2.3&2.4 Flashcards
Double helix
Shape of DNA molecule, due to cooling of two sugar phosphate backbone strands into a right handed spiral configuration
Monomer
Molecule that when repeated makes a polymer, nucleotides monomer of nucleic acids
Nucleotides
Molecule constituent of five carbon sugar, a phosphate group and a nitrogenous base
Polynucleotide
Large molecule containing many nucleotides
DNA polymerase
Enzyme that catalysed formation of DNA from activated deoxyribose nucleotides, using single stranded DNA as a template
Helicase
Enzyme that catalyses the breaking of hydrogen bonds between the nitrogenous pairs of bases in a DNA molecule
Semi conservative replication
How DNA replicates, resulting in two new molecules, each of which contains one old stand and one new strand. One old strand conserved in each new molecule
Gene
A length of DNA that codes for a polypeptide or for a length of RNA that is involved in regulating gene expression
Polypeptide
A polymer made of many amino acid units joined together by peptide binds
Protein
Large polypeptide of 100+ amino acids and terms often used synonymously and insulin described as small molecule
Transcription
Prices of making mRNA from DNA template
Translation
Formation of a protein at ribosomes by assembling amino acids into a particular sequence according to the coded instructions carried from DNA to the ribosomes by mRNA
Active site
Indented area on surface of enzyme molecule with a shape that is complementary to shape of substrate molecule
Catalyst
Chemical that speeds up rate of reaction and remains unchanged and reusable at the end of the reaction
Extra cellular
Outside of cell
Intracellular
Inside of cell
Metabolic/metabolism
Chemical reactions that take place inside living cells or organism
Product
Molecule produced from substrate molecule by enzyme-catalysed reaction
Substrate
Molecule that is altered by an enzyme-catalysed reaction
What’s are nucleotides
Biological molecules that participate in almost all biochemical processes
What is composition of a nucleotide and how is it formed
Phosphate esters of pentose sugar, where a nitrogenous base is linked to C of sugar residue and phosphate group is linked to C5 or C3 of covalent residue by covalent bond formed in condensation reaction
What is the monomer of DNA and RNA
Nucleic acids
What is then pentose sugar in RNA and in DNA
Ribose and deoxyribose
When do nucleotides become phosphorlated nucleotides
When they contain more than one phosphate group
Give an example of a phosphrated nucleotide
ATP adenine triphosphate
What is ATP
Energy rich end product of most energy releasing biochemical pathways and used to drive most energy requiring metabolic processes in cells
What do nucleotides do (pathways by ATP, ADP AND AMP)
Help regulate many metabolic pathways by ATP ADP AND AMP
What may nucleotides be components of and example
Components of many coenzymes like NADP
What is NADP used in
Photosynthesis and of NAD which is a coenzyme used in respiration and of FAD and coenzyme A both also involved in respiration
3 components of nucleotide
Phosphate group, pentose sugar, nitrogenous base
Where is DNA found
In nuclei of all eukaryotic cells and cytoplasm of some prokaryotes cells and in some viruses
What is DNA and what does it carry
Hereditary material and carries coded instructions used in development and functioning of all living organisms
Why is DNA one of the most important macro molecules
It makes up structure of the lining of organisms and makes proteins, carbohydrates and lipids
Structure of DNA (simple)
Polymer made up of many repeating monomeric units called nucleotides
What does a DNA molecule consist of and how is this described
Consists of 2 polynucleotide strands running it opposite directions so described as antiparallel
What are the different nitrogenous bases in DNA
Adenine, thymine, guanine, cytosine
What is a phosphodiester bond
Covalent bond between the sugar residue and phosphate group in the nucleotide
What happens when polynucleotides are synthesised and broken down
Bonds are broken when polynucleotide breaks down and formed when it is synthesised
What do DNA molecules carry
A lot of encoded genetic material
Are DNA molecules long or short
Long
Which nitrogenous bases are purines and how do we know
Adenine and guanine as they have two rings
Which nitrogenous bases are pyrimidine and how do we know
Thymine and cytosine as they only have one ring
What are the two categories the nitrogenous bases are split into
Purines and pyrimidines
How do the two antiparallel strands join together
Hydrogen bonds between two nitrogenous bases
Which groups of nitrogenous bases pair together
A and T, G and C
How do adenine and thymine pair together
By means if two hydrogen bonds
How do cytosine and guanine pair together
By means of three hydrogen bonds
Why do purines always pair with pyrimidines
To ensure equal sized ‘rungs’ on DNA ladder
What happens when DNA molecule is bonded together and what does this provide
Twists into a double helix which provides molecule with stability
What is the purpose of hydrogen bonds in DNA molecule
Allow molecule to be unzipped as they are weak for transcription and replication
What is the upright section of a large DNA molecule resembling a laser formed by
Sugar-phosphate backbone of antiparallel nucleotide strands
What happens at the 5th end of DNA molecule
Phosphate group attaches to C5 of deoxyribose sugar
What happens at 3’ end of DNA molecule
Phosphate group attaches to C3 of deoxyribose sugar
What do the rings on the ladder consist of
Complimentary base pairs joined by hydrogen bonds
Why is it good that DNA is very stable
Integrity of coded information with base sequence is protected
Where is the majority of DNA content of genome found in eukaryotics
Nucleolus
How is DNA kept
Each large DNA molecule is tightly wound around special histone proteins into chromosomes making each chromosome one DNA molecule
What is DNA like in mitochondria and chloroplasts
A loop of DNA without histone protein
What is DNA like in prokaryotes as what is it described as
It is a loop within cytoplasm not enclosed in a nucleus or wound around histone protein so described as naked
What do virus DNA look like
They have it in the form of a loop of naked DNA
What do all DNA within a cell and within all cells in organism carry and why
Coded instructions to make and maintain that organism
What must happen when a cell divides
DNA must be copied so that each daughter cell receives a full set of instructions
When does replication of DNA happen during mitosis
Interphase
What happens in interphase
Chromosomes first join at centromere forming two sister chromatids so each each chromosome gets an identical copy of itself
Does DNA in mitochondria and chloroplasts also replicate each time organelle divides
Yes happens just before cell actively divides
How does DNA make new copies of itself firstly
Unwinds and double helix untwisted but by bit by enzyme gyrase
What happens in DNA replication when DNA unzips
DNA unzips and hydrogen bonds between nucleotides are broken, catalysed by helicase to make 2 strands of DNA with exposed bases
What happens in DNA replication after it has been unzipped
Free phosphorlated nucleotides, present in nucleoplasm, are bonded to expose bases following complementary base pairing
What enzyme catalysed the addition of new bases
DNA polymerase
Which direction is leading strand in and then lagging strand
3” to 5” and lagging is 5” to 3”
What is each single strand described as
Template strand for new bass to be added to
How is leading strand synthesised with addition of new nucleotides
Continuously
How is lagging strand synthesised with addition of new nucleotides
Added in fragments discontinously
What enzyme joins new nucleotides together and zips up the DNA molecule
Ligase
What supply’s energy to make new phosophodiester bonds
Hydrolysis of active nucleotides which release extra phosphate groups which supply energy
What is the product of replication
2 DNA molecules identical to each other and parent molecule
Why is a DNA replication described as semi-conservative replication
Each DNA molecule contains an old strand of DNA and a new strand
Do loops of DNA in mitochondria chloroplast and prokaryotes also replicate semi conservatively
Yes
How does DNA in prokaryotes replicate
A bubble sprouts from loop and unwinds and unzips it and complementary nucleotides join exposed ones till as whole new loop is copied
What are issues that could occur with replication
During replication errors may occur and wrong nucleotides may be inserted which could change genetic code and is a point of mutations
How often does replication errors occur
1 in 10*8 base pairs
What reduces the rate of mutations produced
During replication process there are enzymes which can proof read and edit incorrect nucleotides
Are all mutations harmful
No many genes have changes to their nucleotide sequence called an allele or gene variant
Do all mutations give an advantage or disadvantage and example
No all are (roll your tongue or not) but some are such as animals which are white and live in snow
What can some mutations lead to
Cancer
Why are can helicase break hydrogen bonds easily
As they are weak
What must be added before DNA polymerase can add new bases
A primer must be added
Why is the lagging strand slower
As a new primer must be added for every fragment
What are the fragments on lagging strand called
Okazaki fragments
What is strand that new bases added to called
Template strand
How is RNA different from DNA (4 things)
Sugar molecule in RNA is ribose not deoxyribose, nitrogenous base uracil (pyrimidine) replaces thymine, poly-nucleotide chain is single stranded and shorter, 3 forms of RNA (mRNA, tRNA and rRNA
What is a gene and what does it contain in eukaryotic cells
Each chromosome in nucleus has DNA molecule and on each chromosome their are specific lengths of DNA called genes, each gene contains code that determines sequence of amino acids in particular polypeptide/ protein
What are proteins and how many of them are there in an organism
Account for 75% of organisms dry mass, some proteins are structural like cytoskeleton, others make up cells tool kit like enzymes which many catalyse formation of non protein molecules like lipids and carbs
What determines the amino acid/ primary structure of a protein
A sequence of base triplets found in each DNA molecule
What happens is primary structure of polypeptide is incorrect
It will fold incorrectly and won’t be held in its tertiary structure so it won’t be able to carry out its function
Why is proteins structure important for enzymes
Shape of enzymes active site must be complementary to shape of substrate molecule
Why is proteins shape important for antibodies
Part of antibodies have to be complementary to shape of antigen of invading pathogens surface
Why is shape of protein important for receptors on cell membrane
They must have complementary shape to cell signalling molecule which it much detect (drug/hormone)
Why is shape of protein important for ion channel proteins
Needs hydrophilic amino acids lining protein and lipophilic on outside layer next to the lipid by layer of plasma membrane
Where are genes found and where are proteins made
Gene found in cells nucleus but proteins made in cytoplasm at ribosomes
What happens to gene instructions as they are too big to leave the nucleus
Copy of each gene must be transcribed into a length of mRNA
When gene code is in form of mRNA what are the sequence of base triplets called and what does this now mean
Codons, which can pass out of nucleus
What happens once coded instructions are translated
Protein is assembled correctly from amino acids
Why is genetic code universals
As almost all living organisms have the same triplet if DNA bases code for the same amino acids
Why is genetic code degenerate
For all amino acids except methionine and tryptophan there is more than one base triplet which may reduce effect of the point of mutation as a change in one base of the triplet code could produce another base triplets that still codes for same amino acid
Why is genetic code none overlapping
As it is read starting from fixed points in groups of 3 bases
What happens is a base is added or deleted
Causes frame shift as every base triplet after that and every amino acid coded for is changed
What is the first step in transcript
Gene unwinds and unzips and hydrogen bonds break between complementary nucleotide bases
What happens in transcription once gene is unzipped
Enzyme RNA polymerase catalyses temporary formation of hydrogen bonds between RNA nucleotides and their complementary unpaired DNA bases on the unwound DNA strand (template strand)
What bases go together in RNA pairing
A-T. A-U. G-C.
What is produced after RNA polymerase has finished adding bases
Length of RNA which is complementary to the template strand of the gene is produced and identical to coding strand
What happens once mRNA strand is formed
mRNA passes out of nucleolus through nuclear envelope and attaches to ribosome
Where and how are ribosomes made
Made in nucleolus in two smaller subunits which pass separately out of nucleus via pores and then come together to form ribosomes (magnesium ion helps bind the two subunits together)
What are ribosomes made of
ribosomalRNA and protein in roughly equal parts
Where is tRNA made and where does it go
Made in nucleolus and passes out of nucleus to cytoplasm
What are tRNA
Single stranded polynucleotides which can twist into a hairpin shape
What are at the two different ends of a tRNA molecule
One end is a trio of nucleotide bases that recognise and attach to specific amino acids and at other end is another triplet base called anticodon that is complementary to specific codon it bases on mRNA
What catalyse synthesis of polypeptides
Ribosomes
What does the tRNA do in translation
Brings amino acids and find their place when anti codon binds by temporary hydrogen bonds to complementary codon on mRNA molecule
What happens as ribosomes move along the length of mRNA
It reads the code and when 2 amino acids are adjacent to each other a peptide bond forms between them
What is needed for polypeptide synthesis
Energy in form of ATP
What is the amino acid sequence for a polypeptide determined by
Sequence of triplet nucleotide bases on length of DNA (the gene)
What happens after polypeptide is assembled
mRNA breaks down and it’s component molecules are recycled into new lengths of mRNA with a different codon sequence
What helps newly synthesised polypeptide fold into its 3D or tertiary structure so it can carry out its function
Chaperone proteins
What does mRNA attaching to ribosomes cause
Amino acids to assemble in correct order with the help of tRNA
Why does tRNA fold in on itself into a 3D shape
So they can bind to amino acids at one end and mRNA at the other end
What happens before tRNA arrives at ribosomes
Amino acids attaches by specific enzyme for each different amino acid
What happens once the amino acids are aligned
Peptide bonds formed between amino acids and polypeptide chain is eventually formed
Example of why genetic code is non overlapping
If the code was ACU GCA it would only read it as 2 groups (ACU AND GCA) not ACU then CUG then UGC
What is an advantage of the genetic code being non overlapping
It is more flexible
Cofactor
A substance that has to be present to ensure an enzyme catalysed reaction takes place at the appropriate rate
Enzyme substrate complex
Complex formed by temporary binding of enzyme and substrate molecules during an enzyme catalysed reaction
Enzyme product complex
Enzyme molecule with product molecules in its active site joined temporarily by non-covalent forces
Q10
Temperature coefficient, calculated by diving rate of reaction at (T+10)degreesC by rate of reaction at T degrees C
Concentration
Number of molecules per unit volume
Competitive inhibition
Inhibition of an enzyme where the inhibitor molecule has similar shape to substrate molecule for enzymes active site. Blocks active site and prevents formation of ES complexes
Inhibitor
A substance that reduces or stops a reaction
Non-competitive inhibition
Inhibition of an enzyme where competitor molecule attaches to part of the enzyme molecule but not the active site. This changes the shape of active site which prevents ES complexes forming, as the enzyme active site is no longer complementary in shape to the substrate molecule
What are enzymes
Biological catalysts because the sped up metabolic reactions in living organisms
What do enzymes actions effect
Both structure and function within cells, tissues and organs
What are catalysts
Speed up reactions and remain unchanged at the end of the reaction, so they can be re-used
What can small amounts of catalyst do
Catalyse conversion of large numbers of substrate molecules into product molecules
What is Turnover number
Number of reactions enzymes can catalyse per second
What do chemical catalysts usually need
High temperatures and extremes in pH
How are enzymes different to chemical catalysts
Speed reactions up at much lower temperature and natural pH and normal pressures
Due to enzymes working at neutral pH, low temp and normal pressure what does this mean
They can function in conditions which sustain life
Mare enzymes or chemical catalysts more specific and why
Enzymes as they don’t produce unwanted bi-products and very rarely make mistakes
What do cells do where enzymes are made and/or act in
They regulate their production and activity and o fit the needs of a cell or organism at that time
What does enzymes structure all them to do
Carry out their function like all biological molecules
What my enzymes need when catalysing a reaction
Help from cofactors
Where are instructions for making enzymes found
They are encoded in genes
What happens to making of enzymes if a gene mutates
It alters the order of amino acids in a protein which alters enzymes tertiary structure so it won’t work
What happens when an enzyme which catalyses a metabolic reaction is deficient
Metabolic disorders can occur
What do enzymes catalyse as well as reactions
The formation of organisms structural components like collagen in bone, cartilage and vessel walls
What do some genetic disorders cause, give an example
Cause malfunction of connective tissue and can be harmful and lead to ‘stone man syndrome’
What is enzymes basic structure
Large molecules with a specific area/indentation on molecules surface called active site
How many amino acids does the active site consist of
Only 6-10
What is so special about the tertiary structure of enzymes active site
It is complementary to the shape of the substrate molecule
What does enzymes active site and substrate being complementary mean
Each type of enzyme is highly specific in function as it can only catalyse reactions involving a particular type of substrate that fits into its active site
How can the shape of enzymes active site and its ability to catalyse a reaction be altered
By change in temperature and pH as it affects bonds which hold the protein in its tertiary structure
Do enzymes catalyse intercellular or extra cellular reactions
Both
How many metabolic reactions happen at the same time within organelles in cells and how does this relate to enzymes
1000, each catalysed by a different enzyme but some are part of the same metabolic pathway
What is each metabolic pathway in living cells
Is one of a series of consecutive reactions, every step catalysed by a specific enzyme that produces a specific product
What acts as substrate for specific enzymes
Various reactants and intermediates
What are known as metabolites
Reactants, intermediates, products
What happens in catabolic metabolic pathways
Metabolites are broken down into smaller molecules and release energy
What happens with anabolic metabolic pathways
Energy is used to synthesise larger molecules from smaller ones
What are two examples of complex metabolic pathways and why
Respiration and photosynthesis as many enzymes are involved
Where is catalase found
In almost all living organisms that are exposed to oxygen
Why is catalase so important
Protects cells from damage by reactive oxygen quickly breaking down hydrogen peroxide which is a potentially harmful bi-product if many metabolic reactions of water and oxygen
What is catalase structure
4 polypeptide chains and each contain a haem group with iron
How fast does catalase act
Fastest acting enzyme with a turnover of 6million per second
Where is catalase found in eukaryotes
Inside small vesicles called peroxisomes
When do white blood cells use catalase
When ingesting pathogens, as it helps invade the invading microbes
What is catalase optimum pH
7
What is optimum pH and temp for enzyme catalase
Between pH 4-11 and temp for humans is 45degreesC but for some thermophilic archea it is 90
What happens to enzymes which act extracellularly
Enzymes are secreted from cells where they are made and act on their substrate outside the cell
Give an example of an extracellular and how it works
Fungi(bread mould), releases hydrolytic enzymes from their thread like hyphae, the enzyme digests carbs, proteins and lipids in the bread and the products of digestion-glucose, amino acids, fatty acids, are absorbed into fungal hyphae for use in respiration and growth
What happens to many enzymes in our digestive system
They are secreted from cells lining alimentary canal into the guts lumen where they extracellularly digest large molecules (carb,protein,lipids) and nucleic acids found in food. Products of digestion are then absorbed by epithelial cells of gut wall, into bloodstream to be used from respiration, growth and repair of tissue
Where is amylase produced and where does it act and how does it work
Produced in salivary glands and acts in mouth to digest polysaccharide starch to the disaccharide maltose, amylase also made in pancreas and acts to catalyse starch into maltose in small intestine
Where is trypsin made, act and how does it work
Made in pancreas, acts in small intestine lumen to digest proteins into smaller peptides by hydrolysing peptide bonds
What is trypsin optimum pH
pH7.5-8.5
What is lock and key hypothesis
Substrate fits into enzymes active site as the tertiary structure of an enzymes active site give it a complementary shape to substrate molecule (like a key fits into a lock)
What does the lock and key represent
Lock is enzymes active site and key is substrate molecule
What happens when substrate fits into enzymes active site according to lock and key
Substrate fits into active site and temporary hydrogen bonds hold the two together forming and enzyme-substrate complex
What happens once ES complex formed
Substrate molecule broken into smaller product molecules that leave the active site
What happen when a larger molecule is being formed according to lock and key
Substrates fit in ES complex forming bonds between the two substrates making and enzyme-product complex then the larger molecule leave the active site
What energy do both substrate and enzyme molecule have
Kinetic energy and are constantly moving randomly
What happens when substrate successfully collided with enzyme according to lock and key
ES complex is formed and substrate fits into complementary active site on enzyme
What happens to substrate molecule in active site
Either broken down, or built up into product molecules-forming an enzyme-product complex whilst still in active site
What happens once product molecules leave the active site according to lock and key
Enzyme can form another ES complex
What can a small number of enzymes do
They can convert a large number of substrate molecules into product molecules
Who c up with induced fit hypothesis and how
Koshland modified lock and key hypothesis by suggesting active site is not a rigid structure but the presence of a substrate molecule induces a shape change giving it a good fit
What did Koshland say about induced fit model
When the substrate molecule fits into active site, the active site changes shape to mould itself around the substrate molecule
How is the induced fit model often described
Putting a glove onto a hand
What is similarity and difference between induced fit model and lock and key
Substrate still have a complementary shape but on binding there is a subtle change in the shape of the side chains(r-groups) of the amino acids that make up the active site to give a more precise confirmation that exactly fits substrate molecule
What does induced fit moulding around substrate mean
Enables substrate to bind more effectively to active site, an ES complex is formed and
What forces bind substrate to active site
Non-covalent forces like hydrogen bonds, ionic attractions, Van Der Waals forces and hydrophobic interactions
What is the name for a product molecule that hasn’t left the active site yet
Enzyme-product complex
Why do product molecules detach from enzymes active sites
As they have a slightly different shape from the substrate so they no longer fit
What happens when product leave active site
Enzyme molecule is free to catalyse another reaction with another substrate molecule of the same type
What is the sequence of substrate becoming a product molecule
Enzyme+substrate->ES complex ->enzyme-product complex ->enzyme+product
What do chemical reactions need to begin
Energy
How are chemical reactions often provided with energy to begin them
Heated to provide energy so reactants react together
What happens when chemical reactions are heated
Increases kinetic energy of molecules so that they move faster and more randomly and are more likely to successfully collide together and react together
Why can’t biological reactions active by adding heat
Temp can’t be increased as it would denature proteins and lipids would melt
How do enzymes work to start a reaction without need of excess heat
Enzymes have a specific active site if a substrate, they bring substrate molecules close enough together to react with the need for excess heat so they lower the activation energy and speed up metabolic reactions
What do enzymes involved in catalysing oxidation-reduction and others like it need to work and what is it called
Only work if another small non-protein molecule is attached to them-called cofactors
What is a cofactor which is permanently bound to enzyme called
Molecule permanently bound by covalent bonds to an enzyme molecule is called a prosthetic group
What is an example of an enzyme with a prosthetic group
Carbonic anhydrase contains a zinc ion permanently bound to its active site
Where is carbonic anhydrase found and what does it catalyse
Found in erythrocytes and catalyses interconversion of carbon dioxide and water to carbonic acid which then breaks down to protons and hydrogencarbonate ions
What is true about most enzyme-catalysed reactions
They can happen either way depending on the concentration of product or substrate molecule
Can only enzymes have prosthetic groups
No other proteins can such as haemoglobin has a haem group
How do some enzymes work better not permanently bound to a cofactor but work in the presence of ions
Ions act as cofactors, during enzyme-catalysed reactions, enzyme and substrate temporarily bind forming an ES Complex, presence of certain ions that may temporarily bind to either substrate or enzyme may ease formation of ES complex and increase rate of reaction
What do some cofactors act as
Co-substrates as they and the substrate form the correct shape to bind to the active site of the enzyme
What do some other cofactors do
Some cofactors change the charge distribution on the surface of the substrate molecule or on the surface of the enzymes active site and make temporary bonds in ES complex easier to form
What does the enzyme amylase digest and when will it function
Digests starch to maltose and only functions if chloride ions are present
What is the main difference between cofactors and coenzymes
Cofactors are inorganic and coenzymes are organic
What are coenzymes
Small organic non-protein molecules that temporarily bind to the active site of the enzyme, either just before or at the same time as the substrate
What happens to coenzymes during a reaction and after
They are chemically changed during a reaction and need to be recycled to their original state sometimes by a different enzyme
What do many coenzymes derive from and what happens if these are deficient in human diet
Water soluble vitamins, if these vitamins are deficient in human diet then certain diseases may occur
What is the coenzyme derived from vitamin B12 and what disease is caused it there’s a deficiency
Cobalamin coenzymes and causes pernicious anaemia (progressive and fatal)
What is the coenzyme derived from folic acid and what disease occurs if it is deficient
Tetrahydrofolate and causes megablastic anaemia (large, irregular RBC)
What is coenzyme is derived from vitamin B3, nicotinamide and what disease happens if it is deficient
NAD OR NADP and causes pellagra (diarrhoea, dermatis, dementia)
What is coenzyme derived from vitamins B6, pantothenate and what happens if it’s deficient
Coenzyme A and causes elevated blood-plasma triglyceride levels
What coenzyme derived from vitamin B1, thiamine and what happens if it’s deficient
Thiamine pyprophosphate and causes beriberi (mental confusion and irregular heartbeat)
What are NAD AND NADP and what do they derive form
They are hydrogen acceptors and derived form nucleotides
What does organic mean
Carbon based, associated with molecules in living organisms such as lipids, carbs and proteins
What is inorganic mean
Salts and metals
What do organic cofactors/coenzymes derive from
Vitamins in our diet
What do inorganic cofactors derive from
Minerals in human diet
What is an apoenzyme
Inactive enzyme which is incomplete as no cofactor or co enzyme has been added
What is a holoenzyme
Active whole enzyme as a cofactor or coenzyme has been added
Precursor activation
Many enzymes only activate under certain conditions and when they do they are precursor enzymes, when cofactor added to apoenzyme becomes holoenzyme and that is precursor activation
What energy do all molecules have and what does this cause
Kinetic energy and can continuously more around randomly
What does molecules randomly moving around cause
Molecules collide with each other
What happens to molecules when a substance is heated
The extra energy causes molecules to move faster which increases rate of collisions between molecules and also increases the force with which they collide with as they are moving faster
What happens when the reaction mixture containing enzymes and substrate is heated
Both types of energy will gain energy and move faster, this increases the rate of collision per second, so rate of formation of ES complexes increases and rate of reaction increases and this increases number of enzyme product complexes up to a certain temp, after 37.5degreeC in humans enzymes are at their optimum temp and rate of reaction is at its max
As well as moving faster what does increasing temp do to the molecules
Makes them vibrate
What does temp making the molecules vibrate cause
May break the weak bonds, such as hydrogen and ionic bonds that hold tertiary structure of enzymes active site
What happens as bonds of enzymes active site begin to break
Active site shape will change and substrate won’t fit in so well so rate of reaction will begin to decrease
What happens as more and more heat is applied to enzyme substrate mixture
Active site completely and irreversibly changes so no longer complementary to substrate molecule, so, enzyme has denatured and reaction can’t continue
Does heat break peptide bonds and what does this mean
No, so although tertiary structure of enzyme is altered the primary structure remain the same
What is optimum temp
The temperature at which enzymes work there best and have their max rate of reaction
What enzymes work best in cool temps
Psychrophilic bacteria, live in cold conditions and their enzymes work best in cool temps
What enzymes work best in hot temps
Thermophilic bacteria live in hot springs and there enzymes are heat stable and have more disulphides bonds that don’t break with heat and keep shape of enzyme stable
What does a graph for optimum temp of enzymes look like
Temp will slowly rise and rate of reaction will speed up and up till optimum temp and after that reaction rate will decrease more rapidly until enzymes have denatured
How is reaction rate of graph showing optimum temp measured
Rate of reaction= 1/time taken to reach end point
What does temperature coefficient refer to
Increase in rate of a process when a temp increases by 10degreesC
What is the equation of temp coefficient (Q10)
Q10=rate of reaction at (T+10)degreeC / rate of reaction at T degreeC
For a chemical reaction in test tube where Q10 is 2 for every 10degreeC rise in temp what does this do to reaction rate
Doubles it
For a metabolic reaction catalysed by enzymes, temp between 0-40degreeC what happens to rate of reaction for each 10degreeC increase
Roughly doubled as there is more kinetic energy
For temp above there optimum what happens to value of temp coefficient
It drops as higher temp alters the active site structure so they are no longer complementary to shape of substrate molecules
What does pH indicate
Whether pH is acidic, alkaline or neutral
What is pH 0-6
Acidic
What does pH 7 indicate
Neutral
What pH is alkaline
8-14
What do acids such as hydrochloric acid and sulfuric acid dissociate into
Protons and a negatively changed ion (HCL->H+ + Cl-)(H2SO4-> H+ + HSO4-
What other type of acids are also proton donors, give example
Organic acids, lactic acid dissociates to lactate and H+ and pyruvic acid dissociates to pyruvate and H+
What is a buffer
Something that resists the change in pH
Why is it essential human blood have certain chemicals which help resist change in pH
So blood remains within fairly narrow limits close to pH 7.4, the chemical can accept or donate hydrogen ions
What can some proteins like haemoglobin do in terms of buffers
They can donate or accept protons, so act as buffers
What do you use buffers for in lab experiments
To maintain desired pH for investigating enzyme action at different pH values it to keep pH constant whilst you investigate another factor
What does it mean due to hydrogen ions having a positive charge (proton)
Has a positive charge so it is attracted to negatively charged ions/molecules or parts of molecules
What does excess hydrogen ions interfere with in enzymes
Interferes with hydrogen bonds and ionic forces and so active site of the enzyme molecule will change shape
What happens once the excess hydrogen ions has changed the shape of the enzymes active site
Substrate molecule does not fit well into the active site, then rate of reaction that the enzyme catalyses will be lowered
Why does increasing H+ alter charges on active site and what does this cause
Increasing concentration of H+ ions alters charge on enzymes active site as more protons will cluster round negatively charged groups in the active site which interferes with binding of substrate molecule to active site
Do enzymes work in a narrow pH range
Yes
What can small changes in pH on either side of an enzymes optimum pH do
Slow rate of reaction as shape of active site is disrupted but is normal pH is restored hydrogen bonds can reform and active site shape is restored
What happens to enzymes at extreme pH
Enzymes active site may be permanently changed, when enzyme denature it cannot catalyse the reaction
Is the optimum pH the same for all enzymes
No, they differ for each enzyme
What pH do intercellular enzymes have
pH close to 7
What do extracellular enzymes pH work best at
They differ
During digestion what happens and what pH does it happen at of starch
Food in mouth digested by amylase which digests starch to maltose works best at pH 6.8, as food passes into stomach hydrochloric acid is secreted at low pH, to kill bacteria or pathogens in food
What is the enzyme for digesting protein in the stomach and what pH is it’s optimum and how does it work
Pepsin, pH 1-2, it digests large protein molecules into smaller peptide molecules
What happens as partly digested food moves into small intestines, mention pH
Salt in bile made in liver neutralises the food and raises its pH to 7.8 which is optimal for protein-digesting enzymes, trypsin and enterokinase, that catalyses further digestion of peptides to amino acids in small intestines
What happens to enzyme catalysed reactions if no substrate is present
No reaction happens as no ES complexes can form
What happens as substrate is added to an enzyme mixture
As substrate concentration increases rate of reaction increases
Why does rate of reaction increase as substrate added to enzyme mixture
More ES complexes can form resulting in more product molecules forming
Why is substrate concentration the limiting factor when the concentration of enzymes is fixed
As it is limiting the reaction, as substrate concentration increases, rate of reaction increases
What happens as substrate concentration is the same as the enzyme concentration
Reaction will meet its maximum rate and increasing the substrate even more will not increase the rate of reaction
Why does enzyme catalysed reactions eventually meet a Vmax
As all enzymes active sites are occupied with substrate molecules, if more substrate added they can’t successfully collide with and fit into enzymes active site
What may you be able to change in a lab to do with enzyme concentration
You may be able to change the concentration of a solution of a particular enzyme
In living cells what does enzymes concentration/availability depend on
Rate of synthesis of enzymes and its rate of degradation, each of these rates is directly controlled by the cell
What is enzyme synthesis
Depending on cells needs genes for synthesising particular enzymes can be switched on or off
What is enzyme degradation
Protein components of living cells are constantly being turned over, cells are continuously degrading old enzyme molecules to their component amino acid and synthesising new enzyme molecules from amino acids
What are the advantages of enzyme degradation
Eliminates abnormally shaped proteins that may accumulate and harm cell, regulation of metabolism in the cell by eliminating any superfluous(surplus to requirements) enzymes
What must happen for a cell to regulate its metabolism properly
The control of enzyme degradation is equally important as the control of enzyme synthesis
What happens as enzyme concentration increases
More active site in enzyme become available and more successful collisions between enzyme and substrate occur, more ES complexes can form per unit, so rate of reaction increases
Why is enzyme concentration a limiting factor when substrate concentration is fixed
As enzyme concentration increases so does rate of reaction
When is enzyme catalysed reaction at its max reaction rate with fixed substrate concentration
When all the substrate molecules are occupied in an active site or being released as product molecules
What happens once enzyme catalysed reaction is at its max reaction rate
If enzyme concentration increases further, reaction rate won’t increase as active site of extra enzymes aren’t occupied, enzyme concentration is no longer a limiting factor as enzyme concentration increases rate of reaction doesn’t, substrate concentration become limiting factor as rate of reaction will increase if it increases
Is initial reaction rate for any reaction faster or slower and why
Faster as enzymes and substrate moving randomly at the start have a greater chance of successfully colliding as there aren’t any ES complexes formed yet
What happens to rate of reaction as in continues after initial stage
Substrate molecules used up as they are converted to product molecules so concentration of substrate drops as a result frequency of successful collisions decreases so initial rate of reaction gives max reaction rate for enzymes under a particular experimental situation
What are inhibitors
Substances that reduce the activity of an enzyme by combining with the enzyme in a way that influences how the substrate binds to active site or by affecting enzymes turnover number
What my some enzyme inhibitors do and what may others do
Some may block the active site and some change actives site shape
What do both ways of inhibition do
Inhibit the formation of ES complexes and therefore formation of product molecules
What is a competitive inhibitor
A substance with a similar shape to enzymes substrate molecule, so it fits into active site so substrate molecule can’t enter
What does the amount of inhibition depend on
Relative concentration of substrate and inhibitor molecules
What does the more inhibitor molecules mean
More inhibitors collide with active site and so effects of inhibition is greater
What does effectively increasing substrate concentration do to rate of inhibition
Dilutes the effect of the inhibitors as if enough substrate added, the inhibitor is more unlikely to collide with the enzyme
What happens to rate of reaction with a competitive inhibitors
Rate of reaction is lower but it does eventually reach the original Vmax
What do competitive inhibitors form when they directly compete with substrate
Enzyme-inhibitor complex formed if collision is successful and it is catalytically inactive
Once attached to enzyme what happens to competitive inhibitor
Inhibitor isn’t changed by enzyme as normal substrate molecule would be
What happens due to presence of inhibitors preventing the substrate molecules joining to active site
Reduces the rate of formation of ES complexes and product molecule formation
What do competitive inhibitor do
Reduce the number of free enzyme active sites available for substrate molecules to bind and form ES complexes
What is good about most competitive inhibitors
It is reversible as collisions between enzyme and substrate or inhibitor molecules are random and increasing substrate concentration would reduce effects if reversible competitive inhibition as there would be more chance if an enzyme molecule colliding molecules with a substrate molecule than with an inhibitor molecule
What is it called when a competitive inhibitor binds irreversibly to enzymes active site
Inactivator
How do you know a non-competitive inhibitor is present
If inhibitor molecule binds to enzyme somewhere other than active site
How are non-competitive inhibitors different to competitive
They don’t compete with substrate molecules for a place on enzymes active site
Where do non-compatible inhibitors attach to enzyme
Region known as allosteric site away from active site
What happens when non-competitive inhibitor binds to allosteric site
They disrupt enzymes tertiary structure and change active sites shape so it is no longer complementary to substrate and enzyme can’t bind to active site so no ES complexes form
Does max rate of reaction stay the same or decrease with presence of non-competitive inhibitor
It reduces and the Vmax is lowered
What may adding more substrate do if non-competitive inhibitor is present
It may allow reaction to reach a new lower rate but even very high concentration of substrate won’t allow rate of reaction to return to its uninhibited max
What happens the greater amount of inhibitor molecules present
Greater degree of inhibition as more enzymes are distorted and either can’t form ES complexes it can’t complete the catalytic reaction involving ES complexes
Do non-competitive inhibitors bind reversibly or irreversibly to allosteric site
Some reversible but most are irreversible
What is one way enzyme catalysed reactions may be regulated
By end product inhibition
What is end product inhibition
After catalysed reaction has been completed product molecules stay tightly bound to enzyme, this way enzymes can’t form more of the product that the cell needs and this is an example of negative feedback
What do many metabolic process such as respiration and photosynthesis involve
A series of enzyme catalysed reactions as product of one enzyme catalysed reaction becomes substrate for the next within the metabolic pathway
What does cells not needing to accumulate too much end product mean
Product of last enzyme catalysed reaction in metabolic pathway may attach to a part of the first enzyme in the pathway, but not as its active site, this binding changes the shape of the first enzymes active site preventing pathway from running
What is it when the 1st enzymes active shape changes in a metabolic pathway
It is non-competitive inhibition but reversible
After the first enzymes had been changed on a metabolic pathway how is it reversed
When the concentration of the product within the cell falls, the molecules will detach from enzyme 1 and allow its active site to return to its normal shape
What increases efficiency of metabolic reactions without increasing substrate concentration and how
Multi-enzyme complexes as they keep the enzyme and substrate molecules in the same vicinity and reduce diffusion time
What does many metabolic reactions being carried out in certain regions or organelles of the cell do to reactions efficiency
It increases its efficiency of metabolism, some enzymes within organelles are bound into the organelle membranes
How do many toxins(poisons) exert their effect
They inhibit/inactivate enzymes
How does potassium cyanide (KCN) work
Highly toxic as it inhibits aerobic respiration and catalase
What happens when KCN is ingested
It is hydrolysed to produce hydrogen cyanid which is a very toxic gas that can readily dissociate into H+ and CN- ions
What to CN- ions do once they have be made from hydrogen cyanide dissociating
They bind irreversibly to an enzyme found in mitochondria and inhibit final stages of aerobic respiration, as final stage is inhibited, earlier stages cannot run and aerobic respiration stops
What does venom of a green mamba contain
A chemical that inhibits the enzyme acetylcholinesterase which is important in neuromuscular synapses tissue break down the neurotransmitter, acetylcholine
What happens if acetylcholinesterase is inhibited
Acetylochtine says attached to receptors on muscle membrane and keeps muscle contracted which causes paralysis as movement depends on muscle being able to contact and relax alternately, also if muscle is involved in breathing and is paralysed victim suffocates
How does aspirin work
Salicylic acid binds to enzymes that catalyse formation of prostaglandins, so it prevents formation of these and they are cell signalling molecules produced by cells when tissues are infected or damaged
What do prostaglandins do
They make the nerve cells more sensitive to pain and increase swelling during inflammation
What does aspirin do in terms of blood clots
Reduces risk of blood clots in blood vessels and many people take it to reduce risk of strokes
Why can’t children U12 take aspirin
It can damage their stomach lining
Where is ATPase inhibitors found and what does it do
Extract from foxglove leaves used to treat heart failure and atrial arrhythmia (abnormal beat of atria)
What are ATPase inhibitors now called
Cardiac glycosides or digitalis, digitoxin, digitalin or digoxin
How to cardiac glycosides work
They inhibit sodium potassium pump in cell membrane of heart muscle cells and allow more Ca2+ ions to enter the cell, calcium ions increase muscle contractions and this strengthens heartbeat
What are ACE inhibitors
Medicinal drugs that inhibit angiotensin converting the enzyme (ACE) which normally operates in a metabolic pathway that ultimately increases blood pressure
What are ACE inhibitors used for
To lower blood pressure in patients with hypertension who can’t take beta-blockers, to treat heart-failure and to minimise risk of a second heart attacks and help prevent strokes in patients who have suffered a myocardial infarction
Why is patients blood pressure checked when taking ACE inhibitors
Only a small does can lower blood pressure too much so it is checked incase it falls to low
What are protease inhibitors
Like amprenavir and ritonavir, they are used to treat some viral infections
How do protease inhibitors work
They prevent replication of virus particles within host cells by inhibiting protease enzymes so viral coats can’t be made
Do protease inhibitors inhibit by competitive or non-competitive inhibition
Competitive
What are many anti viral drugs like zidovudine and Abacavir used to treat
Patients how are HIV+
What type of inhibitors are anti-viral drugs used to treat HIV and how does this work
They are nucleoside reverse transcriptase inhibitors as they inhibit enzymes involved in making DNA using viral RNA as a template
