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ESA1 Review > Molecules, Genes and Disease > Flashcards

Molecules, Genes and Disease Flashcards

1
Q

What is the name given to diseases caused by improper polypeptide folding?

A

Amyloidoses

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2
Q

What type of bonds are involved in the primary structure of proteins?

A

Covalent (peptide) bonds

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3
Q

What type of bonds are involved in the secondary structure of proteins?

A

Hydrogen bonds

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4
Q

What type of bonds are involved in the tertiary/quaternary structure of proteins?

A
  • Hydrogen bonds
  • Van Der Waals
  • Hydrophobic Interactions
  • Covalent (Disulphide)
  • Ionic Interactions
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5
Q

What are the main features of the alpha helix?

A
  • 3.6 amino acids per turn
  • 0.54nm pitch
  • Right handed helix
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6
Q

What are the main features of the beta pleated sheet?

A
  • Extended conformation
  • Parallel or antiparallel
  • Multiple inter-strand H-bonds
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7
Q

Which organelles are important for detoxification reactions?

A
  • Endoplasmic reticulum

- Golgi body

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8
Q

What is the function of the plasma membrane of a eukaryotic cell?

A
  • Cell morphology and movement

- Transport of ions and small molecules

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9
Q

Give two benefits of a molecule being hydrophobic as opposed to hydrophilic?

A
  • Can pass through lipid bilayers

- Can be stored anhydrously

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10
Q

What is a zwitterion?

A

A zwitterion is a neutral molecule that has both positive and negative charge

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11
Q

When does a zwitterion become deprotonated?

A

When the pH > pKa of an Amino Acid

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12
Q

What is the isoelectric point of a protein?

A

The isoelectric point is the pH at which the protein has no overall charge.

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13
Q

What two small amino acids are strong helix formers?

A

Alanine and Leucine

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14
Q

Why is proline considered to be a helix breaker?

A

The rotation around the N-C bond is impossible.

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15
Q

Why is glycine considered to be a helix breaker?

A

The tiny R-group supports other conformations.

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16
Q

What effect does 2,3-bisphosphoglycerate (BPG) have on the binding of O2 to haemoglobin? Which way does it shift the oxygen dissociation curve?

A

It decreases the affinity for oxygen binding and shifts the curve right

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17
Q

In what two cases is the concentration of BPG increased?

A
  • High altitudes

- In highly metabolising tissues

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18
Q

What effect do carbon dioxide and protons have on the binding of O2 to haemoglobin? What is this effect called?

A

They decrease the affinity for oxygen binding known as the Bohr effect

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19
Q

What type of oxygen binding does myoglobin exhibit?

A

Hyperbolic O2 binding

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20
Q

What type of oxygen binding does haemoglobin exhibit?

A

Sigmoidal O2 binding

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21
Q

What two states can deoxyhaemoglobin exist in?

A
  • Tense state (doesn’t bind oxygen that readily)

- Relaxed state (binds oxygen easily)

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22
Q

What is a fibrous protein? Give three examples of what a fibrous protein is used for.

A

One repeating primary structure. Proteins for structure, support, protection

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23
Q

What is a globular protein? Give two examples of what a globular protein is used for.

A

Several types of secondary structure structure. Enzymes and regulatory proteins

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24
Q

What causes sickle cell anaemia?

A

It’s an autosomal recessive genetic disorder resulting in the substitution of hydrophilic Glutamate to hydrophobic Valine in the β-subunit of Hb

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25
Q

What is the pathological progress of sickle cell anaemia?

A

A ‘sticky hydrophobic pocket’ formed by Val allows deoxygenated Hbs to polymerise, causing sickle shape. This leads to premature destruction of RBCs and blockage of the cell microvasculature.

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26
Q

What are Thalassaemias?

A

A group of genetic disorders where there is an imbalance between α and β subunits.

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27
Q

What is Km?

A

The substrate concentration that gives half the Vmax

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28
Q

What is Vmax?

A

The maximum rate when the enzyme is saturated with substrate

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29
Q

List the 5 major regulatory mechanisms that control enzyme activity

A
  • Covalent modification
  • Proteolytic activation
  • Allosteric control
  • Substrate/product concentration
  • Enzyme concentration
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30
Q

How does proteolytic activation work?

A

An enzyme secreted as an inactive protein precursor (zymogen) and cleaved by proteases create the active enzyme when needed

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31
Q

What type of regulatory mechanism controls phosphofructokinase activity? What activates and inhibits it?

A

Allosteric regulation:

  • Activators are AMP, fructose-2,6-bisphosphate
  • Inhibitors are ATP, citrate and H+
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32
Q

What is the zymogen of pepsin?

A

Pepsinogen

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33
Q

What is the zymogen of trypsin?

A

Trypsinogen

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34
Q

What is the zymogen of elastase?

A

Proelastase

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35
Q

How many rings does a purine have? What bases are purines?

A

Two rings (A and G)

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36
Q

How many rings does a pyrimidines have? What bases are pyrimidines?

A

One ring (C, U and T)

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37
Q

Which end of the DNA chain has a free phosphate?

A

5’ end

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38
Q

Which end of the DNA chain has a free -OH group?

A

3’ end

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39
Q

Briefly outline the three main steps of DNA replication.

A
  • Initiation
  • Elongation
  • Termination
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40
Q

What is the direction of chain growth in DNA replication?

A

5’ to 3’

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41
Q

What is the genotype?

A

The genetic make-up of an individual

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42
Q

What is the phenotype?

A

All observable characteristics of an individual or the expressed trait as a result of the genetic make-up

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43
Q

Which phase of the cell cycle is all the genetic information duplicated in?

A

S phase

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44
Q

What is the function of the G1 phase of the cell cycle?

A

Cellular content is duplicated

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45
Q

What is the function of the G2 phase of the cell cycle?

A

Double checking everything is correct

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46
Q

What is a gene?

A

A unit of heredity; a length of DNA on a chromosome that contains the code for a protein

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47
Q

What is an allele?

A

An alternative form of a gene; each individual has two alleles for every gene, which can either be the same or different

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48
Q

Name two autosomal dominant conditions. (there are loads)

A
  • Marfan’s

- Familial hypercholesterolaemia

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49
Q

Name two X-linked recessive conditions. (there are loads)

A
  • Haemophilla

- Duchenne muscular dystrophy

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50
Q

Briefly describe the process of initiation during transcription

A
  • Recognition at 5’TATA3’ box
  • Transcription factors bind at this point
  • Attract RNA polymerase
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51
Q

Briefly describe the process of elongation during transcription

A

RNA polymerase travels along forming a complimentary RNA strand

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52
Q

Briefly describe the process of termination during transcription

A
  • Capping - a methyl-guanine ‘cap’ to the 5’ end

- Tailing - polyadenylated (lots of Adenine nucleotides are added)

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53
Q

Outline the process of initiation during translation

A
  • Binding of 40s sub-unit of Met-tRNA to the 5’ cap of mRNA

- Codon 5’AUG binds to anticodon 5’CAU-60S subunit then binds

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54
Q

Outline the process of elongation during translation

A
  • Met-tRNA occupies p site of ribosome and then another aminoacyl-tRNA occupying A site using GTP and peptidyl transferase
  • Formation of peptide bond between amino acids, making the tRNA in P site uncharged
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55
Q

Outline the process of termination during translation

A
  • Stop codon on mRNA reached and no tRNA can bind to it

- Peptide and tRNA are hydolysed to release the protein into the cytoplasm

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56
Q

How can mutations outside the coding region affect gene expression?

A

Mutations to promoter regions where transcription factors bind can affect gene expression

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57
Q

What type of RNA is most numerous in the body?

A

Ribosomal RNA (rRNA)

58
Q

What type of RNA has the most kinds?

A

Messenger RNA (mRNA)

59
Q

What is regulated secretion?

A

-Proteins packaged into vesicles but not released until a signal (hormone)

60
Q

What is constitutive secretion?

A

-Proteins packaged into vesicles and release continuously by exocytosis.

61
Q

Which drug blocks peptidyl transferase?

A

Chloramphenicol

62
Q

What is the function of the drug tetracycline?

A

It can block the binding of aminoacyl-tRNA

63
Q

Give the anagram commonly used for collagen synthesis and briefly outline what each letter stand for.

A

CHADPOGRL:

  • Cleavage of signal peptide
  • Hydroxylation of proline/lysine residues
  • Addition of N-linked oligosaccharides
  • Disulphide bond formation
  • Procollagen - formation of triple helix
  • O-linked glycosylation
  • Golgi then exocytosis
  • Removal of terminal peptides (procollagen peptidase)
  • Lateral aggregations to form fibrils
64
Q

Give a brief overview of the secretory pathway in mammalian cells

A
  • SRP recognises secretory signal sequence at N terminus, binds to sequence and protein synthesis stops
  • SRP (attached to sequence) then binds to the SRP receptor on cytosolic face of the ER
  • SRP is released, protein synthesis restarts
  • Cleavage of signal sequence by signal peptidase after protein synthesis is finished
  • Folding of protein, may require chaperones
65
Q

How does protein modification occur in the golgi?

A
  • Trimming and modification of N-linked oligosaccharides

- O-linked glycosylation via glycosyltransferase-Endo/exoproteases

66
Q

How does protein modification occur in the endoplasmic reticulumn?

A
  • Signal Cleavage (signal peptidase)
  • Disulphide bond formation (protein disulphide isomerase)
  • N-Linked glycosylation (oligosaccharide-protein transferase and dolichol)
67
Q

Briefly describe O-linked glycosylation of proteins

A
  • Modification of the Hydroxyl Groups on serine/theonine

- Glycosyl transferase builds up a sugar chain from Nucleotide Sugar Substrates

68
Q

Briefly describe N-linked glycosylation of proteins

A
  • Oligosaccharide is built up on a Dolichol Phosphate carrier molecule in the membrane
  • Oligosaccharide is then transferred to the Amide group of Asparagine
69
Q

Where is the “pre” segment of a protein removed?

A

Endoplasmic reticulum

70
Q

Where is the “pro” segment of a protein removed?

A

Golgi

71
Q

Formation of insulin is an example of what kind of secretion?

A

Regulated

72
Q

Formation of albumin is an example of what kind of secretion?

A

Constitutive

73
Q

Outline the formation of the mature insulin molecule

A
  • Removal of signal sequence by signal peptidase (preproinsulin to proinsulin)
  • Disulphide bonds form between A and B peptides, cleavage of C peptide by endopeptidases
74
Q

What can C peptide be used as a measure of?

A

Marker for measuring levels of endogenous Insulin in Diabetics

75
Q

Describe the basic structure of the collagen molecule

A
  • Glycine every third position
  • 3 alpha chains
  • Left handed triple helix
  • Mostly hydroxyproline and proline residues in other positions
76
Q

What is the significance of the proline residues in the collagen molecule?

A

Prevents the peptide moving into a different structure than the extended α-chain conformation

77
Q

What is the significance of the hydroxyproline residues in the collagen molecule? How are they formed?

A

Formed from hydroxylation of proline (Prolyl Hydroxylase) and forms many interchain H-bonds

78
Q

What two things are required for Prolyl Hydroxylase to function correctly?

A
  • Vitamin C

- Fe 2+ ions

79
Q

What is scurvy due to?

A

Vitamin C deficiency

80
Q

How are proteins targeted to the nucleus from the cytoplasm?

A
  • Fully folded protein with an NLS is bound to the protein importin
  • Complex translocates through nuclear pore-Release of nuclear protein
  • Importins are moved back out to be reused
81
Q

What does penicillin do? How does it do it?

A

It inhibits the formation of bacterial cell walls by inhibiting the transpeptidase enzyme that forms cross-links in cell wall. Which results in osmotic pressure causing cell lysis.

82
Q

What does rifampicin do? How does it do it?

A

Binds to bacterial RNA Polymerase preventing transcription and therefore preventing DNA replication

83
Q

What does tetracycline do? How does it do it?

A

Competes with tRNA at A site of bacterial ribosome and therefore inhibiting translation

84
Q

What does methotrexate do? How does it do it?

A
  • Impairs the synthesis of tetrahydrofolate (essential for DNA synthesis) from folic acid
  • Done by competitively inhibiting dihydrofolate reductase (DHFR)
85
Q

Give 5 mechanisms by which cells can become resistant to an antibiotic or drug.

A
  • High rate of division (mutation - chance resistance - natural selection)
  • Decreased influx (takes up less of drug)
  • Increased efflux (more kicked out by protein channel being upregulated)
  • Increased Transcription of Target (increasing transcription of target to overwhelm the drug)
  • Altered Target
86
Q

Outline the mechanisms involved in targeting proteins to the mitrochondria (matrix proteins)

A
  • Unfolded and have an amphipathic N-terminal signal sequence
  • Stabilised in the cytosol by interaction with molecular chaperones like MSF
  • Sequence recognised by TOM proteins in the mitochondrial outer membrane - form a protein import channel
  • TIM proteins move across inner mitochondrial membrane (using ATP) and N-terminal signal sequence is removed by MPP-Protein folds into its native conformation using ATP and chaperones
87
Q

Outline the mechanisms involved in targeting proteins to the lysosome

A
  • Lysosomal Hydrolases are targeted by addition of a Mannose-6-phosphate (M6P) signal to N-linked oligosaccharides-M6P added by N-acetylglucosamine phosphotransferase/phosphoglycosidase
  • Golgi has M6P receptors to move vesicles containing the protein in the right direction
88
Q

How is I-Cell Disease caused and what does it result in?

A
  • Genetic defects in the N-acetylglucosamine phosphotransferase enzyme result in a lack of M6P addition to lysosomal targeted proteins.
  • Lysosomal hydrolases mistargeted for secretion - proteins present in blood/urine
89
Q

How do proteins that are meant to remain in the ER but get released get back into the ER?

A
  • Have a KDEL sequence near C terminus

- KDEL sequence binds KDEL receptors and is returned to the ER in transport vesicles

90
Q

Briefly outline the Sanger Dideoxy Chain Termination Method of DNA sequencing

A
  • Fluorescent/Radioactively stained ddNTPs (dNTPs lacking a 3’ OH group) are added terminating the sequence at different points
  • Produces lots of new DNA fragments of different lengths that can be denatured with heat and separated using gel electrophoresis
91
Q

Briefly outline the process of restriction analysis

A
  • Restriction endonucleases are bacterial enzymes that recognise DNA sequences ‘restriction sites’ and the cut the DNA here
  • Cutting of the DNA sequence leaves ‘sticky ends’ - can be reversed/different fragment joined using DNA ligase
92
Q

What can restriction analysis be used for?

A
  • Investigate size of DNA fragments (deletions)
  • Investigate mutations (sickle cell disease)
  • Investigate DNA variation (DNA fingerprinting)
  • Gene cloning
93
Q

Outline the three main steps of gene cloning

A
  • Plasmid is cut using restriction enzymes, gene of interest is added to create ‘recombinant DNA’ molecule
  • Transformation - introduced into bacteria
  • Multiplication of bacteria
94
Q

Outline the four main steps of gel electrophoresis

A
  • A solution of different fragments is placed in a well at the negative anode end
  • A charge of the anodes encourages the (negatively charged) DNA to move towards the positive anode
  • Larger fragments move slowest
  • Fragments of known size are used as a reference.
95
Q

Briefly outline the process of polymerase chain reaction (PCR)

A
  • Denaturation at high temperature (94 – 96 degrees)
  • Renaturation (annealing) at lower temperature (50 - 65 degrees)
  • DNA synthesis at medium temperature (75 - 80 degrees)
96
Q

What type of DNA polymerase is used in PCR?

A

Thermostable Taq DNA Polymerase from Thermus Aquaticus.

97
Q

What is Western blotting an analysis of?

A

Proteins

98
Q

What is Northern blotting an analysis of?

A

RNA

99
Q

Briefly outline the process of Southern Blotting and DNA Hybridisation

A
  • Nylon is used to transfer the DNA fragments from electrophoresis
  • Hybridised with a labelled gene probe to show the specific DNA fragments
  • Radioactive probes can mark specific complimentary DNA fragments
100
Q

What is the process of Southern Blotting and DNA Hybridisation used for?

A
  • Investigate gene structure (deletions/duplications)
  • Investigate gene expansion (triplet repeats)
  • Investigate variation (DNA fingerprinting)
101
Q

How can PCR be used in an allele-specific test?

A

Use primers specific for sequence either side of allele of interest to amplify specific allele.

102
Q

How can restriction analysis be used in an allele-specific test?

A
  • Use restriction enzymes with restriction sites around/within the allele. Analyse the size of fragments produced.
  • If the restriction enzyme cuts the wild type but not sample, the restriction site is mutated/missing.
103
Q

How can DNA hybridisation be used in an allele-specific test?

A

Use a DNA probe that is complementary to either the wild type allele or mutated allele. See which binds.

104
Q

Briefly outline the process of SDS page.

A
  • The detergent SDS (Sodium dodecyl sulphate) denatures protein molecules (breaking 30 structure) and gives the protein a negative charge proportionate to molecular weight
  • Electrophoresis then takes place, with migration from negative to positive electrode, largest molecular weight (more negative charge from SDS) travel further.
105
Q

Briefly outline the process of isoelectric focusing

A

Proteins are applied to a gel containing a pH gradient - protein migrates until a pH that matches it’s pI – at this point it will have no overall charge and so will stop migrating.

106
Q

Briefly outline the process of 2D page.

A

Combination of both SDS page and isoelectric focusing - the gel is run in one way and when two proteins stop at an identical value it is run in a 90 degree angle to the original movement

107
Q

What is an enzyme assay?

A

Methods for measuring enzymatic activity, vital for study of enzyme kinetics/inhibition.

108
Q

What conditions need to be met for an enzyme assay to be taken?

A
  • Optimal pH
  • Optimal temperature
  • Optimal ionic strength
  • Appropriate ions or cofactors
109
Q

How can enzyme assays be used to detect tissue damage?

A

Elevated levels of enzyme in serum can be indicative of damage to the tissue that usually contains that enzyme

110
Q

Which two enzymes can be used to detect liver damage/disease?

A

Aspartate transaminase (AST) and Alanine transaminase (ALT)

111
Q

Which two enzymes can be used for detection of a myocardial infarction?

A

Creatine Kinase (CK) and Lactate dehydrogenase (LDH)

112
Q

Briefly outline the process of Western blotting (don’t bother describing SDS page)

A

Following SDS-PAGE, the separated proteins can be transferred to a nitrocellulose membrane and specific proteins can be visualised by binding with antibodies conjugated to a label

113
Q

Briefly outline the process of Enzyme-Linked Immunoabsorbent Assays (ELISA)

A
  • Primary antibody “stuck” on solid support
  • Solution to be assayed is applied to antibody covered support
  • Secondary antibody conjugated with an enzyme binds to the antibody-antigen complex
  • Amount of binding of second enzyme is measured
114
Q

What would the normal karyotype for a male be?

A

46, XY

115
Q

What would the normal karyotype for a female be?

A

46, XX

116
Q

Describe the components of a chromosome

A

Chromosomes are made up of chromatids which are made up of:

  • Histones
  • DNA/RNA
  • Non histone proteins
117
Q

What is euchromatin?

A

Lightly packed chromatin often under active transcription (beads on a string)

118
Q

What is heterochromatin?

A

Tightly packed chromatin (solenoid)

119
Q

What stage of the cell cycle do chromosomes replicate?

A

S phase

120
Q

What is polyploidy? What is it often caused by?

A

A numerical change in the ENTIRE chromosome set, multiples of all the chromosomes caused by polyspermy.

121
Q

What is aneuploidy? From this explain the terms monosomy and trisomy.

A

An abnormal number that is not a multiple of the haploid number:

  • Monosomy - a chromosome exists singly without a partner (not in pair)
  • Trisomy - A chromosome pair exists as a triplet - one normal and one double
122
Q

How is a ring chromosome formed from one chromosome?

A

Loss of telomeres or ends of both arms and formation of a ring

123
Q

What is an isochromosome?

A

Creation of two non identical chromosomes, one is a combination of the two short arms, the other is a combination of the two long arms.

124
Q

What is a Robertsonian translocation?

A

Q-arms (long) of two acrocentric chromosomes combine to form one ‘super-chromosome’ with the loss of both p-arms.

125
Q

Why is Karyotyping useful?

A
  • Prenatal Screening (raised maternal age, family history)
  • Birth Defects (Malformations, Mental retardation)
  • Abnormal Sexual Development (Klienfelter’s Syndrome)
  • Infertility
126
Q

What is a transversion mutation?

A

Where a purine is produced instead of a pyrimidine (or vice versa)

127
Q

What is a transition mutation?

A

Where a different purine is produced than the original purine OR where a different pyrimidine is produced instead of the original pyrimidine

128
Q

Why can point mutations in non-coding regions or outside genes cause problems?

A

Alter binding sites, promoter sequence, splice sites etc. which can all change how the protein is produced

129
Q

What is a nonsense mutation?

A

A mutation that change the amino acid specified to a stop codon

130
Q

What is a missense mutation?

A

A mutation that replaces one amino acid with another

131
Q

What is a silent mutation?

A

A mutation that does not alter the amino acid specified

132
Q

What is a frameshift mutation?

A

Addition or subtraction of nucleotides not in multiples of 3

133
Q

Name 4 things that can induce mutations.

A
  • Alkylating agents (Remove a base)
  • Acridine agents (Add or remove a base)
  • X rays (Break chromosomes/delete few nucleotides)
  • UV radiation (creates thymidine dimers)
134
Q

What is the wild type trait?

A

The trait that is most common in a population

135
Q

What is excision repair?

A

Damaged DNA is removed by excision of bases and replacement by DNA polymerase.

136
Q

What are the two types of excision repair?

A
  • Nucleotide excision repair replaces up to 30 bases and is used in repair of UV Damage and some carcinogens
  • Base excision repair replaces 1-5 bases and repairs oxidative damage.
137
Q

When does mismatch repair occur and what does it do?

A
  • Occurs when enzymes detect nucleotides that don’t base pair in newly replicated DNA
  • Incorrect base paired is excised and replaced
138
Q

What is the response when DNA repair fails?

A

Protein p53 monitors repair of damaged DNA and if damage is too severe it promotes apoptosis

139
Q

What is formed when a proto-oncogene is mutated?

A

Oncogene

140
Q

Why is PCR important in the diagnosis of genetic disease?

A

Most human mutations are single base changes and therefore hard to detect, PCR makes it easier to detect.

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