Module 2: Biological Molecules pt 2 Flashcards
two word phrase for an enzyme
biological catalyst
4 step process of enzyme Action
1)enzyme + substrate entering active site
2)enzyme/substrate complex
3)Enzyme/product complex (weakly bound)
4)enzyme + product leaving active site
Lock + Key hypothesis
-Active site specific to one substrate like a lock is specific to a key
-substrate binds to active site of enzyme forming enzyme/substrate complex
-R groups in active site react with substrate, putting strain on it
-The strain helps to create or break bonds, separating or joining substrates
-active site remains unchanged
-activation energy reduced
how is Induced fit hypothesis differences to Lock + Key
-Weak initial interaction between enzyme + substrate
-Enzyme tertiary structure changes slightly to bind to substrate
-more strain on substrate, lowering activation energy
What are competitive inhibitors
Inhibitor molecule has similar shape to substrate and block enzymes active site
example of competitive inhibitors
Statins, asprin, antibiotics (penicillin)
for competitive inhibitors what does degree of inhibition depend on
the relative concentration of substrate, inhibitor, enzyme
what are Non competitive inhibitors?
Inhibitor molecule which binds to the enzyme away from the active site (the allosteric site).
It changes the tertiary structure of the actives site so it cannot bind to the substrate
examples of Non competitive inhibitors
cyanide, arsenic, organophosphates
does Increasing substrate concentration effect the degree of inhibition of Non competitive inhibitors
no
How do prosthetic groups help enzymes?
tightly bound- form permanent part of enzyme (active site)
give an example of a prosthetic group of an enzyme and it’s role
Example = Zn^2+
Important part of structure of carbonic anhydrase
Enzyme in the metabolism of CO2
Why is Precursor Activation needed?
- To activate the enzyme in certain conditions
- To prevent the enzyme damaging tissues
What is an inactive precursor
an enzyme found in an inactive form
how does Precursor Activation happen with a inorgancic molecule
what is the enzyme called before and after this
. Addition of cofactor to an inactive precourser
Before this, enzyme = apoenzyme
After, enzyme = holoenzyme
how does Precursor Activation happen without an inorganic molecule
give an example of this
. Change in conditions
Example = pepsinogen
Released into stomach
Acidic pH causes conversion to pepsin
what is a Cofactors
non-protein ‘helper’ inorganic molecule or ion
how are cofactors obtained
Obtained via diet
how do cofactors work
Bind loosely to the enzyme so that a substrate can bind to active site
give an example of a cofactor and its role
Example = Cl-
Needed for amylase to form the correctly shaped active site
what is a Coenzyme
an organic ‘helper’ molecule
waht are coenzymes derived from
Mostly derived from vitamins
example of coenzyme and its role
Example – Vitamin B3 needed to synthesise NAD
NAD = coenzyme used in respiration
are coenzymes changed in the reaction?
yes
+they can also be changed to be used between two enzymes - recycled+
Describe How temperature effects the rate of reaction of a solution containing an enzyme?
As temp increases, so does rate of reaction until optimum (usually around 40°)
Then the rate of reaction decreases and stops
Explain How temperature effects the rate of reaction of a solution containing an enzyme
More heat = more kinetic energy so more frequent collisions + collisions with more energy.
-> More enzyme/substrate complexes formed
Temperature above optimum = enzyme + molecules vibrate more -> H bonds break and active site changes shape -> no more ESC’s formed
Describe How substrate concentration effects the rate of reaction of a solution containing an enzyme?
As substrate concentration increases, so does the rate of reaction. Eventually, rate of reaction plateaus
Explain How substrate concentration effects the rate of reaction of a solution containing an enzyme
More substrate = more collisions with enzyme -> more ESC’s formed until it reaches its V max (maximum rate)
Active sites are all occupied at this point, so adding more substrate has no effect.
Enzyme concentration now limits this reaction
Describe How Enzyme concentration effects the rate of reaction of a solution containing an enzyme
As enzyme concentration increases, so does rate of reaction. Eventually, rate of reaction decreases slowly
Explain How Enzyme concentration effects the rate of reaction of a solution containing an enzyme?
More enzyme = more collisions with substrates -> More ESC’s.
If substrate concentration is limited then there’s more enzymes to deal with available substrate until there are none available.
Adding more enzymes has no effect
Rate of reaction will slow as substrate is getting used up
Explain How Enzyme concentration effects the rate of reaction of a solution containing an enzyme?
More enzyme = more collisions with substrates due to more active sites available -> More ESC’s.
If substrate concentration is limited then there’s more enzymes to deal with available substrate until there are none available.
Adding more enzymes has no effect
Describe How PH effects the rate of reaction of a solution containing an enzyme?
Enzymes have an optimum PH vale.
above and below the optimum PH, rate if reaction slows or stops
Explain How PH effects the rate of reaction of a solution containing an enzyme?
Above and below optimum PH, the charge in Hydrogen ions can break the hydrogen and ionic bonds holding the enzymes tertiary structure in place. This changes the active site so the enzyme becomes denatured
Structure of DNA nucleotide
Deoxyribose sugar (pentose sugar)
phosphate group
Nitrogenous base
How many hydrogen bonds form between adenine and thymine
2
how many hydrogen bonds form between Guanine and Cytosine?
3
(C is 3rd letter in alphabet)
name the 4 possible bases in DNA
Adenine, Cytosine, Thymine, Guanine
What are the nitrogenous base pairs of DNA
Adenine - Thymine
Guanine - Cytosine
Which bases can be classed as Purines?
Guanine + Adenine
which bases can be considered pyrimidines?
Thymine, Cytosine, Uracil
*(TutanCahmUn) pyramid
3 differences between DNA and RNA
-Uracil base instead of Thymine
-Contains ribose sugar instead of deoxyribose
-Single strand rather than double
what’s the difference between a purine and a pyrimidine base
Purine = 2x Carbon - nitrogen rings joined together
Pyrimidine = 1x carbon - nitrogen rings (smaller)
(remember pyrimidine = pyramid so only one )
Which elements do all nucleotides contain?
Nitrogen, Carbon, Hydrogen, Oxygen, Phospherous
What is the use of DNA
store genetic info
what is the use RNA
Used to make proteins from the instructions in DNA
Go through the process of DNA replication
1-6
1)The enzyme DNA helicase travels along the DNA backbone and breaks the hydrogen bonds between the two polynucleotide DNA strands
2)The helix ‘unzips’ to form two single strands. Each of these original strands acts as a template for a new strand
3)Free-Floating DNA nucleotides join to the exposed bases on each original template by complementary base pairing.
4)the nucleotides on the new strand are joined together by the enzyme DNA polymerase, which catalyses the formation of phosphodiester bonds to form the sugar-phosphate backbone.
5)Hydrogen bonds form between the bases on the original and the new strand. strands twist to form double helix
6)This type of copying is called semi-conservative replication as half the strands in each new DNA molecule are from original piece of DNA. others are new
Go through the process of Transcription in protein synthesis
1)In nucleus, RNA polymerase attach to DNA at the start of a gene
2)Move down DNA breaking H bonds between strands
3)one strand used as a template strand and free RNA nucleotides line up with complementary bases alongside strand
4)RNA polymerase joins nucleotides together to make mRNA molecule
5)RNA polymerase goes down DNA until it reaches stop codon
so it stops making RNA and detaches from DNA
6)DNA reforms H bonds and recoils
7)mRNA leaves nucleus through nuclear pore and attaches to ribosome in cytoplasm
Go through the process of Translation in Protein synthesis
1)mRNA attached to ribosome in cytoplasm
2)tRNA molecule with complementary anticodon to the start codon on the mRNA attaches to mRNA by complementary base pairing
3)Second tRNA molecule attaches to next codon on mRNA
4)rRNA in ribosome catalyses formation of peptide bonds between the two amino acids on tRNA
5)ribosome moves along mRNA and releases the first tRNA molecule, leaving the amino acids behind
6) tRNA molecules continue to bring amino acids to mRNA until ribosome reaches a stop codon on the mRNA molecule
7)Newly formed polypeptide chain moves away from the ribosome and folds up to form a new protein
what is mRNA
Messenger RNA
what is tRNA
what does it stand for
Transfer RNA
what is rRNA
Ribosomal RNA
Role of tRNA
where is it found
carries amino acids to ribosomes
-found in cytoplasm
-Single polynucleotide chain folded into a clover shape
role of rRNA
-Forms Larger and smaller subunits of ribosome alongside protein
-helps to catalyse formation of peptide bonds between amino acids
structure of tRNA
(shape and sites)
-Single polynucleotide chain folded into a clover shape
-anticodon site
-Hydrogen bonds between base pairs
-Amino acid binding site
Role of mRNA
-carries genetic code from DNA in nucleus, takes it into cytoplasm where it is used to create a protein
Basic structure of mRNA
when is it created
-Single polynucleotide chain
-created during transcription in the nucleus
What is a codon
three Nitrogenous bases
aka a triplet
What are the three ‘laws/properties’ of codons/triplets
-Non-Overlapping, they don’t share bases
-Degenerate- There are more possible combinations of triplets than amino acids. some amino acids coded for by more than one codon
-Universal- The same base triplets code for the same amino acids in all living things
What are the three types of mutation
define
Point/Substitution - one base replaced by another
Addition/insertion - extra base added to DNA molecule
Deletion- base removed from DNA molecule
what are the two worst types of mutation, why?
Deletion and Addition
they cause a “frame shift” of the codons, changing them all
What is the difference between ADP and ATP
ADP = Adenosine diphosphate so two phosphate groups
ATP= Adenosine Triphosphate so three phosphate groups
How do coenzyme work
They participate in the substrate reaction with active site (kind of like a second substrate) and are changed by the reaction
Act as carriers, moving chemical groups between each enzyme
