Module 2.3 Flashcards
DNA is built from molecules called nucelotides.
Structure of nuecleotide is found in DNA ,
-Dont need to know structure but check sheet .
But nucleotide consists of three parts and we do need to know these …
check sheet
What is in the center of the strucutre?
Contains a five-carbon sugar molecule.
-Sugars with 5 carbon atoms are called pentose sugars .
What is attached to the sugar ?
We find a nitrogen-containing molecule called a BASE .
-Sometimes referred to as nitrogenous ses as they contain NITROGEN .
What is attached to the other side of the sugar molecule ?
We find a negatively charged phosphate group .
-meaning nucleotides contain the elements carbon , hydrogen, nitrogen and phosphorous .
represent nucleotides using a simpalr model
-need to learn this structure , so check the sheet
-nucleotides are used to make both the molecules DNa +RNA
-The nucleotids in DNA + RNA all share the same general structure.
-But tere is specific differences
First difference between DNA + RNA
-In DNA , the pentose sugar is clled deoxyribose .
-Whereas in RNA , the pentose sugar is called ribose .
-Deoxyribose has one fewer oxygen atoms than ribose .
second difference between DNA + RNA
(check sheet )
-In DNA nucleotides , we find four different bases
-If you look at the bases you will see two have a DOUBLE RING strucutre . Adenine +guanine
-Scienists call these PURINES .
-The other two bases - thymine nd cytosine have a single ring strucutre
-scienitsts call these pyrimidines .
Third difference between DNA and RNA
Just like DNA , RNA also contains denine guanine and cytosine .
-Howeveer , RNA DOES NOT containthymine .
-Instead it contains URACIL .
NEED TO KNOW THIS AS THIS IS VERY IMPROTANT .
General strucutre of a nucleotide (check sheet)
-Can see the hydroxyl group on carbon 3 of the pentose sugar.
-That is because it plays a really important role.
What is the important role ?
-If we take two nucleotides (check next page )
-Then we cn form a ond between them -PHOSPHATE GROUP of one nuecleoitde + hydorcyl group onc arbon 3 of the pentose sugar on the othe rnucleotide ,
(check sheet to see bond )
What is the bond called ?
PHOSPHODIESTER BOND - NEED TO KNOW THIS !!!!!!!!
-wHAT HAPPENS WHEN THE PHOSPHODIESTER BOND IS FORMED ?
-Water is released so is an example of a condensation reaction .
-+THIS moelcule we formed is a dinucleotide .
-can break the phosphoidester ond by adding water .
-THIS IS A hydrolysis reaction
-We can continue to add nucleotides by forming phosphodiester bonds .
Have formed a polymer of nucleotides and scientists call is a polynucleotide BOTH DNA RNA are examples of polynucleotide.
Structure of dna
Dna consists of two polynucleotide stands .
-we have the sugar phosphate backbone on the outside with bases on the center .
-the two poly ue Lodi fox’s stands are held together by hydrogen bonds , which form between the bases on opposite strands .
KEY : based on one strand are complementary to the bases on the other strand .
Guanine on one strand always pairs with cytosine on the opposite strand . Adensine slways pairs with thymine .
-this complementary base pairing is central to how Dna functions .
In the last video , we saw both adenine and guanine are purines because of their DOUBLE RING structure .
iWhereas thymine and cytosine are pyrimidines because they have a single ring .
-what this means is that purine on one strand always pairs with pyrimidine on the oppsoite strand .
This means that the distance between the sugar phosphate backbone is constant , all down the DNA molecule.
-the two polynucleotide strands in Dna are anti parallel . Meaning they run in opposite directions .
-looking at the left hand side , we can see that the top of the phosphate group is attached to carbon 5 of the deoxyribose sugar .
At the bottom , we have the carbon 3 hydroxyl at the top .
At the bottom , we have the carbon 5 attached to the phosphate.
The different base pairs form a different number of hydrogen bonds .
Adenine an thymine pair forming two hydrogen bonds
Cytosine and guanine pair forming three hydrogen bonds
Because of the complementary base pairing , the properties of guanine and cytosine are always the same as eachother .
The proportions of Adensine and thymine are also the same as eachotehr .
-this means we can calculate the proportions of the different nucleotide
Check sheet for example question
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The two polynucleotide strands in dna , twist around eachother and form a double helix
We can see that the sugar phosphate backbones on the outside and base pairs in the center .
Structure of rna
RNA is also a polynucleotide but rna is different in a number of ways :
RECAP :
RNA contains the Penrose sugar ribose rather than the deoxyribose found in DNA .
RNA does not contain the base thymine , instead , RNA has the base uracil .
One difference between DNA and RNA
Dna is found in chromosomes of the nucleus whereas RNA is found in the cytoplasm .
RNA plays a key role in protein synthesis .
Second difference between DNA and RNa
DNA is an extremely long molecule .
-Often containing many millions of nucleotides .
-in contrast , RNA molecules are much shorter , making RNA molecules only contain a few hundred nucleotides
Third diffeeence between DNA and RNA
Lastly , Dna is a double stranded molecule , consisting of two polynucleotide starts twisted into a double helix .
Whereas rna molecules consist of only one polynucleotide strand .
Dna replication -everytime a cell undergoes divison , all of the DNA is copied .
The process is called DNA replication .
Stage one of DNA replication
The enzyme DNA helicase attached to the DNA molecule .
-DNA helicase causes the hydrogen bonds between the complementary bases to break .
Stage two of dna replication
This causes the two polynucleotide strands to separate from each other .
Stage theee of dna replication
Now , free nucleotides line up with their complementary bases on the DNA strands .
At this stage , the free nucleotides are only held in place by HYDROGEN BONS between the complementary bases .
-they are not bonded to eachother by phosphodiester bonds .
Notice something different about free nucleotides ?
Thee are called activated nucleotides .
-SHEIN a normal activated nucleotide inactivated nucleotide has three phosphate groups . Where a normal nucleotide contains
Going to the previous diagram , as you can see activated nucleotides are lined up , held in place by hydrogen bonds between the complementary base pairs .
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Stage four of dna replication
At this stage , a second enzyme kow attached . Enzyme is called DNA polymerase .
DNA polymerase or down the molecule and catalyses the formation between the formation of a phosphodiester bond between the activated nueclpetodes . This is an example of a condensation reaction .
Key : when phosphodiester bonds forms , the activated nucleotides lose , their extra two phosphate groups .
As those two phosphate groups leave this provides energy for the reaction .
Now got , two copies of our four double standard molecule .
However , each of the DNA molecules contain one strand from the original DNA molecule and one stand which is brand new .
-this type of Dna replication is called semi consecrate replication
Important dna is coped accurately
But sometimes , an incorrect bade is inserted into the growing polynucleotide strand
This means that the sequence has changed .
Scientists cal this mutation and these can be very harmful to the organisms .
Remember , mutations wre random and occur spontaneously
Heck fhe video girl it’s so illegible
What happens in semi conservative replication
In semi conservative replication , the Dna helix sepearate into two polynuecleotide strands .
-Each strand is then replicaed into a complementary NEW STRAND .
-SSo at the end ONE molecule of DNA has been copeid into two m olecules of DNA .
KEY about semi conservatie replication
Two copies contain one strand fromt he original DNA moleucle and one enw strand ( orginal is in white and new one is in red in the picture )
-When the strucuture of DNA , was discovered int he 19501s , scienitsts did not KNOW how dna is replicaed .
-Semiconservative replication was ONE possilit .
-Another possiilitt was CONSERVATIVE REPLCITION ; a DNA double helix i formed contaning TWO NEW STRANDS .
-The DNA moelcule contains none of the ORIGINAL DNA .
-SO scienistss had ot design an EXPERIEMNT .
so scienitsts had to design an experiemnt to show whether DNA replcited by cosnervaive or semi conservative repliciton .
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experimentnal details and results .
-to udnerstand this experment , need to understand ONE IDEA .
-All of the bases of DNA CONTAIN THE ELEMENT NITORGEN .
Nitrogen exists as two main isotopes , what are they ?
Nitrogen -14+Nitorgen -15 .
-Nitrigen -14 is the most common isotope , With over 99% of nitrogen atoms being nitrogen-14 .
KEY ; ntirogen-15 is sligghtly HEAVIER than atoms of Nitrogen-14 .
Stage one of the experiment
scientists took a sample of BACTERIA .
-Under normal contions , almost all of the nitrogen atoms atoms in the DNA of these bacteria , will be nitrogen-14 (the lighter isotope ) .
stage two of the experiment
scieniets now took some of this bacteria and extracted the DNA .
Stage three of the experiment
they then placed the DNA in a solution and spun this at a very high speed in a centriguge .
stage four of the epxeriemnt
the DNA moved down the solution and formed a band the scientists could detect .
KEY of the experiment
thhe postion of the DNA band depends on how heavy the DNA IS .
-Because of the nitorgen atoms int he DNA were almost all nitorgen-14 .(high nitorgen )
-This forms a banf ear the TOP of the tube .
(I have repreented the DNA containing light nitorgen represented as FAINT LINES )
Stage five of the expweriment
scientists culture the bcteria in a growth medium .
-Which contains only nitrogen whicho ne .
stage six of the experiment
after the bacteria had reproduced many many times .
-Almost all the nitrogen atoms in the DNA was nitogen-15 (heavy nitogen ) .
stage seven of the experiment
when this dna was extracted and centriguged .
-it formed a band near the bottom of he tube .
(DNA containing heavy nitrogen represened as THICK LINES ) .
SUMMARISE
-When bacteria are grown in nitorgen -14 what does this mean ?
-Because their DNA was LIGHTER it formed a band near the top of the tube .
-But when nitrogen as their dna was HEAVIER it formed a BAND neAr the BOTTOM OF THE TUBE . -
STAGE EIGHT OF THE EXperimetn
now scienitsts took a sample of the acteri which ahd been growing on nitorgen- (heavy nitrrogen
-scienitsts transferred these bacteria to nitorgen-14 .
-allowed them to replciate their dna oly ocne .
stage nine of the experiment
the scientists extracted the DN nd spun it in a centriguge .
-What they found out was that this DNA porduced a band inebtween he two bands produced BEFORE
-This told the scienitsts that this DNA containied one strand containing N-14 and one with N-15 .
WHY IS this finding really improtant
this si really improtnt ,as this means tht the DNA must have replciated SEMICONSERVATIVELY
REMEBER - ina semiconservtive repliction the DNA porduced contains one strand fromt he ORIGINAL DNA and one compeltely new strand .
4-In this case , the replicaated DNA , has one strand containig nitorgen-15 and one strand nitrogen-14.
Stage ten of the experiment
At this point , the scienitsts allwoed the bacteria one more time of ntirogen-14 .
-Whent eh DNA ws extracted nd spun it produced a band t the BTTOM shown here .
-We still have the INTERMEDIAR BADN but we now have a band enr the TOP pof the tube .
We can xplain this if we go ack to pur previosu diagram .
-After the second round of replication , we have four DNA molecules .
2 contains one strand of N-14 . and stand with N15 , can see here .
-This represents dgidg
-The two n-1 dna moelcules both contain two strand with oonly n-14 tjese repset the ond .
EXAM –> could e sked to suggest what resuts would show if DNA replicte cosnervatively rather thean semi cosnervaively
remember , conservative rep ends upw ith one moelcuel df DNA continig wo ignal strans .
-ANd oen meolcule of DNA contianin two new stands .
-back to the experiment after one round replication , we would have one dna moelculecontaining only ntirogen -15 and one moelcule with only ntioreng -14.
After two rounds of replciaiton we would sitll only have one moelcule only nitorgen-15 ut 3 dna moelcul continign n-14
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key WE HAVE no dna moelcules CONTAINING both n-14+2-15.
So with conservative rpelciaiton , we would get to see a bdongin pattern , shown here .
-In cells , the DNA is arranged in a speciic way .
this is different between eukaryotes and prokaryotes like bacteria .
one difference between prokaryotes and eukaryotes .
-DNA in prokryotes iss usually circular with no free ends .
HOWEVER ; in euakryotes the DNA mooleucle are linear (got two ines ) .
second difference between prokaryotes and eukaryotes .
In prokaryotes , the DNA molecule are relatively short and compared ot the FN moelcules in eukryotic cells which re much logner .
third difference between eukaryots
in eukaryotes , the dn moelcules re tightly wrapped around poteins called HISTONES . Forming compelx strucutres called chromsomes
-In contrast , the DNA in porakryote is not bound to histones .
So prokaryotes DNA does not exist as a chromsomes .
-Have been discussin DNA found int he Nuclleus of eukaryotes .
where else can we find dna apart from the nueclues of eukarutes ?
-in mtochodnira and chloroplasts .
-This DNA is very simailr to the DNA found in prokarytoes .
(AKA relatively short circulr and not attached to histones .
nucelus of eukaryotic cells –. the dark material in the nueclue is the DNA bound to histones . (not possile to any dsitict chromsomes ) - WHY ?
That is because , at this stage , the chromsomes have a relativley ioen strucutre .
-At this point , we refer to thDNA and histones a CHROMOATIN.
Before a cell divides all of the chormsomoems are copied .
-These two copies remain unattached at point clled the centromere .
-Niw the rtwo dna moelcues are called chromatins left chromtin and right chroamtin .
(now refer to whole strucure as chromosmoes .
the chromsomes CONDESNE (KA Dna and hsitones form densel packed loops and coilks
and chromsomes become visile .
Homologous chromsomosomes
23 from mother
and 23 from tather
-scienists refer to thesr a homogous oaur
jey 2 chromsomes in a homogous pair have the same genses .
-The postion of a gene ona c hromsome is called ALOCUS for tha gene .
WHta is a gene ?
gene is a section of DNA , hich encodes the amino acid sequece of a polypetide .
-Soemtimes , random mtuatins tak eplace and this eans cjamhed on ense can occur .
different versiosn .
-Scienitsts call thiese versions of a gene ALLELES .
A humans inherits one of each of the homogous chromosmes in a pir one from mother and oen from fther .
meaning in a homogus pair , of chromosoems , alleles do not have ot be the same
could e aa bb ab ba .
KEY l a lot of the DNA WE FIND INA CHromsomse , do not code for polypetides , WHat are the reasons for this .
ONE REASON FOR THIS L i that beween the genes , we find larf amounts of amino acids of repeging base sequeneces .
-THese repeating sequenec sequeneces do ot code .
SECOND REASEON - even twithin the funcionl genses ,w e ind strethe of non-coding DNA , these are called introns .
Certaub reguibs if chromsoomes re called GENES
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Genes play role in protein ynthesis
-as the nuecleotide sequenece of a gene eencodes .
-The primary , strucuture of a polypetide (AKA the sequence of aminoa cids ) .
SUMMARY
-There are two main stage of protein synthesis the first stage is transcription and this takes in th NUCELUS .
SUMMARY- PROTEIN SYNTHESIS
-During transcription , they have base sequence of a gene is copied onto a complementary base sequence of a molecule called messenger RNA (mRNA )
SUMMARY of protein syntheiss (2)
the MRNA molecule then ma moves to the cytoplasm .
SUMMARY of PORTEIN SYNTHESIS (3)
in the cytoplasm , the ifnormation encoded int he neucleotide seqeucne of the MRNA is used to join a specific order of aminoa cids , formign the polynucleotide . (scienitsts call this trnslation ) .
TRANSLATION (1)
Part of a gene encoding a specific polypetide .
-Stage one of transcription , DNA helicase breaks the hydorgen bonds becaus eof the stwo strmds.
TRANSLATION (2)
Now the complementary RNA nucleotides move into place and form hydrogen bonds witht hw bases ont he expodes nuecloeitfrs on one of the DNAstrands .
Translation (3)
A t this point , the enzyme RNA polymerase joins the RNAnucleotides by forming phosphodiester bons /
TRANSLATIOn (4)
The enzymes continue to move thier way long the DNA , until they each the end of the gene .
translation (5)
now the produced stand of messenger RNA .
KEY ; if you looka t he messenegr RNA , you will see that the base sequence is the same as the top of the DNA STRAND .
-EXCEPT thymine has been replaced byu racidl .
-we call ths DNA strand the sense strands
the Mrna is complementrary to the other DNA strand + we call this the antisense tempalte strand .
translatino (6)
once the mrna has been syntehsised ,the RNA polymerase deaches from th DNA .
+The DNA foe back to tis normall oduble helix .
translation (7)
At this sgtgae of the MRNA , moes out og he nuecues htorugh a nueclear por . Onc eint he cytoplams , mRNA CAN TAKE PART INTRANSLATION (MRNA SHORTER THAN IT REALLY IS INRL ) .
human hve 23 chromosmes , other orgnisms have more or less .
-All the genes in a cell is called GENOME .
-In eukaryotoes , this include both the genes on the chromosomes and the genes in mitochondira and in chloroplasts .
-As we’ve seen , the nuecleotide nucleotide sequence of a gene , determines the AMINO ACID seencw od POLYPEPTIDE / PROTEIN .
-All of the porteins produved bythe genome of n orgnism is clled the proteome .
-Only a frction of that gene will be those protiens willbe produced in nay particuaalr cell type .
-Cells can produce different rnge of proteins deoedning on what the cell is doing .
Key mRNA nucleotide are read as series of triplets .
scienitst call these tripet GENETIC DOE .
Key features of genetic code one
-MOst amino acids have more than one triplet ,
-e.g iplet .
e.gleaine –> 6 triplets nd a large number of maino acid has four .
-because of this scientusts call the geentic code a DEGENERATE CODE .
key features of a geentic code 2
-the triplet code is non-overlpping
no base is read more than once .
third key feature is genetic code
-The genetic code is universal .
-The same tripets encode the same aminoacids , in the vast majoring of orgnisms on planet EARTH .
As said before ,t he mRNA nucletoide srethe mRNA nucleotide sequence is used to determine where tp dtart tradnslating the mRNA molecule .
-This is called a start triplet .
-The start triplet also ecncodes th amino acid methione .
-3 triplets determine where translation stops . These are called STOP TRIPLETS .
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What happens in translation ?
-in trnalsation the nuecleotide sequence of mRNAENCE OF THE Mth mMRN is used to determined the amino acid sequence of a polypeptide .
showing a sketch of the MRNA , each triplet in the mRNA is clled a CODON .
KEY ; in order for the mRNA to be read , and another type of RNA is invovled .
-GTThis is clled rna (tRNA)
-transfer RNA has two important parts .
Imporrtant part one of tRNA
-t the top of the TRNA moleucle we have the bidning site for an amino acid .
Important part of tRNA two is
-at the bottom we have triplet of bases called the anticodon .
-The tRNA for the aminoacid methione .
-KEY ; the Trna anticodon is complementary to the mRN codon for that amino acid .
-go back to our mRNA , one codon is AUG , this is the start CODON , but also the codon for methione .
-As you can see the , anticodon , ont he tRNA carrying mehtuoine .
–It is compleentarty to the mRNA codon , for methione and infct this is a complementay TRNA for the codons encoding every amino aicds .
REMEMBER ; man amino acids , re encoded bys everal triplet and each of these will have a corresponding transfer RNA .
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Stage one of translation
-Once the MRNA moves from the neuclues to the cytoplas , the small subunits of a ribosome , binds iwth he mRNA at the start codon .
-Ribosomes contain a number of different porteins . They also contin a type of RN called IBSOOMAL RNA .
Stage two of translations .
-Now the tRNA moecule with an anticodon , complementary to the start codon attached .
-This is held in place by HYDROGEN BODS between the complementry base pairs in the mRNA nd tRNA .
Third stage of transltion
-Now a second tRN moelcule moves into place .
-THe ntidcodon on this tRNA is complemenary to the second dondon on the mRNA .
-IN THIS Mrna , THE SECOND CONDON IS CALLED gccg .
-lOOKING AT HE GENETIC CDOE this codnon encodes the amino acid alanine .
four stages of translation
A peptide bond forms between two amino acids .
-This is catakysed by the enzyme petide ransferase .
-which is actually part of he risomes RNA moeucle .
-+The formation of the peptide bond reruies energy porvided by ATP .
Five stage of translation
-now the ribosomes move to the next codon nd forms a peptide bodn to the next amino by enzymes int he cytoplasm .
six stages of translation
-the first rna moleucle is rleeased .
-trna moelcules that have been released re attached to their amino acids by enzymes int he cytoplasm .
seven stage trnalsation
-the ribodomes continues moving down the mRN forming the polypeptie .
stage eight of translation
when the ribsoome comes to a stop codon , it detached the polypeptide chain and is rleased .
key
rleeased .
-I should just point out that one the first ribsoome , has stored another ribsoome can attach to th other stat codona nd start traslating .
-we might see a wole line o ribosomes making htier ay along the mRNA >
-tHIS MEANS that a large of polpeptide moleucles can be produced rapildy .
stage nine of translation
once the polypeptide chain hs crefully foledeit can then carry out its function in the ce;.
Where are covalent bonds formed by consolidation
Condensation reactions .
Nitrogenous base is linked with c1 of the sugar residue and phosphate groip linked to either c5 or c3
Nucleotides consolidation
They become phosphorylase’s nucleotide when they contain more than one phosphide groip
Nucleotide part two
They help to regulate many metabolic pathways xx
An may be components of many coenzymes
Pjosphodester bond is
Covalent bond
Equal sized rings on the fam ladde
Caused by a oriole alwahs pairing worj phrimode
Giving the molecule stability
Consolidation semi convergence replocarion
Look at page 89 bruh
What are the theee forms of rna
Messenger rna
Transfer rna tRNA
And ribosomal rna rrna
Why is the generic code described as ehe rage
As most amino acids fhere is more than one base triplet xx
- this may reduce the effect of loint mutations as a change in one base of the toilet could produce another base triplet thay codes for the same amino acid
What do magnesium ions do for riniodomes
Magnesium ions jelly to bond the ribosome subunits togeyher
What happens after the polypeptide change has been assembled consolidator
The mRNA breaks down and its component loelfilew can be recycled into new lengths of mRNA with different condom sequences. .
Table lists fhe steps involved ind na extraction why is
- sample blended w a mortar and pestle
- detergent added
Protease added - ethanol added
- break down cell walls
- break down fell memebranes
- break down proteins associated with dna
- to precipitate the sna
