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principles year 1 > brief overview of thinsg > Flashcards

brief overview of thinsg Flashcards

1
Q

explain DNA replication

A
  1. initiation - DNA helicase unwinds the 2 strands. DNA primase synthesises a small RNA primer which acts as a kick starter for DNA polymerase. DNA polymerase attaches to the original unzipped strands
  2. elongation - DNA polymerase syntheses new DNA to match the templates. Leading strand 5’ to 3’ and lagging strand 3’ to 5’
  3. termination - the process of expanding the new DNA continues until there is either no more DNA template left to replicate or 3 replication forks meet and terminate. RNAase H removes the RNA primer that was at teh begining of each okazaki fragment and DNA ligase joins fragments together to complete one full strand
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2
Q

what is rRNA

A

combines with proteins to form ribisomes where protein synthesis takes place

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3
Q

what is tRNA

A

carries amino acids to be incorporated into protein

Anticodons consist of 3 nucleotides

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4
Q

what is mRNA

A

carries genetic information for protein synthesis

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5
Q

what is Pol I, II, III

A

Three multisubunit RNA polymerase (Pol) enzymes, Pol I, II, and III, transcribe the eukaryotic genome

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6
Q

what is TFIID

A

general transcription factor required for all Pol II transcribed genes

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7
Q

when are the introns spliced out

A

after transcription and before translation

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8
Q

explain transcription

A
  • RNA polymerase binding
    which requires transcription factors
  • DNA chain separation - unwinding of DNA
  • Transcription initiates
  • Elongation due to addition of further nucleotides to RNA chain in 5’ to 3’ direction
  • Termination - release of finished RNA
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9
Q

explain translation

A

(anticodons of tRNA form base pairs with codons of mRNA)

  • Initiation - GTP provides energy. Ribosomal subunit binds to 5’ end of mRNA and moves along until the start codon is found. Initiator tRNA pairs to start codon. Large subunit joins assembly and initiator tRNA is located in P site
  • Elongation - elongation factor brings aminoacyl-tRNA to A site
  • Peptidyl transferase catalyses peptide bond formation between amino acids in P and A sites
  • Termination - Occurs when A site of ribosome encounters a stop codon (UAA, UAG, UGA). Finished proteins cleaves off tRNA
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10
Q

what are the 3 binding sites in ribosome

A

Exit, Peptidyl, Aminoacyl

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11
Q

what is post translational and co-translational in regards to protein formation

A
  • Free ribosomes in cytosol proteins for - cytosol, nucleus, mitochondria – Post translational
  • Bound ribosomes on rough ER - plasma membrane, ER, Golgi, secretion – Co-translational
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12
Q

what are enzymes without a cofactor and with a cofactor called

A

Without = apoenzyme

With = holoenzyme

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13
Q

what is induced fit

A

binding of the substrate induces a conformational change in the shape of the enzyme resulting in a complentery fit

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14
Q

what carries out phosphorylation reactions

A

protein kinases

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15
Q

what is Vmax

A

maximal rate of reaction at unlimited substrate concentration

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16
Q

what is Km (Michaelis constant)

A

50% of Vmax

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17
Q

what graphs are drawn for enzyme kinetics and what are the axis

A

Lineweaver Burk plots

y axis = 1/V
x axis = 1/[s]

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18
Q

what is seen in a lineweaker Burk plot of a competeitive inhibition

A
  • binds to active site
  • Vmax remains the same
  • Km varies
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19
Q

what is seen in a Lineweaker Burk plot of a non competative inhibition

A
  • bind to other side than active site
  • Km stays the same
  • Vmax varies
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20
Q

where is Vmax on a Lineweaker Burk plot

A

the point at which the line crosses the Y axis

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21
Q

what is allosteric control and what does it show on a graph

A

Allosteric control refers to a type of enzyme regulation involving the binding of a non-substrate molecule, known as the allosteric effector, at locations on the enzyme other than the active site

shows a sigmoidal relationship

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22
Q

what are the functions of lipids

A

Cholesterol

  • present in cell membranes
  • component of the mylein sheath
  • precursor molecule for: steroid hormone, Vit D, bile acid

Triglycerides

  • present in all cell membranes - lipid bilayer
  • highly concentrated energy stores
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23
Q

what enzyme of the TCA cycle is not present in the matrix

A

succinate dehydrogenase in the inner mitochondrial membrane

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24
Q

what is phosphoryl transfer potential

A

free energy change for ATP hydrolysis

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25
Q

what is electron transfer potential

A

measured by redox potential of the compound

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26
Q

what is standard redox potential of a substance

A

measure of how readily it donates an electron

  • Negative = reduced form of X has a lower affinity for electrons than hydrogen
  • Positive = reduced form of X has higher affinity for electrons than hydrogen
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27
Q

what is glycolysis

A

initial pathway for the conversion of glucose to pyruvate

  • per glucose there is a net gain of 2 ATP
  • Hexokinase phosphorylates glucose
  • Phosphofructokinase phosphorylates fructose-6-phosphate
  • Pyruvate kinase converts phosphoenolpyruvate to pyruvate
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28
Q

explain aerobic metabolism of pyruvate

A

Enters mitochondria matrix

Converted to acetyl-coA (catalysed by Pyruvate Dehydrogenase Complex PDC)

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29
Q

explain the TCA cycle

A
  • Pyruvate has been converted to acetyl-coA (catalysed by Pyruvate Dehydrogenase Complex PDC)
  • Condenses with 4C compound to form 6C compound
  • 6C compound decarboxylated twice – yields CO2
  • 4 oxidation reactions – yield NADH + H+ and FADH2
  • GTP formed
  • 4C compound recreated
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30
Q

what is produced form each cycle of the TCA cycle from one acetyl-coA

A
  • 3 NADH + H+
  • 1 FADH2
  • 1 GTP
  • 2 CO2
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31
Q

explain oxidative phosphorylation

A

It is the coupling of respiration to ATP synthesis

2 stages:

  1. Electron transport
    - Respiratory chain – electrons from NADH enter at complex I, electrons from FADH2 enter at complex II (TCA cycle), electrons are handed down from higher to lower redox potentials, transferred onto O2 to form H2O
    - Transfer of electrons through respiratory chain is coupled to H+ transport from mitochondrial matrix to intermembrane space
    - 3/4 complexes pump H+ (1,2,4)
    - Electrochemical gradient – more protons in intermembranous space than matrix, matrix side more negative, protons attracted to matrix – coupled to ATP synthesis
  2. ATP synthesis
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32
Q

what inhibits oxidative phosphorylation

A

cyanide, azide, CO inhibit the transfer of electrons to O2

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33
Q

what is the essence of oxidative phosphorylation

A
  • electrons from NADH and FADH2 used to reduce O2 to H20
  • Their energy used to pump protons from mitochondrial matrix to intermembrane space
  • Protons flow back across the membrane
  • Energy of proton flow used to phosphorylate ADP to ATP
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34
Q

what is the final balance of the breakdown of glucose

A
  • Glycolysis - 2 ATP
  • TCA cycle (2GTP) - 2ATP
  • Glycolysis, PDH, TCA cycle (10 NADH + H+) - 25 ATP
  • TCA cycle ( 2 FADH2) - 3 ATP
  • 1 glucose molecule yield 30-32 ATP molecules
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35
Q

what makes up a chromosome

A

DNA strands associates with proteins (including histones)

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36
Q

when does DNA synthesis occur

A

S phase of the cell cycle

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37
Q

what is an overview of transcription and translation

A
  • DNA transcribed to pre-mRNA
  • Pre-mRNA spliced to mRNA
  • mRNA translated to protein
  • Protein is modified and moved around the cell
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38
Q

what are sequence variations within a gene

A
  • change in promotor sequence

- change in exon sequence

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39
Q

what are sequence variations in DNA between genes

A
  • SNPs (single nucleotide polymorphisms)

- larger duplications or deletions

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40
Q

what are polymorphisms

A
  • Any variation in human genome which has a population frequency >1%
  • Does not cause disease in own right
  • May predispose to common disease
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41
Q

what does aneuploidy mean

A

whole extra or missing chromosome

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42
Q

what are some translocation examples

A 
Rearrangement of chromosomes 
47 XY +21 – Down syndrome, trisomy 21 
47 XY +14 – Miscarriage, trisomy 14 
47 XY +18 – Edward Syndrome, trisomy 18
45 X – Turner syndrome 
47 XXY – Klinefelter syndrome
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43
Q

what is robertsonian translocation

A

Two acrocentric chromosomes stuck end to end

Increases risk of trisomy in pregnancy

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44
Q

what is microarray CGH

A

1st line chromosome test
Detects any missing or duplicated piece of chromosome
Find polymorphisms

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45
Q

what is penetrance

A

the likelihood of you having the disease if you have the gene mutation

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46
Q

what is expression

A

variation in disease severity if you have the mutation

47
Q

what is aCGH (microarray competative genomic hybridisation)

A

1st line for paediatric referrals, checks for deletions/ duplications.

48
Q

what is a polymorphism

A

A genetic variation that is prevalent in the population and not, in itself, disease causing.

49
Q

what is a mutation

A

(Genetic variation that causes a disease)
Promotor and splice site sequence changes
Stop transcription or cause abnormal splicing
Base changing causing amino acid change
Change in protein sequence
May or may not reduce protein function
Base change causing premature stop codon
Insertion or deletion of bases

50
Q

what is a mendelian disorder

A

a disease that is caused by a change in a single gene

51
Q

is X linked inheritance dominant or recessive

A

recessive eg haemophilia

52
Q

‘Only having one working copy is not enough’ mutation

A

haploinsufficiency

53
Q

‘Abnormal protein interferes with normal protein ‘ mutation

A

dominant negative

54
Q

‘mutation activates gene’ mutation

A

gain of function mutation

55
Q

what is Angelman syndrome

A 
Neuro-genetic disorder 
Developmental delay 
Intellectual disability 
Ataxia 
Epilepsy 
Happy demeanour 
Frequent laughing and smiling 
Chromosome 15
56
Q

what are the characteristics gained by cells on progression to cancer

A 
Proliferation 
Evasion of immune response 
Acquire a vascular supply 
Avoid apoptosis 
Metastasis
57
Q

what genes are involved in cancer

A
  • Oncogenes – switch these on for cell division
  • Tumour suppressors – switch these on to stop cell division
  • DNA repair genes – repair DNA damage
  • Drug metabolism – genes that metabolise carcinogens
58
Q

what is FISH

A

Fluorescence in situ Hybridisation

Can light up specific bit of chromosome if you know which bit to light up

59
Q

where is the mutation in breast cancer

A

BRCA1 gene

60
Q

what makes up a eukaryotic cell

A
  • Outer membrane
  • Inner cytosol – solution of proteins, electrolytes and carbohydrates
  • Cytoskeleton – determines shape and fluidity of the cells
    Made from thin, intermediate filaments and microtubules
  • Membrane bound organelles within the cytosol
61
Q

what are the components of the cytoskeleton

A

Microfilaments – 7nm – composed of actin

Intermediate filaments - >10nm – composed of proteins

Microtubules – 25nm – composed of tubulin

  • Originate from organising centre called centrosome
  • Polar
  • Dynein and kinesin attach to them and move along them
62
Q

what are occluding junctions

A

Link cells to form diffusion barrier
Prevent diffusion
Also known as tight junctions

63
Q

what are anchoring junctions

A

Provide mechanical strength
Adherent junctions – link submembrane actin bundles of adjacent cells
Cadherin molecules bind to each other in extracellular space and to actin of cytoskeleton

64
Q

what are hemidesmosomes

A

Hemidesmosomes link submembrane intermediate filaments of cells to extacellular matrix through transmembrane proteins

65
Q

what are desomsomes

A

Desmosomes link submembrane intermediate filaments of adjacent cells

66
Q

what are communicating junctions

A
  • Allow movement of molecules between cells
  • Often termed gap junctions
  • Each junction is circular patch studded with pores (produced by connexion proteins)
  • Found in epithelium, but also in smooth muscle and cardiac muscle
67
Q

what are endocrine cells and their features

A
  • product secreted towards basal end of cell
  • Distributed by vascular system
  • Ductless glands
68
Q

what are exocrine cells and their function

A
  • product secreted towards apical end of cell

- Ducted glands

69
Q

what are the 3 types of connective tissue

A
  • soft
  • hard
  • blood and lymph
70
Q

what are features of soft connective tissue

A

Tendons, ligaments, mesentery, stroma of organs, dermis of skin
Loose
Dense regular if fibres aligned
Dense irregular if fibres run in many directions

71
Q

what are features of hard connective tissue

A
  • Bone and cartilage
  • Strong, flexible, compressible, semi-rigid tissue

3 types of cartilage

  • Hyaline – articular surface, tracheal rings, costal cartilage, epiphyseal growth plates
  • Elastic
  • Fibrocartilage
  • Bone
    Outer shell of cortical bone makes up shaft – diaphysis
    Cancellous/trabecular bone occupies ends – epiphyses
72
Q

what cells are in connective tissue

A
  • fibroblasts
  • adipose cells
  • oesteocytes
  • chondrocytes
73
Q

what are the 3 types of muscle

A

Smooth – involuntary and non-striated

Skeletal – voluntary and striated , multinucleated
Nuclei are elongated at located at the periphery, just internal to cell membrane (sarcolemma)

Cardiac – involuntary and striated
Have intercalated discs – contain multiple intercellular junctions to maintain mechanical integrity

74
Q

what nervous tissue surrounds the CNS and PNS

A 
CNS = meninges 
PNS = epineurium
75
Q

what are astrocytes

A

support and ion transport

76
Q

what are oligodendrocytes

A

produce mylein

77
Q

what are microglia

A

provide immune surveilance

78
Q

what are schwann cells (PNS)

A

produce myelin and support axons

79
Q

where are non-keratinised stratified squamous epithelium found in the GI tract (protective)

A
  • oral cavity
  • pharynx
  • oesophagus
  • anal canal
80
Q

where are simple columar epithelium with villi and tubular glands found (absorptive mucosa)

A

small intestine

81
Q

where are simple columnar epithelium with extensive tubular glands found (secretory)

A

stomach

82
Q

where are simple columar epithelium with tubular glands found (protective and absorptive)

A

large intestine

83
Q

In the large intestine, the outer longitudinal smooth muscle is not continuous – found in 3 muscular strips called

A

teniae coli

84
Q

immunonology on other

A

brainscape

85
Q

gram positive stains

A

purple

86
Q

gram negative stains

A

pink

87
Q

what is a commensal

A

organism that is part of the normal flora

88
Q

what is an opportunistic pathogen

A

probably only cause infection in immunocomprimised individual

89
Q

what is virulence

A

degree of pathogenicity of an organism

90
Q

how does bacterial growth divide

A

binary fission

91
Q

what is an exotoxin

A
  • usually gram positive

- produced inside cell and exported from it

92
Q

what is endotoxin

A
  • usually gram negative

- part of gram negative bacterial cell wall

93
Q

features of mould

A

produce spores and hyphae

  • Aspergillus
94
Q

features of yeasts

A
  • single cells that reproduce by budding

- Candida

95
Q

what are features of streptococcus

A

gram positive cocci

  • Aerobic
  • Cocci chains
  • Alpha haemolysis (partial) – Strep pneumoniae (pneumonia, meningitis), Strep viridans (endocarditis)
  • Beta haemolysis (complete) – Group A Strep (throat, skin infection), Group B strep (neonatal meningitis)
96
Q

features of enterococcus

A

gram positive cocci

  • Aerobic
  • Cocci chains
  • Non-haemolytic
  • Normal gut commensal and cause of UTIs
97
Q

features of staphylococcus

A

gram positive cocci

  • Cocci clusters
  • Coagulase positive (golden) – Staph aureus – wound, skin infections
    Flucloxacillin antibiotic of choice
    Common cause of bacteraemia (bacteria in the blood)
  • Coagulase negative (white) – Staph epidermidis – normal skin commensal, IV line infections
98
Q

features of gram negative cocci

A
  • Diplococci
  • aerobic
  • Neisseria gonorrhoea
  • Neisseria meningitidis
99
Q

features of coliforms

A

Gram negative bacilli

  • Aerobic but can also be anaerobic
  • Gut commensals
    E coli, Klebsiella, Proteus
  • Gut pathogens
    Salmonella, Shigella, E coli O157
  • Gentamicin is first line antibiotic
100
Q

features of strict aerobes

A
  • Gram negative bacilli
  • Pseudomonas aeruginosa
  • Legionella pneumophilia
101
Q

what are spiral or curved gram negative bacilli

A

Campylobacter – food poisoning

Helicobacter pylori – gastritis

102
Q

what is haemophilus influenzae

A

Small gram negative bacillus

Common cause of chest infection, especially in COPD exacerbations

103
Q

features of gram positive anaerobic bacilli

A
  • Clostridium spp.
  • Part of normal bowel flora
  • Produces spores
  • Produce exotoxin that cause severe tissue damage
104
Q

features of gram negative anaerobic bacilli

A
  • Bacteroides spp.
  • Normal gut commensals, only pathogenic when found in other sites
  • Metronidazole is first line treatment for infections caused by anaerobes
105
Q

what is Mycobacteria

A
  • TB
  • thick waxy outer coat
  • acid fast bacilli or ziehl neelson stain
106
Q

what is transformation gene transfer

A

DNA from dead bacteria taken up by living bacteria and incorporated in plasmids or the bacterial chromosome

107
Q

what is conjugation gene transfer

A

Sex pilus (fimbria) produced by one bacteria through which plasmid DNA can be transferred

108
Q

what is transduction gene transfer

A

Viruses infecting bacteria can transfer bits of DNA from one bacterium to another

109
Q

what antibiotics work on the cell wall

A
  • penicillin
  • cephalosporins (ceftriaxone)
  • glycopeptides (vancomycin)
110
Q

what antibiotics prevent protein synthesis

A
  • macrolides (erythromycin, clarithromycin, azithromycin)
  • tetracyclines (doxycycline)
  • aminoglycosides (gentamicin)
111
Q

antibiotics that act on bacterial DNA

A
  • metroniadazole
  • trimethoprim
  • fluoroquinolones
112
Q

what is a side effect of gentamicin

A

renal and VIII nerve damage

113
Q

what is a side effect of ciprofloxacin

A

tendonitis

114
Q

what is a side effect of metronidazole

A

interacts with alcohol

principles year 1 (9 decks)

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