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Protiens Flashcards

1
Q

How many common amino acids are there?

A

20

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2
Q

What 3 categories can amino acids be divided into?

A

non-essential, conditionally essential, essential

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3
Q

What are non-essential amino acids?

A

the body is able to produce them

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4
Q

What are conditionally essential amino acids?

A

supplemented in the diet for young and compromised animals

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5
Q

What are essential amino acids?

A

the body is unable to produce them and they need to be acquired in the diet

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6
Q

Describe the chemical structure of an amino acid

A

central carbon atom, a carboxyl group, a hydrogen atom, an amino group and a variable side chain (R) group

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7
Q

How can the R groups vary?

A

structure, size and electrical charge

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8
Q

What does the variety in the R groups influence?

A

the solubility of the amino acids in water

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9
Q

Can amino acids act as both acids and bases?

A

yes

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10
Q

What does a doubly charged amino acid have?

A

one positive and one negative charge

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11
Q

What are doubly charged amino acids called?

A

zwitterion

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12
Q

How many structure levels do protiens have?

A

4

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13
Q

What are the structure levels of a protien called?

A

primary, secondary, tertiary and quaternary

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14
Q

What does the primary sequence of a protein determine?

A

its 3D conformation and function

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15
Q

What can changes in the amino acid sequence cause?

A

severely compromise the ability of a protien to carry out it’s function

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16
Q

How is a peptide bond formed?

A

when the carboxyl group of one amino acids reacts with the amino group of another amino acid

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17
Q

What is produced as a byproduct in the formation of a peptide bond?

A

water

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18
Q

What are two amino acids joined by a peptide bond known as?

A

a dipeptide

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19
Q

What is a chain of amino acids known as?

A

oligopeptide

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20
Q

What is a large chain of amino acids known as?

A

polypeptide

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21
Q

What does every peptide or protein have at each end of the chain?

A

a free amino group at one end and a free carboxyl group at the other end

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22
Q

Where do disulphide bonds occur?

A

between the R cystine group of cystine molecules

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23
Q

What is eliminated in order to form disulphide bonds?

A

2 hydrogens and 2 electrons

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24
Q

what effect does the removal of hydrogen and electrons in order to form disulphide bonds have on the protein?

A

stabilises the proteins structure

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25
Q

What does the secondary structure of a protien describe?

A

the local special arrangement of amino acids

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26
Q

What is the secondary structure of a protein formed by?

A

hydrogen bonds of the main chain atoms in the polypeptide backbone

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27
Q

What are the two types of protein secondary structure?

A

alpha helix and beta pleated sheet

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28
Q

How are the R groups arranged in an alpha helix?

A

on the outside of the helix in a right handed twist

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29
Q

How is the alpha helix stabilised?

A

by hydrogen bonds between the carbonyl oxygen of a peptide bond and the hydrogen bond of the peptide bond 4 amino acids away

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30
Q

What does the large number of hydrogen bonds in an alpha helix provide?

A

a stable rigid structure

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31
Q

How are R groups arranged in beta pleated sheet?

A

above and below the plane of the polypeptide backbone

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32
Q

Which bonds stabilise the structure of beta pleated sheet?

A

hydrogen bonds between carbonyl oxygen and hydrogen

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33
Q

What two forms can beta pleated sheet be in?

A

parallel and antiparallel

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34
Q

What is the name of the turns which connect the strands of an antiparallel beta pleated sheet?

A

beta turns

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35
Q

What does the tertiary structure of a protein describe?

A

the overall 3D conformation of the polypeptide chain.

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36
Q

What two protein structures do most proteins form in their tertiary structure?

A

extended fibrous structures and compact globular structures

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37
Q

What are the 3 methods of arrangement in tertiary structure of a protein?

A

reversable attractions/repulsions, hydrogen bonds, hydrophillic and hydrophobic R regions

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38
Q

What do hydrophobic and hydrophillic regions form from in protein tertiary structure?

A

arrangements from polar and non-polar R groups

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39
Q

How is globular proteins shape created?

A

different segments of the polypeptide chain fold bakc on each other, generating a more compact shape than seen in fibrous proteins

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40
Q

What does the folding in globular proteins provide for their structure?

A

structural diversity necessary for proteins to carry out a wide range of biological functions.

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41
Q

Name 5 examples of globular proteins?

A

enzymes, transport proteins, immunoglobulins, motor proteins, regulatory proteins

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42
Q

what does the quaternary structure of proteins describe?

A

the 3D arrangements of sub units in a multi-subunit protein.

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43
Q

What does the quaternary structure of a protein result from?

A

specific interactions between sub units

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44
Q

What is the name for 2 and 3 subunits?

A

dimer and trimer

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45
Q

How many sub units does haemoglobin have?

A

4

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46
Q

What is the common precursor of all amino acids

A

glucose

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47
Q

What 3 seperate pathways does glucose undergo?

A

pentose pathway, glycolysis and citric acid cycle

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48
Q

How is amino acid synthesis regulated?

A

feedback inhibition of the first reaction by the end product of the pathway

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49
Q

What other, non-protein, biomolecules do amino acids make?

A

hormones, coenzymes, nucleotides, alkaloids, cell wall polymers, porphyrins, antibiotics, pigments and neurotransmitters

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50
Q

What is a precursor of porphyrins?

A

glycine

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51
Q

What structure do porphyrins have?

A

cylindrical

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52
Q

what are porphyrins?

A

nitrogenous biological pigments

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53
Q

What is one of the best known porphyrins?

A

haem

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54
Q

What is haem the pigment in?

A

red blood cells

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55
Q

What is haem a cofactor of?

A

haemoglobin

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56
Q

What digestive aid is haem the source of?

A

bile pigments

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57
Q

What is haem released from?

A

dying erythrocytes (RBC)

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58
Q

What happens when haem is degraded?

A

free Fe2+ (iron) and bilirubin (ultimately)

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59
Q

What is used to convert haem to biliverdin?

A

haem oxygenase

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60
Q

What catalyses the conversion of biliverdin to biliruben?

A

biliverdin redactase

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61
Q

How can you view the reaction of haem to bilirubin?

A

observing a change in colour (e.g. bruising), black or purple from damaged erythrocytes, green from biliverdin and yellow from bilirubin

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62
Q

How does bilirubin travel in the bloodstream?

A

as a complex with serum albumin.

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63
Q

What happens to bilirubin in the liver?

A

it is transformed to the bile pigment bilirubin diglucuronide.

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64
Q

What happens to bilirubin diglucuronide?

A

it is sufficiently soluble to be excreted with other components of bile into the small intestine.

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65
Q

What happens to bilirubin diglucuronide in the small intestine?

A

it is converted predominantly into urobilinogen by microbial enzymes

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66
Q

What happens to urobilinogen?

A

some is reabsorbed into the blood and transported to the kidney where it is converted to urobilin. the remaining urobilinogen in the intestine is converted to stercobilin.

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67
Q

What is urobilin?

A

the compound that gives urine its yellow colour

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68
Q

What is stercobilin?

A

the compound that gives faeces its red brown colour

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69
Q

What are colorimetric assays and what can they be used to infer?

A

reactions which cause a colour change to infer protein presence or activity

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70
Q

What sort of data does a colorimetric assay provide?

A

semi-quantitative as the results are visually assessed

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71
Q

What compound is often used in colorimetric assays?

A

bromophenol blue

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72
Q

What happens to bromophenol blue when it is exposed to proteins?

A

they change colour

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73
Q

What diagnostic technique are colorimetric assays used in?

A

urine dipsticks

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74
Q

What does SDS-PAGE stand for?

A

sodium dodecyl sulphate polyacrylamide gel electrophoresis

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75
Q

What does SDS-PAGE do to proteins?

A

separates them according to size

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76
Q

What happens during SDS-PAGE?

A

gel forms pores which trap proteins, bigger proteins are less able to pass through it. An electrical current is applied across the gel and proteins which become negatively charged (follow the current)

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77
Q

What happens once the proteins are separated by size in SDS-PAGE?

A

they can be transferred to a thin membrane and specific proteins detected using an antibody

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78
Q

Why may secondary antibodies be added to the proteins?

A

they allow them to be visualized

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79
Q

What is this process of transfer to a membrane and visualization of the proteins known as?

A

Western blotting

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80
Q

What happens during ELISAs?

A

cells are fixed with a fixative (e.g. acetone), the primary antibody is added and allowed to bind to the protein of interest. The labeled secondary antibody is then added to the primary. The secondary antibody is bound to a florescent marker.

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81
Q

When are ELISAs useful diagnostic techniques?

A

when a protein location rather than quantity is informative

82
Q

Give an example of when ELISA may be useful

A

feline infectious peritonitus, feline coronavirus is commonly found in cats guts but if it is found in an abdominal fluid aspiration it is indicative of FIP. This would be detected using ELISA

83
Q

What is immunohistochemistry?

A

using an enzymatic colour-changing reaction to detect proteins of interest in fixed tissue samples from pathology samples

84
Q

What is immunocytochemistry?

A

similar to immunohistochemistry but uses cells rather than tissues

85
Q

What are the advantages of protein testing?

A

identify host or pathogen proteins, can show location (immunohistology), qualitative or quantitative. Convenient, rapid in-house assays (of variable accuracy) available

86
Q

What are the disadvantages of protein testing?

A

variable sensitivity (false negative results), variable prices depending on test. Variable sample stability depending on protein structure and test requirements

87
Q

What happens during protein catabolism?

A

proteins are broken down to amino acids

88
Q

What process do amino acids undergo in order to generate energy?

A

oxidative deanimation

89
Q

What are the 3 metabolic circumstances that oxidative deanimation happens under?

A

normal synthesis and degradation of cellular proteins (protein turnover), when the diet is rich in protein and ingested amino acids exceed the body’s need for protein synthesis, the surplus is catabolised. During starvation or uncontrolled diabetes mellitus, when carbohydrates are either unavailable or not properly used, cellular protein are used as fuel.

90
Q

What is deanimation?

A

the process by which amino acids are broken down

91
Q

Why do amino acids need to go through deanimation?

A

amino acids can’t be stored

92
Q

What is produced when animo acids are deanimated?

A

they produce a carbon skeleton and ammonia

93
Q

Why must ammonia be detoxified before excretion?

A

it is highly toxic

94
Q

What can the carbon skeleton be broken down into and used for?

A

3-4 carbon units used to build fatty acids or glucose

95
Q

What happens to the amino group of many amino acids so they form glutamate?

A

they are transfurred to alpha ketoglutarate

96
Q

What is yielded from oxidatively deanimating glutamate?

A

ammonium

97
Q

What do aminotransaminases do?

A

catalyse the transfer of an amino group from an amino acid to an alpha - ketoglutarate

98
Q

What is left behind once the amino group has been transfurred to alpha - ketoglutarate?

A

the corrosponding alpha-keto acid analog of the amino acid

99
Q

Why is there no net loss of amino group (deanimation) during the transfer of amino acid to alpha-ketogluterate?

A

alpha-ketoglutarate becomes animated as the amino acid is deanimated

100
Q

What happens to the nitrogen atom that is transfurred to alpha-ketoglutarate in the transmission reaction?

A

it is converted to a free ammonium ion by oxidative deanimation

101
Q

What enzyme catalyses the conversion of nitrogen to a free ammonium ion by oxidative deanimation?

A

glutamate dehydrogenase

102
Q

What does glutaminase catalyse?

A

the production of glutamate from glutamine

103
Q

Where does glutamine come from in the body?

A

muscle and other tissues

104
Q

What ion does the production of glutamate from glutamine produce?

A

an ammonium ion

105
Q

What happens to ammonium ions before entering the urea cycle?

A

converted into carbamoyl phosphate

106
Q

What happens in the first step of the urea cycle?

A

citrulline is formed from ornithine and carbomyl phosphate (entry of first amino group)

107
Q

What happens during the second step of the urea cycle?

A

formation of argininosuccinate by addition of aspartate to citruline

108
Q

What does the third step of the urea cycle involve?

A

formation of arginine and by-product fumerase from argininosuccinate

109
Q

What does the formation of arginine from argininosuccinate release?

A

fumarate

110
Q

What does fumarate do?

A

enter the citric acid cycle

111
Q

What happens in the 4th step of the urea cycle?

A

urea is formed and can be excreted

112
Q

How do aquatic species dispose of nitrogen?

A

release ammonia into the surrounding water as this dilutes it

113
Q

How do birds and reptiles dispose of nitrogen?

A

in the form of uric acid

114
Q

What involvement do enzymes have in reactions?

A

biological catalysts which alter the rate of s reactio but are not changed by it.

115
Q

what is an enzymes active site made from?

A

amino acid residues

116
Q

What parts of an enzymes structure are essential to the function of the active site?

A

primary, secondary, tertiary and quaternary

117
Q

What do some enzymes require to form substances with the correct active sites?

A

cofactors

118
Q

What do co enzymes act as?

A

carriers or donors of functional groups

119
Q

What are enzymes classified by?

A

the type of reaction they catalyse

120
Q

how are many enzymes named?

A

by adding the suffix -ase to the name of their substrate or a word or phrase describing their activity

121
Q

What do oxidoreductases do?

A

transfer of electrons

122
Q

What do transfurases do?

A

group transfer reactions

123
Q

What do hydrolases do?

A

hydrolysis reactions (transfur of functional groups to water)

124
Q

What do lyases do?

A

cleavage of C-C, C-O, C-N or other bonds by elimination, leaving double bonds or rings or addition of groups to double bonds

125
Q

What do isomerases do?

A

transfur of groups within molecules to yield different isometric forms

126
Q

What do ligases do?

A

formation of chemical bonds between two macromolecules by condensation reactions coupled to hydrolysis of ATP

127
Q

How do enzymes help with the reaction they are involved with?

A

lower the activation energy for the reaction they catalyse, they therefore can speed up reactions

128
Q

What does the rate of enzyme action depend on?

A

the reaction being catalysed and the concentration of the substrate

129
Q

What does the Michaelis-Menten equation do?

A

relates the rate of product formation (V0) with enzyme affinity (Km)

130
Q

What are the two types of inhibition that enzymes are subject to?

A

competitive and non-competitive

131
Q

What happens during competitive inhibition?

A

an inhibitor molecule blocks the active site of the enzyme

132
Q

What happens during non-competitive inhibition?

A

inhibitor molecule binds to another part of the enzyme and changes the shape of the active site

133
Q

What can be done to control enzyme activity?

A

controlling the supply of substrate, controlling the amount of enzyme, controlling the catalytic activity of regulatory enzymes

134
Q

How can the supply of substrate be controlled?

A

keeping substrates in vacuoles

135
Q

how can the numbers of enzymes in use be controlled?

A

enzymes are tagged to be degraded after use

136
Q

What 3 ways can catalytic activity of regulator enzymes be controlled?

A

Allosteric control, proteolytic cleavage, covalent modification

137
Q

How does allosteric control control the catalytic activity of regulator enzymes?

A

allosteric regulators act as non-competitive inhibitors and alter its activity

138
Q

How does proteolytic cleavage catalytic activity of regulator enzymes?

A

many enzymes are produced in an inactive precursor (zymogen) form which is then activated by proteolytic cleavage.

139
Q

What sort of enzymes are often produced in zymogen form to stop them damaging the cells they are made in?

A

digestive enzymes to stop them from digesting the cells that make them

140
Q

How does covalent modification control catalytic activity of regulator enzymes?

A

Phosphorylation by a kinase or dephosphorylation by a phosphatase are common modifications which can increase or decrease enzyme activity.

141
Q

What level is serum concentration of cellular enzymes at?

A

low

142
Q

Why may enzyme activity in plasma be increased?

A

cell proliferation or damage (e.g. cancer, cell death, trauma)

143
Q

What does the amount of enzyme in serum depend on?

A

the amount of enzyme in the damaged tissue, the organ or tissue mass, the degree of damage and the rate at which the enzyme is cleared from the plasma

144
Q

What can analysis of serum enzymes provide?

A

information about which tissue has been damaged

145
Q

Why can activity of diagnostic enzymes increase or decrease?

A

Increase: Proliferation of cells which normally produce it, Death of cells which contain it, Trauma or over-use (especially muscle)
Decrease: Reduction in the number of cells which produce it, Presence of inhibitors

146
Q

Why is correct protein folding important?

A

misfolded proteins cannot perform the functions they were intended for and can accumulate in cells or tissues

147
Q

When does protein folding occur?

A

very rapidly in newly synthesised cellular proteins

148
Q

What happens to those proteins which cannot fold correctly when surrounded by a polar solvent?

A

they need help from a pre-formed chaperone protein

149
Q

What happens to these proteins without the assistance of chaperone proteins?

A

they can become misfolded

150
Q

What re misfolded proteins called?

A

prion proteins

151
Q

What can prion proteins cause?

A

other proteins to misfold and create aggregates

152
Q

What happens if misfolded proteins are not downgraded in the cell?

A

aggregates can form deposits that cause disease

153
Q

What can these aggregate deposits present as in humans?

A

alzheimers

154
Q

What do misfolded protein aggregates form in animals?

A

spongiform encephalothopy. Can be present as bovine, feline or transmissible.

155
Q

what is spongiform encephalothopy colloquially known as?

A

mad cow disease

156
Q

What does loss of protein structure lead to

A

loss of function

157
Q

What is the destruction of the 3D shape of a protein known as?

A

denaturation

158
Q

What does denaturation involve?

A

the disruption of the interactions responsible for secondary and tertiary structure and reduces the polypeptide to a random coil

159
Q

What are some denaturing agents?

A

heat, pH, organic solvents, urea and mercaptoethanol, detergents

160
Q

What happens if a protein denatures?

A

enzyme active site can no longer work to catalyse reactions, co-enzymes and carrier proteins are unable to bind to substrate, reducing transportation of other biomolecules throughout the cells and organs, receptor sites of signalling protein molecules become denatured so cell signalling is affected.

161
Q

can enzymes refold after the denaturing agent is removed?

A

very few can, most are irreversibly damaged

162
Q

What is pancreatitis?

A

inflammation of the pancreas

163
Q

What effect can inflammation of the pancreas have on zymogens?

A

can activate them prematurely

164
Q

When are zymogens usually activated?

A

once inside the GI tract

165
Q

Why are zymogens activated inside the GI tract?

A

prevents them from breaking down tissues outside this area

166
Q

Where are zymogens often stored?

A

zymogen granules

167
Q

What are the main causes of pancreatitis?

A

very high fat diet, with or without concurrent obesity. Can also be caused by medical treatment or steroids. It can happen spontaneously without obvious cause (idiopathic)

168
Q

What are the consequences of pancreatitis?

A

digestive enzymes spill into abdominal cavity, digestive enzymes begin to digest tissues in the body and can case lasting damage to surrounding organs (liver, bile ducts, gall bladder, intestines

169
Q

How can pancreatitis be treated?

A

IV fluid therapy, anti-emetics, analgesia, resting the pancreas (24h starvation), longer term dietary changes and weight loss management

170
Q

What is hyperammonaemia?

A

when ammonia is not converted to urea and remains in the body in excess

171
Q

What are the signs of ammonia excess?

A

neurological e.g. vomiting, ataxia, headpressing, seizures, coma and death

172
Q

What is the most common cause of hyperammonaemia?

A

portosystemic shunt, where an extra blood vessel bridging between the vena cava and the portal vein allows blood to avoid being filtered by the liver

173
Q

Why must blood be filtered by the liver?

A

that is where protein deanimation and the urea cycle occur. blood is filtered through the liver by the portal vein so that ammonia and other waste products can be detoxified before being sent to the kidneys for excretion

174
Q

What are other causes of hyperammonaemia?

A

lack of enzymes for urea cycle resulting in reduced rate of urea production

175
Q

How can hyperammonaemia be treated?

A

surgery can close PSS but the patient must be stabilised first. This is done by restricting dietary protein intake to reduce nitrogen in the diet and medical management to help excretion of ammonia. If the cause is lack of urea cycle enzymes, enzyme precursors and substitute molecules can be supplemented

176
Q

Where are many exocrine enzymes produced and what is their function?

A

in the pancreas and they catalyse the breakdown of fats, carbohydrates and proteins

177
Q

What happens if the pancreas is not able to produce enough of these enzymes?

A

the body is unable to digest the molecules they break down and they cannot pass out of the digestive tract. This usually results in weight loss despite a normal/increased food intake

178
Q

What other causes can weight loss despite an increased appetite have?

A

lymphoma, parasites, infectious agents

179
Q

What is very important in diagnosing EPI?

A

clinical history and trypsin-like immunoreactivity

180
Q

What does trypsin-like immunoreactivity test?

A

the levels of trypsin (an enzyme that digests protein) and trypsinogen (the precursor to trypsin) in the blood.

181
Q

What disease is indicated by levels of trypsin and trypsinogen below normal range?

A

diagnostic for EPI

182
Q

How is EPI treated?

A

supplemented with pancreatic enzymes (powders or tablets.) Switched on to highly digestible, low fat diets to compensate for the reduced levels of exocrine enzymes. Important to treat the cause of the EPI, which can be chronic pancreatitis.

183
Q

What do coenzymes act as?

A

Carriers and donors of functional groups

184
Q

Why do coenzymes usually have dietary precursors?

A

They cannot be fully synthesised by the body

185
Q

What happens if the body is unable to synthesise coenzymes that require dietary precursors?

A

If they are not readily present in the diet this will cause issues

186
Q

What are two of the most common coenzymes deficiencies?

A

Thiamine (vitamin B1) and cobalamin (vitamin B12)

187
Q

What is thiamine the precursor to?

A

Thiamine pyrophosphate

188
Q

What molecule does thiamine form a compound with to create thiamine pyrophosphate?

A

ATP

189
Q

What functional group is thiamine pyrophosphate a carrier for?

A

Aldehyde ( -CHO)

190
Q

What reaction is thiamine pyrophosphate a coenzyme in?

A

Catabolism of sugars and amino acids

191
Q

What happens if thiamine is not present in the diet?

A

There is incomplete breakdown of sugars

192
Q

What are the early signs of thiamine deficiency?

A

Non specific such as lethargy and anorexia

193
Q

What are the signs in the later stages of thiamine deficiency?

A

Neurological signs such as in coordination, circling, head tilt, and abnormal gait which can progress to tremors or seizures

194
Q

What is a way to test for thiamine deficiency?

A

Administer thiamine and see if the patient improves

195
Q

What is cobalamin a coenzyme for?

A

Enzymes in three different classes

196
Q

What 3 classes of enzyme is cobalamin a coenzyme for?

A

Isomerases, transfer hydrogens to create different isomers.
Methyltransferases, transfer methyl.
Dehalogenases, only in bacteria

197
Q

What are the enzymes that cobalamin is a coenzyme for, involved in?

A

DNA synthesis and amino acid metabolism

198
Q

What clinical signs are shown if there is a deficiency in cobalamin?

A

Poor body condition, inability to gain weight, weakness, lethargy, vomiting and diarrhoea

199
Q

For what reason may signs of cobalamin deficiency be seen in the very young?

A

It can be congenital

200
Q

How is cobalamin deficiency treated?

A

Cobalamin supplementation

X Pre Clinical Science (17 decks)

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