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Foundations of health and disease > microbiology > Flashcards

microbiology Flashcards

1
Q

what is molecular cell biology

A

The study of molecular mechanisms at the cellular level and how such observations relate to cell function

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2
Q

what is a biomarker

A

A characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention

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3
Q

what is translational research

A

Applying basic research to a clinical setting

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4
Q

what is stratified medicine

A

We identify subgroups of a population with exhibit distinct characteristics of disease

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5
Q

what is personalised medicine

A

A tailor-made clinical model whereby therapy is delivered on an individualised basis

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6
Q

what is physiology

A

studies the characteristics (chemical, physical and mechanistic) that contribute to function and the processes of life.

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7
Q

what is pathophysiology

A

studies pathology in the context of physiology. For example, this could be disease process or injury

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8
Q

what is negative feedback

A

is the process where biological systems maintain defined constant conditions in response to an altering environment.

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9
Q

what is positive feedback

A

the process of amplifying change

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10
Q

what is a solution

A

solute dissolved in a solvent

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11
Q

what is diffusion

A

the movement of a molecule down a concentration gradient, from an area of its high concentration to an area of its low concentration.

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12
Q

what is simple diffusion

A

molecules move directly across the membrane without the aid of a carrier protein

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13
Q

what is facilitated diffusion

A

passive movement down a concentration gradient with the help of carrier proteins

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14
Q

what is the equation for rate of diffusion

A

(surface area x concenctration gradient) / length of diffusuon pathway

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15
Q

what is osmosis

A

Osmosis is the process by which water molecules pass through a semipermeable membrane, from a less concentrated solution into a more concentrated one.

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16
Q

what is a hypotonic environment

A

when more water is on the outside

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17
Q

what is hypertonic

A

when more water is on the inside

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18
Q

what is active transport

A

the movement of molecules from an area of lower concentration to higher concentration

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19
Q

what is co transport

A

Some membrane proteins involved in facilitated diffusion or active transport can carry multiple molecules or ions at once

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20
Q

what is a symporter

A

when molecules move in the same direction through a facilitator protein

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21
Q

what is an antiporter

A

when molecules move in different directions through a facilitator protein

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22
Q

what is carbonic anhydrase

A

is an enzyme that catalysis the reaction of H2O and CO2 to generate carbonic acid and subsequently bicarbonate.

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23
Q

what is voltage

A

is the potential difference between two points in an electrical field

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24
Q

what are features of excitable cells

A

Excitable cells can produce OR respond to electrical signals
Excitable cells can propagate action potentials

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25
Q

which cells are excitable

A

neurons, skeletal muscle cells, smooth muscle cells, cardiac myocytes

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26
Q

what is the features of a cell membrane

A
  • Hydrophilic phosphate head groups orientate toward the aqueous internal / external environments
  • Hydrophobic lipid tails orientate towards each other.
  • Cholesterol alters the fluidity of the plasma membrane.
  • One of the most common lipids in the PM is phosphatidylcholine
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27
Q

what are examples of membrane proteins on the cell membrane

A
  • Catalysts – enzymes.
  • Transporters, pumps and ion channels.
  • Receptors for hormones, local mediators and neurotransmitters.
  • Energy transducers.
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28
Q

what is the function of a cell membrane

A
  • Forming a continuous, highly selectively permeablebarrier
  • Allowing the control of an enclosed chemical environment
  • Communication
  • Recognition
  • Signal generation
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29
Q

what is the permeability of gases in the cell membrane

A

permeable

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30
Q

what is the permeability of small uncharged polar molecules in the cell membrane

A

ethanol is permeable but water and urea are slightly permeabe

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31
Q

what is the permeability of large uncharged polar molecules in the cell membrane

A

impermeable

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32
Q

what is the permeability of charged polar molecules in the cell membrane

A

impermeable

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33
Q

what is the permeability of ions in the cell membrane

A

impermeable

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34
Q

what does the RER do

A

takes developing proteins from the cytosol and continues their development prior to completion in the golgi apparatus.

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35
Q

which proteins do the RER develop

A
  • Secretion into the extracellular matrix e.g. mucus and enzymes.
  • Association with the cell membrane e.g. receptors and channels
  • Membrane bound vesicles e.g. enzymes of lysosomes.
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36
Q

what does the SER do

A

The smooth endoplasmic reticulum is important in the synthesis of lipids, phospholipids and steroids.

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37
Q

what does the golgi apparatus do

A

The golgi apparatus modifies proteins and lipids that it receives from the endoplasmic reticulum. These biochemicals leave the golgi byexocytosisbefore being delivered to differentintracellularorextracellulartargets.

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38
Q

what is protein processing in the golgi

A

carbohydrate regions of glycoproteins are altered by addition, removal or modification of carbohydrates.

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39
Q

what is protein processing in the golgi

A

dds phosphate groups and glycoproteins to lipids from the endoplasmic reticulum (such as cholesterol) to create the phospholipids that make up the cell membrane.

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40
Q

what are lysosomes

A

are acidic membrane-bound organelles found within cells,
Lysosomes contain numerous hydrolytic enzymes which catalyse hydrolysis reactions.

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41
Q

what is the structure of mitochondria

A

Mitochondria have an inner and outer membrane, with an intermembrane space between them

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42
Q

what is the function of the mitochondria

A

The mitochondrion is the site of ATP synthesis for the cell
Store caspases responsible for triggering apoptosis.
Are able to transiently store calcium contributing to calcium homeostasis.

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43
Q

what is the role of the cytoskeleton

A

Is involved in the processes such as mitosis

Acts as a highway for intracellular vesicles

Provides support to the plasma membrane

Enables cellular locomotion

Controls the shape of the cell

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44
Q

what are the primary filament systems of the cell cytoskeleton

A

microtubules
actin filaments
intermediate filaments

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45
Q

what do stem cells divide into

A
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46
Q

DNA vs RNA

A
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47
Q

what are features of stem cells

A

They can divide indefinitely
Are not terminally differentiated
Daughters have a choice: differentiate or remain a stem cell

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48
Q

what are introns

A

. Introns are removed by RNA splicing as RNA matures, meaning that they are not expressed in the final messenger RNA (mRNA) product

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49
Q

what are exons

A

exons go on to be covalently bonded to one another in order to create mature mRNA.

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50
Q

why do large variations of the genome exist

A

mechanisms of disease
targeted therapeutics
gene therapy
predictive use (testing and reproductive ethics)

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51
Q

what are purines

A

adenine and guamine

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52
Q

what are pyrimidines

A

cytosine
uracil
thymine

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53
Q

what is the structure of DNA

A
  • DNA is a double helix formed by base pairs attached to a sugar-phosphate backbone.
  • Sugars are connected via phosphate groups
  • This phosphodiester bond occurs between the 3’ and 5’ carbon atoms
  • The helix is antiparallel
  • Opposite bases on each strand compliment each other.
  • The outer edges of the bases are exposed in the major and minor grooves.
54
Q

how many hydrogen bonds do AT have

A

2

55
Q

how many hydrogen bonds do CG have

A

3

56
Q

what are the stages of the cell cycle

A

g1
s
g2
m

57
Q

what happens during the g1 phase

A

cell increases in size
cellular contents are duplicated

58
Q

what happens during the s phase

A

dna replication

59
Q

what happens during the g2 phase

A

cell grows more
organelles and proteins develop in preperation for cell division

60
Q

what happens during the m phase

A

mitosis followed by cytokensis
formation of two identical daughter cells

61
Q

how is the cell cycle regulated

A

This cycle is also closely regulated by cyclins which control cell progression by activating cyclin-dependent kinase (CDK) enzymes.

62
Q

what happens during prophase (mitosis)

A

Each chromosome is made of two genetically identical chromatids, joined by a centromere. mitotic spindles begin to form.
The spindles attach to the centrosome.
the centrosomes begin to move in opposite directions.

63
Q

what happens during metaphase (mitosis)

A

the chromosomes align at the metaphase plate. The centrosomes are located at opposite ends of the cell.
the cell will check that all the chromosomes are aligned along the metaphase plate.

64
Q

what happens during anaphase (mitosis)

A

sister chromatids are pulled to opposite ends of the cell.
The spindle fibres contract, breaking the chromatids at the centromere and moving them to opposite poles of the cell.

65
Q

what happens during telophase (mitosis)

A

reformation of two nuclei
The chromosomes decondense and the mitotic spindles fibres are broken down.

66
Q

what happens during cytokinesis (mitosis)

A

Cytokinesis is the division of the cytoplasm to form two new cells.

67
Q

what happens during initiation of DNA replication

A

DNA synthesis is initiated at origins which have specific coding regions.
DNA helicase unwinds the double helix by hydrolysing the ATP used to form the bonds between the nucleobases
DNA primase synthesises a small RNA primer, which acts as a ‘kick-starter’ for DNA polymerase.

68
Q

what happens during elongation of DNA replication

A

Once DNA Polymerase has attached to the two unzipped strands of DNA it is able to start synthesising new strands of DNA by adding free nucleotides to the 3’ end.
One of the template strands is read in a 3’ to 5’ direction, therefore the new strand will be formed in a 5’ to 3’ direction.

69
Q

what happens during termination of DNA replication

A

The process of expanding the new DNA strands continues until there is either no more DNA template strand left to replicate.

70
Q

what it meiosis

A

the process of cell division by which gametes are made

71
Q

what is meiosis I

A

In meiosis I, homologous chromosomes are separated into two cells

72
Q

what happens in prophase I (meiosis)

A

chromosomes replicate to form sister chromatids. The nuclear envelope disintegrates and the chromosomes begin to condense.
Spindle fibres appear
crossing over on the chiasmata

73
Q

what happens in metaphase I

A

homologous chromosomes align along the equator of the cell.
independent assortment occurs

74
Q

what is crossing over

A

To further increase genetic diversity, homologous chromosomes exchange small parts of themselves, such that one chromosome contains both maternal and paternal DNA
the points at which this occurs on a chromosome is the chiasmata.

75
Q

what is independent assortment

A

this is when maternal and paternal chromosomes line up and randomly align themselves on either side of the equator.

76
Q

what happens during anaphase I

A

each of the homologous chromosomes get pulled towards opposite poles of the cell as the spindle fibres retract. This equally divides the DNA between the two cells which will be formed.

77
Q

what happens during telophase I

A

the nuclear envelope reforms and spindle fibres disappear

78
Q

what happens during cytokinesis I

A

the cytoplasm and cell divide resulting in two cells that are technically haploid – there is one chromosome and two chromatids for each chromosome (2c, n).

79
Q

what happens during prophase II

A

The nuclear envelope disintegrates and the chromosomes begin to condense.
Spindle fibres appear

80
Q

what happens during metaphase II

A

chromosomes line up in single file along the equator of the cell.

81
Q

what happens during anaphase II

A

sister chromatids are pulled to opposite poles of the equator

82
Q

what happens during telophase II

A

the nuclear envelope reforms and spindle fibres disappear

83
Q

what happens during cytokinesis II

A

the cytoplasm and cell divide producing 2 non-identical haploid daughter cells.

84
Q

what do recombination errors lead to

A

gene duplications (or loss)and to inversions and translocations

85
Q

what is turner syndrome

A

XO female, reduced height, underdeveloped ovaries, and may have neck webbing, heart and kidney defects

86
Q

what is Klinefelter syndrome

A

XXY male, reduced fertility, may affect general development

87
Q

where can dna damage occur

A

germline or soma

88
Q

what are mutations

A
  • Changes in the DNA
  • Source of all genetic variation
  • Random and can be harmful, neutral or advantageous
  • Mutation rates are generally low
89
Q

what are routes of DNA repair

A
  • Polymerases involved in DNA replication have 3’-5’ exonuclease activity, this allows proof reading
  • Base excision repair (BER), nucleotide excision repair (NER) and mismatch repair (MMR) systems that act throughout cell life repairing DNA damage
  • A specific system exists to repair double stranded breaks, this is related to the system that allows recombination
90
Q

what are mitochondrial diseases

A

Mutations in mitochondrial genes can also cause a range of maternally-inherited diseases

91
Q

what is Leber’s hereditary optic atrophy (LHON)

A

a midlife, acute or subacute, painless, central vision loss that results from one of arrange of mtDNA mutations

92
Q

what is myoclonic epilepsy

A

mutation at nucleotide that results in a defect in translation of all mtDNA-encoded genes

93
Q

what is cystic fibrosis

A

CTRF protein Cl- channel is expressed in a number of epithelial tissues and mutations may be in the form of blocked channels or few channels on the membrane surface.

94
Q

what is xerderma pigmentosum

A

is an autosomal recessive dissorder

95
Q

what is DNA transcription

A

the process by which the genetic information contained within DNA is re-written into messenger RNA (mRNA) by RNA polymerase. This mRNA then exits the nucleus, where it acts as the basis for the translation of DNA. By controlling the production of mRNA within the nucleus, the cell regulates the rate of gene expression.

96
Q

what is the initiation of DNA transcription

A

Transcription is catalysed by the enzyme RNA polymerase, which attaches to and moves along the DNA molecule until it recognises a promoter sequence.
Once bound to the promoter sequence, RNA polymerase unwinds a portion of the DNA double helix, exposing the bases on each of the two DNA strands.

97
Q

what are transcription factors

A

Transcription factors are proteins that control the rate of transcription; they too bind to the promoter sequences with RNA polymerase.

98
Q

what is the elongation of DNA transcription

A

One DNA strand (the template strand) is read in a 3′ to 5′ direction, and so provides the template for the new mRNA molecule. The other DNA strand is referred to as the coding strand.

RNA polymerase uses incoming ribonucleotides to form the new mRNA strand. It does this by catalysing the formation of phosphodiester bonds between adjacent ribonucleotides

99
Q

what is the termination of DNA transcription

A

Elongation continues until the RNA polymerase encounters a stop sequence. At this point, transcription stops and the RNA polymerase releases the DNA template.

100
Q

what is splicing

A

Splicingallows the genetic sequence of a single pre-MRNA to code for many different proteins, conserving genetic material.
Removal ofintrons(non-coding sequences) viaspliceosome excision

Joining together ofexons(coding sequence) byligation

101
Q

what is DNA translation

A

is the process by which the genetic code contained within a messenger RNA (mRNA) molecule is decoded to produce a specific sequence of amino acids in a polypeptide chain.

102
Q

what is the initiation of DNA translation

A

thestart codonis recognised.
the small 40s subunit of the ribosome binds. Subsequently, the larger 60s subunit binds to complete theinitiation complex.

103
Q

what is the elongation of DNA translation

A

The ribosome hastwo tRNA binding site; thePsite which holds thepeptide chain and theAsite whichaccepts the tRNA.

While tRNA occupies the P site, the tRNA that is complementary to the next codon binds to the A site,
The ribosome thentranslocatesalong the mRNA molecule to the next codon

104
Q

what is termination of DNA translation

A

One of the threestop codonsenters the A site. The small and large subunits of the ribosomedissociate

105
Q

what are microRNA’s

A

micro RNAs (miRNA) are non-coding RNAs that play a critical role in gene expression.

106
Q

what do amino acids consist of

A
  • the amino group
  • carboxyl group
  • the R group
107
Q

what is the chemistry of non-polar aliphatic r groups

A

hydrophobic

108
Q

what is the chemistry of aromatic r groups

A

hydrophobic but functional groups may alter polarity

109
Q

what is the chemistry of polar r groups

A

polar uncharged hydrophllic

110
Q

what is the chemistry of polar r groups

A

polar uncharged hydrophllic

111
Q

what is the chemistry of positively charged r groups

A

basic
hydrophilic and possess a significant charge at pH 7

112
Q

what is the chemistry of negatively charged r groups

A

acidic
hydrophilic and possess a significant charge at pH 7

113
Q

what are features of the protiens primary strucutre

A

multiple amino acids bound together via strongcovalent peptide bondsto form apolypeptide chain.
The peptide bond has a partial double bond character

114
Q

what mutations form from a proteins’ primary structure

A

can affect protein folding in the subsequent stages of protein structure, leading to problems with the protein’s function.

115
Q

what bonds come from the primary structure of a protein

A

electrostatic attraction
London forces
hydrogen bonds
interchain disulfide bonds
intrachain disulfide bonds

116
Q

what is the secondary structure of a protein

A

folding of polypeptide chains by hydrogen bonds between the hydroxyl (OH) group and the hydrogen molecule of the adjacent amino acid

117
Q

what is an alpha helix

A

a coil formed by hydrogen bonds between the carbonyl group and the amino group
The strong bonds and stability of this structure gives it a strong tensile strength

118
Q

what is a beta-pleated sheet

A

is formed by hydrogen bonds between the carboxyl group of one amino acid on one sheet and the hydrogen molecule of an amino acid on another sheet. The sheets can be in parallel or anti-parallel.

119
Q

what is a beta-turn

A
  • These connect the polypeptide chains between secondary structures such as ⍺-helices and β-sheets.
  • The turn brings about a 180 change in direction for the polypeptide chain.
120
Q

what is the tertiary structure of a protein?

A

the folding of the polypeptide chain into aunique 3D structure.
Folding of the polypeptide chain occurs viainteraction between the R groupsof amino acids.

121
Q

what is protein denaturation?

A

disruption to the bonds between R groups. This causes the structure to lose its shape, resulting in a loss of function

122
Q

what bonds are present in the tertiary strucutre

A

hydrostatic
electrostatic
covalent disulphide
hydrophobic

123
Q

what is a hydrostatic bond

A

forms between the hydroxyl (OH) group and an adjacent hydrogen molecule, providing a strong bond between polar R groups.

124
Q

what is a electrostatic bond

A

forms between positive and negative charge. They can be disrupted by presence of other charged molecules near them.

125
Q

what is a covalent disulphide bond

A

form between sulphide groups within the R group of amino acids. They usually occur between two cysteine amino acids, which contain sulphur within their R groups.

126
Q

what is a hydrophobic bond

A

form between non-polar groups and commonly involve the benzene group.

127
Q

what is the quaternary protein structure

A

he combination of multiple polypeptide chains that link together to form a functioning unit. It is formed via bonds between the R groups of different amino acids within the polypeptide chains,

128
Q

what factors affect protein folding

A
  • Hydrogen bonds between groups form cooperatively:
  • Ionic interactions / salt bridges: strength increases if salt bridge formed within more hydrophobic interior of a protein
  • Disulphide bonds: additional covalent bonds that join together different parts of the polypeptide to help form the final 3-D structure of the protein.
129
Q

what are protein domains

A
  • Proteins may fold into multiple domains
  • Domains usually have a distinctive function or role.
  • Such roles include: DNA binding, protease, spanning plasma membranes
  • Domains can often be “found” in the primary sequence as SEQUENCE MOTIFS
130
Q

what are chaperone proteins?

A

proteins that help other proteins fold correctly

Foundations of health and disease (21 decks)

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