Principles Flashcards
1
Q
What are biomolecules made up of?
A
Atoms
2
Q
What are atoms made up of?
A
- Proton (positive)
- Neutron
- Electron (negative
3
Q
What is a covalent bond?
A
Shared pair of electrons between non-metal atoms
4
Q
What is an ionic bond?
A
Attraction of opposite charges
5
Q
What is a hydrogen bond?
A
Sharing of a H atom (intermolecular)
6
Q
What are hydrophobic interactions?
A
Interactions of non-polar substances in the presence of polar substances (especially water)
7
Q
What are Van der Waals forces?
A
Interaction of electrons of a non-polar substances
8
Q
What is the electronegativity of an element?
A
The attractive force that an atomic nucleus exerts on the electrons of another atom.
9
Q
What is phosphorylation?
A
Addition of a phosphate group
10
Q
What is dephosphorylation?
A
Removal of a phosphate group?
11
Q
What is acylation?
A
Addition of an acytl group (carbon with double bond to oxygen)
12
Q
What is carboxylation?
A
Addition of a carboxyl group
13
Q
What is esterification?
A
Reaction of an alcohol and a carboxylic acid to form an ester
14
Q
What is a condensation reaction?
A
Joining compounds together by removing water
15
Q
What is hydrolysis?
A
Breaking up a compound by adding water
16
Q
What is oxidation?
A
Loss of electrons
17
Q
What is reduction?
A
Gain of electrons
18
Q
What is a redox reaction?
A
When one molecule is oxidised and the other is reduced.
19
Q
What is a reducing agent?
A
Molecule that causes another molecule to be reduced by itself being oxidised
20
Q
What is an oxidising agent?
A
Molecule that causes another molecule to oxidise by being reduced itself.
21
Q
What are the oxidation stated of carbon?
A
Alkane–> alcohol–>aldrehyde–>carboxylic acid–>carbon dioxide
22
Q
What are main functions of biomolecules?
A
- Information storage eg DNA
- Structural eg teeth, bones
- Energy generation eg glycolysis, TCA cycle
4.Energy currency eg ATP
Recognition/communication eg receptors, hormones and enzymes
23
Q
What are the major classes of biomolecules?
A
PEPTIDES AND PROTEINS- made from amino acids
LIPIDS- made from trigycerides, phospholipds and steroids
NUCLEIC ACIDS- DNA and RNA
CARBOHYDRATES -mono/di/trisaccharides
24
Q
Give an example of a monosaccaride.
A
Glucose
25
Give 4 examples of disaccarides.
Lactose
Maltose
Sucrose
Cellobiose
26
Give two examples of polysaccharides.
Cellulose
| Glycogen
27
What is the first law of thermodynamics?
Energy is neither created nor destroyed only transferred
28
What is the second law of thermodynamics?
When energy is converted from one form to another, some of that energy becomes unable to do work
29
What is enthalpy?
Heat content
30
What is entropy?
Disorder
31
How do you calculate the free energy of a reaction?
ΔG = ΔH – TΔS
32
How do you calculate the change in free energy?
ΔG = (energy of the products) – (energy of the reactants)
33
When is a reaction feasible?
If the free energy change is -ve
34
What is an endergonic reaction?
Reactions in which the total free energy of the products is more than the total free energy of the reactants. Free energy change is +ve
35
What is an exergonic reaction?
Free energy of the products is less than the reactants.Free energy change is -ve.
36
What is the equation for determining free energy of a reaction?
ΔG = ΔGo’ + RTln([C][D]/[A][B])
| unit is kJ/mol
37
What are standard conditions?
T=298K
1atm pressure
1M concentration
38
What is ΔGo?
ΔGo’ is the change in free energy under standard conditions
39
What is ATP?
Used as a universal energy currency because its breakdown has a very negative standard free energy
The reaction
ATP + H2O → ADP + Pi + H+
has a very negative ΔGo’ (-30 kJ/mol)
40
Why is ATP less stable than ADP?
The negative charges close together in ATP put a strain (electrostatic repulsion) on the molecule that makes it less stable than ADP
Strain is relieved (partially) by removing one or more phosphate groups
Anhydride bonds are ‘high energy’ bonds
41
What is metabolism?
All the reactions taking place in the body
42
What is catabolism?
Breakdown of complex molecules into smaller ones to release energy
43
What is anabolism?
Synthesizing complex molecules out of smaller ones in energy consuming reactions
44
What is glycolysis?
Initial breakdown of glucose for the generation of ATP
Uses two ATP molecules
Generates Four ATP-->net gain of TWO
45
What is gluconeogenisis?
Making new glucose from non carbohydrate precursors eg pyruvate
Anabolic reaction
46
What is meant by a polar molecule?
The electrons are not shared equally in the molecule due to it's electronegativity
47
Describe the molecular shape of water.
Water is bent and forms a dipole- it is therefore tetrahedral shaped.
48
What does hydrophilic mean?
'Water-loving' i.e. a substance that dissolves in water
49
What makes a molecule hydrophilic?
It must be ionic or polar.
| Like dissolves like.
50
Describe the formation of hydrogen bonds in water.
A covalent bond between hydrogen and a more electronegative atom (e.g. oxygen) creates a polarized bond
hydrogen has partial positive charge
This hydrogen can interact with unshared electrons from another electronegative atom
This interaction is called a hydrogen bond
Individually much weaker than covalent bonds but can be strong collectively
51
What substances are hydrophobic (insoluble in water)?
Non-polar substances
52
Why are non polar molecules hydrophobic?
Hydrogen bonds BETWEEN water molecules prefer to interact with each other than the non-polar substance
53
What is the hydrophobic effect?
When non-polar substances are not dissolved when mixed with water eg hydrocarbons and water do not mix
54
What are amphipathic molecules?
Molecules that are both hydrophilic and hydrophobic.
| They have a hydrophilic head and a hydrophobic tail
55
How does water interactions affect the organisation of amphipathic molecules?
Hydrophilic head interacts with water and is in contact.
| Hydrophibic tail does not, it is sequestered from the water-->forming MICELLES
56
Give an example of an amphipathic molecule.
Sodium palmitate (a fatty acid)
57
What is the importance of cell membranes?
They act as a selective and controllable barrier to the outside world
Aid compartmentalization by isolating organelles.
58
What is contained within the cell membrane?
Lipids- phospholipid bilayer
| Proteins
59
Describe the general structure of amino acids.
```
The building blocks of proteins.
An alpha carbon bonded to either:
-an amino group
-a carboxyl group
-a hydrogen
-a side chain
```
60
What is the classifications of amino acids?
Polar
Non-polar
Basic
Acidic
61
Describe the steriochemistry of amino acids.
Comes in D and L forms which are non superimposable mirror images.
62
What is a peptide bond?
Bond between two amino acids.
63
Describe the characteristics of a peptide bond.
Unidirectional (N to C)
Partial double bond character
Planar
Strong and rigid
64
What is an acid?
Molecule that donates a proton
65
What is a base?
Molecule that accepts a proton
66
How is the strength of an acid measured?
By how well is dissociates ie. its acid dissociation constant
67
What is the equation for measuring the amount of protons in a solution in strong acids?
pH = -log10[H+]
68
Give an equation for calculating the pKa of an acid.
pKa=-log10[Ka]
69
What is the Henderson-Hasselbalch equation used to measure?
The pH of weak acids
70
What is the Henderson-Hasselbalch equation?
pH=pKa +log [A-]/[HA]
71
What is a buffer?
A solution in which the pH remains constant when small amounts of acid or base are added.
72
What happens close to the pKa value during a titration of an acid with a base?
pH remains relatively unchanged
73
What is the isoelectric pH (pI) of a molecule?
the pH at which a molecule has no net charge
74
Explain why an uncharged amino acid has two titratable groups.
Uncharged amino acids exist as zwitterions in a neutral solution- no net charge
Contain two titratable groups- therefore have two pH pKa values.
75
Explain how proteins can act as buffers.
The ends of proteins can be ionised.
| They can therefore act as buffers eg haemoglobin in blood
76
Explain the impact of pH of amino acids and thus proteins.
Changes in pH can change the ionisation in amino acids and thus proteins which can lead to changes in the structure and function of that protein
77
What is the primary structure of a protein?
The sequence of amino acids
78
What is the secondary structure of a protein?
The localised conformation of the polypeptide backbone. IMPORTANT ONLY CONSIDERS BACKBONE.
79
What is the tertiary structure of a protein?
The 3D structure of an entire polypeptide, including all of its side chains
Arrangement of all atoms of a polypeptide in space
Consists of local regions with distinct secondary structure
80
What is the quaternary structure of a protein?
The spatial arrangement of polypeptide chains in a protein with multiple subunits
81
What are the three types of secondary protein structures?
Alpha helix
Beta strands and sheets
Triple Helix
82
Describe the alpha helix in secondary protein structures.
```
Rod-like
One polypeptide chain
Mostly right-handed
-C-O group of one amino acid forms a hydrogen bond with the -N-H group of an amino acid four residues away
Proline residues break alpha helices
```
83
Describe the beta sheets structure of secondary proteins.
```
Polypeptide backbone almost completely extended
Can involve more than one chain
Two directions possible:
parallel
antiparallel
Turns between strands (glycine and proline
Repeated ‘zigzag’ structure
also called pleated sheet)
```
84
Give an example of secondary protein structures.
Phosphoglycerate kinase
Contains both alpha helix and beta sheets.
Can have more than one type in one protein
85
Give an example of a molecule with a triple helix secondary protein structure.
Collagen.
Three left-handed helical chains twisted around each other form a right-handed superhelix
Tropocollagen
Repeating sequence of X-Y-Gly in all strands
X = any amino acid
Y = proline or hydroxyproline
also contains hydroxylysine
Inter-chain H-bonds (no intra-chain)
involving hydroxylysine and hydroxyproline
Covalent inter- and intra-molecular bonds
86
Why is collagen relevant clinically?
Influences the strength of connective tissue
Weakened collagen results in bleeding gums
Covalent crosslinking increases with age
Scurvy-bleeding gums, skin discolouration
the enzyme which hydroxylates proline requires ascorbic acid (vitamin C)
dietary deficiency of vitamin C results in reduction in hydroxyproline
results in weakened collagen
87
What are the two types of tertiary proteins?
Fibrous
| Globular
88
Describe fibrous proteins
Contain polypeptide chains organized approximately parallel along a single axis. They
consist of long fibers or large sheets
tend to be mechanically strong
are insoluble in water and dilute salt solutions
play important structural roles in nature
89
Give examples of fibrous proteins.
Keratin- hair and wool
| Collagen- bones, teeth, skin. blood vessels
90
Describe globular proteins
Proteins which are folded to a more or less spherical shape
they tend to be soluble in water and salt solutions
most of their polar side chains are on the outside and interact with the aqueous environment by hydrogen bonding and ion-dipole interactions
most of their nonpolar side chains are buried inside
nearly all have substantial sections of alpha-helix and beta-sheet
91
Give examples of globular proteins
Myoglobin
| Haemoglobin
92
What forces interact between tertiary protein structures?
```
Covalent disulphide bonds
Electrostatic interactions = salt bridges
Hydrophobic interactions
Hydrogen bonds
backbone
side chain
Complex formation with metal ions
```
93
Give an example o how changing of a single nucleotide can result in altered protein function
Sickle cell anaemia
| results in the change in haemoglonin in low oxygen- rigid, sickle shaped cells
94
What can happen when proteins fold too slowly?
protein may begin to fold incorrectly before it is completely synthesised
it may associate with other proteins before it is folded properly
95
Give examples of clinical conditions resulting from slow protein folding.
Alzheimer's
Parkinsons
CJD
96
What are chaperones?
Specialised proteins which aid the folding process
97
Give examples of clinical diseases caused by incorrect protein folding
Mad cow disease- infection
Creutzfeld-Jacob Disease
Prion protein diseases
98
What can denature a protein?
Heat- increased vibrations
Extreme pH- interupt elextrostatci interactions
Detergents, urea, guanidine hydrochloride- disrupt hydrophobic interactions
Thiol agent, reducing agents- disrupt disulphide bonds
99
Name an example of a tertiary structure.
Lysosyme
| Myoglobin
100
Describe the structure of myoglobin
```
Globular protein
Contains a haem group
which contains an iron ion, Fe(II)
prosthetic group
haem group binds oxygen
one oxygen molecule per myoglobin protein
Stores oxygen in muscle
```
101
Name and describe a quaternary protein structure example.
```
Haemoglobin
Proteins which contain more than one polypeptide chain
between 2 and more than a dozen subunits
identical or different subunits
Haemoglobin
four subunits
two and two chains
each contains a haem group
each subunit can bind one oxygen molecule
Binding of one oxygen changes affinity of the other subunits
see allosteric regulation
Transports oxygen in blood
```
102
What is the central dogma?
DNA-->RNA-->PROTEIN
103
What is the chemical structure of the nucleic acid in DNA?
Deoxyribose
Base
Phosphate group
104
What is a nucleoside?
Base + sugar
105
What is the chemical structure of RNA?
Ribose sugar
Base
Phosphate group
106
What is a nucleotide?
Base + phosphate group
107
What four bases occur in DNA?
Adeninie
Guanine
Cytosine
Thymine
108
What are the four bases in RNA?
Adenine
Guanine
Cytosine
Uracil
109
What is the nucleoside for the bases of DNA and RNA?
```
Adenosine
Cytosine
Guanosine
Thymidine
Uridine
```
110
What bond is formed between nucleic acids?
Phosphodiester
111
What are the details of a phosphodiester bond?
A phosphodiester bond is formed between a free 3’ OH group and a 5’ triphosphate
Consumes two high-energy bonds!
112
What direction is DNA synthesized?
5 to 3
| New nucleotides are only added to the free 3 end
113
Describe the structure of the DNA double helix?
Two antiparallel nucleotide strands
One is 5 to 3, the other 3 to 5
Sugar phosphate backbone
Base pairs on inside
114
How many bonds are formed between A and T?
Two -double bond
115
How many bonds are formed between C and G?
Three
| triple bond
116
Why is DNA replication important?
So that daughter cells have a complete genome
117
What are the features of DNA replication?
Semi conservative
118
What is the catalyst in DNA replication?
DNA polymerase
119
What is require before DNA replication can occur
Existing nucleic acid
| RNA primer
120
Explain the origins of replication in eukaryotes?
Have many origins of DNA replication
| Bidirectional to ensure DNA replication finishes in a reasonable amount of time
121
What is the leading strand?
ALways has a free 3 end
122
What is the lagging strand
Has to be replicated in short segments called okazaki fragments
123
What are the steps of DNA replication?
```
Helicase unwinds DNA
DNA polymerase synthesises a complementary strand
Primase synthesises an RNA primer
Gaps are filled by DNA polymerase
Primers are degraded
```
124
How does DNA polymerase 'proof read' the DNA?
has a 3 to 5 exonuclease activity
| removes incorrect nucleotide
125
Describe the general structure of RNA.
single stranded
can create stem-loops= local streches of intramolecular basepairing
contains uracil instead of T
126
What are the three main clases of RNA?
ribosomal
transfer
messenger
127
What is the function of rRNA?
combines with proteins to form ribosomes where protein synthesis takes place
128
What is the function of tRNA?
carries the amino acids to be incorporated into the protein
129
What is the function of mRNA?
carries the genetic information for protein synthesis
130
What are the stable RNAs?
rRNA
| tRNA
131
What enzyme makes RNA?
RNA polymerase
132
How many types of RNA polymerazes are there in eukaryotes?
three
| Pol 1, poll II and poll III
133
How can RNA polymerases be distinguished?
By their sensitivity to toxins like alpha amanitin
134
WHich RNA polymerase synthesises mRNA?
Pol II
135
What is tRNA?
Adapter between nucleic acid code and amino acid code
136
What is an anti codon?
Three nucelotides
| specific amino acids attach to it at the 3 end
137
What is the shape of tRNA?
three dimensional
| cloverleaf when flattened
138
What are the steps of transcription?
```
RNA polymerase binds
DNA chain separate
Transciption initiated
Elongation
Termination
```
139
What is the TATA box?
present about 25 nucelotides before transcrition starts
| site for binding of promoters
140
What is TBP?
TATA box binding protein
141
What is TFIID?
a general transcription factor
| rquired for all Pol II transcibed genes
142
What is the role of TBP?
Introduces kink into DNA- determines transciptional start and direction
Provides a landing platform for furthur transcription factors and for RNA polymerase
143
What is required to initiate transcription?
general transcription factors
precise order of assembly
Pol II and TFIIF extend transcript of their own
TFIID allows transcription at low basal rates
144
Describe the process of transcription elongation.
RNA synthesised 5 to 3
New RNA complementary to template
Identical to the coding strand
145
Describe transcription termination.
Newly synthesised RNA makes a stem-loop structure
followed by a stretch of Us
A specific enzyme cleaves the (now finished) RNA
RNA is released
polymerase dissociates
146
Name a specific example of a transciption regulator.
Steroid receptors
147
Where are steroid receptors located?
Cytoplasm (inactive)
148
How are steroid hormones transported in the blood?
Bound to albumin or specific transport proteins
149
Describe the process of how steroids regulate transcription?
Free steroids enter target cells by diffusion
Bind to inactive steroid receptor in cytoplasm
Activates receptor
Translocates to nucleus
Binds to response elements
usually as homodimer
Coordinated regulation of a set of genes
150
Where does the steroid bind to the DNA?
At steroid response elements (SRE's)
151
What is an exon?
Coding region of DNA
152
What is an intron?
Non-coding region of DNA
153
Describe the process of slicing
Extrons and introns are transcribed
| Introns have to be removed before translation into protein
154
How are the ends of mRNAs processed?
Addition of poly(A) tail
| addition of 5' cap
155
What is the function of an anticodon?
Forms base pairs with codons
156
How many nucleotides are in codons and anticodons?
Three
157
What is the name for the three nucleotides on a codon or anticodon?
Triplets
158
What do the anticodons code for?
Amino acids
159
What is meant by the face that amino acids are degenerate?
Amino acids can have more than one codon
160
What is meant by the fact that each codon is unambiguous?
Each codon codes for only one amino acid
161
What are the components of translation?
```
Amino acids
tRNAs
Aminoacyl-tRNA synthetases
A specific set of protein factors for each of
initiation of protein synthesis
elongation of polypeptide chain and translocation
termination
ATP and GTP as sources of energy
Ribosomes
mRNA
```
162
What is the function of Aminoacyl-tRNA synthetase?
Binds amino acids to their corresponding tRNA molecule
163
What kind of bond is between the amino acid and its tRNA?
covalent- requires ATP
164
How many rRNA molecules are contained within a ribosome?
four
| three in bacteria
165
How many tRNA binding sites are present on a ribosome?
three
166
Describe the initiation of translation.
Requires initiation factors (IFs)
GTP is hydrolysed to provide energy for initiation
Small ribosomal subunit binds to 5’ end of mRNA
Moves along the mRNA until AUG (start codon) is found (ATP-dependent)
Special ‘initiator’ tRNA with UAC anticodon base-pairs with the start codon
carries methionine
Large subunit joins assembly and initiator tRNA is located in P site
167
Describe the elongation process of translation.
An elongation factor (EF-1a), brings the next aminoacyl-tRNA to the A site
anticodon (here: CGU) base-pairs with codon (here: GCA)
GTP is hydrolysed, EF is released from tRNA
A second elongation factor (EFbg) regenerates EF1a to pick up the next aminoacyl-tRNA
168
What enzyme catalyses peptide bond formation between the amino acids in the P and A sites?
Peptidyl tranderase
169
What are the names of the tree different binding sites for tRNA?
```
A= acceptor
P= peptidly
E= exit
```
170
Describe peptide bond formation and translocation.
Peptidyl transferase catalyses peptide bond formation between amino acids in the P and A sites
peptide now located in A site
Elongation factor EF-2 moves ribosome along the mRNA
by one triplet
‘Empty’ tRNA moves to E site
can exit and become reloaded with an amino acid
tRNA with the growing peptide moves from the A to the P site
A site is free for the next aminoacyl-tRNA
171
Describe the process of termination of translation.
Occurs when the A site of the ribosome encounters a stop codon
UAA, UAG or UGA
No aminoacyl-tRNA base-pairs with stop codons
Release factor RF binds stop codon
GTP hydrolysis
Finished protein is cleaved off tRNA
The components – rRNA, mRNA and tRNA – dissociate from one another
Whole process starts all over again with small subunit being bound by IF ready for translation of a new protein
172
What is a polysome?
Cluster of ribosomes bound to an RNA molecule
173
Name the five possible overall mutations.
```
Point
Missense
Nonsense
SIlent
Frameshift
```
174
What is a point mutation?
Change in a single base in DNA
175
What is a missense mutation?
Results in a change of amino acid sequence which can change protein function
176
What is a nonsense mutation?
Created new termination codon
| Changes length of protein
177
What is a silent mutation?
No change in amino acid sequencw
DUe to degeneracy of the genetic code
No effect on protein
178
What is a frameshift mutation?
Addition of deletion of a base (or two)
| Changed the reading frame of translation into protein
179
Name the four types of base mutation.
Insertion
Deletion
Altered base- single amino acid change
Altered base- no amino acid change
180
Name the four chromosomal mutations.
Deletions
Duplication
Inversions
Translocation
181
What is protein targeting?
Moving a protein to its final cellular destination
182
What is protein modification?
Addition of further functional chemical groups
183
What is protein degradation?
Damaged or unwanted proteins must be removed
184
What is the difference between a free and a bound ribosome?
Free ribosomes are in the cytosol whereas bound ribosomes are on the rough ER
185
Where do free ribosomes make proteins for?
Cytosol
Nucleus
Mitochondria
Translocated post translationally
186
Where do bound ribosomes make proteins for?
```
Plasma membrane
ER
Golgi apparatus
Secretion
Translocation co-translationally
```
187
Giv examples of post-translational modifications.
Glycosylation- addition of a carbohydrate
| Formation of disulphide bonds
188
What condition can be caused by a post-translational misfolding of the alpha- antitrypsin protein
Emphysema
189
Name and describe a disease caused by incorrect protein targeting?
I cell disease (mucilipidosis II)
inherited recessive disorder of protein targeting
proteins normally destined for lysosomes are not properly sorted in the Golgi
end up secreted from cell
lysosomes can not properly digest material, become clogged
death before age 8
190
What are enzymes?
```
Catalysts
Proteins- exception ribozymes
Efficient
Specific
Potent
```
191
What is a cofactor?
'Helper' molecules for enzymes
192
What is the name for an organic cofactorr?
Coenzyme
193
What is the name for a tightly bound enzyme?
Prosthetic group eg. haem in haemoglobin
194
What is the name for an enzyme without a cofactor?
Apoenzyme
195
What is the name for an enzyme with cofactor?
Holoenzyme
196
Give an example of a metal ion cofactor
Zinc, iron, copper
| Involved in redox reactions
197
Give an example of a Coenzyme
Many are dervived from vitamins and are involved in redox reactions
NAD+, FAD
Others involved in group transfer processes eg CoA transfers acetyl groups
ATP transfers phosphate groups
198
How does coenzymes relate to vitamin deficiency?
Most vitamins function as coenzymes- symptoms of vitamin deficiencies reflect the loss of specific enzyme activities.
199
What is the difference between dietary and functional deficiency?
Dietary- inadequate intake
| Functional- caused by drugs or toxins which inhibit co enzyme synthesis
200
What does NAD+ stand for?
Nicotinamide adenine dinucleotide
201
Where does the substrate bind to?
Active site eg a cleft or crevice
202
What are the features of an active site?
Contains amino acids which are specific and essential for catalytic activity.
203
What is the lock and key model?
Active site of unbound enzyme is complementary to the shape of the substrate
204
What is the induced fit model?
Binding of substrate induces a conformational change in enzyme, results in complementary fit
205
Name an example of an induced fit enzyme?
Hexokinase
206
What effect do enzymes have on the transition state?
Bind to it and stabilize it
207
What is the transition state?
Reaction intermediate that has the greatest free energy
208
What effect to enzymes have on the activation energy of the reaction?
Reduce it by providing alternative reaction pathways
209
Describe the bonding specific to the chymotrypsin active site?
Hydrophobic pocket binds aromatic amino acids
210
Describe the bonding specific to trypsin active sites?
Negatively charges Asp interacts with positively charged Lys or Arg
211
Describe the bonding at elastase active sites
Active site partially blocked, only amino acids with small or no side chains can bind
212
Why is the trypsin acive site affected so greatly by pH?
Trypsin active site – carboxyl group part of active site – essential that this is charged – reduction in pH would reduce the extent of ionisation of this functional group and therefore decrease efficacy of active site.
213
What is an isozyme?
Isozymes are isoforms of enzymes, they catalyse the same reaction but have different properties and structure (and sequence)
214
Give an example of a developmental varying isozyme?
Haemoglobin
| Different during various stages of development- foetal and embryonic varieties have a higher affinity for oxygen
215
Give an example of tissue specific isoforms
```
Lactate dehydrogenase (LDH)
Two types- one in heart and one in muscle
Tetramer- five possible combinations
```
216
What does an increase in LDH suggest?
Myocardial infarction
217
Describe how the isozyme, creatine kinase is useful clinically?
Dimeric protein that binds to muscle sacromere
M form on skeletal muscle
B form in brain
Heart has both in a heterodimer (MB)
Appearance of brain type in blood- STROKE
Appearance of heart type suggest -MI
218
Name an example of reversible covalent modification.
Phosphorylation- can convert inactive for to active form
219
Which enzymes carry out phosphorylation?
Protein kinases
220
What is a zymogen?
Inactive presursor of an enzyme
221
Describe what is meant by irreversible covalent modification
Zymogens are irreversibly transformed into active enzymes by cleavage of a covalent bond
222
Describe examples of irreversible covalent modification
in pancreas: trypsinogen and chymotrypsinogen, inactive precursors, are formed
in small intestine: enteropeptidase cleaves trypsinogen to form active trypsin which cleaves chymotrypsinogen to form active chymotrypsin
Other examples:
digestive enzymes, blood-clotting enzymes, clot-dissolving enzymes
223
Why is the trypsin acive site affected so greatly by pH?
Trypsin active site – carboxyl group part of active site – essential that this is charged – reduction in pH would reduce the extent of ionisation of this functional group and therefore decrease efficacy of active site.
224
What is an isozyme?
Isozymes are isoforms of enzymes, they catalyse the same reaction but have different properties and structure (and sequence)
225
Give an example of a developmental varying isozyme?
Haemoglobin
| Different during various stages of development- foetal and embryonic varieties have a higher affinity for oxygen
226
Give an example of tissue specific isoforms
```
Lactate dehydrogenase (LDH)
Two types- one in heart and one in muscle
Tetramer- five possible combinations
```
227
What does an increase in LDH suggest?
Myocardial infarction
228
Describe how the isozyme, creatine kinase is useful clinically?
Dimeric protein that binds to muscle sacromere
M form on skeletal muscle
B form in brain
Heart has both in a heterodimer (MB)
Appearance of brain type in blood- STROKE
Appearance of heart type suggest -MI
229
Name an example of reversible covalent modification.
Phosphorylation- can convert inactive for to active form
230
Which enzymes carry out phosphorylation?
Protein kinases
231
What is a zymogen?
Inactive presursor of an enzyme
232
Describe what is meant by irreversible covalent modification
Zymogens are irreversibly transformed into active enzymes by cleavage of a covalent bond
233
Describe examples of irreversible covalent modification
in pancreas: trypsinogen and chymotrypsinogen, inactive precursors, are formed
in small intestine: enteropeptidase cleaves trypsinogen to form active trypsin which cleaves chymotrypsinogen to form active chymotrypsin
Other examples:
digestive enzymes, blood-clotting enzymes, clot-dissolving enzymes
234
What is the michaelis constant?
The substrate concentration where the initial reaction rate is half maximal
235
What is Vmax?
The maximum velocity of a reaction in infinite substrate concentrations
236
What is Vo?
The initial reaction rate
237
What is equilibrium?
The rate at which there is no net change of substrate to product
238
What are the units of Km?
concentration (m)
239
What does a low Km mean?
Enzyme has a high affinity for the substate
240
What does a high Km mean?
Enzyme has a low affinity for the substrate
241
How do you determine Vmax on a linewearver-burk plot?
Intersection of the straight line with the Y axis
242
How do you determine the Km for a lineweaver-burk plot?
Intersection with the X axis
243
Give an example of an enzyme with a low Km?
Hexokinase- can work at near Vmax even when blood glucose level is very low
Glucokinase is an isozyme- activity increases as glusose levels rise
244
What is MODY?
MODY (maturity-onset diabetes of the young)
caused by mutations in pancreatic glucokinase which affect KM or Vmax
reduced glucokinase activity results in reduced insulin secretion for a given blood glucose level
245
What is the difference between a reversible and irreversible enzyme inhibitor?
Reversible inhibitors are substances which bind to an enzmye but can be released- irreversible inhibitors cannot be released
246
What is the difference between a competitive and non competitive inhibitor?
competitive inhibitor: binds to the active (catalytic) site and blocks access to it by substrate
noncompetitive inhibitor: binds to a site other than the active site, inhibits the enzyme by changing its conformation
247
How can a competitive inhibitor be 'out- competed'?
By the addition of lots of substrate
| Non competitice inhibitors cannot be out competed in this way
248
What is a common mechanism of allosteric control.
In feedback inhibition- where by the product of a biochemical pathway can act as an allosteric inhibitor of a rate limiting enzyme nearer the beginning of the pathway
249
What is the shape of an allosteric enzymes rate curve?
Sigmoidal
| They do not follow the Michaelis-menten kinetics- not a hyperbola
250
How can allosteric enzymes be controlled
Allosteric inhibitors
| Allosteric activators
251
What is co-operativity?
The influence that the binding of a ligand to one protomer has on the binding of ligand to another protomer in an oligomeric protein
252
What is an allosteric site?
BInding site on an enzyme disctinct from the active site
253
Give an example of allosteric regulation
Binding of oxygen to haemoglobin
254
Describe the allosteric actions of oxygen and haemoglobon
Positive co-operativity- as oxygen increases haemoglobins affinty for oxygen in its other subunits increases
255
What is the R form of an enzyme?
Relaxed- binds substrate tightly- ACTIVE
256
What is the T form of an enzyme?
Tight- binds substrate less tightly- INACTIVE
257
When are more enzymes in the T from?
In the absence of substrate- activate in the presence of substrate
258
What is the sequential model of allosteric regulation?
The binding of substrate induces a conformational change from the T form to the R form
The change in conformation is induced by the fit of the substrate to the enzyme
Other subunits subsequently change as well
259
How do allosteric inhibitors work?
By locking the subunits of the enzyme in the T form
260
How do allosteric activators work?
By locking the enzyme subunit in the R form
