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Sport Science Y1S1 > Biochemistry + Cell Biology > Flashcards

Biochemistry + Cell Biology Flashcards

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1
Q

What are isotopes?

A

Molecules with the same chemical formulae but different structural formulae
- different numbers of neutrons
- are naturally occurring + many are radioactive

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2
Q

What does it mean that isotopes are radioactive?

A

They decay spontaneously but remain stable

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3
Q

What can radioactive isotopes be used to determine?

A

(14C) can be used to determine the age of organic artefacts = radiocarbon dating
- measures decay of 14C by its fixed half life

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4
Q

What is the simplest form of carbohydrates?

A

Saccharides
1 saccharide present = monosaccharide

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5
Q

What are monosaccharides used for and what is their chemical formulae? List some examples

A

Used for cellular energy and building nucleic acids
- (CH2O)n where n = 3/5/6
- glucose, fructose, galactose

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6
Q

Name of carbohydrate when there are…
1. 2 saccharides present
2. 3-10 saccharides present
3. >10 saccharides present

A
  1. Disaccharide
  2. Oligosaccharide
  3. Polysaccharide (starch)
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7
Q

List the key disaccharides and what they are formed of

A

Sucrose = glucose + fructose

Lactose = glucose + galactose

Maltose = 2x glucose

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8
Q

What causes a lactose intolerance?

A

Lactose is not broken down by lactase + utilised by gut flora

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9
Q

What are the main uses of lipids?

A
  • long term energy storage
  • protection/ insulation
  • neuron myelination
  • absorption of fat-soluble vitamins (A,D,E,K)
  • hormone production (oestrogen, testosterone)
  • cell membranes (lipid bilayers)
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10
Q

What is the simplest forms of lipids?

A

Fatty acids compounds which are organic chains with a functional carboxyl group
E.g. butyric acid (butanoic acid) = 4 carbon atoms or palmitic acid (hexadecenoic acid) = 16 carbon atoms

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11
Q

What are the 3 sub-groups of lipids?

A

Triglyceride
Phospholipids
Sterols

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12
Q

What are triglycerides?

A

Glycerol backbone with 3 bonded fatty acids (carboxyl to hydroxyl group bond)
- can be saturated (all single carbon bonds) or unsaturated (at least 1 carbon double bond)

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13
Q

What are the 2 geometries that doubles bonds can be in triglycerides?

A

Cis = same side of double bond
Trans = opposite sides of double bonds

  • trans fats = linked to increased cholesterol levels + onset of CV diseases
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14
Q

What are phospholipids?

A

Glycerol group with associated phosphate group and only 2 fatty acids
- arranged into bilayers = help transport of fats in blood
- have a hydrophilic head + hydrophobic tail

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15
Q

What are sterols?

A

Cyclic organic compound found in grains, nuts, seeds etc
- sub group of steroids e.g. cholesterol

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16
Q

What are proteinogenic amino acids?

A

Amino acids found in nature - only 20 genetically encoded in DNA
- vital in formation of enzymes, antibodies, hormones, structural proteins + receptors

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17
Q

What is the structure of proteins?

A

Made up of a long chain of alpha amino acids joined by peptide bonds (written N-terminus to C-terminus)

  • all have same configurations - L-alpha-amino acids (apart from glycine so no chirality)
  • peptide bond between carboxyl + amine groups
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18
Q

List and describe the 4 levels of protein structure

A

Primary: amino acid sequence from N- to C- terminus

Secondary: alpha helix + beta sheets via hydrogen bonding

Tertiary: overall protein conformation caused by side chain interactions (folding of polypeptide chain into 3D shape)

Quaternary: higher order structure e.g. dimers (multiple subunits joined)

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19
Q

What is an alpha helix?

A

Each C=O (residue i) forms a hydrogen bond with the amide hydrogen of residue i + 4
- formed between the carboxyl + amino groups

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20
Q

What is a beta sheet?

A

The angular conformation of a peptide chain causes a ‘zig-zag’ shape
- backbone is able to form hydrogen bonds between each segment
- exist in either a parallel or anti-parallel structure

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21
Q

What is avogrados constant + what does molar conc refer to?

A

6.02 x 10^23 = 1 mole

  • molar conc refers to the number of moles of a substance in a defined volume
  • where 1 mole of a molecule is always its molecular weight in grams
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22
Q

What are the 3 main functional groups of compounds?

A
  1. Hydroxyl (OH)
  2. Amine (H2N)
  3. Carbonyl (COH)
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23
Q

What is an aromatic ring + pi pi stacking?

A

Every other carbon has a double bond
- very stable structures
- many amino acids have these

Pi Pi stacking is when aromatic rings slightly offset each other so don’t repel

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24
Q

List the equations linking mass, molecule weight (MW), moles

A

Mass = molecular weight x moles

Molecular weight = mass / moles

Moles = mass / molecular weight

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25
Q

Define the 1st Law of Thermodynamics

A

The total amount of energy within a system and its surroundings is constant

Energy can neither be created nor destroyed

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26
Q

Define the 2nd Law of Thermodynamics

A

The total entropy (level of disorder) of a system and its surroundings always increases

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27
Q

Define the 3rd Law of Thermodynamics

A

The entropy of a system approaches a constant value when its temperature approaches absolute zero

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28
Q

What do the terms system and surroundings refer to in the laws?

A

System = whatever part of the universe we are interested in
- closed = cannot exchange matter across boundaries
- open = can pass matter back and forth

Surroundings = everything that surrounds the system

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29
Q

What is enthalpy + give the equation

A

Enthalpy is the heat storage capacity of a system

Enthalpy = internal energy + (pressure x volume)
H (J or J/mol) = E (J) + (P (Pa) x V (m3))

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30
Q

What are exothermic and endothermic reactions?

A

Exothermic = release of heat energy during a reaction

Endothermic = heat energy is absorbed during a reaction

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31
Q

What does entropy refer to?

A

Refers to the level of disorder in a system (how energy is distributed)

Solid = low entropy
Liquid = entropy increasing
Gas = high entropy

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32
Q

What is Gibbs Free Energy (G)? Give the equation

A

The amount of energy available to do work
- tells us if a biochemical process will occur on its own (spontaneously or not)

Gibbs Free Energy (kJ/mol) = change in enthalpy (J) - (Temperature (K) x change in entropy (J/K))

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33
Q

What does it mean when…
G < 0
G > 0

A

When G < 0 = a spontaneous process

When G > 0 = not a spontaneous process

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34
Q

What’s the conversion for degrees C to Kelvin

A

37 degrees = 310 Kelvin

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35
Q

What are coupled reactions for?

A

Fundamental to metabolism
- reaction cannot occur spontaneously if G is > 0 so an energy input is required

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36
Q

What are the 2 types of coupled reactions + give the examples?

A

Anabolic reaction = constructing molecules from smaller units
- 2 x glycine = glyclglycine
- endergonic (unfavourable)

Catabolic reaction = breaking down molecules to form smaller subunits
- ATP + Water = ADP + Pi
- exergonic (favourable)

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37
Q

What do activated carriers do (thermodynamics)?

A
  1. Energy released by oxidation of organic molecules can be stored, preventing it being lost as heat
  2. Energy is stored in activated carriers, as either transferable chemical group or electrons
  3. Then used for endergonic reactions or other cell activities
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38
Q

What is ATP? - not the acronym but what does it drive etc

A

Most important activated carrier molecule
- the phosphorus-oxide bonds assists in storing lots of energy
- drives non-energetically favourable (endergonic) reactions in our body

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39
Q

What are the energy losses/ gain from ATP re-synthesis + hydrolysis?

A

ATP re-synthesis:
- G = +30.5 kJ/mol

ATP hydrolysis:
- G = -30.5 kJ/mol

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40
Q

How do cells obtain energy?

A

Via the oxidation of organic molecules (food)
- energy is stored in covalent bonds of these organic molecules

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41
Q

What do the terms oxidation + reduction mean?

A

Oxidation = removal (loss) of electrons from a molecule

Reduction = addition (gain) of electrons from a molecule

  • electrons are never lost, so if one molecule is oxidised, the other must be reduced
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42
Q

What are NADH + NADPH + what are they involved in?

A

NAD+ = nicotinamide adenine dinucleotide

NADP+ = nicotinamide adenine dinucleotide phosphate

  • they pick up energy in the form of 2 high energy electrons and a proton (a hydride ion H-)
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43
Q

What type of proteins are enzymes?

A

Globular proteins - polypeptide chain folds up into a compact shape, like a ball, with an irregular surface
- their tertiary / quaternary structures are quite complex

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44
Q

What are the active and inactive forms of enzymes called?

A

Active = holoenzyme

Inactive = apoenzyme

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45
Q

Briefly explain enzymes involvement in diseases

A

A malfunction in enzyme activity disrupts homeostasis

  • DNA mutations resulting in under or overproduction/ deletion in a single critical enzyme results in disease
  • a single amino acid substitution = destabilise protein structure/ disrupt binding etc
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46
Q

What are the 2 key theories of enzyme binding?

A
  1. Lock + Key Model = geometric complementarity, considered rigid + fixed
  2. Induced Fit Model = induces a conformational change on binding (more supported)
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47
Q

What determines substrate specificity?

A

Amino acid residues

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48
Q

What are the 2 sites of binding?

A

Active site - non-polar environment that enhances binding

Allosteric site - induces a conformational change as mechanism of regulation

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49
Q

Define the following terms…
1. Cofactor
2. Coenzyme
3. A prosthetic group

A

Cofactors = any factor essentially required for enzyme activity or protein function (inorganic)

Coenzyme = cofactor which is directly involved in enzyme catalysed reaction (organic)

A prosthetic group = covalently associated non-protein constituent required for a particular function

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50
Q

What is the common enzyme inorganic cofactor?

A

Metal co-factors otherwise called metalloenzymes
- cannot function without a metal ion in active site

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51
Q

What is an example of co-enzyme deficiency?

A

Scurvy - connective tissue disease due to lack of vitamin C

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52
Q

What is the transition state in relation to enzymes reaction?

A

Transient molecular state that is no longer substrate, but not yet product

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53
Q

Name some factors that cause activation energy to be lowered

A

Binding

Spatial + chemical complementarity

Induced fit

Specific amino acid R-groups

Orientation

Microenvironment (hydrophobic so no water)

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54
Q

Describe the 4 main catalytic mechanisms

A
  1. Metal ion catalysis - metal ions in active site
  2. Covalent catalysis - covalent bond between substrate + enzyme
  3. Catalysis by approximation - easier as come closer together
  4. Acid-base catalysis - use side chains to catalyse (chymotrypsin)
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55
Q

What is the equation for enzyme kinetics?

A

Rate of reaction is called velocity (V0)

= amount of substrate (S) converted to product (P) per unit of time

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56
Q

Describe the rules about the relationship between S and V0 (enzyme reaction rates)

A

Doubling S also doubles V0

Enzyme saturation means no further increase in V0

Reaction rate dependant on P dissociation from enzyme

Double E will double V0

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57
Q

Describe the Michaelis- Menten graph (enzyme kinetics)

A

Shows substrate conc on X against reaction rate on Y
- Vmax = highest rate of reaction
- Km (michaelis constant) is half Vmax and is a measure of enzyme affinity for substrate
- a low Km indicates weak binding and vice versa

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58
Q

What is the effect of increasing temp + pH on enzyme activity?

A

Rise in temp = increased thermal energy = overcome activation energy = increase in rate

Beyond optimal temp = breaks multiple weak bonds = alters active site = denaturation

(pH)
Small deviations results in decrease activity (ionisation of groups in active site)
- large deviations - denaturation

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59
Q

What are the 3 types of reversible inhibitors for enzymes?

A

Competitive
Non-competitive
Uncompetitive

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60
Q

How do competitive inhibitors work?

A
  • they have some affinity for active site
  • similar shape/ binding properties as substrate
  • substrate is competing for access to active sites
  • therefore reduced rate of activity
  • can be overcome by increasing substrate levels
  • Km increases but Vmax stays same
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61
Q

How do non-competitive inhibitors work?

A

Binds to allosetric site
- conformation of active site changes so substrate cannot bind

Km stays the same but Vmax is reduced

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62
Q

How does a uncompetitive inhibitor work?

A

Binds only when enzymes-substrate complex is formed
- binds to allosteric site

Vmax is much lower + Km is lower
- so enzyme has better affinity for substrate (substrate is always bound to active site)

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63
Q

What are the 3 other types of regulation of enzyme activity?

A
  1. Reversible covalent modification
  2. Proteolytic activation
  3. Apoptosis (programmed cell death)
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64
Q

What is glycolysis, where does it occur?

A

Oxidation of sugars

  • occurs in cytosol of cells
  • ATP is used in reactions 1 + 3 to phosphorylate the sugar + couple the reaction to make it energetically favourable
  • NAD is reduced
  • steps 1-5 = energy investment phase
  • steps 6-10 = energy generation phase
  • end with 2 molecules of pyruvate
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65
Q

Key Step

Explain step 3 of glycolysis - (PFK)

A

PFK (phosphofructokinase) is the most important regulatory + rate limiting enzyme in glycolysis (allosteric enzyme)

  • activated by AMP + F 2, 6 BP and is inhibited by ATP, low pH + citrate
  • low activity of PFK = slower glycolysis + vice versa
  • causes shift in graph to left = more active PFK
  • ATP is broken down to form ADP + Pi in this step
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66
Q

Key Step

Explain step 6 of glycolysis

A
  • enzyme 1 binds to G3-P + catalyses its oxidation
  • NAD+ accepts the electrons and is reduced
  • enzyme 1 becomes displaced by Pi to create a high energy sugar-phosphate (1,3-biphosphoglycerate)
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67
Q

Key Step

Explain step 7 of glycolysis

A
  • the sugar-phosphate intermediate binds to enzyme 2 which catalyses the transfer of Pi to ADP, creating ATP + generates carboxylic acid (3-phosphoglycerate)
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68
Q

(Extra Step 11 of glycolysis)

What happens when no O2 is available as an electron acceptor

A

NAD+ must be regenerated for glycolysis to continue
- When no O2 is available to act as an electron acceptor, NADH passes electrons to pyruvate which forms lactate

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69
Q

What is the net ATP gain of glycolysis?

A

2 ATP

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70
Q

After glycolysis, where do the products of pyruvate go?

A

Moves into the mitochondria where it is decarboxylated to form acetyl CoA

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71
Q

How are fats (lipids) oxidised to form acetyl CoA?

Beta Oxidation

A
  • Fatty acyls (FA’s) are converted to fatty acetyl CoA + transported to mitochondria
  • then enters beta oxidation
  • this is a series of 4 enzymatic reactions which reduced the number of carbons on fatty acyl CoA (2 per decarboxylation)

= produces acetyl CoA, 1 NADH + FADH2
- continues until fatty acid is completely degraded

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72
Q

Describe the TCA (KREBS) Cycle

A
  • Acetyl CoA (2C) is transferred to a 4C oxaloacetate to form the 6C tricarboxyllic acid (citric acid)
  • following series of 8 reactions (4 oxidation) regenerate oxaloacetate
  • energy release is captured in… 3xNADH, 1xFADH2, 1xGTP
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73
Q

How can the TCA cycle be controlled?

A

2 enzymes can be allosterically regulated…

  • isocitrate dehydrogenase = stimulated by ADP, NAD+ and inhibited by ATP + NADH
  • alpha ketoglutarate = stimulated by ADP and inhibited by succinyl CoA, ATP + NADH
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74
Q

Where does amino acid metabolism occur + what parts of amino acid are used to generate energy?

A

At the liver

  • amino acids can be degraded + used as fuels
  • nitrogen (amine group) cannot be used to generate energy so must be removed = leaving carbon skeleton for use
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75
Q

Step 1 amino acid metabolism

Explain transamination

A

Amino group of amino acid is transferred to keto acid
- typically then transferred to alpha ketogluterate
- this is accepted by the first keto carbon
(catalysed by enzymes called aminotransferases)

  • oxaloacetate (another keto acid) can also accept the amino group
  • this forms aspartate = required for urea formation + can be transaminated to form glutamate
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76
Q

Step 2 of amino acid metabolism

Explain deamination

A

(Glutamate has amino group)

  • amino group is removed = deamination
  • redox reaction catalysed by glutamate dehydrogenase
  • removal of amino group as ammonia (TOXIC)
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77
Q

After ammonia is formed in mitochondria, what happens to it?

A

UREA CYCLE

  • apartate comes from transamination reactions
  • fumerate can be used in TCA cycle or to generate glucose
  • urea enters blood + is transported to kidneys
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78
Q

What happens to the carbon skeletons?

A

Start with 20 amino acids

  • 7 become metabolic intermediates
  • Leu + Lys become ketogenic amino acids
  • Ile, Phe, Try + Tyr = Keto + glucogenic amino acids
  • glucogenic amino acids = 14 other amino acids
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79
Q

Some amino acid metabolism occurs in the muscle…

Glucose-Alanine Cycle

A

Muscle used BCAAs for fuel during prolonged exercise
- muscle doesn’t have urea cycle (no enzymes for it)

So buildup of glutamate causes alanine to be formed
- alanine is released into blood + taken up by liver
- alanine is transaminated + amino group is removed

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80
Q

What is gluconeogenesis?

A

Formation of glucose from non-carbohydrate sources

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81
Q

What are the main non-carb precursors for gluconeogenesis?

Where does it occur?

A

Lactate, glucogenic amino acids + glycerol

Occurs in liver = responsible for maintaining blood glucose
- essentially reversal of glycolysis = energetically favourable

82
Q

Why do we have mitochondria?

A

Endosymbiosis
- prokaryote grows
- plasma membrane forms infoldings + pinches off in places forming membrane around organelles/ endomembrane system
- engulfs aerobic bacterium

83
Q

What makes mitochondria special - what do they have?

A
  • own genome
  • own symbiotic machinery = making RNA + proteins
84
Q

Describe the mitochondrial genome

A

Single circular chromosome in mitochondrial matrix
- 37 genes in total (2 rRNA, 22 tRNA, 13 protein encoding)
- mitochondrial DNA = oocytes

85
Q

What’s do the terms fusion and fission mean?

A

Fusion = join

Fission = break apart

86
Q

How are proteins transported into mitochondria?

A

Must have signal sequence to go into mitochondria
- enter via translocases of outer + inner membrane = TOM/TIM

  1. Signal sequence binds to import receptors
  2. Insertion into membrane by TOM complex
  3. Translocation into matrix by TIM23 complex
  4. Cleave by signal peptidase
87
Q

How does pyruvate move into mitochondria?

A

Mitochondrial membrane contains porins (small channel proteins)
- pyruvate passes into matrix via mitochondrial pyruvate carriers

88
Q

How do fatty acids move into mitochondria?

A

Beta oxidation cycles
- acyl-CoA combines with carnitine in cytosol to form acyl-carnitine
- this can move into inter membrane space from cytosol via CPT1
- then moves into matrix via a translocase + breaks apart releasing acyl-CoA

89
Q

How does NADH move into the mitochondria?

A

Malate aspartate shuffle
1. NADH is oxidised to NAD via malate dehydrogenase
2. Oxaloacetate is reduced to form malate
3. Malate can pass from cytosol to inner mitochondrial matrix via porins
4. Inside mitochondria, malate is dehydrogenated to form oxaloacetate which reduces NAD to NADH

90
Q

Give a brief overview of the electron transport chain - what enters, what is formed etc?

A

Involves 4 protein complexes
- high energy electrons, carried by NADH + FADH2, are passed into ETC + accepted by series of carriers
- high energy electrons lose energy as are passed along chain
- energy is used to pump protons (H+) across inner membrane of mitochondria
- oxygen accepts electrons, forming water

91
Q

Explain what occurs at complex 1 of ETC

A

Called NADH-CoQ reductase (largest complex)
- NADH transfers its electrons into complex 1
- complex 1 passes electrons along with 2H+ to CoQ to form CoQH2
- energy released is used to pump 4H+ across membrane into inter membrane space

92
Q

Explain what occurs at complex 2 of ETC

A

Called succinate-CoQ reductase
- (step 6 of TCA cycle) - succinate is oxidised to form fumerate + FADH2
- FADH2 remains coupled to succinate dehydrogenase + then immediately passed into complex 2 to Fe-S clusters
- electrons are ultimately passed to CoQ along with 2H+ to form CoQH2
- FAD is recycled
- H+ are not pumped across membrane as not enough energy is released

93
Q

Explain what occurs at complex 3 of ETC

A

Called cytochrome c reductase
- CoQH2 from either complex 1/2 donate their electrons to complex 3 via Fe-S clusters and then to cytochromes
- the 2 protons are released into intermembrane space
- each electrons is passed to a cytochrome c = 2 reduced cytochrome c molecules being formed
- energy released pumps 2 more H+ across membrane

94
Q

Explain what occurs at complex 4 of ETC

A

Called cytochrome c oxidase
- 4 electrons enter at complex 4 which couple with 4 protons + some oxygen to form 2 molecules of water
- 2 x electrons per NADH (2 cytochrome c carriers) = accepted by 1/2 oxygen + 1 proton = water ^^^

95
Q

Describe the steps of oxidative phosphorylation + ATP synthase role

A
  1. Protons enter ATP synthase through F0 region
  2. Protons move to c subunits of F0 causing them to rotate (mechanical energy) then exit into matrix
  3. In turn, the y subunit (shaft) rotates very quickly
  4. ADP + Pi bind to specific sites between alpha + beta subunits
  5. When the y subunit rotates it causes a conformational change to F1 region + catalyses formation of ATP from ADP + Pi
96
Q

List some key functions of plasma membranes

A
  • physical + chemical barrier
  • communication
  • recognition
  • energy conversion
  • platform for cellular processes
97
Q

Describe the structure of plasma membrane

A

Very thin film of lipids + proteins held via non-covalent interactions
- impermeable barrier to water soluble (polar) molecules
- phospholipids = amphipathic
- two HYDROPHOBIC fatty acid chains + a phosphate containing HYDROPHILIC head

98
Q

What are fatty acids?

A

Long hydrocarbon chains with a carboxyl end (COOH) and a methyl end (CH3)
- can be free or covalently bonded to glycerol via ester linkage

99
Q

What are some other types of membrane lipids?

A

Sterols (cholesterol) = rigid rings attached to hydroxyl group + short fatty acid

Sphingolipids = sphingosine backbone (first carbon attached to fatty acid + second attached to amine group)

100
Q

What is important about polar/ non-polar molecules regarding thermodynamics in lipid bilayers?

A

Polar molecules can dissolve = energetically favourable, more disordered = increased entropy

Non-polar molecules cannot dissolve = energetically unfavourable, more ordered = decreased entropy

101
Q

How do lipid bilayers form?

A

The amphipathic nature

  • to avoid water forming cage structures around hydrophobic regions, the hydrophobic tails cluster together, exposing only the hydrophilic head to water
102
Q

What can regulate the fluidity of lipid bilayers?

A
  • Cis double bond make phospholipids more difficult to pack together + makes it thinner
  • cholesterol
103
Q

What are lipid rafts in membranes?

A

Locations in membranes that are more rigid than rest of membrane
- Van der Waals interactions are not strong enough to hold molecules together
- sphingolipids have long + saturated fatty acid chains and the attractive forces are strong enough to hold adjacent molecules together = rafts

  • proteins often congregate here in prep for vesicular budding + transport
104
Q

What are glycoproteins, glycolipids + glycocalyx?

A

Glycoproteins = proteins glycosylated in RER + golgi
Glycolipids = lipids from SER glycosylated in Golgi
- always found on the non-cytoplasmic side of membrane

= forms a CHO coating to the membrane termed the glycocalyx = protective

105
Q

What are the 2 types of membrane proteins?

A

Transmembrane proteins
- spans membrane only once (single pass)
- e.g. alpha helix / beta sheet

Peripheral membrane proteins
- span membrane multiple times (pores/channels) = multi pass
- embedded in membrane
- or covalently bonded to lipid in membrane

106
Q

What are the 4 groups of molecules and their transport across membranes?

A

Hydrophobic molecules = non-polar so can dissolve in bilayer + diffuse across

Small, uncharged polar molecules = OK to move across, just very slowly

Large, uncharged, polar molecules = need a transporter of some sort

Ions = need specialist mechanism

107
Q

Explain the difference between carrier and channel proteins

A

Carrier = bind a solute + undergo a conformational change to transfer across membrane

Channel = interact only weakly with a solute - form an aqueous pore that solutes can pass through quickly

108
Q

What are the 2 mechanisms by which eukaryotes carry out active transport?

A
  1. Coupled carriers (secondary active transport)
    Symporters
    - uses stored energy from electrochemical Na+ gradient + free energy released from transport of Na+
    - energy is used to pump glucose in same direction (against conc gradient)
    Antiporters
    - transport solutes in different directions e.g. aspartate cycle
  2. ATP driven pumps (primary active transport)
    - Na+/K+ pump
    - uses free energy released by ATP hydrolysis to pump 3Na+ out of cell + 2K+ in to cell
109
Q

How is the acidity in a lysosome maintained?

A

Through pumping H+ ions across the membrane via an ATPase pump

  • example of active transport
110
Q

What are the 3 kinds of gated ion channels?

A

Voltage gated = open/close via stimulation from neurons

Ligand-gated = open/close via binding of ligand

Mechanically gated = open/close based on physical disruption

111
Q

What is a cytoskeleton?

A

A large dynamic network of protein filaments that supports the cell

112
Q

What are the 3 main functions of the cytoskeleton?

A

Shape - cell shape, position of organelles, organisation of cytoplasm

Strength - prevents cell from being damaged

Movement - provides a mechanism by which things can move within a cell + by which cells themselves can move

113
Q

What are the 3 main types of protein filament in cytoskeleton + their roles?

A

Actin filaments = shape of cells surface, whole-cell locomotion, pinching one cell into two

Microtubules = position of organelles, intracellular transport, mitotic spindles

Intermediate filaments = mechanical strength

114
Q

Explain the role of cytoskeletal filaments in the small intestine

A
  • actin filaments enable microvilli formation (important for absorption)
  • also creates a physical barrier by connecting to cell junctions
  • Intermediate filaments anchor across the cell providing structure + strength via cell junctions called desmosomes
  • microtubules run from basal to apical surfaces providing a intracellular transport network (polarity)
115
Q

How are actin filaments formed?

A

By polymerisation of globular actin monomers (G-actin)
- non covalent bonds between adjacent molecules (dimer, then a trimer)
- the monomers form a protofilament
- 2 protofilaments twist to form a helix (F-actin)

  • F-actin has a large cleft where ATP binds
116
Q

What is nucleation?

A

The first step in the formation of a new structure via self-assembly

  • 2 ATP G-actin subunits bind to each other weakly
  • when 3 ATP G actin subunits form a trimer it acts as a nucleus from which a larger filament can form
  • polymerisation + depolymerisation can occur at both ends but assembly is preferred at + end and disassembly at - end
117
Q

What does treadmilling refer to?

A

Subunits are added much faster at + end and dissociate much faster at - end due to differences in Cc
- causes + end to grow and - end to shrink
- the overall length of the F-actin therefore remains constant = essential for cell motility + alterations in cell shape

118
Q

What are the 2 types of protrusions that are important in actins role in cell motility?

A
  1. Lamellipodia = actin filaments in branched network
  2. Filopodia = narrow, finger like protrusions where actin filaments are in bundles
119
Q

How are microtubules formed?

A

By the polymerisation of tubulin heterodimers consisting of alpha tubulin and beta tubulin

  • non-covalent bonds between alpha + beta tubulin
  • tubulin subunits form protofilaments
  • 12 protofilaments form long hollow cylinders with a central lumen = essential for intracellular trafficking
120
Q

What gives microtubules polarity (cell shape)

A
  • beta tubulin exposed at + end
  • alpha tubulin exposed at - end
121
Q

Explain what is meant by dynamic instability regarding microtubules

A

Driven by the rate of tubulin addition + rate of GTP hydrolysis in beta tubulin

  • if rate of GTP hydrolysis is greater than rate of tubulin addition = formation of a curved shape
  • tubulin GDP dissociation is favourable + tend to extend/ shrink from + end
  • the - end is stabilised at the microtubule organising centre (MTOC)
122
Q

What is the MTOC actually called for microtubules?

A

The centrosome
- the - end remains anchored to the centrosome
- consists of 2 features = a pair of centrioles + pericentriolar material (matrix of proteins)

123
Q

Describe what pericentriolar material is

A

The most important component in the synthesis of microtubules

  • contains the amorphous material (a disorganised area of proteins)
  • as well as containing the gamma-tubulin ring complex (y-TURC)
  • y-TURC = multiple copies of y-tubulin complexed with numerous other proteins and is the specific site of nucleation for microtubules
124
Q

What are the 2 associated motor proteins responsible for movement along microtubules?

A
  1. Kinesin = moves towards the + end of microtubules = Anterograde (away from centre)
  2. Dynein = moves towards the - end of microtubule = Retrograde (towards centre)
125
Q

Describe the 6 step process of intracellular trafficking (microtubules)

A
  1. Starts with microtubule surface + kinesin molecules
  2. Lagging head is ATP bound + strongly associated with MT and the leading head is ADP bound + weakly associated with MT
  3. The hydrolysis of ATP causes lagging head to dissociate from MT
  4. Leading head binds to ATP and causes a conformational change
  5. Lagging head moves forward (hand-over-hand mechanism)
  6. Cargo gets transported along MT’s
126
Q

Describe intermediate filaments

A
  • Provide mechanical strength
  • Multiple types composed of different protein subunits
  • non polar + no associated motor proteins
  • great heterogeneity
  • hierarchail structure
  • high tensile strength due to lateral association between tetramers
127
Q

What are the 4 main categories of tissues?

A
  • epithelial
  • muscle
  • nervous
  • connective
128
Q

Describe epithelial and connective tissues

A

Epithelial = sheets of cells that line surfaces of the body
- ECM (extra cellular matrix) is present as a very thin sheet called basal lamina

Connective = cells produce ECM and are sparsely populated within a dense matrix

129
Q

What are the 3 types of cell junctions + what do they do?

A

Anchoring junctions = anchor cytoskeleton between cells/ between cells + ECM

Occluding junctions = prevents passage of ions + small molecules between cells

Communicating junctions = direct connections between cytoplasm of 2 cells
- allows passage of small water-soluble molecules from cell to cell

130
Q

What are the 2 superfamilies to which cytoskeletal linked transmembrane proteins belong to? (Anchoring junctions)

A

Cadherins = cell-cell attachment

Integrins = cell-matrix attachment

131
Q

Describe cadherins binding

A

C terminus of cadherins binds to cytoskeleton (inside cell)

N terminus binds to another cadherins = homophilic adhesion

  • binding is dependant on extracellular Ca2+
132
Q

Type of Cadherins binding 1

What are adherens junctions?

A

Connects actin filament bundles in 1 cell with that in next cell by cadherins
- intracellular binding to cytoskeleton is indirect as it uses adaptor proteins (catenin)
- these adaptor proteins assemble on C-terminus of cadherin + mediates binding
- catenines link cadherin to F actin

133
Q

Type of Cadherins binding 2

What are desmosomes?

A

Connects intermediate filaments in 1 cell to those in next cell by cadherins
- also uses adapter proteins
- only found in vertebrates
- most plentiful in tissues subjected to great mechanical stress (heart + skin)

134
Q

Describe integrins

A

They are composed of 2 glycoprotein subunits
- both subunits span the plasma membrane (single pass)
- small intracellular C terminus + large extracellular N terminus

135
Q

Types of integrins binding 1

What are focal adhesions (also called actin-linked junctions)?

A

In the extracellular domain, they bind to a specific amino acid (AA) sequences in ECM proteins

  • integrins binds to fibronectin (in ECM) which has a RGD sequence (arginine, glycine, aspartate)
  • intracellular domain binds to a complex of several proteins which link to F actin (involve talin + Vinculin)
136
Q

Typos of integrins binding 2

What are hemidesmosomes?

A

They connect the ECM to intermediate filaments within a cell
- use integrins in same way as focal adhesions
- most prominent cell-matrix junction in epithelial cells
- rely on specific integrins termed alpha6 beta 4 integrin

137
Q

What are occluding junctions formed from + describe in greater detail what they are?

A

Also called tight junctions in which they seal gaps between epithelial cells
- ensures that molecules/ fluid entering cells at apical side cannot diffuse back peripherally

They are formed of sealing strands = long row of transmembrane homophilic adhesion proteins

138
Q

What are 2 types of sealing strands in occluding junctions?

A

Claudins = essential mediators of tight junction formation - if knocked out of cells genetically then tight junctions will not form

Occludins = non-essential but important for limiting permeability of junction

139
Q

Describe communicating junctions in greater detail

A

Provide channels which connect the cytoplasm of 2 cells
- permeable to small molecules up to 1000 Da (ions, AAs, sugars) so macromolecules cannot pass
- Normally gated = sensitive to voltage, pH, Ca2+, neurotransmitters etc)

140
Q

What are the 2 proteins that span the gap in communicating junctions

A

The 2 membranes come very close together and the gap is spanned by channel forming proteins…

  1. Connexins = vertebrates
  2. Innexins = invertebrates
141
Q

What is the extracellular matrix, what’s its role + what is it secreted by?

A

Intricate network of proteins, carbs + water (except bone as has no water)

  • provides support for cells + tissue
  • Is an important regulator for cellular signalling

It is secreted by cells (e.g. fibroblasts) in which its organisation is tissue dependant

142
Q

What is the composition of the ECM - 3 major families of macromolecules/proteins?

A
  1. Glycosaminoglycans (GAGs) = oligosaccharides covalently bonded to a protein = proteoglycans
  2. Fibrous proteins (collagens)
  3. Glycoproteins
143
Q

What do the terms histone and nucleosome mean?

A

Histone = protein that binds to DNA to form eukaryotic chromosomes

Nucleosome = a protein-DNA complex containing 8 histone proteins
- most basic level of chromosome packaging

144
Q

Define the terms chromatin, chromosome and sister chromatids

A

Chromatin = repeating nucleosome structure like beads on a necklace
- also bound to non-histone proteins

Chromosomes = defined region of chromatin that carries info relating to a specific set of genes
- 23 pairs in nucleus

Sister chromatids = identical copies of same chromosome
- formed via DNA replication
- only seen during metaphase of mitosis

145
Q

Describe the 4 main features of the nucleus

A
  1. Nuclear envelope that separates nucleus from cytoplasm
  2. Nuclear lamina that lines inside of envelope
  3. Inner + outer membrane forms phospholipid bilayer
  4. Perinuclear space between the 2 membranes
146
Q

What is the nuclear pore complex (NPC)

A

It is an extremely large protein structure (quaternary) forming an aqueous channel that connects the nucleoplasm to the cytosol
- has a very ordered 8 fold symmetry
- as well as cytosolic fibrils (long proteins) that reach into the cytosol
- has a cage like structure = nuclear basket

147
Q

Explain these 3 types of transport through a nuclear pore complex…
1. Molecules of size < 5000 Da
2. Proteins up to 60 KDa
3. Proteins > 60 KDA

A
  1. Freely diffuse through NPC
  2. Can diffuse through, just takes a lot longer
  3. Cannot diffuse through so requires a specialist mechanism + energy
148
Q

What is a nuclear localisation signal?

A

They tell a protein to go into the nucleus
- proteins are synthesised on a cytosolic ribosome containing a NLS

149
Q

What do nuclear import receptors do?

A

They recognise nuclear localisation signals
- nuclear import receptor binds to FG repeats on nucleoporins in the cytosolic domain of NPC
- proteins move through the NPC binding sequentially to FG repeats

150
Q

Describe the process of nuclear import [12]

A
  1. Protein destined for nucleus is synthesised on an 80S ribosome with a nuclear localisation signal in its primary sequence
  2. Nuclear localisation signal is recognised by a nuclear import receptor and the import receptor binds to the localisation sequence and the protein itself
  3. The protein complex binds to cytosolic fibrils of nuclear pore complex
  4. The protein complex moves through the nuclear pore complex by binding, dissociating + rebinding with special nuclearporins containing FG repeats
  5. Protein complex arrives in nucleoplasm
  6. Ran-GTP binds to nuclear import receptor
  7. Nuclear import receptor releases its protein cargo into nucleoplasm
  8. Empty import receptor bound to Ran-GTP moves through nuclear pore complex to cytoplasm.
  9. Ran-GTP is bound by a ran binding protein, and it releases the nuclear import receptor
  10. Ran-GAP hydrolyses Ran-GTP to leave Ran-GDP + Pi
  11. Ran-GDP is transported from cytoplasm to nucleus through nuclear pore complex
  12. Ran-GEF coverts Ran-GDP to Ran-GTP
151
Q

Describe the step of Nuclear Export [8]

A
  1. Ran-GTP binds to nuclear export receptor
  2. A protein to be exported from the nucleus binds to the NER
  3. Export receptor and its cargo bind to nucleoporins on nuclear basket
  4. Protein complex moves through nuclear pore complex by binding, dissociating + rebinding with special nucleoporins containing FG repeats
  5. Protein arrives in cytoplasm
  6. Ran-GTP is bound by a ran binding protein and Ran-GAP + GTP is hydrolysed to GDP
  7. NER releases its cargo + Ran-GDP
  8. Ran-GDP moves back through to the nucleoplasm through nuclear pore complex
152
Q

What are the 2 types of chromatin in the nucleolus?

A

Heterochromatin = transcriptionally inactive + densely packed (dark regions) - hinders transcriptional machinery

Euchromatin = transcriptionally active + loosely packed (light regions)

153
Q

What are the sizes of the large and small subunit of a ribosome + what are these made up of?

A

Large = 60S (3 pieces rRNA + 49 proteins)

Small = 40S (1 piece rRNA + 33 proteins)

154
Q

Where are rRNA genes found, what ones are transcribed by what?

A

rRNA genes are clustered together on a DNA sequence as tandem repeats (adjacent to each other)
- speeds up rRNA transcription
- also spacer regions between tandem repeats = non-coding DNA sequence

18S, 5.8S and 28S rRNAs are transcribed in the nucleolus by RNA polymerase I
5S is transcribed in the nucleoplasm by RNA polymerase III then imported into nucleolus

155
Q

In the nucleus, ribosomes are synthesised… describe ribosomal biogenesis [8]

A
  1. RNA polymerase I transcribes pre-rRNA inside nucleus
  2. Ribosomal proteins enter nucleus via nuclear pore complex + translocate to nucleolus
  3. Ribosomal protein associate with 45S pre-rRNA
  4. 90S pre-ribosome is formed
  5. SnoRNPS modify rRNA in 3 ways…
    (i) Methylation of hydroxyl groups on ribose
    (ii) conversion of uridine to pseudouridine
    (iii) cleavage of 45S pre-rRNA by exo/endonucleases
  6. RNA polymerase III transcribes 5S rRNA in nucleoplasm which is transported to nucleus
  7. 5S rRNA associates with 28S + 5.8S rRNA to form the 60S ribosomal subunit
  8. 40S and 60S subunits leave the nucleus using Ran-GTP mediated nuclear export
156
Q

How do the following 3 methods of RNA modification work?

(i) Methylation of hydroxyl groups on ribose
(ii) conversion of uridine to pseudouridine
(iii) cleavage of 45S pre-rRNA by exo/endonucleases

A

(i) it stabilises RNA
(ii) isomerisation reaction improves the affinity of RNA to tRNA during protein synthesis
(iii) SnoRNPs contain exoribonucleases that cleave + removed externally transcribed spacers and endoribonucleaus that remove internally transcribed spacers

157
Q

What are the key functions of the smooth endoplasmic reticulum?

A
  • synthesis of lipids (phospholipids + cholesterol)
  • synthesis of steroid hormones (testosterone) - adrenal cortex is rich in sER
  • storage + release of Ca2+ from sarcoplasmic reticulum
  • detoxification (alcohol) - lots in liver
158
Q

What are the key functions of the rough endoplasmic reticulum?

A

Site of protein synthesis + processing for transmembrane proteins destined for…
- ER
- Golgi
- Plasma membrane
- Lysosomes
- Endosomes

159
Q

What is co-translational translocation (protein synthesis)?

A

In mammalian cells most proteins are imported to ER during protein synthesis
- Co-translational = happening at same time as translation
- translocation = translocating to another part of the cell (ER)

One end of the protein is attached to the ribosome whilst the other inserts itself to the ER

160
Q

When is post-translational translocation seen?

A

When a chaperone protein binds + escorts other proteins (preventing folding/damage)
- then imported to mitochondria via TIM/TOM complex

161
Q

For co-translational translocation, the signal sequence must…

A
  1. Be recognised (by signal recognition particle/ SRP)
  2. Be recognised by the ER and embedded within the ER membrane (via SRP receptor + translocator)
162
Q
  1. Be recognised (by signal recognition particle/ SRP)

Describe what a SNP is/ what do it does?

A

What it does
- It recognises the signal sequence on the N terminal of the growing polypeptide

It has 2 specific regions:
1. Translational pause domain = binds to ribosome + translation of domain is paused
2. Signal sequence binding pocket = binds to signal on protein itself

163
Q
  1. Be recognised by the ER and embedded within the ER membrane (via SRP receptor + translocator)

Explain this process

A
  1. Ribosomes free in the cytosol start to translate the protein
  2. A signal sequence emerges from the ribosome which is recognised by SRP
  3. One part of the SRP binds to ribosome + one part binds to signal on protein
  4. This causes a pause in translation
  5. The ribosome (with help of SRP) moves to the membrane of ER
  6. SRP binds to a SRP receptor while the protein starts to be transported into a protein translocator
  7. The SRP + receptor are freed from the ribosome + separated = for use in new cycle
  8. Ribosome stays bound to ER membrane
  9. Translation will continue while protein is being translocated to ER
164
Q

What happens after the ribosome has translated in co-translational translocation?

A

The mRNA is released back to the free ribosome pool

  • the mRNA may still remain bound to the ER as it is translated by multiple ribosomes
  • ultimately mRNA will be degraded
165
Q

Once the protein has been translated + is in the ER, what are the 2 ways it will be modified?

A
  1. Fold into its 3D conformation via binding
  2. Glycosylation
166
Q

What is protein glycosylation?

A

It refers to the addition of a sugar to a protein to form a glycoprotein
- a precursor oligosaccharide composed of 14 sugars is added to the N terminus of an asparagine side chain of the protein

It is very specific to proteins that enter the ER:
- quality control
- recognition
- protection

167
Q

Why is glycosylation important, explain it?

A

Quality control - to recognise correctly folded (mature) proteins

  1. If the protein is correctly folded, 3x glucose are cleaved from N-linked oligosaccharide
  2. If it doesn’t fold correctly, glycosyl transferase enzyme adds a single glucose back
  3. Calnexin (chaperone protein) binds to unfolded protein to prevent aggregation
  4. Removal of the terminal glucose (enzyme called glucosidase) releases protein from calnexin
  5. Glycosyl transferase determines if protein is correctly folded, if not single glucose is added back
  6. If protein remains misfolded, then it will be released from ER + targeted for degradation within a cell
168
Q

When misfolded proteins accumulate within a cell, what do it cause?

A

Causes ER stress and triggers an Unfolded Protein Response (UPR)

  1. Inhibit protein synthesis
  2. Degrades misfolded proteins
  3. Increase transcription of chaperones (BiP, Calreticulin, calnexin)

If problem persists it leads to apoptosis

169
Q

What are the different ER receptors in unfolded protein response?

A

PERK = responsible for pausing translation

IRE1 + ATF6 = protein degradation + activation of genes to increase protein folding capacity

170
Q

What are the 3 pathways in intracellular membrane traffic?

A

Secretory pathway = exocytosis

Endocytic pathway = endocytosis

Retrieval pathway

171
Q

What is the movement of proteins in intracellular membrane traffic mediated by?

A

Vesicles from donor to target compartment by budding + fusion

  • movement of vesicle is through movement on microtubules
172
Q

What are the 3 types of vesicles in protein transport?

A

COPII coated vesicles - from the ER

COPI coated vesicles - from the Golgi

Clathrin coated vesicles - from plasma membrane (endocytosis) as well as between Golgi + endosomes

173
Q

How do vesicles find the right membrane?

A

By the GTP binding protein called Rab-GTP
- found on the cytosolic surface of vesicles

  • when it is GDP bound = inactive (in cytosol)
  • when it is GTP bound = active (in vesicle membrane)
174
Q

How is Rab-GTP formed?

A

GEF found on a vesicle membrane activates Rab-GDP in the cytosol to form Rab-GTP

  • Rab-GTP then binds to a Rab effector protein on the target membrane = tethering of the vesicle to the target membrane
175
Q

Describe the process of membrane fusion [7]

A
  1. At start the vesicle has the correct v-SNARE and Rab-GTP on surface
    1. It binds to the Rab effector protein on target membrane (tethering)
    2. Effector protein changes conformation and brings vesicle close to target membrane (docking)
    3. T-SNAREs and V-SNAREs intertwine = trans-SNARE complex
    4. Membranes can slip + fuse with each other = fusion of vesicle with target membrane
    5. (during process of docking + fusion) - Rab-GAP causes Rab to hydrolyse GTP to GDP
    6. Rab-GDP is then released from vesicle + bound by Rab-GTP dissociation inhibitor (GDI) to keep Rab inactive
176
Q

Protein Sorting
What is the purpose of the further processing of oligosaccharide chains (by Golgi)?

A
  • promote correct folding of proteins
  • prevent unwanted aggregation
  • act as signals for sorting and targeting to correct pathway
177
Q

What are the 2 pathways within exocytosis for protein sorting?

A

It’s for if cargo is coming from ER through golgi to outside of cell

Constitutive secretory pathway
- vesicle reaches plasma membrane + is excreted from cell

Regulated secretory pathway
- vesicle is made but stored in cytosol
- only fuses with plasma membrane + release cargo upon receiving a signal (e.g. insulin)
- insulin is stored in vesicles + when blood sugar levels are high, vesicles move forward + release insulin into blood

178
Q

What are lysosomes?

A

They are degradative organelles - digest unwanted material

  • contain lots of enzymes to break down macromolecules
179
Q

When are lysosomes active + how is their pH maintained?

A

Only active at pH 4.5-5 = important protective mechanism

  • pH is maintained via vacuolar ATPase
180
Q

What kind of vesicles must be used to transport proteins from Golgi to lysosomes?

A

Clathrin coated vesicles
- these are also mannose-6-phosphate tagged

181
Q

What are endosomes, late endosomes and what forms endolysosomes?

A

Endosomes = term for saying cargo is packed in vesicles + proteins are destined to be degraded

Late endosomes = contain material that has been ingested by the cell

  • fusion of late endosomes with lysosomes generates endolysosomes
182
Q

Describe the endocytic pathway of protein sorting [7]

A
  1. Protein is made in ER and transported to golgi
  2. To be directed to lysosomes – they have to have M6P
  3. Within golgi there is addition of P-GlcNAc (phosphorylated N-acetylglucosamine) to protein
  4. Phosphate group is then transferred to mannose = M6P
  5. Protein is then packaged in a vesicle (clathrin coat)
  6. Buds off golgi + transported to fuse with early endosome
  7. Due to specific pH inside, proteins are going to dissociate from receptor = hydrolase enzyme
183
Q

Retrieval pathway
After an endocytic vesicle fuses with an early endosome, the ingested material can either be…

A

Degraded - it moves towards the centre of the cell and membrane composition alters. It no longer recycles + starts degradation

Recycled - vesicles containing material for recycling to the plasma membrane bud off and fuse with a recycling endosome

184
Q

What are the reasons for controlling cell growth + division?

A
  • Embryogenesis
  • early growth
  • wound healing
  • menstruation
  • muscle growth
185
Q

What are the 2 halves and the subunits within cell cycle?

A

Interphase (majority of time)
- G0, Gap 1, S phase, Gap 2

M phase (roughly 1 hour)
- prophase, prometaphase, metaphase, anaphase, telophase

186
Q

What roughly occurs in the following stages…
1. M phase
2. Interphase
- G1 Phase
- S Phase
- G2 Phase

A
  1. Mitosis (nuclear division), usually ending in cell division (cytokinesis) (4)

2a. G1 = cell is metabolically active + growing (1)

2b. S phase = DNA replication takes place (2)

2c. G2 = cell growth continues + proteins are synthesised (3)

187
Q

How is the cell cycle regulated?

A

By a series of control points
- START is a major control point, controlling the progression from G1 to S
- once they pass START they are committed to the cycle
- in most animal cells, the restriction point in late G1 functions like START
- if the appropriate growth factors are not present in G1 = progression stops at restriction point + enters resting G0 stage

188
Q

What is the role of DNA damage checkpoints and spindle assembly checkpoint?

A
  1. Ensure that damaged DNA is not replicated + passed on to daughter cells
  2. Stops mitosis at metaphase if chromosomes are not properly aligned on spindle
189
Q

What is the role of MCM helicase during cell cycle?

A

Bind either side of origin recognition complex + serve to open up DNA so DNA replication machinery is allowed in to replicate DNA

190
Q

What are Cdk1 and Cyclin B - cell cycle?

A

Cdk1 = a protein kinase cell cycle regulator - adds a phosphate group as it is a kinase enzyme

Cyclin B = regulatory subunit required for catalytic activity of Cdk1 protein kinase

These 2 bind to form a maturation promoting factor (MPF) which is regulated by phosphorylation/ dephosphorylation of Cdk1
- when Cdk1 is phosphorylated = inactive form
- when Cdk1 is dephosphorylated = active form

191
Q

Explain what occurs during G2 of the cell cycle regarding Cdk1 and Cyclin B

A
  1. Cyclin B is synthesised + forms complexes with Cdk1
  2. Cdk1 is phosphorylated by Wee1 and inhibited, this leads to the accumulation of inactive Cdk1/cyclin B complexes
  3. CDK1 is dephosphorylated by phosphatases + becomes active = cells progress through G2
  4. Cyclin B is then degraded by ubiquitin-mediated proteolysis
  5. The destructions of cyclin B inactivates Cdk1, so the cell exits mitosis + undergoes cytokineses = return to interphase
192
Q

List the complexes of cyclins:cyclin-dependent kinases during the following stages…
1. Early G1
2. Past restriction point (for cell to go into S phase)
3. S phase
4. G2
5. M Phase

A
  1. Cyclin D binds to Cdk4 and 6
  2. Cyclin E + Cdk2
  3. Cyclin A + Cdk2
  4. Cyclin A + Cdk1
  5. Cyclin B + Cdk1
193
Q

How is the activity of Cdks regulated?

A
  1. Cdk/Cyclin association is controlled by Cyclin synthesis + degradation
  2. Activation of Cdk/Cyclin complexes requires phosphorylation of threonine at position 160 (catalysed by CAK)
  3. Inhibitory phosphorylation of tyrosine near Cdk amino terminus (catalysed by Wee1) means Cdks are then activated by dephosphorylation by Cdc25 protein phosphatases
  4. Binding of inhibitory proteins - Cdk inhibitors (CKIs)
    - 2 families = Ink4 + Cip/Kip
194
Q

What does Cyclin D do and how is it synthesised?

A

It provides one link between growth factor signalling + cell cycle progression

  • growth factors stimulate cyclin D synthesis through the Ras/Raf/MEK/ERK pathway
  • it is synthesised as long as growth factors are present
195
Q

What is Rb - cell cycle?

A

A substrate protein of Cdk4,6/Cyclin D complexes + is frequently mutated in many human tumours
- it is the prototype of a tumour suppressor gene, who’s inactivation leads to tumour development

196
Q

What is Rb’s role during G0/ early G1?

A

It binds to E2F transcription factors, which suppresses expression of genes involved in cell cycle progression

Rb is then phosphorylated by Cdk4,6/Cyclin D as cells pass through the restriction point + dissociates from E2F, allowing transcription to proceed

197
Q

How do cells progress through the restriction point?

A

Mediated by activation of Cdk2/Cyclin E complexes
- in G0 + early G1, Cdk2/Cyclin E is inhibited by p27 (part of Cip/Kip family)

Cyclin E synthesis is stimulated by E2F after Rb is phosphorylated + transcription of p27 is inhibited by growth factor signalling
- the resulting activation of Cdk2/Cyclin E leads to activation of MCM helicase + initiation of DNA replication

198
Q

What mediates cell cycle arrest at DNA damage checkpoints?

Explain what happens

A
  1. Mediated by protein kinases (ATM ands ATR) that are activated in response to DNA damage
  2. They then activate a signalling pathway that leads to cell cycle arrest, DNA repair + sometimes apoptosis
199
Q

What do the protein kinases ATM and ATR recognise what do this lead to?

A

ATM recognises double-strand breaks

ATR recongises single-stranded on unreplicated DNA

  • they phosphorylate + activate the checkpoint kinases Chk1 and Chk2
  • these then phosphorylate + inhibit Cdc25 phosphatases, which are required to activate Cdk1 and Cdk2
  • inhibition of Cdk2 results in cell cycle arrest in G1 and S
  • inhibition of Cdk1 results in arrest in G2
200
Q

What is the role of p53 in G1 arrest?

A

It is a tumour suppressor protein - transcription factor whose increased expression leads to activation of Cdk inhibitor p21
- p21 inhibits Cdk2/Cyclin E complexes, leading to cell cycle arrest in G1
- It is phosphorylated by both ATM and Chk2

Sport Science Y1S1 (3 decks)

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