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ESA1 Emily > MGD > Flashcards

MGD Flashcards

0
Q

What happens to an acid if pK is lower than pH?

A

Deprotonated

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1
Q

What is the relationship between acidity of a protein and pI?

A

Acidic proteins have a low pI

Basic proteins have a high pI

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2
Q

What are the 4 ways we can classify amino acids?

A

Polar/non polar
Aliphatic/aromatic
Charged/uncharged
Essential/non essential

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3
Q

Describe a peptide bond

A

Forms between amino group of one amino acid and carboxyl group of another.
Key features are TRANs orientation, rigid, planar
double bond properties
Covalent bond with removal of water molecule

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4
Q

Beta pleated sheet properties

A

Antiparallel or parallel
Extended conformation
Interconnecting hydrogen bonds between chains-stability

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5
Q

Alpha helix properties

A 
Right handed 
0.54nm pitch 
R groups on outside 
3.6 amino acids per turn 
Hydrogen bonds stabilise structure
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6
Q

Helix formers

Why?

A

Leucine, alanine

Small hydrophobic residues

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7
Q

Helix breakers

Why?

A

Proline, glycine
Proline has a large R group and so gives no rotation around the C-N bond
Glycine has a small R group and so promotes other conformations

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8
Q

How can you classify a quaternary structure?

Examples?

A

Heteromeric/homomeric
Hetero- haemoglobin
Homo- tropocollagen

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9
Q

Globular protein features

A

Compact
Involved in catalysis and regulation
Many secondary structures involved
E.g. Enzymes

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10
Q

Fibrous protein properties

A

Long strands/sheets
Involved in shape and support
One repeating secondary structure
E.g. Collagen

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11
Q

Myoglobin structure

A

Single polypeptide with one subunit
One harm group
153 aa
75% alpha helical

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12
Q

What is found in haem

A

4 nitrogen atoms

1 iron ATOM

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13
Q

How is iron atom bonded to haemoglobin?

A

Histidine residues on either side of ring

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14
Q

What happens when oxygen binds to myoglobin or haemoglobin?

A

Iron atom normally slightly below plane of ring. Oxygen binding causes movement of iron into the plane of the ring, leading to a small overall change in conformation

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15
Q

Bohr effect. Describe.

A

Large amounts of hydrogen ions and carbon dioxide released from metabolic processes in metabolically active tissue LOWER affinity for oxygen
Shifts curve to right
Oxygen more readily released at low partial pressure in tissues where it is required.
Process couples delivery of oxygen to demand

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16
Q

Where is 2,3-BPG found?

A 
High altitudes 
Metabolic processes (glycolysis intermediate)
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17
Q

What is the effect of 2,3-BPG on oxygen dissociation curve of haemoglobin?

A

Shifts curve to right

Lowers oxygen affinity by stabilising T state

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18
Q

Why is carbon monoxide poisonous?

A

Carbon monoxide binds 250 times more readily than oxygen and blocks oxygen transport to tissues from the lungs.
Fatal when carbon monoxide associated haemoglobin exceeds 50%

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19
Q

Define enzyme

A

Biological catalyst which increases rate of a reaction by providing an alternative reaction pathway with a lower activation energy
Facilitates formation of transition state

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20
Q

Define international unit of enzyme activity

A

One unit is amount of energy that produces a certain amount of enzymatic activity which is the amount which catalyses conversion of 1micromole per minute

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21
Q

Limeweaver burk plot axis and intercepts

A

y axis- 1/Vo
x axis- 1/S concentration

Y intercept- 1/vmax
X intercept- -1/km

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22
Q

What are the five mechanisms of enzyme control?

A 
Allosteric 
Covalent modification 
Substrate/product concentration
Proteolytic cleavage
Long term change in rate of synthesis/degradation
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23
Q

Describe allosteric inhibition

Give an example

A

Increase in proportion of enzymes in the T state
Decreasing enzyme activity
E.g. Multi-subunit enzymes enabling inhibiting and activating molecules to bind- phosphofructokinase

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24
Q

How does a kinase work?

A

Phosphorylates molecules by transfer of terminal phospahte from ATP to OH of certain amino acids (Ser, thr, tyr)

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25
Q

How are Gla domains formed?

A

Carboxylation of glutamate residues in liver

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26
Q

What are the 4 steps converting fibrinogen to fibrin and subsequent clot formation?

A
  1. Thrombin cleaves A and B peptides (fibrinopeptides) from central globular domain
  2. Beta and gamma chains at C terminus interact with beta and alpha at N terminus to form a clot
  3. Clot is stabilised by amide bond formation between lysine and glutamine side chains
  4. Cross linking catalysed by transglutaminase
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27
Q

What 3 methods terminate clotting?

A

Localisation of prothrombin by blood flowing past diluting site
Digestion by proteases e.g. Protein C
Specific inhibitors e.g. Anti-thrombin 3

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28
Q

What are methods of regulation of the blood clotting cascade? (6)

A

Inactive zymogens are present at low concentrations
Amplification of signal by cascade mechanism
Feedback activation by thrombin
Multiple termination mechanisms
Clustering factors at site of damage
Clot breakdown controlled by proteolytic activation

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29
Q

What is the polarity of a DNA chain?

A

Phosphate molecule at 5’ end

Hydroxyl group at 3’ end

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30
Q

What bonds are found within DNA chains of double helix?

A

Phosphodiester bonds between nucleotides (sugar phosphate backbone)
Hydrogen bonds form between complementary base pairs

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31
Q

Key features of DNA double helix

A 
Right handed 
0.34nm pitch 
Antiparallel complementary stands 
Bases on inside of helix 
Deoxyribose and phosphate molecules on outside of helix
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32
Q

What is a histone?

A

Positive charged protein molecule which DNA wraps around to form nucleosomes which give beads on a string structure

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33
Q

Define chromosome

A

Structure found in cell nucleus which contains one double stranded molecule (or two identical double strands after DNA replication)

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34
Q

Define gene

A

Unit of heredity
Length of DNA
Codes for a protein to be transcribed

35
Q

Differences between mitosis and meiosis

A

2xdiploid v 4xhaploid
Somatic cells v gametes
Growth and repair v spermatogenesis and oogenesis
Identical v genetic variation from independent assortment of chromosomes and crossing over

36
Q

Genotype

A

Genetic make up of an individual

37
Q

Phenotype

A

All observable characteristics resulting from the genotype

38
Q

Allele

A

Alternative forms of the same gene

39
Q

Complementation

Give an example

A

More than one gene is responsible for phenotype

Albinism

40
Q

What are examples of autosomal dominant diseases?

A

Marian’s, Huntingtons, osteogenesis in-perfecta, achondroplasia, malignant hyperthermia

41
Q

How is transcription initiated?

A

Transcription factor binds to TATA initiation codon upstream of gene and attracts RNA polymerase which separates DNA strands to produce template and begin production of mRNA

42
Q

ORF

A

Open reading frame

Area of gene holding code for amino acid residues of gene product

43
Q

How is translation initiated?

A

40S subunit with Met-tRNA binds to 5’ end of mRNA
Start codon 5’AUG is recognised by anticodon on tRNA
60S subunit binds and elongation begins

44
Q

What do the different sites of the ribosome do?

A

P- holds peptide chain

A- binding of tRNA molecules

45
Q

What enzyme is involved in translation

A

Peptidyl transferase

Catalyse formation of peptide bonds between amino acids

46
Q

How is prokaryote protein synthesis different from eukaryotes?
Think MITOCRPS

A

M- no modification post-transcriptional or splicing
I- different initiation mechanism
T- different transcription and translation factors
O- one type of RNA polymerase
C- coupled transcription and translation
R- simple ribosomes
P- simple promoter sequence
S- short lived mRNA

47
Q

How does rifampicin work?

A

Inhibits transcription by binding to RNA polymerase

48
Q

Methotrexate

A

Inhibits dyhydrofolate reductase, preventing synthesis of tetrahydrofolate from folic acid

49
Q

How does penicillin work?

A

Inhibits transpeptidase so cross links in bacterial cell walls cannot form. Resulting in lysis from osmotic pressure

50
Q

How does Tetracycline work?

A

Inhibits translation by competing with tRNA at A site of bacterial ribosome

51
Q

What are the different ways in which bacteria can become resistant to drugs?

A

Increased efflux of drugs from cell so they cannot help treat it
Decreased influx of drug through membrane by causing reduced expression for carrier protein
High division rate (therefore higher rate of mutation and natural selection of best bacteria)
Increased transcription of target to overwhelm drug
Altered target, lowering affinity for drug

52
Q

When would mutations outside of coding region affect gene expression?

A

If occur in promotor sequences and splice sites

53
Q

What are the steps of the secretory pathway?

A 
Protein synthesis at free ribosome 
N terminus signal sequence produced
SRP and GTP bind to ribosome 
Protein synthesis stops 
SRP guides ribosome to SRP receptor on cis-ER membrane 
SRP released
Protein fed through pore into ER 
N terminal sequence cleaved by signal peptidase 
Ribosome dissociates
54
Q

Glycosylation at ER

A

N linked

Used N-acetylglucosaminase phosphotransferase enzyme

55
Q

Golgi glycosylation

A

O linked

Glycosyl transferase enzyme

56
Q

How does I cell disease occur

A

In ER- there is a lack of N-acetylglucosaminase phosphotransferase enzyme
In then targeting to lysosomes no addition of mannose-6-phosphate to create signal patch so mistargetting of secretion of lysosomal hydrolases (seen in blood and urine in elevated levels)

57
Q

How is insulin stored in cells before release?

A

Margination secretory granules

58
Q

How is mature collagen formed from secreted collagen?

A

C- cleavage of signal peptidase from preprocollagen
H- hydroxylation of proline/leucine
A- addition of N-linked oligosaccharides and galactose
S- disulphide bond formation
P- procollagen formed (N and C terminal peptides present prevent collagen forming in a cell)
O- o linked glycosylation
G- exocytosed to Golgi in transport vesicle
R- removal of N/C terminus by procollagen peptidase to form tropocollagen
L- lateral aggregation to form fibrils and covalent cross linking by lysyl oxidase to form collagen fibre

59
Q

Why is vitamin C important for collagen synthesis?

A

Scurvy!
Vitamin C and iron ions area required by enzyme prolyl hydroxylase (converting proline to hydroxyproline)
This enables more hydrogen bonds to form which strengthens tropocollagen molecules

60
Q

What is an enzyme assay used for?

A

Measure of enzyme activity

Indicator of tissue damage if enzymes normally contained in tissues are found in plasma

61
Q

How are southern and western blotting different?

A

Southern blotting involves transfer of DNA after electrophoresis to a nylon membrane and annealing of radioactive DNA probes to expose fragments under X-ray

Western blotting involves transfer of proteins after SDS-page to a nitrocellulose membrane and binding of antibodies conjugated with a label as markers to visualise proteins

62
Q

What are ddNTPs?

A

Used in DNA sequencing as terminator molecules by preventing further polymerisation of nucleotide strand, due to lack of 3’ OH

63
Q

How is restriction analysis used in allele specific tests?

A

If restriction enzyme cuts wild type but not sample (around allele of interest) then restriction site is missing it mutated. You can check for differing length using gel electrophoresis

64
Q

Purpose of array analysis

A

Screen for sub-microscopic chromosome deletions for which locus cannot be deduced from patients’ phenotype

65
Q

What is FISH

A

Fluorescence in situ hybridisation
Detect chromosome abnormalities in DNA sequences on chromosomes in tissues through hybridisation of fluorescently labeled probes

66
Q

A silent mutation may be serious when?

A

If occurring in a binding site, promotor sequence or splice site of DNA

67
Q

How do spontaneous mutations occur?

A

Tautomeric shift- nucleotides briefly change to tautomeric form so behave as altered template bases in replication

DNA strand slippage- template or new strand loops out during replication causing imperfect base pairing

68
Q

What chemicals cause mutation?

A

Nitrous acid
Ethyl methane sulphonate
IQ

69
Q

What kind of radiation can induce mutation?

A

X Rays

Radon gas in environment

70
Q

What are the repair mechanisms of DNA?

A

Excision repair- base for oxidative damage and nucleotide for UV damage

Nucleotide mismatch repair- proof reading (patch of DNA replaced)

P53- monitors and promotes apoptosis when severe damage occurs

71
Q

How do genes become homozygous (for cancer formation)

A

Loss chromosome containing wild type allele
Deletion of wild type allele on chromosome
Point mutation on chromosome which originally held wild type allele
Mitotic recombination

72
Q

How is cystic fibrosis identified?

A

PCR and southern blottingb

73
Q

How is sickle cell anaemia identified?

A

Southern blotting

74
Q

What are the different types of histones?

A

H1- responsible for beads on a string structure

Others react directly with DNA

75
Q

What is a numerical chromosome abnormality?

A

A number of chromosomes any number but 46

E.g. Polyploidy, aneuploidy

76
Q

What is aneuploidy?

A

Abnormal number of chromosomes not a multiple of the haploid number
Monosomy, trisomy

77
Q

What are structural chromosome abnormalities?

A

Physical changes to one or more chromosomes
Balanced/ unbalanced
Reciprocal translocation, Robertsonian translocation

78
Q

What mutations can occur in one chromosome

A

Deletion
Inversion- (single chromosome undergoes breakage and rearrangement within self)
duplication
Ring chromosome (loss of telomeres and formation of ring)
Isochromosome

79
Q

What mutations can occur between 2 chromosomes?

A

Reciprocal translocation

Robertsonian translocation

80
Q

Karyotype

A

Picture of systematic assortment of the complete set of chromosomes of an individual- starting with chromosome 1 and ending with sex chromosomes

81
Q

When should PRIBA be referred for karyotyping?

A 
Congenital:
P- prenatal screening 
R- recurrent foetal loss
I- infertility 
B- birth defects
A- abnormal sexual development

Or acquired: leukaemia etc

82
Q

What does FISH identify?

A

Rearranged chromosomes
Marker chromosomes
Microduplications
Microdeletions

83
Q

Why is imprinting important in UPD?

A

Imprinted chromosomes show differential expression of specific genes depending on parental origin
If chromosome involved is not imprinted then UPD has no phenotypic effect
E.g. Prader-willi, maternal imprinting

84
Q

What is most common mechanism to generate UPD?

A

Trisomy rescue

85
Q

What can NIPT be used for?

A

Chromosome aneuploidy, foetal sex, single gene disorders

ESA1 Emily (3 decks)

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