3.8 Onwards Flashcards
1
Q
Where is peptidoglycan transferase found
A
In RIBSOMES.
2
Q
Nucleus acid context
A
Was discovered in cell nuclei so that’d why they were given this name , two types dna and and rna and both have roles in storage and transfer of genetic information, scythe did for proteins and basis for heriditwryn
3
Q
What makes a nhcelic acid a nuclei acids
A
Nuclei acids are polymers from nucleotides l every nucleotide has
- a pentose monosaccharide = either ribose or deoxyribose
- a phosphate group
- a NITROGENOUS BASE
Thus all elements are C, H, O ,P and N !
4
Q
More on ntitigounednbade?
A
Nitrogenous base contains either one or two carbon rings and hss nitrogen
5
Q
How do they join
A
Nucleotides join by condensation reactions forming covalent bonds
These happen between the phosphate group of one nucleotide which is connected to the FIFTH CARBON and the hydroxyl group of another nucleotide in the third carbon
This makes ohosphodiedyer bonds
Sgsin phonation grouo on 5th carbon connected to hydrolysis group on third
When they join like this they make a long chain of nucleotides that from the sugar phosphate backbone m which is only broken in hydro lido
6
Q
5’ 3’?
A
The the first top bit will be 5’ as it starts here and ends at 3’ , the other chain of nuckeoditded will be from 3’ to 5’ AS THEY ARE ANTIPARALLEL
7
Q
Now specifically for DNA = DEOXYRIBOSE NUCLEIC ACID?
A
= pentode monosaccharide is DEOXYRIBOSE ( and its ribose but without one oxygen. )
- phosphate group
- and can have between 4 nitrogenous base sugars = adenine guanine cytosine thymine
8
Q
Ribose vs deoxyribose
A
Both have hydroxyl group on OH on carb 3 which necessary for onophiduedyer
It ribose had a O on csrbknn3 Sewell , deoxyribose DOESNT!
9
Q
The 4 nitrogenous bases can be split into purines and purdimsidined bssed on how many csrbknnringd they have (1 or 2) which ones
A
Basically if it has Y so cytosine and thymine , then pYrimidine !
If no y then purine
PURINE ARE PURE SO THEY ARE BIGGER , this means they have a DOUBLE CSRBIN RING STRUCTURE
And thus pyramiding has single carbon ring structure
So it onyl binds from purine to pyrimidne so pure is adenine guanine and bigger and they bind to thymine and cytosine smaller sndnoruinidne ?
10
Q
Why are AT AND CG COMPLIMENTARY TO EACH OTHER ?
A
because they may a specific amount of hydrogen bonds with each other which couldn’t happen another way
- purines bind with oyrmidines so AT and CG , thryncomplimentsry becaude they form specific amounts of hydrogen bonds here
AT = 2 CG = 3,
11
Q
What is the actual arrangement of nucleotides dna nuclotidesin a molecule of dna ?
A
- made from two strands of polynucleotides (oh yah multipe nucleotides join to make polyneucletoudes .
- two strands are coiled to make a DOUBKE HELIX , where both strands are comolimenttaily base paired , with hydrogen bonds in between
- the. Two strands run opposite to each other and thus are antiparallel, this is thronly way they can successfully pair and be srrnsged
- here this is 5’ to 3’ and then then anitparallel is 3’ to 5’
So start from I discuss nucleotides that join by phosphodiedter bonds, thennteo dtrsndshydrogen bonds complimentary and sntiparlalle thstbcoil to make a double helix ,
12
Q
Why is base pairing properties importemt
A
The pairing between bases allows DNA to be copied and transcribed EXACTLY - and these are key properties required of the molecule for heridatwy , if it bonded differently each time it would not be able to perfection transcribe etc
13
Q
Now that we have our genetic information stored in sequence of bases, how is this transferred = WHAT IS RNA
A
ribonuclease acid
- nucleotides still
- with a phosphate group,
- ribose pentose monoscshride (had whole OH on carbon 2)
And also nitrogenous base
- this can be adenine guanine cytosine but not thymine, replaced by URACIL when copying
As thymine was pYrimidine with singl carbon ring, so is URACIL!
this transfer needs to happen because dna to bug snd two ssvrednto leave and come back each times so a section is copied and used instesd
This is transcribed into a messenger RNA and thus mRNA molecule
And the fact AT makes 2 AU makes 2 hydrogen bonds too, the fact this happens means base pairing rules still apply and copies are cal,
Here indifuak RNA nuekcotides also join in exact same way by 5 and 3 pjophodiedter bonds
Once dome
14
Q
What happens once finished
A
RNA molecule degrades in cytoplasm , where lhosphidetder bonds hydroksied snd rna nucleotides released and reused
KEY DIFFERENCE =
15
Q
KEY DIFFERENCE BETWEEN DNA AND mRNA
A
DNA IS OF TWO STRANDS, MRNA ONLY ONE!
16
Q
Why still complimentsyrb
A
As it still makes 2 hydrogen bonds, it emsns suit is still coplemit entry
17
Q
How do DNA extraction from plant material and why , what does each step do?
A
1) grind sample with pestle and mortar
- grinding will BREAK DOWN CELL WALLS
2) ADD either DNA extraction buffer or constituent home made ones , this contains = detergent , salt , protease enxumes
- the detergent interferes and breaks up cell membranes due to structure cussing them to form little micelles and break up like fats . This releases the Contents of the cell out into the solution
- now yius dd salt, which breaks the hydrogen bonds between the DNA and userounfing Ayer
- then you add protease enxumes , and these breakdown the HISTONE PROTEINS dna is wounded with , now you have dna free
3) at this point filter than add ICE COLD ETHANOL INZ
- this causes DNA to predeipate out of the solution
- and DNA is no longer protected here ss it is exposed so the soil keeps it protected
5) ss if precipices, ectrsctnusing dolit at angle without damaging
18
Q
Explanation sgsin
A
1) use a pestle snd Mortar to crush the sample and this removes cell walls
2) now add detergent - this breaks down cell surface membranes by interfering with steufture, causing content of cell to be relesded into the mixture
3) now add salt which breaks hydrogen bonds that are made between dna and water
4) now add protease enxumes and breaks down his tone proteins in between , exposing dna from not being as compact
5) pour it in to a COLD layer of ethanol, which caused the DNA to predicate out, and ethanol protects
6) use splits to extract st angle to not damage the dna
You could do it better by hosting first to cause proteins to denature already +
19
Q
How to do it there?
A
Heat and this caused protease to break down etc , can also use RNAse which will cause rna to break down too
20
Q
Why need to denature enxumes?
A
Stops any enxumes from actually breaking the DNA instead
21
Q
Why do cells require energy for in three typed?
A
Synthesis = large molecules such as proteins from small require energy
- transport = pumping molecules or ions across cell membranes for active transport
- movement = protein contractile fibres in muscles to cause movement
22
Q
How is energy supplied
A
Through ATP , adenosine triphoohste , which is a nucleotide that easilky gives energy
23
Q
Steufture ATP = Remember it’s a nucleotide ?
A
= - pentose monosaccharide which is ALWAYS RIBOSE
- nitrogenous base which is always ADENINE
- and three phosphate groups
= adenosine (adenine and ribose ) triphoohste atp
24
Q
Why is ATP called universal energy currency! Is it just human “
A
No it is the molecules used for energy transfer in ALL LIVING THINGS, not just humans
25
Why do ATP not make chains ?
Three phosphate groups negatively charged and close so will repel each other
- this makes it unstable , so chains couldn’t be ,ade, but useful too as you can use thidnproteryb
26
How does ATP release energy overalls
Small amount of energy used to break bonds but large amount for energy released when that phosphate group reacts with other stuff, so overall more energy relessed
This can be thought as energy releasing from the bind breaking to generalised , nit technically but by
27
How is atp cycle happen
Energy from respiration using products like glucose or lipids etc isn’t used straight away , the energy is used to convert ADP into ATP in ohodohykstion reactions , this used energy from respiration and almost stored it here, in condensation reactions
Then when energy needed by cells, the phosphate bond “breaks and released the energy”, and this required water , so hydrokysidn, and this only happens with other revstuond rewuirijg energy snd they are coupled
Respiration energy used to phoohykside and make atp in cindesnrjson
When needed nhdrolysis releases energy
Reason for this is because getting energy from there is hard and stored in ATP first
28
Why atp still used even if can’t store that much energy
Can’t store that much energy , unlike csrbihdyrsted or domething , but rapid ply reformed by khidohykisatuonn, meaning for a decent amount of ATP they don’t all need energy , but rather it is a good IMMEDIATE STORE that has other benefits
1) small and can easily move in and out if cells
2) UNIVERSAL , universal store of energy you can use for anything I’m body , and professes could be different if different energy stieesused each time
- it is SOLIBULE and can deliver energy to aqueous environemtd
- here’s main - RELEASES ENERGY IM SMALL AMOUNTS , WHOCH MEANS LESS ENERGY LOST SD WATSE LIKE HEST FOR WHEN NOT NEEDED (like glucose would rrlesdetoo much energy and this goes to ester ), and thus cells get EXACTLY WHAT THEY NEED
- easily regenerated rapidly by respiration do effeicnet too
And thus good immediate energy store
29
Again main
Released energy in small mskiutnd and less so energy jot wstded unlike glucose, d,all can fit everywhere, soluble for aqueous , UNVIERSAL for whole body, essilky regnerated by respiration so good , and energy small enough for cellular reactions but don’t wastes, do good universal currency
Good immediate too because energy given off instantly due to instability wheress kthers may take tike , and this is ebvause onionykstioj and hydroksied of aaatp happening all the time do energy given and restored , so more immediate, but none goes to waste too so makes Dinesen why to sue
30
DNA replication semi conservatively - what does this mean
This means that for eshc new molecule of dna it had half the old strand and half a new stand , so one old and one nee, so semi conservative
31
Why is this dine
Ensured that if mistakes are made the amount if these are reduced, as there will always be at least half the molecule correct , and that can salvage something
32
How is DNA replicated then with enzymes etc?
DNA must unzip and break hydrogen bonds, free nucleotides match up comokineyrsiky , then hydrogen binds remade and then phophidedter bonds but how does this happen
1) DNA helical enzyme travels along DNA backbone and catakydes reactions that breaks hydrogen bonds between the two strands - unzipping
2) BOTH ACT AS TEMPLATES lnow free nucleotides in the nucleus line up comokinetsriky against the exposed section of strands . Hydrogen bonds are then REMADE
3) finally DNA polymerase catalysed the reactions to make ohophiduedter bonds between the nucleotides again , creating the sugar ohojate backbone
Okay polymerase first then hydrogen
33
What is continuous and discontinuous variation , limitation of DNA pilymerase, how is this overcome and what is called, what enzyme is used snd what are stands called etc
- problem = DNA polymerase can only catalyse resctions to make phophodiedter bonds in the 3’ 5’ direction , attaching to the 3’ end . So it can only move in the direction of this location
- for the strand that goes in this direction , as the DNA unwinds, this is fine, the polymerase can just keep on catalysing revsvtions as strand continues to unzip and is fine. This is the LEADING STRAND And Undergoes CONTINOUSE REPLICSTION
- however other strand running from 5’ to 3’ end had to wait for a decent enough section to unfold first , before catalysing revstuond in the little 3 to 5’ , but then wait for snither section to open up. Thus it catksyded in fragments , known as Okazaki fragments . This is the LAGGING STRAND AND UNDERGOES DISCONTINOUS REPLICATION
in order to fix this, DNA kinase ensyme cstksyded resctions snd makes ohophdiedter bonds between Okazaki fragments ,
why can’t it just open all the way first and both happen?
- dna helcisde will break hydrogen bonds for the SHORTEDT time possible so that dna isn’t exposed as this increases chance of days,e, that’s why it does it as we go along, reokcistionnsnd unwilling st the same time so dna is proretcetd !
34
What is a mutation
Although dna relkcistionnshd to be really accurate to ensure generic information is conserved it can slip up. A mutation s an error in the cooying of dna in a strand. These are RANDOM and spontaneous and lead to a new chain
= a RANDOM ERROR IN THE DNA BADE SEQUENCE after replication
35
What is the genetic code
The fact that dna is what codes for all proteins in any animal, and that oroteins are based on a sequence of amino acids, then the dna must code for the sequence of skink acids , and this is the genertic code
It is the the sequence of base triple tee that code for amino acids for protrind, and this is present in all organisms each and every one ,
Three features of the genetic code = degenerate , universal and non overlapping
36
What does universal mean
Each codon ever coded comes from a base triolet, but this will be the sa,e for all organisms in the world, same triplet codes for same amino acid.
Also the fact that all organisms have the same 4 bases shows genetic code is universal
37
Genetic code just means?
That bases on dna codes for the amino acids of proteins for all organisms
38
What does degenerate mean
For evrything 4 baded means there are 4 x4 x 4 combinations possible , so 64 possible codons inckudijtna start and stop codon , yet there are only 20 amino acids to code for in the human body that makes all our proteins
The fact that there are MORE combinations then amino aicds means that more than one combination codes for the same amino acid,- this is known as the genetic code being DEGENERATE
- advantage
39
What advantage of being degenerate
Good becaude if mutation occurs that only changes one bsse, high chance it couks still code for the SAME AMINO ACID , and so no effect actuallyhappens, because there are more than one combinations for the same amino acids !, so chance of damage from mutations is REDCUED
40
What does non iverlapping mean
The fact that there is A START CODON means dna is always read from the first base and gied in threes after that, not from base 2 or 3 which WOUKD RUIN EVERYTHING this also helped by having a STOP CODON , So dna read ecstasy hoe it should be codon by codon
Thus non overlapping
41
If a mutation occurs ?
= random error in copying if dna base sequence. This could lead to a different sequence if baded which means a different amino acid than intended was coded and thus the wring amino acid in the sequence of proteins leads to a massive change if shape and thus say if it is an enzyme who’s active site ruined can’t carry cpjib etc
This is becaudechange in sequence leads to wrojt amino acid sequence which means primary structure is changed , leading to changes in deocnsayr and thus 3D structure of tertiary structure and perhaps quaternary do functions can’t happen
However this may not happen at all, as it is degenerate it judt may cause same amino acid and thus protein to be formed
Or it may happen and the effects not damaging like dimples
Or it may happen and the effects are actually ADVANTAGEOUS to the current selection pressure, making it more likely to survive !
42
Transcription and translation
Again dna to big to leave and dangerous so trsncrioted into mRNA first
43
Sense strand etc
The dense strand is the strand in the double helix that ACTUALLY ZCODEENFOR THE PROTEINS to be synthesised, and this runs from 5’ to 3’ end
The other strand is the antisense strand and acts as a t epilate to be copied, so that the mRNA molecuke had the EXACT SAME INFIRMSTJON SD THE DENSE DTRSND
44
Sense strand must be protected st all costs
The fact that this in a double helix means bases are not exposed , second strand doesn’t code for anything but atlesdy protected
X the fact that tid too big means it’s locked up safe under nuclear envelope from anything like hydrologic enzymes from dsmsged lysosome ir die thing
45
So process if transcription
1) section containing gene for protein to be synthesised unwinds by way of DNA helicase starting at start codon
2) as said before antisense strand acts as template so mRNA has same info as sense
- here free nucleotides in the nucleus lije against the antisense strand due to complimentary base pairs
HERE INSTEAD OF THYMINE , URACIL IS COMOELMETSRY TO ADENINE , SND REPLACES PYRIMIDEINE SO STILK AHS ONE CARBIN RUNG AND FIRMS TWO HYDROGEN BINDS , thymine shill still bind to adenine here . Here temporary binds between bases are made
3) now RNA pOlymerase catksyded revstuond to form phospodiester bonds between the RNA nucleotides , AND RHIS goes all the way until end of gene. This whole molecule now shoukd have exact same bases as sense strsnd but just uracil
4) finally mRNA detsched from antisense strand and leaves nuekcusd vis nuckesr pore , dna doubke helix reforms and mRNA completed molecule leaves to go to RIBSOMES on RER for translation
46
Summary
1) dna hkicase breaos hydrogen bonds between gene ,
Free nucleotides line up and form temp bonds against antisense strand which runs 3’ to 5’
Comolimnrwrtu abdenlairing occurs, but instead if thumine uracil other
Then rna polymerase makes ohospdiester binds
Then detached snd dna double helix results
mRNA molecule leaves by nuclear pores
47
Now mRNA goes to ribose but what is steufture of ribsome?
- RIBSOMES made from two subunits, one small and large
- but also equal amount if protein as fork if RNA called rRNA so ribosomal RNA
Purpose of rRNA is it plays a bicohemicsl role in catalysing reactions to make the PEPTIDE BONDS BETWEEN AMINO ACID , it also plays role ijndyeifyrusk stability if protein dyntheidensewuence (rRNA. Holds the mRNA I’m place ) SO THAT it can read
48
And wher die gin
After leaving nuckeud snd going to RIBSOMES it goes to the small subunits, which holds the mRNA in place and reads it and decides it is mini acids in translation
Here rRNA plays role structurally
49
tRNA structure and role
TRNA is transfer RNA and helps trnsldrsioj happen
- steufture =
- has three bases on one end of molecule called ANTICODON, which will compel fairly base pair with a real codon
- in the other end it’s got an amino acid that matches the codon
So tRNA brings amino acids based on codons on mRNA base sequence, which is exactly same as 5’ to 3’ sense strand
50
So whole process of translation thenn
1) the mRNA binds to the small subunit on the ribosome at its start codon (non overlapping)
2) the mRNA is “read” and a tRNA with an anticodon with complimentary bases forms bonds with codon start, along with tRNA it brings the start amino acid
3) now the next codon is read and a resulting tRNA with anticodon lined up binds due to comokinrwty base pairs and another respective amino acid is brought . Here a maximum of TWO tRNA CAN BE BOUND AT THE SAME TIME
4) Niw the first amino acid binds to the secind one. This is done and calaysed by peptidyl transferase, which is an enzyme and rRNA component of the ribosome l here peptide bind is madel
- now the first tRNA can detach and another can bind based on next codon
This process is fully repeated until the entire mRNA molecule is resd snd comokemkrsry amino acids are brought snd bonds are msde, now the protein is made and it can undergo its folic to
Polypeptide released
51
Next
Protein foods into secondary ferisry whatever
At RER, may be packaged into transport vesicles and make way to Golgi a appsrsud via cytoskeleton
Here can undergo more modifications (such as attaching csbrihdyrste chain or lipid ) and repackaged inti secretory vesicle snd either stay if ensyme hydrologic kysiixme or go and edit
52
Go over trnsldstion sgsin
53
What happens at the end
RIBSOMES can follow on the mRNA behind the first mRNA , the ribodke can do the same on another mRNA molecule do multilingual IDENTIFSL polypeptide chains can be suthendied st once
Finally mrna broke down and rna nucleotides go back to the nucleotide to be reused!
54
Enxumes why need to be used
Processes importsmt to life required chemical reactions k and these jeed to happen faster
To do this we need higher temps or pressure, but this nit oossibke as it woukd causes damage snd more nearby in bodies
Thus enxumes are used, which are bioiguvsl catksyded and speed up rate if reaction without being used up themselves
55
Two types of reaction
And where can these be (intracellusr and example was repsirsiton )
Extrsfeuklar like tryosinnsmylsde or fungi how they do
Catalyse anabolic reactions = making larger molecule from smaller
- such as proteins in musckes
Also catalyse catabolic reactions = making smaller molecules breakdown from larger
- such as digestion
Theee can be both intracuellar (so enzymes in the cell such as enzymes for repsirsiton , classes)
Or also extraceukalr = so enzymes like tryoisjnfor proteins, amylase for starch
Even outside of bacteria like fungi who secrete external enzyme d
56
How enzymss helps
They offer a different reaction pathway which required less activation energy , which is minimum amount for nergy needed for a reaction to start and so helps reaction happen at lower temps and pressures
Two ways
57
Steufture of enzymes
- have an active site, and this is where the substrate binds to, which is determined by the TERITIARY 3D FOLDING OF THE PROTEIN
- for an enzyme to work dubdtrste hsd to fit exactly and be comokiniwrty to the active duet
- and this allows ensyme shbstrste comoled to be made
- if they aren’t it won’t work = this make highly soecidc
58
Two ways = lock and key hypothesis
| Indie fed fit hyprotheid
1) in the same way how only one key fits into a lock, only one specific substrate will “fit” into the ensyme, due to them being highly specific. And this only happens if the substrate is COMOLEMTNARY TO THE ACTIVE SITE (determined by tertiary structure )
2) next wHen it binds, an enzyme substrate complex is formed. Reaction happens, and products are formed, making an ENZYME PRODUCT SUBSTRSTE , and then the products detach, leaving the enzyme unchsnged and able to tskenosrt in another reaction
So ensyme shbrate k react ensyme product, releaded
59
What about induced fit hypothesis
New hypothesis suggesting that the active site of the enzyme actuslly changes as sub rate approaches
Here intisl interactions between enzymes and subtract are weak, but these inrptervstiosn cusse rapid changes in enzymes TERITSRY STEUCTURE , chsnging the shape of the active site a bit
Thus the substrate doesn’t only have to fit in, but idncud a change such that the active site changes in a way that it fits in perfectly too! So even more specific, have to make active site change exactly to match comokinrwrty shape as changed happen
Now ensyme substrste ocmoelx made, then ensyme produced, then they release snd can happen again
60
But how does the binding actually lower the activation energy of reaction?
If anabolic
- two substrste molecules need to John, and enzymes HOLDS THE SUBSTRSTED IN A WAY THAT THE RIGHT grouod of atoms are held close enough so they can react, and counters repulsion felt, this means resctions can happen essilky which what would have othereise rewuired probably pressure to negate repulsion
For CATABOLIC
-fitting into the ensyme causes strain on the bonds in substrste, and this makes it easier to break so less energy required
Here the r groups on active site ensyme interacts with the substrste in temporsry bonds, but these temporsry bonds put strain in existing bonds making it easier
Again anabolic = holds atoms close together even though reclusion kesjd it can bind essilky
Catabolic. = trmprosyr bidns between r groups and substrste sooly strain weakening snd making it easier to react due to lower sfrifsruojnejergy e
61
Exaowl of extrsfukskr ensyme amylase snd Maltese for starch digestion ,
1) starch first digested and broken down by AMYLASE (assum starch exists as Amy,odd that’s why) into disaccharide maltose . This happens in the mouth where amylase released by saliva but produced in pancreas and salivary glands
2) now maltose is broken down by maltose into glucose, which is small enough to be adoberver by vikinlining the small intensive.
62
Why ensyme needed
Can’t just inject nutrients as too big
63
And example of proteins digested dextran,Umar
Trypsin is found in small intestine , and produced in onacress
It catksyded snd breaks down long chsind of polypeptide chains into dmsller ones which can then be worked in by other protease
Eventually the amino sicds monomers do small can be dbrorbed by blood stream
64
Again where everything found
Most thing small intensity snd produced pancreases, Amy,add also preiuced slavery grandad and digested there too, the maktsde and protesde trypsin both haooen small itneditine until small enigubt I be absorbed
65
Factors affecting rate of reaction for ensyme d
Temp , pH, substrste snd enzyme conc
66
Effect of increase of temp to ensyme rate of reaction
- increasing tmeorature increases kinetic energy of the enzyme and substrates
- as a result they vibrate and collide more frequently, which leads to more successful collisions and more ensyme substrste complexes being made = rate of reaction increases
However this only happens to an optimum temperature , where the rate of reaction is the highest
- past the optimum temperature an increase of temp cause the atoms snd bonds to vibrate a lot and eventually this puts strain on the binds between the tertiary and quaternary structure like hydrogen bonds .
- eventually they break, and breaking if these binds causes change in tertiary structure of proteins , and thus the active site if the enxumes changes
£ this means even with induced, the active site is no longer comokinatsrybti the substrate , and so an enxukensusbtrste complex can’t be made, so the enxyme isnnow densturedn
- rate if reaction will then rapidly decrease up until all the enzymes have denatured
By the way, only a small increase last optimum temowryred is needed to caused Thurman as only a slight change in the 3D structure is needed for substrate tonjot be comokinrwrty = remember high soecityb !
67
Decrease rate off reaction?
Reduce kinetic energy vibrations and frequency coloiodjndo rate if reaction decrease
However decrease in rate of reaction below optimum temp is less rapid because enzyme does nkt actually densture here
68
What is q10 ?
When does this not soluble
This temperature foeffiedjrn and is a measure of how much the rate if reaction increases with a 10° rise in temoertsuren
Thus you di rate if revstuond after / before
Normally thidnid 2 which means it doubled
Haowever thid does not solely after enxumes have been densturedn
And this is for everything elde constant
69
Rememebr which bonds broken
Ionic and hydrogen and in tertiary not quaternary
70
Extreme temp sdsltusojd
```
Cold = less tsbke so small change in tmeortsure will denature them
Hot = need more bonds to be stable such as DISULFIDE bridges snd hydrogen snd withstand temoersturen increase
```
71
How does oh vhange cause change I. Structure
Hydrogen and ionic bonds result in polar and charged interwvtiojennof regroups
Hydrogen ions interact with these polar and charged R groups, which changes the degree of interaction between R groups already , so the polar snd hydrogen bonds
- these interactions also affect the interactions of r groups with each other = and this causes changes
An increwse in hydrogen bonds ,meow ph , means the less r grouod are able to interact with each other , ajdnthis leads to bonds breaking and thus shape of enzyme chsngeing due to change in tertiary structure , which changed shape of active site and thus enxyme can’t make complex snd rstebif reaction decrease
This is true for when lower h+ ions and ph is high, the amount the r groups can intersct with each other decreases and leads to breakage of bonds
This meand that a change of lH both ways causes envy,Ed to denature and so they only functioning within a narrow range
- here the active site will only be at the most correct correct shape when the optimum pH is met- and so greatets rate of reaction. When the pH changes from the optimum the shape changes due to h+ ions affecting the degree of interactions r groups csn make from each other. this lowers rate if reaction , HOWEVER IF PH BROUGHT BACK , then shape returns and it will resume the normal rate , this is RENATURATION, but this can only happens within a narrow range
Past this it will peremsnrley denature
72
PH summary
- H+ ions affect the degree of interactions R groups can make with each other, but also the degree of interactions of Hydrogen bonds and ionic bonds
- thus an increase/ decrease of H+ ions (pH) leads to a lower degree of interaction between R groups, which leads to bonds breaking , change in 3d structure, change in active site, denature, rate reaction decrease
- happens for both high and low pH , and permanent denaturation
- yet if this happens within a smaller range, renaturation can happen such that it returns to its optimum pH and reacts jsut as good
73
Thud how to increase rate of resctions to optimum
Increase or decrease lH increase lH to tooting , but past this will cause it to denature , if returns d calm, but if too much no
74
Rate reaction highest at start
Highest amount to concentration of substrate , so draw a gradient at t = 0
75
What do we know about substrste concentration
Increase substrste concentration= increase ror until all the active sites of enxyme are occupied, and so you reach a saturation limit, increase past and no more
Increase becaude higher frequcney of collisions and higher chanced of enxyme substrate complex being made
For enxumes , increase concentration = increase frequency of collisions and increase the rate of reaction , however again this is to a point until the substrates are all catksyded and rate reaction decreases
This is known as v max
76
Again
Increase substrate cind means higher chance collid snd lead to successful collisions and thus rate of reaction increase due to more being made
But then stsursutin all active sites used = v max, and now enxyme concentration is limiting factor not substrate
V max achieved enxyme concentration once all the substrsted catalysed
Remember fornrate reaction to be 0 it has to go down
The graph is rate of reaction vs concentration of substrate or endyme
So for substrste, it steady increase until all used, and this v max
For enxyme it stead increase until nine left and goes to 0?
77
Substrate cocn against time graph
Is starts high and then as time increase reduce as more and more catksyded, and rate of reaction decreases as concentration of reactant used up
78
Rate of reaction edpeiment ?
Measure the increase of product produced over time, decrease reactant
Here we measure the amount of oxygen released based on enxyme catalase catalysing hydrogen peroxide into water and oxygen
Use an upturned flask to collect oxygen , or a gas syringe and take reading so
Add hydrogen oeridode in and then using suringe catksyded , every time interval measure
Now you can do different experiments by changing conditions and see how much more based one ste if reactions, draw groans
So like hydrogen periodise higher temp
HERE THEY USE LIVER TISSSUE AS A SOURCE OF CATALASEnornally snd then denatur or something
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How else can change in that practical
Change concentration if the substrate by dilution, lH by acificing, but csntwith the enxyme add more or leds, temp etc
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How to find difference conch
| How to change the concentration of the catalyse
Di this using SERIAL DIKUTIONS , add 10 of full, then take one out and put into, add 9 , take one out , each tike you are diluting by 10
Grind down liver or potato to make a solution which is known as 100%
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Why do enzymes need to be I hibtued sometimes?
If hey happen too fast then too many products when not needed are made, and also resourced wstded
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Competitive inhibition
This is when a molecule has similar shape to the substrste of the enzyme and is also complementary to the active site if the enxyme competed with the substrste for the active site,
This blocks the substrste from forming a complex such that reaction takes place snd decreases rate of reaction
Again
A molecule that is structurally dimilsr to the substrate in the dense thstbit is comolemtsry to the enxyme active site , competed for the sctive site with the substrate
If it succeeds snd binds the enxyme can not catakyde the reaction levels and is I HIBITER
- this redcued the amount for nxyem substrate complexes rhstbsre made in a given time snd reduces the rstebif rsvruinn
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Are they temp or permanent
Some are permsntnet bust most of them are temporary
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What happens to the VMAX of the rate of reaction with a competitive inhibitor?
Nithing , VMAX is still achieved but after a longer time, as rate of reaction is reduced due to I hbiotr but assuming it is reversible eventually all the dubtared will be cstlsuded .
This id
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How to reverse affect of the comeltive in inhibitor
Increasing substrate concentration reversed the effects as increase means for a constant inhnit, there is a higher chance substrate molecules makes a complex and so rate of reaction increases until it ends up being the same as before without a comoetive incubator, the more you increase, the less dominant the effect was
Do increase substrate concentration increases rate of reaction but ssme VMAX is achieved just a bit quicker
This is because eincrease means substrate molecules OIT COMPETE THE INIBITOR DTURGCURSLLY DIMILAR SCRICE SITE INED
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Non competitive inhibitor
The inhibitor binds at a site that’s not the active site , at an allots Eric site
This changes the 3D shape of the protein due to binds formed
And this changed the shape of the active site meaning the subdtrste can no longer make a complex and is I hi inter due to it no longer being fomolemtwry
As the inhibitor does not compete for the active site = non comeptive inhibitor
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Increasing substrste or endyme
If you increase the condensation of the substrste , it won’t make a difference because once inhibited thidnid normally per,ant snd that enxyme is not able to cstsksdyd sgsin. If you increase enxyme theh yh if not inhibited rate reaction starts to go up again
If you increases inhibitor, rate if reaction inky goes even more down as more and more accorded sites become unsvislbie
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This time what changed?
Increase inhibit or give a certain amount, then VMAX WILL DECREASE, this is because the maximum rate of reaction can’t happen as there are less enzymes
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Are they reversible or irreverisble
They can be both but tend to to be irrrveisble
Just because they are doesn’t reman good or necessarily bsd
Such as one can ireeveisobekninhibt enxyme necesssry for nerve transmission daudijg cramp and paralysis etc forever
But to treat long term indigestion you may need something that irrrveidbke permsntly stops hydrogen ions pump ion and Laing acidic, which actually saves you?
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End product inhibitor
Thidnid when the procutnof the cayskysstion is used to inhibit the reaction from happening even more
This served for a NEGSTIGE FEEDBSCK SYSTEM , so that EXCESS PRODUCTS ARE NOT MADE AND RESOURCES ARE NOT WASTED . This is non competitive , but REVERISBLE INHIBITOJ (non competive because product could not be same shape so wouldn’t be competive , and can’t be fully irrevdibke because you can then never use that reaction again
Example
- for example atp system , when atp made form glucose it binds to allosteric site in enxyme that breaks down glucose to stop mor eglucose form being broken down. This means when levels of ATP are high, less are encouraged to be made
- but when atp leveks are low then ledd atp is a bale to bind to sllosteric site, meaning more glucose is broken down and levels of atp rise again = negtosve feedbsck and non competive and revseible i hibit,
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Cyanide metabolic poison inhnitor?
Consider is non comeptive and IRREVDIBKE inhibit of cytochrome c oxidase , which catksyded repsirsiton resctiojsn, cells that can’t respire due
This binds to allosteric site irrevdibke which stood respiration of happening snd causes death CYANIDE IFREVIBSLE NON COMEPTIVE OF CYTOCHROME C OXIDDASE RELISNIBKENFOR CSLTYSIFN REDOIREITON RESCTIOND , KILLING THEM
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What are inactive precursors
Enxumes sometimes made so thst they are inactive until something happens. This works by a ,ole uncle in place inhibiting its function by an enxyme. Only when the molecule is removed can the enxyme inhibit
Example is some protease enxumes , you don’t want the, to damage the cells they are made in, so they have molecule that inky in presence of high pH is removed so stomach and then they can work
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Difference between prosthetic group cofactors and coenzymes
They all are a NON PROTEIN grouo that helps the enzyme function as a biologicsl cstlsdyt
Cofactors are inirgsnjc + they are TEMPORARILY BOUND
Coexnymes are organic
Prosthetic group are cofactors that are PERMANELTY BOUND and form a permanent feature of ensyme
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How do these three help enzymes
They could form part of the active site, or also hellmtrsnsfer atoms or groups from one reaction to another
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How are cofactors and coenzymes different
Cofactors tmeorwirly and organic, and thede are NOT CHANGED INNRESCTION , often help form part of the active site
COENZYMES are Organic, and they are often changed in resctiond, BUT ALWAYS RECYLED BSCK (do one changed , then stats is changed bsck)
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Examples you need to know for exam = chlorine ion and an 2+ zinc
Amylase which catksyded star act into maltose used COFACTOR (looedley bound) cl-
And carbonic anhyrase for metabolism of carbon dioxide uses prosthetic group ZN2+
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Coexnjem
Derived from vitamins, NAD is needed for respiration
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So back to inactive precursors, that need a change to tertiary structure to work , how is this achieved
1) Adding a cofactors , before this is called apoenzyem , after cofactors it is called holoenzyme
2) also by other enxyme working in enxyme like protease , this is proenxyke
3) or change like oH like inactive pepsinogen ,which itherwide fell effects of pepsin
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How to design practical
Identity variables independent depdennt and everything control
Procedure and safety
CONTROL EACH TIME
how you can vary
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Again enxyme
Competive inhibit = competed soteucturslly similar withstand Clive side tend to be reveiebl
Non competive binds to sollaodteric site which caused change int ertwiry snd I hints, this means can’t react , and for example cyanide to cytochrome oxidase
Now end prices inhibtion is a way for negative feedbsck system to work,product of one inhibits own pathways / reaction, such as atp for glucose, so low glucose it makes and high glucose it inhibits
Then inactive eorecurose needs tome adjustment before work thisnto protect body fromitdkef, such as change ph pepsiongen so it fit. Fidget self, and sdftion if cofactor goifn from apoenxyem to haloenxyme or work done by smother enxyme like protease so sporenxyme
Corfsctor irrevrdileb organic, often nit changed snd help active site, example is cl- in amylase
Coexnyme is a cofactors other organic , derfived form vitamins like b3 to make NAD, hereiftenget changed but recycled and help transfer atoms between enxumes
Cprotethic grouo is cofactors permanent , xn2+ on carbonic anhdyrase
