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foundations Flashcards

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1
Q

what is an amphipathic phospholipid?

A

A phosopholipid with a partially charged area (polar) and partially uncharged (non-polar)

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2
Q

What causes the liquid crystalline phase in biomembranes?

A

The mono-unsaturated lipids in the tails can produce a kink, ensuring tails cannot be packed too closely together.

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3
Q

Can different biomembranes have different lipid concentrations of lipid? why?

A

Yes. Due to the different functions of membranes.

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4
Q

What is the function of flippases?

A

To maintain the asymmetry of lipid concentration in biomembranes (due to different phospholipids at either side of the membrane).

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5
Q

Whats an integral protein?

A

A protein embedded deep in the lipid bilayer.

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6
Q

Whats a transmembrane protein?

A

An integral protein that transverses the membrane (could be many times), The transmembrane segments are composed of amino acids with non-polar side chains, these can interact with the lipid tails to form complex structures.

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7
Q

What is a peripheral protein?

A

Not embedded in the bilayer but linked to integral membrane proteins or membrane lipids.

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8
Q

What type of substances would use simple diffusion and what type active transport across a membrane?

A

Simple non-polar molecules would use diffusion

More complicated polar molecules would use active transport.

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9
Q

What are the three types of transporters? explain each.

A

Uniport - just transports one intended molecule.

Symport - transports two molecules together from one side to the other.

Antiport - Transports one molecule in one direction and another in the other direction.

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10
Q

What is primary active transport?

A

When ATP directly changes the shape of a transmembrane protein to directly transfer molecules across the membrane (one at a time).

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11
Q

What is secondary active transport? example?

A

When ATP is used indirectly to transport a molecule across the membrane. For example when a substance is actively transported using ATP to the cytoplasm and then used in antiport to transport a molecule out of the cell.

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12
Q

What is an ABC transporter?

A

An ATP Binding Casette, used in primary active transport.

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13
Q

Two types of bases and their differences?

A

Purines and Pyrimidines. Purine has two cyclic carbon rings and pyrimidine has only one.

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14
Q

Which bases are Purines which are pyrimidines?

A

A and G are purines, T,U and C are pyrimidines.

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15
Q

What is the bond that joins two bases together in the same strand?

A

Phosphodiester bond.

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16
Q

DNA is described as anti-parallel what does this mean?

A

That one strand runs in a 3’ to 5’ direction and the other in a 5’ to 3’ direction.

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17
Q

What bonds do signalling molecules bind to their receptors with?

A

Non-permanent non-covalent bonds.

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18
Q

Five different classifications of primary signalling molecules?

A

Neurotransmitters.

Hormones.

Growth factors and cytokines.

Vitamin A and Vitamin D derivatives.

Nitric Oxide.

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19
Q

What is a neurotransmitter made up of, how many (range)?

A

Amino acids or their derivatives (5-35 long).

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20
Q

What is GABA?

A

Primary inhibitory neurotransmitter in the brain, anti-stress effects.

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21
Q

What are eicesanoids?

A

Hormones derived from arachidonic acid. All involved in inflammation, prostaglandins and leukotrienes are examples.

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22
Q

How do some anti-inflammatory drugs such as aspirin function?

A

Anti-inflammatory blocks the pathways and synthesis of prostaglandins.

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23
Q

How do steroid hormones bind to their receptors?

A

They pass through the plasma cell membrane and bind to their receptors in the cytoplasm or nucleus.

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24
Q

where do hydrophilic protein hormones bind to their receptors?

A

On the plasma cell membrane. (Plasma membrane receptors)

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25
Q

Three major classes of plasma membrane receptors?

A

Ion channel receptors.

Receptors tyrosine kinases.

G-Protein coupled receptor.

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26
Q

What do all three major classes of plasma membrane receptors have in common (2)

A

Has three domains and extracellular, membrane spanning and intracellular domain.

Rapid and immediate effects on cellular ion levels or the activation/inhibition of enzymes.

changes in the rate of gene expression for particular proteins.

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27
Q

What is a kinase?

A

An enzyme that causes the phosphorylation of another molecule.

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28
Q

What is a phosphatase?

A

Opposite to a kinase. Removes a phosphate group.

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29
Q

What can activate a receptor tyrosine kinase?

A

Growth/differentiation factors

Metabolic regulators e.g. insulin.

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30
Q

What happens to receptor tyrosine kinase’s in order for them to illicit a response?

A

Form a dimer, activating the tyrosine kinase portion of the receptor (intracellular) autophosphorylation of the tyrosine residues means they can then phosphorylate relay proteins - activating them. The relay proteins can then illicit a response in the cell.

one tyrosine kinase receptor can activate over 10 different relay proteins.

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31
Q

What is sequential kinase activity?

A

Three or more consecutive kinase enzymes, each activated by phosphorylation allowing kinase activity on the next enzyme in the chain.

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32
Q

Why are RTK’s sometimes the target of cancer drugs?

A

Abnormal receptor tyrosine kinases that activate without a ligand binding have been linked to some forms of cancer.

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33
Q

What is the MAP kinase cascade? (sorry) (10)

A
  1. Growth factor binding to receptor tyrosine kinase causes dimerisation.
  2. Autophosphorylation of tyrosine residues.
  3. Allows an adaptor protein to dock (Grb)
  4. Grb binds sos.
  5. The gdb-sos complex binds ras.
  6. RAS activates a MAPKKK (Raf)
  7. Raf activates a MAPKK (MEKK)
  8. MEKK activates a MAPK (ERK)
  9. ERK (the MAPK) migrates to the nucleus and activates transcription factors through phosphorylation.
  10. Transcription factors bind to the promotor region and the gene is expressed.
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34
Q

What is Herceptin (Trastuzumab)?

A

Monoclonal antibody that targets HER2 receptors (tyrosine kinase receptors) found on 25% of breast cancer cells. This blocks the natural ligand from activating proliferation in tumour cells.

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35
Q

How are MAP kinases switched off?

A

Protein phosphatases.

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36
Q

What is a G-protein coupled receptor made up of, and what are it’s features?

A

7 alpha helix domains (like subunits).

Binds a G-protein, extracellular domain in specific

no kinase activity - the signal is transacted through the G-protein.

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37
Q

What is a G-protein made up of?

A

Alpha, beta (ß) and gamma subunits.

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38
Q

Process by which a G-protein coupled receptor illicit a cellular response after a primary signalling molecule binds?

A
  1. The associated G-protein exchanges GDP for GTP and one of it’s 3 subunits dissociates and activates adenylyl cyclase.
  2. second messengers e.g. cAMP is created from ATP.
  3. Activates protein kinase A.
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39
Q

How does cAMP illicit a cellular response?

A

Via protein kinase A in two main ways:

  1. Phosphorylates a large number of enzymes in the cytosol.
  2. alters gene-transcription in the nucleus.
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40
Q

features of cAMP?

A

Transmits the signal of hormones such as glucagon and adrenalin.

cAMP can stimulate a variety of cellular activities unlock the first messenger.

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41
Q

in G-protein coupled receptors how is the signal amplified?

A

One receptor-ligand complex can activate many G-proteins.

The G-proteins can go on to activate many adenylyl cyclases.

Many adenylyl cyclases can go on to activate many cAMP molecules which can then go on to activate enzymes which produce many products.

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42
Q

Is a G-protein coupled receptor always stimulatory?

A

No can be inhibitory.

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43
Q

Will one ligand (primary signalling molecule) always produce the same result at every cell?

A

No can produce several results on the same cell by stimulating different receptors.

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44
Q

Can GTP bound proteins activate other secondary messengers? Example?

A

Yes, e.g. phospholipase C.

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45
Q

What is the effect of the activation of phospholipase C?

A

Phospholipase C is an enzyme and degrades cell membrane PTI, releasing IP3. and leaving DAG.

IP3 diffuses through cytosol to the ER and binds to receptor releasing Ca2+

DAG activates protein kinase C, initiating a series of phosphorylation reactions.

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46
Q

Give an example of a defective G-Protein coupled receptor disease? what was affected?

A

Retinitis pigmentosa - Rhodopsin receptor.

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47
Q

Give an example of a Defective G-protein disease? what was affected?

A

Pituitary - thyroid tumours.

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48
Q

Similarities in G-protein coupled receptors and Receptor tyrosine kinases?

A

Membrane receptors.

Ligand activated.

Both require ATP.

Multiple downstream signalling cascades.

Initiate activation by phosphorylation.

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49
Q

Differences in G-protein coupled receptors and Receptor tyrosine kinases?

A

G-protein:

7-transmembrane domains.
second messengers amplify signals

Receptor tyrosine Kinases:

Two monomers become a dimer.
adaptor proteins need to be recruited.
autophosphorylation.

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50
Q

What function does nitric oxide play in the body and why is it a special case?

A

Formed from amino acid arginine and oxygen by NO synthase. acts as both a primary and secondary messenger locally (why it is special).

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51
Q

How many different Interleukins are there?

A
  1. From IL-2 to IL-13 and IL alpha and beta (which do similar things.
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52
Q

How many different Interferons are there?

A
  1. Alpha Beta and Gamma.
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53
Q

What does IL-2 do? and where is it released from?

A

Causes proliferation of B cells and and activated T cells also NK functions.

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54
Q

What do both Interferons (INF) alpha and beta do?

A

Antiviral effects, induction of MHC I on all somatic cells, activation of NK cells and macrophages.

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55
Q

What is Erythropoietin? Where is it produced? What is it’s function?

A

A growth factor. The Kidneys. promotes proliferation and differentiation of erythrocytes.

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56
Q

What is IGF-I? Where is it produced? What is it’s function?

A

A growth factor, produced in the liver and promotes the proliferation of many cell types.

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57
Q

What is glucagon? Where is it produced? What’s it’s function?

A

A hormone, produced in the pancreas, stimulates the hydrolysis of glycogen.

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58
Q

Can RNA fold into 3D structures?

A

Yes.

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59
Q

Can RNA have structural and catalytic functions?

A

Of course.

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60
Q

What’s rRNA?

A

Ribosomal RNA form the basic structure of the ribosome and catalyse protein synthesis.

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61
Q

What are cytokines classified as?

A

Proteins or glycoproteins.

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62
Q

Difference in transcriptional activators and general transcription factors?

A

Transcriptional activators help attract RNA polymerase II to the promotor, General transcriptional factors help RNA polymerase II bind to the promotor.

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63
Q

What tells RNA polymerase to stop in Eukaryote’s and prokaryote’s?

A

In prokaryotes there are termination sequences in the DNA.

In eukaryotes transcription continues until after the polyadenylation signal.

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64
Q

How many types of RNA polymerase are there?

A

Three I, II and III

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65
Q

How many stages of transcription are there?

A

Initiation

Elongation

Termination

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66
Q

What happens in the initiation stage of transcription?

A

At a promotor transcription factors help RNA polymerase bind to the promotor.

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67
Q

What happens in the elongation stage of transcription?

A

RNA polymerase makes a complementary strand to the template strand.

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68
Q

What happens in the termination stage of transcription?

A

RNA polymerase stops when it recognises a termination sequence or after the polyadenylation sequence in eukayotes.

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69
Q

What is the polyadenylation signal?

A

The addition of a Poly(A) tail to the mRNA.

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70
Q

Give an example of a virus that has only RNA as it’s genetic information?

A

Retroviruses such as HIV.

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71
Q

What enzyme do RNA containing viruses use to copy their RNA to DNA in a cell?

A

Reverse transcription.

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72
Q

What are Nucleoside analogues, how do they work? What is an example?

A

Compete with normal bases (are incorporated into normal genome) and terminate DNA chain elongation, they are specific to viral DNA polymerase but also may affect mitochondrial DNA e.g. AZT

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73
Q

What are non-nucleoside reverse transcriptase inhibitors, how do they work? Example?

A

Inhibit the reverse transcription enzyme e.g. neverapine.

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74
Q

What is heterochromatin, features??

A

it is highly condensed DNA, it is always inactive and condensed, it is made of largely repetitive DNA.

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75
Q

What are transposons? how can they cause DNA?

A

‘junk DNA’ Multiple copies of short DNA sequences arising from short stretches of DNA that insert themselves in other DNA.

If they insert close or in a gene they can cause disease.

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76
Q

Definition for a gene?

A

A DNA sequence that encodes for an RNA product.

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77
Q

What is the open reading frame?

A

The protein coding section. Between the initiator codon and stop codon

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78
Q

Can genes vary in size and exon content?

A

Yes some have only 1, some e.g. dystrophin have 89.

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79
Q

How is it we have around 100,000 proteins and only around 22,000 genes?

A

Alternative transcription and processing.

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80
Q

What are alternative promotors?

A

A type of alternative transcription and processing.

When the promotor binds at a different start exon on a gene, or alternative internal promotors.

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81
Q

What are three ways in which alternative transcription and processing occur?

A

Alternative promotors

Alternative splicing

RNA editing

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82
Q

What is alternative splicing?

What is it regulated by?

A

The splicing of exons in anything other than a sequential manner.

Results in the generation of many different protein isoforms from 1 primary transcript

Regulated by RNA binding proteins.

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83
Q

What is RNA editing?

A

The insertion, deletion or substitution of nucleotides at the RNA level. This is mediated by enzymes.

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84
Q

How is mRNA exported from the nucleus?

A

Through highly specific nuclear pores.

85
Q

How is mRNA recognised as ‘mature’ or ‘export ready’?

A

By the binding of proteins that indicate splicing is complete, binding to both the 5’ cap and poly A tail.

86
Q

What 4 things are needed for translation to occur?

A

mRNA, Amino acids, tRNA, Ribosomes.

87
Q

At pH 7 will the carboxyl and amino groups be ionised or non-ionised? what will their chemical formula be?

A

Ionised, NH4+ and COO-

88
Q

what are the three general groups for amino acids?

A

Charged polar

Uncharged polar

Non-polar

89
Q

What is the bond that exists between amino acids in proteins?

What type of reaction forms it and what is lost?

A

Peptide bond,

Condensation: loss of H2O

90
Q

What are the two ends of a polypeptide chain called? which direction is the sequence represented?

A

The amino terminus (N-terminus), and carboxyl terminus (C-terminus)

N to C from left to right.

91
Q

The features of the genetic code? (6)

A

Redundant (one amino acid may be coded for by more than one codon, but each codon only codes for one amino acid)

Triplet

Non-overlapping

Defined start

Defined stop

Universal (across all species) almost.

92
Q

What are ribosomes made up of?

A

proteins and rRNA

93
Q

What is tRNA formed from?

A

Longer precursors

94
Q

RNA editing after transcription formed what in tRNA

A

Modified bases

95
Q

What is the structure of tRNA?

A

A cloverleaf structure (four arms, three looped), with a D-arm, T-arm and an anticodon loop and an amino acid loop with CCA at one end.

96
Q

What is wobble in tRNA?

A

The fact that the non-standard nucleotides added to tRNA through RNA editing result in the ability for the anticodon to pair with different amino acids. This is because the third base pair is a ‘wobble’ pair with a non-standard nucleotide.

This is why there are only 48 tRNA’s for 61 codons.

97
Q

What enzyme ‘activates’ amino acids by coupling them to the correct tRNA?

A

aminoacyl-tRNA synthetase, there is one for each amino acid.

98
Q

What fuels the energy for the coupling reaction between an amino acid and tRNA?

A

The ester bond between the tRNA and aa

99
Q

Details on the three steps of translation?(not in-depth)

A

initiation - an initiation complex is formed where the ribosome is bonded to the start site on the mRNA, the initiator tRNA is annealed to the initiator codon.

Elongation - addition of further amino acids to form the polypeptide

Termination - recognition of the end of the open reading frame and release of completed polypeptide.

100
Q

What are rRNA’s responsible in the ribosome?

A

Overall structure

ability to position tRNAs on mRNA

catalytic activity in forming covalent peptide bonds, (ribozyme - not and enzyme)

101
Q

What are the three ribosomal sites?

A

A (Amjnoacyl-tRNA)
P (peptidyl-tRNA)
and E (exit)

102
Q

Detailed description of initiation in translation?

A

An initiation factor (protein) binds to the A site.

This forms a complex with the small ribosomal subunit, other initiation factors then bind to the 5’ cap and poly A tail and the small subunit the binds to the start of the mRNA.

This proceeds downstream until the AUG

The large ribosomal subunit binds with the initiator aminoacyl tRNA in the P site.

103
Q

Detailed description of elongation in translation? (5)

A
  1. Aminoacyl tRNA’s are picked up by an elongation factor (with GTP), they enter the ribosome on the empty A site.
  2. The anticodon on the aminoacyl tRNA is matched against the codon on the mRNA until the correct match is reached.
  3. When the right aminoacyl tRNA enters peptidyl-synthase (on the ribosome) forms a peptide bond between the amino acids.
  4. This leaves an empty tRNA in the P site and a new petidyl tRNA in the A site
  5. The ribosome moves forward one codon and the peptidyl tRNA moves to the A site, the empty tRNA moves to the E site and exits
  6. Repeat (from step 1).
104
Q

details of the termination stage of Translation?

A

Elongation continues until a stop codon is reached.

A release factor binds to the A site another release factor cleaves the bond between peptide and tRNA releasing a new polypeptide

Ribosome dissociates.

105
Q

Differences in eukaryotic and prokaryotic translation?

A

In eukaryotes the first tRNA - the initiator tRNA carries Met (Methionine) in prokaryotes a modified fMet is carried.

There is no 5’ cap in prokaryotes so a specific Shine-Delgarno sequence in the mRNA marks an area where a ribosome may bind, bacterial ribosomes can therefore start anywhere on an mRNA and are often polycistronic (mRNA that codes for several proteins)

106
Q

What are polyhistrionic mRNAs?

A

RNA that can code for several proteins usually found in prokaryotes.

107
Q

What are the four levels of protein structure? (brief description on each)

A

primary - type number and order of amino acids (no bonding)

Secondary - Hydrogen bonding and interaction between the R groups

Tertiary - Folding into a 3D shape.

Quaternary - interactions between multiple polypeptides to form a functional molecule.

108
Q

What conformation does a protein fold into it’s highest or lowest energy conformation?

A

Lowest.

109
Q

What proteins help to fold proteins in a living cell?

A

Chaperone proteins.

110
Q

Why is protein folding constrained? (3)

A

Peptide bond is inflexible, due to it’s nature as a partial double bond, resulting in no free rotation around the C-N bond.

The many weak non-covalent bonds e.g. van der waals, hydrogen and ionic bonds.

The distribution of both non-polar and polar side chains, and their interactions with H2O in an aqueous environment.

111
Q

Two common secondary folding patterns? due to what bonding?

A

a-helix

B-sheet

Due to hydrogen bonding between N-H and C=O

112
Q

What is a protein domain?

A

A substructure of the polypeptide that can fold independently to produce a stable conformation.

113
Q

What is one protein domain often produced from?

A

1 exon.

114
Q

Where are protein binding sites and active sites often found?

A

often at domain junctions.

115
Q

In the quaternary structure what is each polypeptide considered?

A

a subunit.

116
Q

In the quaternary structure what bonding associates the subunits together?

A

Hydrophobic interactions

Hydrogen bonds

salt bridges/ion pairs

117
Q

Two different classifications of protein?

A

Fibrous - structural proteins, insoluble in water, often arranged in long strands.

Globular - folded together in ‘knot shape’, possess dynamic functions.

118
Q

Some examples of fibrous proteins?

A

Actin, myosin, collagen and keratin.

119
Q

What type of bonds do only extracellular proteins normally contain? Where are these formed?

A

disulphide bridges. in the ER, before export.

120
Q

Examples of types of globular proteins?

A

Enzymes, Hormones, Antibodies, transport proteins (e.g haemoglobin), binding proteins e.g. myoglobin, membrane proteins e.g. receptors

121
Q

What type of common folding pattern is normally seen spanning lipid membranes?

A

a-helix’s, normally seen in membrane spanning proteins.

122
Q

What is meant by the fact that protein folding is normally co-translational?

A

Folding starts from the N-terminal as soon as it exits the ribosome.

123
Q

What proteins help correct folding?

A

Molecular chaperone proteins.

124
Q

What can incorrectly folded proteins cause? why?

A

Disease, due to the possibility of aggregation and precipitation out of solution.

125
Q

What are the main mechanisms for protein transport?

A

Gated transport - Regulated by complexes of proteins forming a selective gate.

Transmembrane transport - Relies on signal peptide to redirect proteins across the membrane

Vesicular transport - Involves vesicles budding off one membrane with enclosed cargo and fusing with another membrane.

126
Q

Examples of post-transcriptional modification?

A

Proteolysis - cleavage into fragments

addition of carbohydrates - e.g. glycosylation

addition of lipids e.g. myristoislation

addition of other compounds e.g. phosphorylation, methylation acetylation.

127
Q

What is genomics?

A

The scientific study of genomes?

128
Q

Give some examples of the uses of genomic medicine.

A

Chromosome abnormalities

Single gene - myogenic examples

Pharmocogenetics (personalised medicine)

129
Q

What is cytogenetics?

A

The study of the structure of chromosomes.

130
Q

What is it called if all cells are abnormal?

A

Constitutionally abnormal.

131
Q

What is it called if only some cells are abnormal?

A

Somatic abnormality.

132
Q

What is the chromosomal banding pattern? it’s use?

A

A way to identify regions of chromosomal abnormality. They are produces from Giemsa staining.

133
Q

Process of Karyotyping?

A

Tissue sample is cultured to induce proliferation

Mitotic spindle disrupted, nuclear membrane lysed and stain applied

The dye stains regions dense in A and T bases

Images counted and structures analysed and organised in a visual format.

134
Q

What are numerical chromosome abnormalities?

A

Abnormalities involving the gain or loss of complete chromosomes.

135
Q

What is polypoidia?

A

A numerical chromosome abnormality. Extra set of complete chromosomes so you would have 69XXX

136
Q

What is aneuploidy

A

A numerical chromosome abnormality involving the loss/gain of one or more chromosomes

137
Q

What are structural chromosome abnormalities? What are the two types?

A

Abnormalities involving an altered structure of a chromosome. Balanced (no loss of genetic material) or imbalanced (loss of genetic material)

138
Q

What are disorders of imprinting?

A

When normal karyotypes are pathogenic due to the wrong parental origin. Methylation patterns are sex-specific, only one copy of a gene is expressed.

139
Q

Definition for mutation?

A

Permanent transmissible change in the genetic material

140
Q

What is polymorphism?

A

The existence of two or more alleles in the population, they may be neutral or predispose to disease.

141
Q

4 different types of mutation?

A

Point mutation - single base pair change may be silent (no change), missense (wrong amino acid) or nonsense (stop codon).

Deletion (of one triplet code)

Insertion (of one triplet code)

Frame shift - one base pair deletion or addition which causes the whole rest of the code to change.

142
Q

Two types of mutations?

A

Spontaneous - mistake in biological process

Induced - altered by mutagens

143
Q

Causes of spontaneous DNA mutations?

A

DNA nucleotides are unstable

DNA polymerase can make mistakes

Meiosis is not perfect.

144
Q

Mechanisms of induced DNA mutations?

A

Chemicals that have covalently bonded to nucleotide bases.

Some chemicals add chemical groups to DNA bases.

Radiation damage.

145
Q

The accumulation of DNA errors can result in what three things?

A

Senescence (ageing)

Cancer

Apoptosis.

146
Q

what is a monogenic disorder?

A

A disorder caused by a single gene.

147
Q

If a monogenic disorder is sex-linked where has the mutation occurred?

A

On the X-chromosome.

148
Q

What is a herterozygote advantage?

A

When a carrier of a recessive condition has a selective advantage over others who are not carriers.

149
Q

What are complex genetic diseases?

A

Common diseases that are polygenic, often combined with environmental effects e.g. hypertension.

150
Q

How can a genetic component to a common disease be discovered?

How are these genes identified?

A

Family studies, twin studies.

Association studies (case control).
Linkage analysis.
151
Q

Generally speaking how do enzymes work?

A

They bring together substrates into favourable orientations in the enzyme substrate complex, reducing the activation energy for a reaction.

152
Q

Four different types of enzyme catalysis?

A

Metal ion catalysis - metal ion serves as electrophilic catalyst.

Electrostatic catalysis - Active site residues or cofactors form ionic bonds with the intermediate.

Covalent catalysis - Active site residues or cofactors for transient covalent bonds with the intermediate.

Acid - base catalysis - active site contains proton donors or acceptors.

153
Q

The 6 EC classes of enzymes?

A

EC1 Oxidoreductases (oxidation-reduction)

EC2 Transferases (transfer functional groups)

EC3 Hydrolyases (hydrolysis)

EC4 Lysases (addition to double bonds or it’s reverse)

EC5 isomerases (isomerization reaction)

EC6 Ligases (formation of bonds with ATP cleavage)

154
Q

Examples of how enzymes are regulated? (5)

A 
Inhibition through feedback
Gene expression controlling enzyme synthesis
Co-factor binding
Enzyme sequestration
Post-translational modifications.
155
Q

Three examples of enzyme co-factors?

A

Co-enzymes - soluble and may diffuse between enzymes e.g. NADH and ATP.

Metal ions - Often bound by dipole interactions with histidine and other amino acids with lone pairs

Prosthetic groups - strongly bound to the enzyme through covalent bonds or other means e.g. haem

156
Q

Main divisions of enzyme inhibitors?

A

Non-specific and specific.

Within non-specific there is denaturing.

Within specific there is reversible and irreversible.

157
Q

Features of irreversible, specific, enzyme inhibitors?

A

Often artificial,

Often poisonous

Often tightly bound to enzyme e.g. covalently.

158
Q

Features of Reversible, specific, enzyme inhibitors?

A

Rapid dissociation of enzyme/inhibitor complex

One of Competitive, uncompetitive or non-competitive/mixed.

159
Q

Describe the four types of reversible inhibitor.

A

Competitive: competes with natural substrates for the active site.

Non-competitive: Binds allosterically to the enzyme equally well whether the substrate is bound or not.

Uncompetitive: Binds allosterically to the ES complex and not the free enzyme

Mixed: Binds to either free enzyme or ES complex.

160
Q

Series of enzyme reactions that degrade alcohol?

A

Alcohol —> acetaldehyde (Alcohol dehydrogenase)

acetaldehyde —-> acetic acid (Aldehyde dehydrogenase)

161
Q

What is Vmax and Km? (enzymes)

A

Vmax = maximum rate.

Km = Affinity

162
Q

What is specificity referring to in diagnostic tests?

A good way to remember?

A

Proportion of true negatives that are correctly identified.

Specific = Terrific (terrific not to have the disease

163
Q

What is sensitivity referring to in diagnostic tests?

A good way to remember?

A

Proportion of true positives that are correctly identified.

Sensitivity = sense to have gone and get the test.

164
Q

What is the Positive predicted value?

A

The proportion of patients, expressed as a percentage, with a positive result that are correctly diagnosed.

165
Q

What is the negative predicted value?

A

The proportion of patients, expressed as a percentage, with a negative result that are correctly diagnosed.

166
Q

What is the main difference between sensitivity/specificity and PPV/NPV?

A

PPV and NPV are dependent on the prevalence of the disease yet sensitivity and specificity are not.

167
Q

Three different categories for diagnostic tests?

Two examples of each.

A

Genetic:

Cytogenetic: Karyotyping, FISH - Fluorescent In Situ Hybridisation
PCR - Polymerase Chain Reaction with sanger sequencing.

Immuno-detection (using antibodies):

IHC - Immuno-histochemistry
ELISA - enzyme-linked-immuno-sorbent-assay

Biochemical:

Enzyme activity assays
Direct chemical detection

168
Q

How does FISH work?

A

Specific DNA sequences that are complementary to areas of DNA that are to be identified are produced and flourescently labelled.

The DNA and complementary sequences heated and cooled resulting in hybridisation and areas becoming fluorescent.

169
Q

Brief description of how PCR works, followed by sanger sequencing?

A

Primers encompassing the desired region are synthesised, followed by sequential heating and annealing, followed by replication using DNA polymerase, results in amplification of desired region of genome in an exponential manner.

Analysis of the last base of the DNA sequence resulting from elongation of the primer.

170
Q

Clinical uses of PCR and sanger sequencing? (3)

A

Pathogen detection

Phenotype identification

Cancer detection

171
Q

Brief description of immuno-histochemistry?

A

Use primary antibody, followed by secondary with a method for detection.

172
Q

Brief description of ELISA?

A

Get an antibody coated gel, add antigen, add enzyme coated secondary antibody and finally add substrate and measure colour.

173
Q

How do cells obtain bases?

A

Can be synthesised de novo (from simple compounds) or salvaged following normal cell turnover.

174
Q

What is a nucleoside and what is a nucleotide?

A

Nucleoside is the base plus a sugar (deoxyribose or ribose)

A nucleotide is a nucleoside plus a phosphate group.

175
Q

Steps in purine nucleotide synthesis?

A

Preformed ribose-5-phosphate,

Activated to form PRPP (inhibited by ADP and ADP)

IMP is then formed, through multiple steps, two ATP’s are added. (inhibited by every product AMP, ADP and ATP and GMP, GDP and GTP)

IMP either uses GTP to convert it to adenylosuccinate (inhibited by AMP) and then to AMP

OR

Converted to XMP (inhibited by GMP) and then GMP.

176
Q

How do sulphonamides inhibit purine synthesis? why does this affect bacteria but not humans?

A

Inhibit the synthesis of folic acid, bacteria produce their own folic acid but humans do not, this means only bacterial purine synthesis is inhibited.

177
Q

What is methotrexate?

A

A folic acid analogue that competes with dihydrofolate reductase and so competitively inhibits tetrahydro-folic acid synthesis

Used to treat Cancer as it will slow the production of DNA, also used to treat psoriasis, neoplastic disease and rheumatoid arthritis.

178
Q

What is tetrahydro-folic acid?

A

The compound produced from folic acid that is used in amino acid and purine synthesis.

179
Q

What is mycophenolic acid? what is it used for?

A

A reversible inhibitor of inosine-monophosphate (IMP) dehydrogenase.

Used as an immunosuppressant used to prevent graft rejection, this is because it deprives rapidly proliferating B and T cells of key components of nucleic acids.

180
Q

How are nucleoside mono phosphates converted to diphosphates? and then how to triphosphates?

A

To diphosphates: Using base-specific nucleoside monophosphate kinase’s, using ATP usually as the donor e.g:

GMP + ATP = GDP + ADP or AMP + ATP = 2ADP

To triphosphates using nucleoside diphosphate kinase.

181
Q

What is Lesch-Nhyan syndrome

A

An X-linked recessive disorder associated with the inability to salvage Guanine and hypoxanthine in normal cell turnover.

This results in increased levels of PRPP and decreased levels of IMP and GMP (salvaged from hypoxanthine and Guanine) this results in increased de novo purine synthesis.

Results in production of excess uric acid causing urolithiasis (kidney stones) and crystals in joints (gouty arthritis)

182
Q

What enzyme is used to convert ribonucleotides to deoxyribonucleotides?

A

Ribonucleotide reductase.

183
Q

Where does dietary purine degradation occur? what are they converted into?

A

In the small intestine, converted into uric acid.

184
Q

Three enzymes essential in purine degradation?

A

Adenine deaminase

Purine Nucleoside phosphorylase (PNP)

xanthine oxidase (produces uric acid)

185
Q

What are the consequences of adenine deaminase deficiency?

A

Can cause SCID, this is due to severe lack in T, B and NK cells (lympoctyopenia)

186
Q

What is gout?

Treatment?

A

Tophi (crystal deposits of uric acid) accumulate at joints and in kidneys

Associated with diet rich in seafood and meat.

Underexcretors (more common) such as anti-inflammatories and other drugs that increase excretion.

Overproducers e.g. allopurinol (structural analogue of hypoxanthine - inhibits xanthine oxidase.

187
Q

Are pyrimidines regularly salvaged in humans?

A

Hardly - the ring is cleaved giving rise to highly soluble products.

188
Q

The formation of Carbamoyl phosphate is inhibited and activated by what?

A

Inhibited by UTP, and activated by PRPP.

189
Q

What is MAO?

A

Breaks down cytosolic Noradrenaline in the pre-synaptic cell

190
Q

What are the four polar head groups?

A

Choline

Serine

Inositol

ethanolamine

191
Q

Where are glycosidic bonds found?

A

Inbetween sugars

192
Q

What is the BCR_ABL chromosome abnormality, also called the philadelphia chromosome?

A

A translocation between chromosome 9 and 22.

193
Q

What does semi-conservative DNA replication mean?

A

that each strand of DNA is kept together in DNA replication but both strands are not (conservative model) and the strand is not split up (dispersive model)

194
Q

Where does DNA replication start?

A

A replication fork

195
Q

What is meant by the fact DNA synthesis is semi-discontinuous?

A

Strands are synthesised in opposite directions. The one towards the fork is synthesised continuously but the one in the other direction is synthesised in fragments.

196
Q

How does DNA polymerase know where to start?

A

RNA primer.

197
Q

Main facts to know about DNA replication?

A

It is semi-conservative.

Starts at the replication fork.

Unwound by DNA helicase

Synthesized by DNA polymerase

Semi-discontinuous

The RNA primer signals where DNA polymerase should start.

198
Q

How do DNA polymerases ‘proof read’?

A

Using 3’ - 5’ DNA exonuclease activity to remove incorrectly paired bases.

199
Q

How is the RNA primer used in the lagging strand, how is a full strand made?

A

RNA primer originally binds and DNA polymerase synthesises an okazaki fragment, the RNA primer is then removed and replaced by DNA by DNA polymerase, DNA ligase joins the fragments and an new RNA primer is synthesised.

200
Q

Are there many enzymes at the replication fork?

A

Yes - many enzymes cooperate in DNA synthesis at the replication fork.

201
Q

What are 6-mercaptopurine and 5-fluorouracil?

A

Base analogues used as chemotherapy agents.

202
Q

What is the nuclear envelope made up of?

A

Two membranes, the inner is continuous with the ER.

203
Q

What is a nucleosome?

A

How DNA is packaged, made up of eight histone proteins with DNA coiled around them.

204
Q

What is a chromatin fibre?

A

A compact string of nucleosomes.

205
Q

What are the different stages of DNA packaging?

A

First There are nucleosomes, that are wound together to form a chromatin fibre, that is wound around a scaffold, which produces many loops of chromatin fibre.

206
Q

How do mitochondria produce ATP?

A

Through oxidative phosphorylation.

207
Q

Stages of mitosis?

A

Interphase, prophase metaphase anaphase then cytokinesis.

208
Q

4 examples of transcriptional control?

A

Binding of RNA polymerase

Long range control

Chromatin remodelling

DNA methylation

209
Q

What are the intracellular changes on activation of a1 a2 and ß receptors?

A

a1 - phospholipase C pathway.

a2, ß - adenylyl cyclase.

Molecular cell biology (1 decks)

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