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Zoology Semester 1 > APS138 Cell And Molecular Biology - Leegood > Flashcards

APS138 Cell And Molecular Biology - Leegood Flashcards

1
Q

What is a glycosome?

A

A peroxisome involved in glycogen storage and metabolism

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2
Q

What is the volume and total membrane area of a hepatocyte?

A

5000 micrometres^3

110,000 micrometers^2

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3
Q

What percentage of the volume of the cytosol is protein?

A

20-30% (200mg.ml^1)

In choloroplasts the protein concentration is even higher (280mg.ml^1)

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4
Q

Why are cells so small?

A

Metabolism needs fuel from outside and produces waste products
Exchange is limited by surface area to volume ratios
Small cells are easier to turnover than large cells

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5
Q

How long does a protein take to traverse e.coli cytoplasm vs the cytoplasm of a mammalian cell?

A

~10ms vs

~10s

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6
Q

How are some cells specialised for high material exchange?

A

Surface area increased by microvilli and mitochondria abundant

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7
Q

What feature do Sarum canadense roots have for material exchange?

A

Mycorrhizal arbiscules

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8
Q

What adaptions may very large cells such as bubble algae have?

A

Coenocytic structure with multiple nuclei and chloroplasts and a large central vacuole

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9
Q

What do membranes allow within cells?

A

Compartmentalisation

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10
Q

Why do cells and organelles have compartments?

A

Different environments (pH for example)
Metabolic regulation by keeping enzymes, substrates and regulators in separate locations
Locally high metabolite concentrations
Sequestration of toxic substances

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11
Q

What pH do compartments of choloroplasts and mitochondria have and why?

A

Acidic pH to drive ATP synthesis

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12
Q

What is the nucleus for?

A

Genome, DNA replication, transcription, RNA processing

Compartmenting the genome from the cytoplasm allows regulation of gene expression (e.g. post-transcriptional processing, such as alternative splicing)

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13
Q

What is the cytoskeleton made up of?

A

Motor proteins and protein filaments

Protein filaments form a 3D mesh for rigidity shape and structure.
Motor proteins form trackways for movement

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14
Q

In muscle cells, how much of the total cell protein is comprised by actin?

A

10%

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15
Q

What are microtubules?

A

Cylindrical tubes (20-25nm diameter) of Tubulin. Highly dynamic

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16
Q

What are microfilaments and what are they for?

A

Actin fibres (3-6nm diameter)

For gliding, contraction and cell cleavage. With myosin are responsible for muscle contraction

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17
Q

What are microtubules for?

A

Determining cell shape, provide a trackway for movement of cell organelles and vesicles. Form spindle fibres in mitosis. Found inside cilia and flagella.

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18
Q

What are intermediate filaments?

A

Anchor and position nucleus and give cell flexibility (8-12nm diameter)

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19
Q

What are movers (motor proteins) powered by?

Include Kinesin, Dynein, myosin (muscle)

A

ATP

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20
Q

In which direction does kinesin travel in?

A

Towards ‘plus’ end away from the nucleus

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21
Q

Which direction does dynein travel in?

A

Towards ‘minus’ end towards the nucleus

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22
Q

What are melanocytes?

A

Cells used by fish, amphibians, crustaceans, cephalopods and reptiles to change colour

Motor proteins transport pigments in melanosomes along microtubule/actin tracts

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23
Q

How do microtubules aid cell wall synthesis in plants?

A

Cortical microtubules form a template for the deposition of cellulose in bands

Turgid driven growth is constrained along the axis of elongation

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24
Q

Cells produce molecules that have to be delivered to other places inside the cell, or exported out of the cell, at exactly the right moment. Where are these molecules parcelled within?

A

Vesicles

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25
Q

What does the RER do?

A

Synthesises proteins and packages them in vesicles

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26
Q

What does the SER do?

A

Synthesises lipids

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27
Q

What do transport vesicles do?

A

Takes proteins and lipids to Golgi apparatus

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28
Q

What does the Golgi apparatus do?

A

Modified lipids and proteins, sorts and packages them in vesicles

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29
Q

What vesicles travel to the cell surface membrane and expel materials?

A

Secretory vesicles

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30
Q

What do lysosomes do?

A

Contain digestive enzymes that break down cell parts or substances entering by vesicles

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31
Q

What proportion of genes code for proteins that enter the ER?

A

1/3

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32
Q

What must happen to proteins before they are transpired to targets?

A

They must be folded and modified correctly in the ER

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33
Q

Where does protein translocation occur in the ER membranes?

A

Translocation pores

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34
Q

What is removed while the nascent polypeptide is emerging into the ER lumen?

A

N-terminal signal peptide

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35
Q

What does nascent mean?

A

Emerging/ forming

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36
Q

What is the ER lumen specialised for?

A

Folding, assembly, modification, quality control and recycling of proteins

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37
Q

Name 2 examples of processes used to enhance protein stability before secretion in the ER

A

Disulphide bond formation and glycosylation

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38
Q

What is ER movement dependent on in plants vs animals?

A

Actin/myosin in plants

Microtubules in animals

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39
Q

What enables vesicles to dock and fuse with their target membranes precisely

A

A protein complex

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40
Q

In milk secretion what is the role of the Golgi apparatus?

A

Synthesis of lactose form Glc and UDP-Gal

Sorting and packaging

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41
Q

What is the main type of protein body used in plants, to store proteins and provide C, N and S for rapid growth?

A

Vacuoles

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42
Q

What type of plant contains ricin and what is ricin?

A

Castor bean seeds

A potent cytotoxin

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43
Q

What is ricin for and how does it work?

A

Anti-herbivory - inhibits protein synthesis by irreversibly inactivating eukaryotic ribosomes

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44
Q

Where in castor bean cells is ricin stored?

A

Protein bodies - when seed germinates, ricin is rapidly degraded

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45
Q

When is ricin not catalytically active until?

A

It is proteolytically cleaved within the protein bodies.

Plant thus avoids poisoning its own ribosomes

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46
Q

Demand for insulin will potentially double over the next 10 years. How much insulin is found in safflower and how many hectares would be required to meet the worldwide demand?

A

0.4kg.ha^-1

6,500 hectares

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47
Q

What happens to proteins that are incompletely or incorrectly folded (e.g. mutants)?

A

They are recognised and retained within the ER and targeted for degradation by lysosomes or proteasomes

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48
Q

What are chaperones?

A

Proteins that assist the correct intercellular folding and assembly of polypeptides

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49
Q

What does ERAD stand for?

A

Endoplasmic Reticulum-Associated protein Degradation

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50
Q

What is CFTR?

A

Cystic Fibrosis Transmembrane conductance Regulator - a chloride ABC transporter

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51
Q

In cystic fibrosis what do the epithelia lining sweat gland ducts fail to take up efficiently?

A

Cl from the lumen

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52
Q

What does lack of CFTR allow the accumulation of?

A

Mucus

- in the lungs, and in the pancreas, so digestive enzymes cannot get into the intestine

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53
Q

What does cystic fibrosis stop from happening during quality control?

A

The mutant protein from leaving the ER

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54
Q

Lack of Phe^508

A

70% of cystic fibrosis sufferers

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55
Q

In which types of organisms are vacuoles and lysosomes found?

A

Plant and fungal cells

Some protist, animal and bacterial cells

56
Q

What are lysosomes for?

A

Autophagy, lysis and recycling misfolded proteins

57
Q

What proportion of leaf epidermal cell volume is comprised by vacuoles and lysosomes?

A

99%

70% in leaf mesophyll cells

58
Q

What are vacuoles for?

A

Storage of carbohydrates, organic acids, anthocyanins, seed storage proteins

Isolation of toxic substances

Anti-herbivory (eg cyanogenic glycosides)

Maintaining internal hydrostatic pressure (turgor)

59
Q

How many species use cyanogenesis as a method of anti-herbivory?

A

3000 species

Including cassava - major source of calories for people in sub-Saharan Africa - chronic cyanide poisoning can occur

60
Q

Sorghum leaves

A

Hydrolysis of dhurrin occurs only after tissue disruption (by herbivory)

61
Q

A few species of insects are able to synthesise cyanogenic glycosides. E.g…

A

Larvae of the burnet moth sequester then from their food plants, storing them in viscous droplets in cuticular cavities.

Adult females release HCN as a pheromone to attract males. Makes give cyanogenic glycosides to females as gift during mating - helps females protect eggs

62
Q

What is the theory of how chloroplasts and mitochondria came from aerobic and photosynthetic bacteria called?

A

Endosymbiotic theory

63
Q

What are some similarities between prokaryotes and mitochondria and chloroplasts?

A

70S ribosomes
Binary fission
1 single circular chromosome containing DNA
Similar size (approx. 1-10micrometres)
Positive porins
Same initiating amino acid (N-formylmethionine)

64
Q

What evidence for endosymbiosis can be found in arabidopsis?

A

Genes for Cyanobacteria peptidoglycan (cell wall) synthesis still present

Cardiolipin

65
Q

What theory is suggested for why plastids often have many envelopes (membranes)

A

Secondary (Multiple) endosymbiosis

66
Q

How do sea slugs display similarities to endosymbiosis?

A

Ingest chloroplasts and can use for photosynthesis and survive for months without eating, running in “solar power”

67
Q

How many arabidopsis protein-coding genes were acquired from cyanobacteria?

A

~4,500 (18% of total)

Transfer of organelle DNA to nucleus, increasing nuclear complexity

68
Q

What does mitochondrial DNA code for?

A

rRNAs, tRNAs, 13 our of ~85 components of oxidative phosphorylation system

69
Q

What does chloroplast DNA encode?

A

About 80 genes: some rRNAs, tRNAs, ribosomal proteins, RNA polymerase subunits and some genes for photosynthesis

70
Q

Why is mitochondrial DNA inherited maternally (from the mother)?

A

Simple dilution (egg contains 100,000 to 1,000,000 mtDNA molecules, sperm contains only 100 to 1000)

Degradation of sperm mtDNA in the fertilised egg

Failure of sperm mtDNA to enter the egg

71
Q

How do proteins cross chloroplast membranes?

A

Most proteins are nuclear encoded. A signal peptide is a target sequence of amino acids that is recognised and cleaved by a signal peptidase at the chloroplast envelope

(2 signal sequences if also entering thylakoid membrane)

72
Q

What size are the ribosomes used to synthesise the large subunits in rubisco?

A

70S (chloroplast plastid DNA)
Chaperones are required
80S ribosomes in the cytoplasm are used to translate the pre-SS polypeptide which then enters the chloroplast as the small subunits, and rubisco is formed (L8S8)

73
Q

Name a plant without plastid genomes

A

Rafflesia lagascae

A parasite that has plastid-like structures but no intact genome

74
Q

The freshwater alga polytomella has…

A

A plastid but no trace of a plastid genome

75
Q

What are apicomplexa?

A

Parasitic single-celled eukaryotic organisms deriving from red algae, loss of plastids.
Malaria, toxoplasma, coccidiosis (loss to poultry industry worldwide)

76
Q

Plasmodium in malaria - still retains its plastid genome. How many membranes do its apicoplasts have?

A

4

Suitable target for drug treatments

77
Q

What has cryptosporidium lost?

A

Apicoplast

78
Q

Expressing a large genome is expensive. What do mitochondria contain for efficient energy generation in eukaryotes?

A

A large area of internal membranes

79
Q

What is an advantage of chloroplasts and mitochondria?

A

They expand and diversify the genome in eukaryotes

Mitochondria increased number of cel proteins by 4-6 orders of magnitude

80
Q

List functions of proteins

A

Catalysis (enzymes)

Energy production (light harvesting, electron transport, rotary ATPases)

Host/pathogen interaction: antibodies, mucus

Structural: keratin, collagen

Motion: cytoskeleton, muscle, flagella

Organisation of DNA and regulation: histones

Regulation: kinases

Storage: seeds and eggs

Toxins and venoms

Transport: membrane proteins, haemoglobin

81
Q

What do proteins consist of?

A

Chains of amino acids joined by peptide bonds

82
Q

What does the polypeptide protein backbone have?

A

Amino acid side chains (may be polar or non polar)

83
Q

How many amino acids with different side chains with different properties are there?

A

20

The polypeptide backbone is identical in all proteins

84
Q

What do side chains determine?

A

How the polypeptide chains of the protein interact and how the protein is folded

85
Q

How many levels of structural organisation are there in proteins?

A

4

86
Q

What does the quarternary structure involve?

A

The association of two or more polypeptides into multi-subunit complexes

Rubisco has 16 subunits

87
Q

Where are h bonds found in a helices?

A

Between side chains within the same polypeptide

88
Q

Where are I bonds found in ß pleated sheets?

A

Between different polypeptide chains

89
Q

Sulfide bonds can be interchain or intrachain

A

Yes they can joey well done!

90
Q

What processes may proteins go through to increase their stability before secretion?

A

Sulfide bond formation and glycosylation

91
Q

In the cytosol the gluthione reduction potential is…

A

Reducing

92
Q

What is mucin?

A

A glycosylated protein used to produce mucus.

Large extracellular glycoproteins with hundreds of oligosaccharide chains linked to a protein backbone.

Either anchored or secreted

93
Q

What does high glycosylation mean for mucin

A

It is resistant to acids (stomach acid), proteolysis, adds gel like properties found in mucosal barriers

94
Q

What percentage of the amino acids in keratin are cysteine?

A

25%

95
Q

What gives keratin polypeptide chains great stability?

A

Disulfide bridges (cross linkage of chains)

96
Q

What is the major extracellular insoluble fibrous protein and most abundant protein in animals

A

Collagen

97
Q

What is collagen for?

A

Helps tissues withstand stretching

98
Q

What happens to collagen if there is an absence of vitamin c (ascot if acid)?

A

Helices cannot form, blood vessels, tendons and skin become fragile, leading to scurvy

99
Q

What makes silk so strong in structure and tensile strength?

A

High glycine content, small non-polar side chains allowing for tight packing of the anti parallel ß sheets

100
Q

What happens to silk when water is present?

A

It is stored as an emulsion as the C-terminus ensures solubility and the core is hydrophobic.
It can be spun into a thread when water is absent

101
Q

What does gluten form (that traps CO2 bubbles)?

A

A matrix

Gluten proteins are linked by hydrogen bonds and disulphide bridges

102
Q

What are enzymes?

A

Proteins folded into complex shapes that allow substrate molecules to fit into the active site

They do not change during reactions, they simply facilitate the interaction of reactants and speed up the rate of the reaction.
They are the most powerful and selective catalysts known.

103
Q

What do nucleases do?

A

Break down nucleic acids by hydrolysing bonds between nucleotides

104
Q

What do synthases do?

A

Synthesise molecules by condensing two small molecules

105
Q

What do isomerases do?

A

Rearrange bonds within a single molecule

106
Q

What do kinases do?

A

Add phosphate to molecules (eg sugars or proteins)

107
Q

What do phosphatases do?

A

Remove phosphate group

108
Q

What is the total number of enzymes in a person?

A

Approx 75,000

109
Q

What percentage of plant enzymes have unknown functions?

A

60%

110
Q

How is enzyme protein abundance regulated?

A

Transcription and translation

111
Q

How does the cell regulate the catalytic activity of enzymes?

A

Direct fine-tuned control of protein activity and kinetics by metabolites and regulators

Specific post-transcriptional modification

Transcription and translation regulation

112
Q

How many types of post-translational modifications are there?

A

Over 300

113
Q

What are the two types of repression for the tryptophan pathway?

A

Inhibit activity of the first enzyme in the pathway (rapid response)

Depress expression of the genes for all the enzymes needed for the pathway (longer-term)

114
Q

Name some types of PTMs

A

Addition of functional groups - phosphorylation, glycosylation

Structural changes - reduction/oxidation

Changes to amino acids

Addition of proteins or peptides - ubiquitunation can increase protein lifespan and stability

Some PTMs are fixed for the life of the protein, while other changes are reversible

115
Q

Many proteins have two or more different functions, for example…

A

Some crystalline, structural proteins in the lens of the vertebrate eye, are also metabolic enzymes. E.g. duck crystalline is lactate dehydrogenase.

Aconitase in man is both an enzyme of the Krebs cycle and involved in iron homeostasis

Called moonlighting proteins

116
Q

Extended aerobic respiration required a regulated supply of…

A

Carbon from glycogen and lipids

117
Q

How many glucose units in a glycogen granule around its core protein of glycogenin?

A

Approx 30,000

118
Q

What advantages does branching give glycogen?

A

More soluble

Exposure of more C4 ends means that glycogen can be both synthesised and degraded more quickly than a single starch chain with the same number of residues

119
Q

What percentage of the arabidopsis genome is protein kinases?

A

5.5%

120
Q

Name 3 hormones controlling glycogen metabolism in mammals.

A

Insulin, glucagon, adrenaline

121
Q

Why is glucagon and adrenaline action selective?

A

Only liver cells have receptors

122
Q

What are glucagon and insulin used to do?

A

Maintain a constant concentration of blood glucose ~5mM

123
Q

What is glycogen synthase b?

A

Phosphorylated (by protein kinase a) and inactive

124
Q

What is protein kinase A activated by?

A

cAMP (formed by adenylyl Cyclades pathway)

125
Q

Why is transport necessary in eukaryotic cells?

A

Metabolism needs fuel and produces waste products.
Organelles must be able to transport materials to and from the cytosol.
Proteins need to be seceted.
Signalling within and between cells

126
Q

What are gap junctions?

A

Channel proteins (connexins in vertebrates, innexins in invertebrates) for the rapid exchange of ions and metabolites between cells

127
Q

How many connexins are in the human genome?

A

~20

128
Q

What are plasmodesmata?

A

Gaps in the cell walls of plants that allow trnasport of materials between cells (as cell walls are impermeable to most substances) - enable cytoplasmically interconnected fields of cells called symplasm.

There is also a tubule of ER that passes through plasmodesmata

129
Q

Which types of molecules easily pass through the phospholipid bilayer?

A

Hydrophobic molecules, very small uncharged polar molecules (H2O)

130
Q

What are aquaporins?

A

Membrane channels for transport of water, glycerol, CO2 etc.
An extremely hydrophobic protein
They facilitate the diffusion of small uncharged molecules (water, glycerol, urea, CO2)
Occurence correlates with high water fluxes (e.g. kidney)
Activity can be regulated by phosphorylation

131
Q

what are the 3 ways of driving active transport?

A
  • Coupled transporter
  • ATP-driven pump
  • Light-driven pump (e.g. halobacteria)
132
Q

What do P-type pumps (P-ATPases) transport?

A

Specific ions e.g. H+, Na+, K+, Mg2+, Ca2+.

One or two polypeptides (less than rotary ATPases)

133
Q

What do ATP-Binding Cassette (ABC) transporters transport?

A

lipids and sterols, ions and small molecules, drugs and large polypeptides
e.g. Cystic Fibrosis transmembrane conductance regulator (CFTR) is an ABC Cl- trnasporter

134
Q

What do rotary ATPases transport and why?

A

H+ pumps with a role in energy conversion

135
Q

Ion channels can be opened by different stimuli, including….

A

Voltage, temperature, pH, stretch, ligands

Zoology Semester 1 (16 decks)

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