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ISCM > BIOCHEMISTRY > Flashcards

BIOCHEMISTRY Flashcards

1
Q

what are proteins

A

complex biopolymers whos structure is determined by the sequence of amino acids

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2
Q

how many amino acids are there and how are they different

A

20, differentiated by the R side chains

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3
Q

describe the structure of an amino acid (left to right)

A

starts with and amine group (NH3) then the alpha C with H ontop and R group below then there is the carboxyl group (COOH)

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4
Q

why are amino acids called zwitter ions

A

they both a negatively charged end (carboxyl group) and a positively charged end (amine group)

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5
Q

how many stereoisomers exist

A

2 steroisomers called enantiomers/optical isomers

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6
Q

which enantiomers are found in living things

A

L-animo acid enantiomers. it is asymmetric and this allows for highly specific molecule recognition

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7
Q

what are the different groups of amino acids

A
  • nonpolar and hydrophobic
  • aromatic
  • polar,hydrophillic and acidic
  • polar,hydrophilic and basic
  • hydroxylic, sulfur containing and amidic
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8
Q

why is methionine special

A

conatins sulfur and is the first amino acid in a polypeptide chain

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9
Q

what is special about cyteine

A

contains sulfur and is highly reactive and therefore used in enzyme active sites. it can also form disulfide bonds

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10
Q

how does a peptide bond form

A

when the OH from a carboxyl group links to the H from the amine group they from water so the (C=O-NH) is the peptide bond

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11
Q

what does the primary structure mean

A

the primary structure determines how the peptide folds into a 3D shape

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12
Q

what is the secondary structure

A

it is how it is more complexly folded eg alpha helix, beta pleated sheets

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13
Q

what type of bond is the secondary structure dependent on

A

on hydrogen bonds between O and H

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14
Q

what does it mean that the alpha helix is right handed

A

the side chains are pointing outwards from the central helix

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15
Q

which direction can the beta sheets form

A

either parallel or anti parallel

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16
Q

what is the tertiary structure

A

this is the arrangement of the secondary structures forming a more complex molecule

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17
Q

what are the different types of bonds in the tertiary structure

A

electrostatic attraction, hydrogen bonds and van der waals forces

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18
Q

what is the quaternary structure

A

the 3D structure which is several subunits bonded by non covalent bonds

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19
Q

what are the functions of proteins

A 
structural proteins 
catalytic proteins-enzymes 
signalling proteins 
proteins involved in cell adhesion and recognition
membrane transport proteins
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20
Q

examples of structural proteins

A
  • extracellular matrix proteins eg collagen and elastin
  • muscle proteins
  • cytoskeletal proteins
  • antibodies, complements
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21
Q

how to detect proteins

A
  • using SDS page gels which are 1D and 2D
  • mass spectrometry
  • crystallography
  • edman sequencing
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22
Q

what is the function of ubiquitin

A
  • regulates major cellular processes such as cell division, immune responses and embryonic development.
  • marks proteins for degradation
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23
Q

what is the function of the proteasome in protein breakdown

A

the proteasome recognizes the ubiquitin and cleaves off the ubiquitin. it then feeds the protein through a channel and then chops it into smaller pieces

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24
Q

how many heme groups does the quaternary structure of haemoglobin have

A

4

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25
Q

how does abnormal primary structure affect protein function and give examples

A
  • mutations leading to misfolding, sickle cell disease
  • mutations leading to trapping of protein in the ER, cystic fibrosis
  • mutations leading to premature stop codons and hence unfinished proteins, Duchene Muscular Dystrophy (DMD)
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26
Q

how does abnormal secondary structure affect protein function and which disease does it lead to

A

leads to amyloidosis which is the collection of amyloid which is a collective name for the congregation of abnormal proteins that cannot easily be broken down. theyre folded into beta sheets leading to extracellular deposits. alot of beta sheets leads to alzheimers disease

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27
Q

what are prions

A

it is also caused by abnormal secondary structure. prions are proteinaceous infectious particles (no DNA/RNA).

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28
Q

what is the function of a prion protein (PrPC)

A

normal neuronal protein involved in cell adhesion, ion channel activity and neural excitability

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29
Q

what is the shape of PrPC

A

normally an alpha helix secondary structure but when abnormal it changes into beta sheets

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30
Q

when ribosomes synthesize proteins which end do they start from

A

N-terminal of the amino acid, amine side

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31
Q

what type of amino acids can form hydrogen bonds

A

hydrophillic

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32
Q

which protein detection methods is most suitable to analyse protein structures

A

crstalography

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33
Q

which protein detection methods is most suitable to check the occurrence of a specific protein

A

immunoblots

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34
Q

what are enzymes

A

proteins with unique structures that are folded to create active sites which enable recognition of specific substrates they transform

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35
Q

what do oxidoreductases do

A

oxidation and reduction reaction

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36
Q

what do transferases do

A

transfer amino,carboxyl,acyl,carbonyl,methyl,phosphate and other groups between molecules

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37
Q

what do hydrolases do

A

cleavage bonds by adding water

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38
Q

what do lysases do

A

cleavage of carbon-carbon,carbon-sulphur and carbon-nitrogen but not peptide bonds

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39
Q

what do isomerases do

A

rearrangement of bonds

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40
Q

what do ligases do

A

formation of bonds between carbon and oxygen, sulphur and nitrogen

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41
Q

what is a catalyst

A

a protein which increases the rate of reaction without beinf changed itself in the overall process

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42
Q

how does a catalyst affect a reaction

A

helps change the rate not the equilibrium however equilibrium is reached faster

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43
Q

what is the induced fit model

A

when two substrates fit into the active site and form a enzyme-substrate complex. the activation energy is lowered and the two substrates form one product

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44
Q

what is the transition state theory

A

when one substrate binds to the active site forming an enzyme substrate complex, it undergoes catalysis and the two products stay in the active site now called an enzyme product complex/transition state and the product is then released

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45
Q

how do enzymes reduce the activation energy

A

they bind to the transition structure stabilizing it which leads to a lower activation energy

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46
Q

how is the transition state stabilized

A

the substrate binds in the correct orientation and binds tightly

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47
Q

what is an example of the transition state theory

A

lysozymes

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48
Q

how does the active site in the induced fit model reduce the activation energy

A

they bind the substrate in a favorable orientation but also allows the shape to be closer to that of the transition state

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49
Q

what do the enzymes do in the induced fit model

A

they can change their shape based on the substrate and need a chain reaction to return back to the original shape

50
Q

what affects the rate of reaction

A

temperature, pH and substrate concentration

51
Q

describe a graph of rate of reaction (y )against substrate concentration(x)

A

it is a curve starting from zero zero and plateauing at the higher substrate concentration.

52
Q

how can you determine the enzyme capacity by using the curve

A

the height of the curve is the enzyme capacity

53
Q

why does the rate of reaction plateau

A

all the active sites are occupied so that is the maximum rate of reaction despite increasing substrate concnetration

54
Q

what is the symbol for when the enzymes are fully saturated

A

Vmax and it is dependent on enzyme concentration. its at the top when it starts to plateau

55
Q

what is Km (its a constant )

A

it is the affinity of the substrate for the enzyme. Km is equal to the substrate concentration at which the enzyme converts substartes into products at half of its maximal rate

56
Q

what is the relationship between the Km and the affinity for the enzyme

A

the higher the Km the lower the substrates affinity for the enzyme

57
Q

what does having the same Vmax and having the same Km mean

A

same Vmax means- same enzyme concentration

same Km means - same affinity for the enzyme

58
Q

what are isoenzymes

A

catalyse the same reaction but different structures

59
Q

what is cytochrome P450

A
  • catalyse oxidation
  • superfamily of microsomal (liver) enzymes
  • named as CYP+number+letter
60
Q

what are competetive inhibitors

A
  • they bind reversibly to the active site
  • Km increases (reduces affinity for the enzyme)
  • Vmax remains unchanged
61
Q

what are non-competetive inhibitors

A
  • inhibitor binds outside the active site, decreasing raate of reaction
  • Km remains unchanged
  • Vmax decreases
62
Q

what are allosteric regulators

A

-they are multi-subunit proteins with multiple active sites

63
Q

what happens during allosteric regulation

A

-inhibitors bind to a site that is not the active site and this reduces Vmax and increases Km(reduces affinity)

64
Q

what is an allosteric activator

A

attaches outside the active site and it allows the substrate to bind at a higher affinity

65
Q

what is feed forward activation

A

when a metabolite produced activates an enzyme that catalyze a reaction further down the pathway

66
Q

give an example of feed forward activation

A

pyruvate kinase in glycolysis is activated by fructose-1,6- biphosphate

67
Q

what is gibbs free energy

A

the energy of products minus the energy of the substrate

68
Q

what is the purpose of biochemical profiling

A

to assess the physiological status of an individual

69
Q

what is patient stratification

A

separating patients to different treatment streams based on some characteristic

70
Q

how to measure biomolecules in the laboratory

A

each molecule absorbs light differently and at a certain wavelength. if a light source passes through a solution containing those molecules the amount of light absorbed will be in direct proportion to the number of molecules

71
Q

what equipment is used and what are the units

A

spectrophotometer in optical density (OD)

72
Q

what are colorimetric assays

A

this is when biomolecules being measured produce a color complex of a particular wavelength

73
Q

how is blood glucose measured

A

the glucose is converted by glucose oxidase into D-gluconic acid. simultaneously the glucose oxidase coverts the oxygen into hydrogen peroxide which reacts with horse radish peroxidase (HRP) which forms a color complex with a wavelength absorption of 540-570nm

74
Q

how do you convert optical density values into concentrations

A

the optical density of known concentrations of the sample are measured and plotted. a standard curve or line of best fit is drawn and the concentration can be found using the OD of the unknown samples

75
Q

what are screening tests

A

provide preliminary physiological data to reflect the general conditions of an individual. less complicated tests are involved and normally can be performed within a short period of time

76
Q

what are specific function tests

A

will provide more details to indicate whether a particular body system is performing their normal function or if there is any damage to particular organs

77
Q

what is the most common biochemical test request

A

urea and electrolytes

78
Q

what is the difference between blood plasma and blood serum

A

plasma is the liquid, cell free part of blood that has been treated with anticoagulants whereas serum is the liquid after coagulation therefore void of fibrinogen and other clotting factors

79
Q

why and how do we use serum as a test

A

whole blood is collected and the samples will be left to allow for clot formation and all the clot with blood cells is removed by centrifugation since fibrin and cellular components interfere with assay results

80
Q

why and how do we use plasma as a test

A

specific types of tests may require preservation of analyses by addition of enzyme inhibitors or preservatives e.g. adding fluoride oxalate to prevent the breakdown of the glucose being tested

81
Q

why is venous blood sampling more common than arterial

A

due to high pressure in arteries are compared to veins

82
Q

when do we use venous blood samples

A

for analyzing blood cell contents

  • glycosylated hemoglobin( raised level in diabetes )
  • white blood cell count
  • red blood cell count
83
Q

when do we use arterial blood samples

A
  • blood gas analysis for arterial pressure of O,CO2 and pH

- blood gas analysis to indicate hypoxaemia

84
Q

when do we use capillary blood samples

A
  • in young children
  • people with fragile veins e.g. old people
  • patients with severe burns
85
Q

how can we manage acid base disorders

A

if symptoms are indicative of an acid base imbalance the first step is to collect arterial blood and examine the hydrogen ion concentration. then we consider change in pCO2 and HCO3 and manage accordingly

86
Q

why do we look at HCO3

A

it forms an important part of the buffering systems in our body

87
Q

how is urea made

A

urea is the breakdown product of amino acids processed to ammonia in liver. ammonia plus CO2 is processed to urea

88
Q

how do we measure urea in clinical samples

A

-take a sample of clotted venous blood from your patient and extract the serum after centrifugation. urease converts urea to ammonium. 2-oxyglutamate and ammonium is converted to glutamate using glutamate dehydrogenase (GLDH) which also converts NADH to NAD and NADH measured at 340nm

89
Q

what is the relationship between NADH and urea concentration

A

the higher the absorbance of NADH the lower the concentration of urea

90
Q

what key roles do electrolytes undertake

A

osmolarity, pH maintenance and biochemical reaction co enzymes

91
Q

what are three rules when interpreting electrolytes

A
  • one third of the fluid is extracellular where as two thirds is intracellular
  • water isn’t restricted to one compartment but sodium is
  • water follows sodium so if sodium leaves water leaves leading to dehydration
92
Q

which ions are present more in the ICF than the ECF

A

potassium
magnesium
phosphate

93
Q

which ions are equally present in the ECF and ICF

A

calcium

94
Q

which ions are more in the ECF than the ICF

A

sodium
chloride
bicarbonate

95
Q

how do we measure electrolytes

A

using an ion selective electrode ,ISE

96
Q

how does ISE work

A

there are two electrodes , the reference electrode allowing all ion influx into the electrode and sample/indicator electrode which only allows a certain electrode

this creates a potential difference and so the current created reflects the abundance particular ion in the sample

97
Q

what are possible conditions linked to electrolyte imbalance

A
  • chronic renal malfunction
  • dehydration
  • liver failure
98
Q

what is reference range

A

It indicates the concentration range within which results of a non-symptomatic individual would fall into

99
Q

what does a liver function test measure

A
  • total protein
  • albumin
  • bilirubin
  • enzymes
100
Q

what enzymes does a liver test measure

A
  • alanine aminotransferase ALT
  • aspartarte aminotransferase AST
  • alkaline phosphatase ALP
  • gamma glutamyl transferase
101
Q

what protein is used to analyze heart damage and what do abnormal levels indicate

A

analyses by cardiac troponin and shows ischaemic cardiac damage

102
Q

what proteins form the troponin complex

A

TnC ,TnI and TnT

103
Q

why is detection of TnI and TnT more specific than TnC

A

TnC is released by other muscles while the other two are specific to the cardiac muscles

104
Q

how do we use measures of Tn levels to show heart damage

A

comparison between time points e.g. between three hours since the start of symptoms and if there is a 20% increase it shows cardiac muscle damage

105
Q

what is an epitope

A

a specific part of a protein the antibody binds to

106
Q

how can we detect troponin in hospitals

A

magnetic beads are coated in anti cTnI (cTnI means cardiac TnI) antibodies against one epitope
the anti cTnI are conjugated to alkaline phosphatase ALP for a second epitope
this allows for the antigen in the patient serum if present to be sandwiches between the two antibodies and then a chemical is acted which reacts with ALP to produce a light measured by a luminometer

107
Q

what are the three ways pH is maintained

A
  • buffering of intracellular and extracellular buffers
  • alveolar ventilation which controls PaCO2
  • renal H+ excretion which controls plasma HCO3 conc
108
Q

what are the major buffering systems of the body

A
  • HCO3- / H2CO3 buffering in the lungs
  • HPO4- / H2PO4- buffering
  • NH3 / NH4+ buffering in the kidney
109
Q

how does the carbon buffering system work

A

when excess H+ ions are added to bow fluids due to an acid they combine with HCO3- and produce H2CO3 which is broken down into H20 and CO2 which is removed by respiration so the buffer system never reaches equilibrium

110
Q

what are the three steps of gas transfer in the lungs

A
  • O2 binds to deoxyhaemoglobin and forms oxyhemoglobin with the release of H+
  • the H+ binds to HCO3- to form H2CO3
  • the H2CO3 dissociates into CO2 and H2O
111
Q

what are the three steps of gas exchange in tissues ( providing them with oxygen )

A
  • oxygenated Hb dissociates to release O2 into the tissues and the deoxygenated Hb is produced
  • CO2 generated in the tissues is hydrated to form H2CO3 which ionizes to form H+ and HCO3-
  • the deoxygenated Hb accepts the H+
112
Q

what is the structure of Hb

A

four subunits 2 alpha and 2 beta each with haem groups

there Is a ferric ion Fe2+ in the center of the haem group

113
Q

what happens during oxygen unloading

A

once the oxygen is unloaded in the tissues 2,3-bisphosphoglycerate (BPG) binds to beta chains

the 2,3 BPG binding induces a confirmational change of all four chains disabling O2 binding so it cant be taken away

when 2,3 BPG levels are low it dissociated from Hb enabling O2 to bind again

114
Q

how is haemoglobin synthesised

A

occurs in the mitochondria of an immature RBC

the Fe2+ ions are delivered by transferrin where they translocate to the mitochondria

inside the mitochondria the alpha aminolaevulinic acid ALA is synthesised, processed in the cytoplasm and is transported back to the as protoporphyrin which binds the Fe2+ to form haem groups

115
Q

what is reparatory acidosis

A

failure of the lungs to excrete sufficient CO2

116
Q

what is metabolic acidosis

A

failure to excrete enough endogenous acid by the kidneys

117
Q

what 2 functions must the kidney perform to maintain pH

A
  • reabsorption of all filtered HCO3-

- excretion of the daily H+ load

118
Q

how can sulphuric and phosphoric acid be removed through the carbonate buffer system

A

H2SO4 + 2NaHCO3- goes to NaSO4 + 2H2CO3–> 2H2O + 2CO2

119
Q

where does the phosphate come from

A

high conc in the cel. many processes use ATP and signaling pathways use phosphorylation

120
Q

where does the ammonia come from

A

generated from the amino acid glutamine. ammonium ions NH4+ are excreted as a chloride salt NH4Cl

ISCM (19 decks)

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