H H H H I N 0 0 0 0 JC N I T 39 c 0amp0 sugar phospha re 1 H N backbone N n i I H o To NH 1 quot Cy 39 osme CH 3 0 Nko 4 H H u u WafsonCrick base pairing in DNA H N N H O CH3 AdenineN NHN Thymine N N o H N 0 H N GuanineN NH cytosine N N HO a z Rosalind Franklin Kings College photographed x ray diffraction patterns from DNA bers Watson and Crick constructed a model of DNA with Features that made chemical sense and was consistent with Franklin s x ray diffraction data 539 m 339 end 4 Su arr hos hate backbones 1 g P P Mam 9mm MA nu aw Major and minor grooves in DNA Rotate so degrees nmund M39s axis rumor groove RNA can also form base pairs A U CG 2 s rrands of base paired RNA Base paired DNA and RNA helices are quite different in structure Why are DNA and RNA helices so diFFeren r in s rmc rure Why are DNA and RNA helices so different in sfruc rure RNA RNA DNA OH group in RNA H bonds wifh oxygen on ribose oF adjacen r nucleo ride This H bond in uences fhe orien m rion oF fhe ribose ring in RNA RNA can Form complex structures RNA JEv 1aof A stem loop in a viral RNA A pseudoknof within a messenger RNA 1 u Central dogma of molecular biology n o 49 cl transm lion translation 3 DNA P mRNA gt Prateln messenger RNA DNA replicalion is carried oul by an enzyme called DNA polymerase DNA polymerase lls in single slranded DNA lo make double slranded I 392 3 nmnll 131m 1 e a39llyu llV MS llWl WT 3 quotcf Mx W a DNA replicafion is carried ouf by feams of DNA polymerase enzymes defails fo come in chapfer 17 0 quot 0 4 DNA lranszriptian mRNA Iranxlnllan Protein messenger RNA Transcrip rion is carried ou r by RNA polymerase repI AA I W3 39 IampIVI39 I x r RNA polymerase makes a s rrand of RNA rha r is complemen rary ro rhe bo r rom s rrand of a DNA rempla re RNA polymerase reads DNA as ACGT wri res RNA as ACGU transm39 lion I anslar on DNA p mRNA 4 Protein messenger RNA Transla rion is carried ou r by a ribosome amp JrransFer RNA fRNA man The ribosome amp JrRNAs read Jrhe mRNA and make profein using amino acids DNA sequence codes For mRNA mRNA codes For pro rein sequence DNA 5 C T C A G T G C C 339 339 G A G T C A C G G 539 transcription RNA polymerase mRNA 539 CUCAGU GCC 339 rransla rion ribosome amp RNA Protein Leucine Serine Alanine The Standard Genetic Code TABLE 373 The standard genetic code 39 First Third position Sccond position position d 5 en U C A G 3 end U lIUl39 Plu llCl 39 Scr UAU 39I39yr HUN 8 U Ul 1C Phc ICC Sm UAC 39I39yr l ICC 7p C HI IA Lu IICA Sur 1AA Slop UCLA Sn up A Ul VG mu IICG Sm NAG Sn up UGO Trp G C Cl l39 hu CCU Pm Alf H b CG U Am J Cl 1C In CCC Pru CAC H b CGC Am C Cl 1A nu TA Pm AA Gln CGA Am A C 1 IO Lcu CCG Pm quotAG Gin CC G Am G A Al VII llc Mill I39hr AAI Asn A l Sm U Al K2 lk ACC I hr AM Asn Am 5a C Al VA Ilc At A I39hr AM l39s AGA Arg A All Mm I hr AM kw Am Arg 6 G il39ll zll 1139 Alz l GM Asp Zlf 11 U M Yul I Ala At Asp 1m 391y C UA Va A Ala HA In ZGA 213 A ltU al 1 Ala 2M Ju 00 Hy G quotl39lw 2 amino zu xlsurc uHxynnlud ALL alanine Mg gdUIJIIMIX lu gllnnnmlu Hts thdinu llu ismurine 5ch amino Thr 39I39hluxmwfl lp uypuzplun Tu luvsine and Val Ilhlu Learn how to use this table to convert a DNA sequence Into an amino acid sequence lrgimne sn Ls39mmghw Asp uspzlrlutr 1w awnI m Iy glyl39l ncz Hn Lw lemme Lys lysuxh ch nmhlunlnc l ho phonyiulunlnc Pm pmlmu Some rools of nucleic acid chemis rry 1 De rec ring DNA mel ring by UV absorbance 2 DNA sequencing 3 Polymerase chain reac rionquot or PCR 1 Detecting melting of DNA by change in absorbance of UV light Absorbance of UV tight by nucieic acids increases by about 30 when the base pairs are meited 1quot 5 K39d a Absorbnnce of UV We llghf at 260 nm A Temperature deg c rom a meiting curve such as above it is possibie to determine the meiting temperaturequot of nucieic aci s Why is there a change in UV absorbance upon melting DNA or RNA A change in absorbance at 260 nm that is associated with changes in base stacking Remember Beer39s law A 8 C 5 For nucleic acids is lower when base stacking occurs because base stacking changes the energies oF the 1 gt JI electronic transitions that give rise to the absorbance at 260 nm 2 DNA sequencing DNA sequencing uses DNA polymerase and dNTPs with a li r rle dideoxyNTPsquot ddNTPs mixed in OCH2 0 base H H H H H H 2 3 Dideoxynucleoside triphosphate ddNTP numumma my on mm mm aaaa r When the DNA pol uses a ddNTP the polymerization stops The resul ring DNA ends with a ddNTP nucleo ride which can not be ex rended Fur rher Labeled terminator ddNTP Sf jiTnTr rFT WHH 3 r S I L Denature separate DNA strands 3r n1 I I 5 Add short DNA primeri 5 3 3lli 35 Add DNA polymerase dNTPs ddNTPsi The DNA pol extends the top strand starting at primeri ddNTFgt terminates the chain ddN milllllllll I J Separate DNA strands to sequence top strands ddNn Mixture of DNA strands of g Trn WI UW different lengths all terminated with a ddNTPi ddNTP Mixture oF DNA strands oF diFFerent h 39W lengths all terminated wit a ddNTPl The ddATP ddCTP ddGTP ddTTP have diFFerent Fluorescent colors so you can tell which type oF nucleotide terminated the chain DNA strands to migrate through an electric eld which separates them by size This tells you the order oF the nucleotide sequence on the original DNA strands gt4PDDPPDBI DQDPBQOBIInoID I Detect the uorescent color as the DNA passes this point Figure From the text showing DNA strands oF various lengths migrating through an electric eld The color identi es the type A C G or T oF the ddNTFgt that terminated the strand t V J i I z mm 4 mm mame cuunnting The whole human genome was sequenced a Few years ago 1 a a 5 s 1 e C 2 HROMOSOM cu u 2 u 5 x lt 1 14 15 15 17 1a 1 Order your free copy of the Human Genome Landmarks poster E coli bacteria have about 4000 genes For 4000 different proteins Metabolism 21 Unknown 38 Structure 55 Replication transcription translation 85 Regulation Phages transposons 2 4 0 Other Transport activities 1 o 11 Functions of E coli genes 3 Las r fool oF nucleic acid chemis rry For ioday Polymerase chain reac rionquot or PCR PCR is used o make many copies of a sequence of DNA So iF you have jus r a li r rle bi r of DNA you can make many iden rical copies and ge r enough DNA For sequence analysis PCR is used ro make many copies of a sequence of DNA Sfep 1 One DNA quotprimersquot 3 y 3 m 6 quot 997 L m4 ml Sfep 2 3 51M am I J i Lu buA 940mg ole lh nub El 3 2 molecules of DNA 5quot l Repeal Sfeps 123 Sfep 3 4 molecules of DNA 8 molecules of DNA Repeal Sfeps 123 Wha r Jrhings do you need Jro do PCR DNA Fempla re Fo be copied amp DNA shor r primers dNTPs mixed dATP dCTP dGTP dTTP DNA polymerase preferable Fhermos rable so if can s rand Fhe hea ring and cooling cycles A popular DNA polymerase For use in PCR DNA pol From Thermus aqua ricus Taq polyerasequot DNA pol From Pyrococcus Furiosus PFu polymerasequot From a Fhermophilic archeaon Found near Vulcano Island I raly The polymerase chain reaction gure af end of chapfer 3 Maybe move rhis ro pro reins lec rure 2 add sec rion on recombinan r pro reinquot More rools oF nucleic acid chemis rry 3 Res rric rion enzymes Cu r DNA a r speci c sequences 5 GAATTC 3 3 CTTAAG 5 G AATTC CTTAA G Sticky ends G AATTC CTTAA G Blunt ends 5 GATATC 339 3 CTATAG 5 l GAT ATC CTA TAG Production of a recombinant DNA molecule cul anneal rigam 4 4 4 Plasma Recommnam DNA Farewgn DNA Dauuersxmnum wasmm cnnlammg gene m be muugemzed meal Imsmalcnsdpnmers Dnmmnxlunstan nmtmomv mm 91 my v Many mm m mm alumna DNA wnn mulngsmmd gm Sitedirected mutagenesis swmm haw w J Knowledge of RNA grea rly increased wi rh Jrhe defermina on of Jrhe ribosome s rruc rure by x ray crys rallography in 2000 Secandary Slruplure arge summu nbusuma RNA 539 I39mI The Complete Atomic Structure of the Large Ribosomal Subunit at 24 A Resolution Nand Ianquot yam lemnquot Jellny Huuux rem a Mam nmm A snm39 I Sugarphosphate backbones Hypochromism in nucleic acids De ned as a change in absorbance at 260 nm that is associated with changes in base stacking Remember Beer s law A 5 C e For nucleic acids is lower when base stacking occurs because base stacking changes the energies of the n gt n electronic transitions that give rise to the absorbance at 260 nm Hypochromism in nucleic acids De ned as a change in absorbance at 260 nm that is associated with changes in base stacking Remember Beer s law A 5 C e For nucleic acids is lower when base stacking occurs because base stacking changes the energies of the n gt n electronic transitions that give rise to the absorbance at 260 nm 1 g k 5 torka Luquk L RafJAMQA 914 exhnuA JIWJVK 5 3 0 Envnnkug skMJamp L E Arm quot393 Hypochromism provides a means For de rec ring s rruc rural changes in nucleic acids For example hm From a mel ring curvequot such as above if is possible ro quan ri ra rively evalua re nucleic acid s rabili ry 250000 bp DNA I I transcription Unspliced Liiii iiiiiirl mRNA I splicing 6129 bases SPIiCEd mRNA 12 l l 4444 bases 1480 codons I translation 1480 amino acids Protem page 69 Splicing Introns and Exons mRNA See p 599 601 Normal gene mRNA Protein Mutated gene mRNA Protein 504 505 506 507 508 509 510 511 GAA AAT ATC ATC TTT GGT GTT TCC Glu Asn lle lle Phe Gly Val Ser 504 505 506 507 508 509 510 511 GAA AAT ATC AT T GGT GTT TCC Glu Asn He He Gly Val Ser One of the abnormalities found in Cystic Fibrosis L39nnumhered page 09 2 Deletion 512 TAT Tyr out 512 TAT Tyr no Transcrip rion as described in the fex rbook Coding strand nontemplate Noncoding strand template 25m w in in i mi 7 4 Ur Digestion of bacteriophage


Buy Material

Are you sure you want to buy this material for

25 Karma

Buy Material

BOOM! Enjoy Your Free Notes!

We've added these Notes to your profile, click here to view them now.


You're already Subscribed!

Looks like you've already subscribed to StudySoup, you won't need to purchase another subscription to get this material. To access this material simply click 'View Full Document'

Why people love StudySoup

Steve Martinelli UC Los Angeles

"There's no way I would have passed my Organic Chemistry class this semester without the notes and study guides I got from StudySoup."

Kyle Maynard Purdue

"When you're taking detailed notes and trying to help everyone else out in the class, it really helps you learn and understand the I made $280 on my first study guide!"

Jim McGreen Ohio University

"Knowing I can count on the Elite Notetaker in my class allows me to focus on what the professor is saying instead of just scribbling notes the whole time and falling behind."


"Their 'Elite Notetakers' are making over $1,200/month in sales by creating high quality content that helps their classmates in a time of need."

Become an Elite Notetaker and start selling your notes online!

Refund Policy


All subscriptions to StudySoup are paid in full at the time of subscribing. To change your credit card information or to cancel your subscription, go to "Edit Settings". All credit card information will be available there. If you should decide to cancel your subscription, it will continue to be valid until the next payment period, as all payments for the current period were made in advance. For special circumstances, please email


StudySoup has more than 1 million course-specific study resources to help students study smarter. If you’re having trouble finding what you’re looking for, our customer support team can help you find what you need! Feel free to contact them here:

Recurring Subscriptions: If you have canceled your recurring subscription on the day of renewal and have not downloaded any documents, you may request a refund by submitting an email to

Satisfaction Guarantee: If you’re not satisfied with your subscription, you can contact us for further help. Contact must be made within 3 business days of your subscription purchase and your refund request will be subject for review.

Please Note: Refunds can never be provided more than 30 days after the initial purchase date regardless of your activity on the site.