1. Cellular & Molecular Structure & Function

Question 1

Why are we interested in understanding macromolecular structure?

Answer 1

It is the basis of biological structure and function.

Question 2

What is the most common way of determining 3D protein structure?

Answer 2

X-ray crystallography

Question 3

What is the general clinical importance of GPCRs?

[Clinical extra info]

Answer 3

• 6 of the top 10 and 60 of the top 200 best-selling drugs in the US in 2010 target GPCR
• This is because there are over 375 GPCRs encoded by the human genome, of which 225 have known ligands

Question 4

What are the two main types of biophysical techniques that can be used to study proteins?

[Experimental extra info]

Answer 4

• Spectroscopic -> Study the environment of various atoms to deduce structural information
  
  • CD, UV
  • Fourier transform infrared
  • NMR
  • X-ray absorption fine spectrum
• Scattering -> Form an image of the species under study
  
  • Dynamic laser light scattering
  • Microscopy
  • Neutron scattering
  • Small-angle X-ray scattering
  • X-ray diffraction

Question 5

Why are X-rays ideal for studying macromolecular structure?

[Experimental extra info]

Answer 5

The wavelength of X-rays is similar to the size of atoms, which is what we want to study.

Question 6

Describe briefly the process of X-ray crystallography.

[Experimental extra info]

Answer 6

• Purification
• Cystallisation
• Data collection (via diffracting X-rays using the crystal)
• Map calculation
• Map interpretation

Question 7

What are some of the different types of electron microscopy used in studying proteins and why is each useful?

[Experimental extra info]

Answer 7

• Single particle cryo-EM -> Allows large macromolecules to be imaged that cannot otherwise be crystallised
• Cryo-electron tomography -> Allows images to be obtained of cells and their machinery
• Correlative light (fluoresence) and electron microscopy (CLEM) -> Allows for multicolour labelling and Angstrom range resolution of cellular components

Question 8

Give some examples of macromolecules and what they are made from.

Answer 8

• Proteins -> Made from amino acids
• Polysaccharides -> Made from monosaccharides
• Nucleic acids -> Made from nucleotides
• Fats -> Made from fatty acids

Question 9

What type of reaction is the formation of macromolecules usually?

Answer 9

Condensation (or dehydration)

Question 10

Draw the formation of a peptide bond, noting the functional groups involved.

Answer 10

Question 11

Draw the formation of an ester bond, noting the functional groups involved.

Answer 11

Question 12

Draw the formation of a glycosidic bond, noting the functional groups involved.

Answer 12

Question 13

What is another name for a glycosidic bond?

Answer 13

Ether bond

Question 14

Describe the different levels of protein structure and the interactions at each level.

Answer 14

• Primary -> The order of amino acids in sequence -> Covalent bonding (i.e. peptide bonds)
• Secondary -> The regular folding into an alpha helix or beta pleated sheet -> Repetitive hydrogen bonding
• Tertiary -> The more complex forlding of regular structures -> Hydrophobic effect, ionic, disulfide, Van der Waal’s forces, hydrogen bonding
• Quaternary -> The interaction of multiple structured polypeptides (and non-protein components) -> Hydrophobic, ionic, disulfide, Van der Waal’s forces, hydrogen bonding

Question 15

Draw the general structure of an amino acid.

Answer 15

Question 16

What are the two carbons in an amino acid called?

Answer 16

• The ‘central’ carbon (the one with the R group attached) is called the alpha carbon
• The carbon in the carboxyl group is just a carbon atom

Question 17

Which functional groups in an amino acid are involved in peptide bonds?

Answer 17

COO^- and NH₃⁺

Question 18

How many commonly encountered amino acids are there?

Answer 18

20

Question 19

Does the charge of an amino acid ever change?

Answer 19

Yes, it varies depending on the pH.

Question 20

Describe the charges of an amino acid at different pHs.

Answer 20

• Physiological pH -> Both sides of the amino acid have a charge (NH₃⁺ and COO^-)
• Low pH -> Only NH₃+ side is charged (i.e. both sides are protonated)
• High pH -> Only COO^- side is charged (i.e. both sides are deprotonated)

Question 21

What are the main functional types of amino acid side group?

Answer 21

• Charged -> Acidic and basic
• Uncharged polar (hydrophilic)
• Uncharged non-polar (hydrophilic)
• Special cases / Structural

Question 22

Draw a diagram showing the main functional types of amino acid side chain.

(Note: You do not need to know an specific structures)

Answer 22

Question 23

What charge do the acidic and basic amino acids show an physiological pH?

Answer 23

• Acidic -> Negative because they have already lost their an H -> They contain a carboxyl group and function similar to a carboxylic acid
• Basic -> Positive because they have already picked up an extra H -> They contain an N and function similar to ammonia

Question 24

What anagram can be used to remember the amino acid side chain functional types?

Answer 24

LHA-AG STAG VITALPTM CSGP

Read as: Laaaaaaaag, stag, vital post-translational modification, computer science GP

Question 25

What are the charged amino acids?

Answer 25

Basic (positively charged):

• Lysine
• Histidine
• Arginine

Acidic (negatively charged):

• Aspartic acid
• Glutamic acid

Question 26

What are the uncharged polar (hydrophilic) amino acids?

Answer 26

• Serine
• Threonine
• Asparagine
• Glutamine

Question 27

What are the uncharged non-polar (hydrophobic) amino acids?

Answer 27

• Valine
• Isoleucine
• Tryptophan
• Alanine
• Leucine
• Phenylalanine
• Tyrosine
• Methionine

Question 28

What are the special cases of amino acid?

Answer 28

• Cysteine
• Selenocysteine
• Glycine
• Proline

Question 29

What makes glycine unique?

Answer 29

• It contains a hydrogen as its side chain
• This means that there is much more conformational flexibility in glycine.
• What this means is that glycine can reside in parts of protein structures that are forbidden to all other amino acids (e.g. tight turns in structures).

Question 30

What makes proline unique?

Answer 30

• It is the only amino acid where the side chain is connected to the protein backbone twice, forming a five-membered nitrogen-containing ring.
• So proline is unable to occupy many of the main chain conformations easily adopted by all other amino acids.
• In this sense, it can be considered to be an opposite of glycine, which can adopt many more main-chain conformations.
• For this reason, proline can often be found in very tight turns in protein structures (i.e. where the polypeptide chain must change direction).
• It can also function to introduce kinks into alpha helices, since it is unable to adopt a normal helical conformation -> i.e. It is an alpha helix breaker

Question 31

Which amino acid is often found in parts of proteins that need to move, such as hinges?

Answer 31

Glycine, because it is so small and flexible.

Question 32

What are the alpha helix breakers and why?

Answer 32

• Proline (Classic helix breaker) -> The side chain interferes strically with the backbone of the chain, forcing a kink in the helix. Also cannot form hydrogen bonds as effectively.
• Glycine -> Its high conformational flexibility makes it entropically expensive to adopt the relatively constrained α-helical structure.

Question 33

Describe the concept of amino acid conformers.

Answer 33

• WITHIN the side chain of amino acids that have a C-C bond (i.e. not glycine, alanine and proline), there exist many variations, which exist due to the tetrahedral arrangement of atoms around each carbon.
• Looking down the axis of the bond, these appear staggered so that the atoms around one carbon appear in the gaps between the atoms around the other carbon.
• Therefore, the different conformations differ by 120*.
• Generally, there exists a set of preferred conformations.

Question 34

What is a post-translational modification?

Answer 34

A modification that happens to a protein after translation, usually controlled enzymatically and caused by the synthesis or breaking of covalent bonds.

Question 35

Give some examples of post-translational modification to amino acids in collagen. How are these clinically relevant?

Answer 35

• Hydroxyproline
  
  • Permits sharp twisting of the collagen helix and stabilises the triple helix conformation
  • Requires vitamin C to form, so a deficiency results in weaker collagen (scurvey)
• Hydoxylysine
  
  • Provides linkage sites for sugars or short polysaccharides, allowing cross-linking of collagen molecules
  • Mutations in the lysine hydroxylase enzyme result in diseases -> e.g. Ehlers-Danlos syndrome (spidery fingers and highly flexible joints)

Question 36

What are the main post-translational modifications?

Answer 36

On syllabus:

• Disulfide bonding
• Cross-linking
• Peptidolysis
• Glycosylation
• Phosphorylation
• Adenylation
• Farnesylation

Others:

• Methylation
• Acetylation
• Hydroxylation
• Isoprenylation
• Ubiquitination
• Deamidation

Question 37

Remember to add flashcards on the different PTMs.

Answer 37

Do it, using Miffy’s essay.

Question 38

Around which carbon atom do amino acids show chirality?

Answer 38

Alpha-carbon

Question 39

Which is the only amino acid that does not show chirality?

Answer 39

Glycine, since it does not have 4 different atoms around it.

Question 40

Define chirality.

Answer 40

The existence of 4 different atoms around a carbon in an amino acid so that two different configurations are possible that cannot be superimposed.

Question 41

What are the two configurations for an amino acid called?

Answer 41

Enantiomers:

• D-(Dextro)
• L-(Laevo)

Question 42

Which is the only amino acid enantiomer found in living organisms?

Answer 42

L, which can be worked out using the CORN law:

• Look at the amino acid alpha-carbon from the direction of the hydrogen atom
• In an L-amino acid, the atoms around the carbon should spell out CO-R-N in a clockwise direction

Question 43

Describe the structural properties of a peptide bond and discuss the significance of this.

Answer 43

• The peptide bond is a single C-N bond in a CO-NH system
• However, this bond exhibits the resonance hybrid model, where charge is redistributed through the CO-NH system as shown in the diagram
• This gives the C-N bond the characterstics of a double bond, so that there is no rotation around it
• Therefore a rigid planar structure arises that limits the number of possible conformations

Question 44

Draw the resonance hybrid model of a polypeptide.

Answer 44

Question 45

What are the angles in a polypeptide called and why?

Answer 45

They are called dihedral angles because the angles around each side of a peptide bond are planar (and a dihedral angle is defined as the angle between two planes).

Question 46

What are the different angles in a polypeptide and what values do they tend to take on?

Answer 46

• ω (omega)
  
  • Angle of rotation of the peptide bond (C-N)
  • Is usually 180* (trans) or more rarely 0* (cis)
• Φ (phi)
  
  • Angle of rotation of the C_α-N bond
  • Is between -180* and 180*
• ψ (psi)
  
  • Angle of rotation of the C_α-C bond
  • Is between -180* and 180*

Note that the phi and psi angles tend to take on values of 60, 180 or -60*.

Question 47

Label:

Answer 47

Question 48

What values does the omega angle in a polypeptide take on and when is each possible?

Answer 48

• The 180* trans variation is most common, since the cis variation tends to result in too much steric clash
• Only really proline tends to take on the 0* cis version, since both the cis and trans variations show a similar degree of clash, meaning that both are relatively viable

Question 49

What is a good way of remembering the psi and phi bonds and their symbols?

Answer 49

• The psi bond has the PSame atoms on each side of the bond, and the symbol is like PSoidon’s trident
• The phi bond has diPHIrent atoms on each side of the bond, and the symbol looks like a pie being cut in half (pie rhymes with phi)

Question 50

What is the name for the plot used to show phi and psi angles?

Answer 50

Ramachandran plot

Question 51

What is a Ramachandran plot?

Answer 51

A plot showing the different psi and phi angles allowed in a polypeptide chain.

Question 52

What is on each axis of a Ramachandran plot? How can you remember this?

Answer 52

• Phi on the x-axis and psi on the y-axis
• You can remember this by thinking that the phi and psi correspond in alphabeticity to x and y

Question 53

Draw a simple Ramachandran plot.

Answer 53

Question 54

Draw a Ramachandran plot with the following points labelled:

• Anti-parallel beta sheet
• Parallel beta sheet
• Left-handed alpha helix
• Right-handed alpha helix
• Collagen helix

Answer 54

Question 55

Define a domain in protein structure.

Answer 55

A fundamental unit of tertiary structure, defined as a polypeptide chain, or part thereof, that can fold independently into a stable structure.

Question 56

Describe how a domain is made up of smaller structures.

Answer 56

• There are 3 main classes of secondary structure elements: alpha helices, beta sheets and turns/loops.
• Secondary structures can be connected to form simple motifs, which are supersecondary structures (e.g. beta hairpin)
• These combine to form a domain, which is the fundamental unit of tertiary structure

Question 57

What are the different forces that hold polypeptides together?

Answer 57

• Covalent bonds (also disulfide bonds)
• Hydrogen bonds
• Ionic interactions
• Van der Waals interactions
• Hydrophobic effect

Question 58

What is the most common type of hydrogen bond in proteins and how does the strength vary with distance?

Answer 58

• Between C=O and N-H groups
• Strength falls off as 1/r⁶ (i.e. very short range)

Question 59

Describe how Van der Waals forces occur and draw a graph to show how they vary with separation.

Answer 59

• Exist as attractive or repulsive interactions
• Attractive forces exist due to fluctuations in the electron densities of neighbouring non-bonded atoms -> Favour tight packing in macromolecules
• Repulsive forces result from close approaches of electron density clouds
• The graph shows a decrease of 1/r⁶

Question 60

Describe the structure of the alpha helix.

(Angles, residues per turn, hydrogen bonds, directionality, dipole)

Answer 60

• Angles: Around Phi = -60*, Psi = -50* (both negative)
• Residues per turn = 3.6
• Hydrogen bonds between the C=O of residue n with the NH residue of n+4 -> So all groups are hydrogen bonded except for the first and last
• Directionality -> Always right handed (since they are made from L-amino acids)
• R groups point outwards and do not affect helix
• Dipole: 0.5 to 0.7 units from C to N terminus

Question 61

What are some variations of the alpha helix?

Answer 61

The standard is the n+4 helix, but rarely there may also be:

• 3₁₀ helix -> n+3
• π helix -> n+5

Question 62

Where are alpha helices commonly found?

Answer 62

Membrane proteins (e.g. channels, receptors and transporters)

Question 63

Draw the dipole that exists in alpha helices.

Answer 63

Question 64

Describe the structure of the beta sheet.

(Angles, hydrogen bonds, directionality, dipole)

Answer 64

• Angles: Around Phi = -140*, Psi = 130*
• Made of strands that are almost completely extended called beta strands
• These can run either parallel or antiparallel to each other
• In each strand, the R groups alter between being above and below the strand
• Regular hydrogen bonds exist between the C=O and N-H of adjacent strands

Question 65

Draw the structure of a parallel beta sheet.

Answer 65

Question 66

Draw the structure of an antiparallel beta sheet.

Answer 66

Question 67

Where are beta sheets commonly found?

Answer 67

Globular proteins

Question 68

What are loops and turns? What is the difference between them?

Answer 68

• Loops are the structures that connect the alpha and beta structures
• They are often on the surface, while the alpha helices and beta strands are in the hydrophobic centre
• Turns are similar to loops, except they contain internal hydrogen bonding between two end residues that makes them tighter and sharper than loops

Question 69

Describe the structure of loop regions.

Answer 69

• They are often on the surface of proteins
• Have free C=O and N-H groups to make hydrogen bonds with water molecules
• Also often have charged and hydrophilic residues
• The loop is not as sharp as a turn

Question 70

Where are loop regions commonly found?

Answer 70

Usually on the surface of proteins, so they often act as:

• Binding sites
• Enzyme active sites

Question 71

Give a specific example of the role of loop regions in proteins.

Answer 71

Antigen binding sites on antibodies are composed of 6 loop regions. These loop regions vary in length and in amino acid sequence between different antibodies.

Question 72

Are loops and turns always considered to be different?

Answer 72

Yes, but sometimes turns are seen as a subset of loops, containing fewer than 5 residues and being much sharper.

Question 73

What are the regions that connect two antiparallel beta strands called?

Answer 73

Hairpin loops, although short hairpin loops are called reverse turns (or just turns).

Question 74

What are the types of turn and how do they differ? Draw diagrams.

Answer 74

Type I and Type II -> They differ by the positional restraints on the amino acid R².

Question 75

What is a synonym for a simple motif?

Answer 75

Supersecondary structure

Question 76

Give some examples of common simple motifs.

Answer 76

• Helix-turn-helix motif -> Found in DNA binding proteins and calcium binding proteins
• Hairpin beta motif -> Two adjacent antiparallel beta strands joined by a loop
• Greek key motif -> 4 adjacent antiparallel beta strands
• Beta-alpha-beta motif -> A common way to connect beta strands

Question 77

Explain the concept of structural homology.

Answer 77

If there are large similarities between the amino acids in two domains, then the domains will have similar structures.

Question 78

Do motifs always need the same amino acid sequences to form?

Answer 78

No, so the similar domain structures frequently occur in different proteins with different functions and with different amino acid sequences.

Question 79

What are the two states of a protein?

Answer 79

• Native -> When a protein is properly folded and/or in the assembled form, which is operative and functional.
• Denatured -> When a protein loses the secondary, tertiary and quaternary structure that gives it its functionality.

Question 80

Is the native state always the most stable conformation for a protein?

Answer 80

No, at various temperatures and pressures the native state may not be the most stable.

Question 81

What is the most important driving force in protein folding and why?

Answer 81

• Hydrophobic effect
• Because the universe tends towards disorder (second law of thermodynamics) and non-polar segments of the protein restricts the conformational freedom of the surrounding water molecules
• Therefore, folding the non-polar regions away from the water is more thermodynamically favourable

Question 82

Describe the counter-acting forces of proteins at equilibrium.

Answer 82

The attractive forces in the folded state overcome the unfavourable restrictions on the conformational freedom of the polypeptide chain.

Question 83

Describe what disulfide bridges are and where they may be found.

Answer 83

• Covalent bonds between two cysteine residues (S-S)
• These may be within a single polypeptide or between polypeptide chains (like in insulin)

Question 84

What are the different types of electrostatic interaction and how does the strength of each change with distance?

Answer 84

• Charge-charge
• Charge-dipole
• Dipole-dipole

E = q₁q₂/εRⁿ

Question 85

What is the importance of the change in energy of an electrostatic interaction?

Answer 85

The rate at which some of the stronger electrostatic interactions decrease with distance is relatively slow, meaning that they may act over long distances and contribute to tertiary and quarternary structures.

Question 86

What is the strength of electrostatic interactions in the centre of a protein like?

Answer 86

These interactions tend to be stronger because the interior of the protein is hydrophobic and so the dielectric constant is lower.

Question 87

What are the different types of multi-subunit proteins?

Answer 87

• Homo-oligomeric -> All of the subunits are identical (e.g. dimer, trimer)
• Hetero-oligomeric -> Made of more than one type of sub-unit

Question 88

What is the Levinthal paradox?

Answer 88

• Proteins cannot randomly sample the theoretical number of possible conformational states that would enable them to find the correct, native fold.
• If each residue had two states, either 𝛼 or 𝛽, a 100 residue peptide would have 2¹⁰⁰ or 10³⁰ possible conformations. If the rate of conversion was ~ 10^-13 seconds, then it would take ~ 10¹⁰ years…
• Therefore it was decided that proteins must have evolved mechanisms of efficient, guided folding pathways.

Question 89

Describe the thermodynamics of protein folding and what determines whether a protein’s native state is stable.

Answer 89

• The Denatured to Native transition can be notated as:
  
  • ∆G_{D → N} = G (N) – G (D)
• If ∆G_{D → N} is negative then the reaction is spontaneous and therefore the protein is stable.

Question 90

How can the stability of a protein be affected by mutations?

Answer 90

• Mutations may increase the Gibbs free energy of the native state, so that the energy difference between the native and denatured state is reduced.
• This reduces the stability of the protein and shifts the equilibrium towards the denatured state.

Question 91

Give an alternative way of considering the denatured to native state protein transition.

Answer 91

Question 92

How can protein folding be observed?

Answer 92

Removing the denaturant from the protein, so that it can fold.

Question 93

Describe the 3 stages of protein folding that are observed.

Answer 93

1. Fast collapse and secondary structure formation. Formation of what is commonly called the ‘molton globule’ state. Characterised by a reduction in the radius of gyration to 10% larger than the native state.
2. Appearance of tertiary structure (ms to seconds). Interactions between nascent secondary structure elements build up, mutually stablising their states through interactions. Side chain conformations are still mobile, although the core of the protein starts to fix.
3. Final formation of the native state, typically less than a second. Resulting in the locking together of buried side chains to form highly ordered compact networks of interactions.

Question 94

What are molecular chaperones and how do they work?

Answer 94

• Enzymes that assist with the folding of a protein
• They work by unfolding misfolded proteins and allowing the protein to try again at folding

Question 95

What is a co-factor?

Answer 95

• A non-protein chemical compound or metallic ion that is required for an enzyme’s activity as a catalyst, a substance that increases the rate of a chemical reaction.
• It can either be a metallic ion or organic molecules (called coenzymes)

Question 96

Give an example of a process that uses many co-factors.

Answer 96

Electron transfer

Question 97

Describe the main tertiary domain types.

Answer 97

• Alpha structures
• Beta structures
• Alpha-beta structures -> Including alpha/beta and alpha+beta structures

Question 98

What are alpha domains?

Answer 98

Proteins whose core structures have mostly alpha helices in their secondary structure.

Question 99

What are beta domains?

Answer 99

Proteins whose core structures have antiparallel beta sheets in their secondary structure. This usually involves two sheets with strands of various lengths and numbers.

Question 100

What are alpha-beta domains?

Answer 100

Proteins with a mixture of alpha and beta secondary structures. The most common type are alpha/beta, which consist of a central beta sheet surrounded by alpha helices.

Question 101

For each domain type, list the different protein types it can be found in.

Answer 101

Alpha domain:

• Membrane proteins (e.g. channels, receptors, transporters)
• DNA & RNA binding proteins (e.g. transcription factors)
• Connective tissues (e.g. collagen)
• Coagulating proteins (e.g. fibrinogen)

Beta domain:

• Enzymes
• Transport proteins
• Antibodies
• Cell surface proteins
• Virus coat proteins

Alpha-beta domain:

• Enzymes
• Proteins that bind and transport metabolites

Question 102

Consider adding more flashcards on the different tertiary domain types.

Answer 102

Do it!

Question 103

Give an example of a protein where mutliple domains are combined to give the functional protein.

Answer 103

Ligand-gated ion channels

Question 104

Give an essay plan outlining the different post-translational modifications. (Make full notes on this later!)

Answer 104

Phosphorylation

• add phosphate groups onto aa’, negatively charged so can attract positive side chains via ionic interactions
• particularly important in intracellular signalling protein kinases
• eg MLCK phosphorylation inactives MLCK in intracellular signalling for smooth muscle relaxation
• increasing inotropy in the heart
• regulation of translation : insulin can trigger an intracellular cascade leading to the phosphorylation of 4E binding proteins, which would usually prevent the 5’ methylated guanosine cap from forming, preventing ribosome from being recruited, but phosphorylation prevents this action to increase and regulate translation

Hydroxylation

• hydroxylase enzymes adds -OH groups onto collagen, fibrous protein with sequence of Gly-X-Y, glycine-hydroxylysine-hydroxyproline
• lysyl and prolyl hydroxylases will add -OH groups to proline and lysine residues, meaning water can form OH bonds with them, underlying collagens tensile strength due to cross links between triple helix, water providing incompressibility

Ubiquitination

• misfolded proteins tagged to be broken down by ubiquitin ligases, and directed to proteasomes
• prevents protein from carrying out disruptive function or aggregating

Glycosylation

• process of adding oligosaccharides to proteins to make glycoprotein
• lectins are proteins that glycans add to specifically
• usually added to -OH groups on serine, threonine, tyrosine, via O-linked glycosylation taking place extracelluarly or N-linked glycosylation occurring where glycan added to N atom on an aa’
• glycoproteins produced from this reaction are important for cell signalling, interaction and adhesion
• eg fibronectin and laminin glycoproteins in basement membrane which bind integrins, and blood group tags

Adenylation

• uses cAMP as a substrate, addition of AMP to proteins
• important in cell signalling

Farnesylation, addition of c15 goup, also important in cell signalling

-Important in order to activate amino acids for example aminoacyl tRNAs are found through activating the amino acid thorugh adding AMP and this facilitates the addition of tRNAs.

Acetylation

• addition of acetyl-coA groups to proteins, by acetyltransferases eg histone acetyl transferase
• histone proteins H2A H2B H3 H4
• masks positive charge of lysine, so histone group less attracted to DNA
• can be used to control gene expression, important in differentiation when cell type specific gene expression is required to retain cells in their terminally differentiated state

Allosteric regulation

Important for proteins in order to activate and inactive enzymes but also important in molecules such as DNA as they show cooperativity due to allosteric binding.

Cleavage

Can be used in order to active pro hormones to hormones that would otherwise be damaging to a cell.

Additional

Addition of cofactors

Question 105

Give two examples of co-operativity or allostery in proteins.

Answer 105

• Haemoglobin -> One oxygen binding makes it easier for another to bind. This results in a sigmoidal dissociation curve.
• Phosphofructokinase -> One of the most important regulatory enzymes of glycolysis. Allosteric inhibition can be used to regulate the rate of respiration in response to chemical levels (e.g. levels of ATP).

Question 106

What are the two functional types of fibrous proteins?

Answer 106

• Active proteins
• Passive structural proteins

Question 107

Describe the amino acid sequence in fibrous proteins.

Answer 107

It is often a repeating sequence of amino acids, although this repetition does not need to be perfectly consistent.

Question 108

Describe the structural types of fibrous proteins.

Answer 108

• Coiled coil alpha helices -> Keratin, Myosin
• Collagen triple helix
• Beta sheets in amyloid fibres and silks

Question 109

Describe the structure of collagen.

Answer 109

• Made up of 3 left-handed polypeptide strands that are coiled into a right-handed collagen helix
• Each strand contains lots of glycine because it is the only amino acid small enough to fit into the crowded interior of the triple helix
• General structure: -Gly-X-Y-Gly-X-Y-
  
  • X: typically proline
  • Y: typically hydroxyproline
• Collagen molecules are assembled parallel to each other but are staggered, forming a long fibril -> These fibrils are stabilised by cross-linkages, largely between the hydroxylated amino acids, like hydroxylysine
• Fibril assembles into a collagen fibre

Question 110

What type of protein does collagen exemplify?

Answer 110

Fibrous

Question 111

What are the causes and symptoms of Ehlers-Danlos syndrome?

Answer 111

• Causes: Different types, all caused by defects in collagen, usually genetic
• Symptoms: Stretchy skin, Joint hyperflexibility, Weak and easily bruised skin

Question 112

What is the name for the immature and mature form of collagen?

Answer 112

• Immature = Procollagen
• Mature = Tropocollagen

Question 113

Describe the process of maturation of collagen.

Answer 113

• Collagen molecules are laid down by fibroblasts as procollagen
• Peptidases cleave the amino and carboxy termini allowing the formation of the mature form, tropocollagen.

Question 114

Give an example of a globular protein.

Answer 114

Histones

Question 115

Describe the structure of histones.

Answer 115

• They are globular proteins
• 8 histone proteins form an octamer -> When DNA wraps around this, the whole unit is called a nucleosome

Question 116

What is the need for histones?

Answer 116

They save space in the nucleus by packing the DNA very tightly.

Question 117

Define catalysis.

Answer 117

The increase in rate of a chemical reaction by a catalyst, which is unchanged at the beginning and end of the reaction.

Question 118

Define enzyme.

Answer 118

A catalyst that is produced by a biological organism.

Question 119

Describe whether an enzyme is changed by the reaction it catalyses.

Answer 119

The enzyme is not changed at the beginning and end of a reaction, but it can be changed during the reaction.

Question 120

What are the units for Gibbs free energy?

Answer 120

kJ mol^-1

Question 121

Describe how an enzyme affects the energy and rates in a reaction.

Answer 121

• An enzyme speeds up a reaction by providing a pathway that has a lower energy path
• Larger k₁ and k_-1
• Lower ΔG₁ and ΔG_-1 (energy changes of the formation of the transition state and formation of the product respectively)
• But ΔG⁰ (energy change of reaction) remains the same

Question 122

Explain why there are dips in the graph for the catalysed reaction.

Answer 122

When an enzyme-substrate complex is formed, there is a drop in energy.

Question 123

Explain what transition states and reaction intermediates are.

Answer 123

• Transition states are the states in which the reactants exist just before the product is formed (i.e. when all the bonds have been broken). They are the highest points on an energy-time graph.
• Intermediates are entities that are formed as a result of the substrates reacting, and which will react again to form the final product. They are indicated by any dips in the graph.

Question 124

Name some classes of biochemical reaction you need to know.

Answer 124

• Hydrolysis
• Ligation
• Condensation
• Group-transfer
• Redox
• Isomerisation

Question 125

What are hydrolysis reactions?

Answer 125

Organic chemical reactions that involve adding water to break apart molecules.

Question 126

What are ligation reactions?

Answer 126

• Reactions where two DNA fragments are joined by a phosphodiester bond
• This is catalysed by a ligase enzyme

Question 127

What are condensation reactions?

Answer 127

A reaction where two molecules are joined and a small molecule is released. It is often water.

Question 128

What is the difference between a condensation and a dehydration reaction?

Answer 128

• Condensation -> When a small molecule is released
• Dehydration -> When thesmall molecule released is specifically water

Question 129

What are group-transfer reactions?

Answer 129

A reaction where one or more groups of atoms is transferred from one molecule to another.

Question 130

What are redox reactions?

Answer 130

A type of chemical reaction that involves a transfer of electrons between two species. One species is oxidised while another is reduced.

Question 131

What are isomerisation reactions?

Answer 131

When one molecule is transformed into another molecule which has exactly the same atoms, but the atoms have a different arrangement e.g. A-B-C → B-A-C

Question 132

What is the importance of the active site in terms of action of enzymes?

Answer 132

• It is the site of catalysis
• It allows for specificity

Question 133

What are multimeric enzymes?

Answer 133

Enzymes that contain more than one polypeptide chain.

Question 134

What are isozymes and why are they important?

Answer 134

• Enzymes that have a different amino acid sequence and are encoded by different genes, but catalyse the same reaction
• They usually have different kinetic parameters, such as a different Km, so that they can be used to mediate a process to the level at which it is required for that tissue at that stage of development

Question 135

Give an example of an isozyme.

Answer 135

• LDH (lactate dehydrogenase) is an enzyme used in converting lactate to pyruvate and back
• There are 5 different isozymes for LDH -> There are 4 subunits in LDH and each one can be one of two different types

Question 136

What are multienzyme complexes?

Answer 136

• Stable assemblies of more than one enzyme, generally involved in sequential catalytic transformations.
• Note that they are different from multienzyme polypeptides, where multiple active sites are within one polypeptide chain.

Question 137

Give an example of a multienzyme complex.

Answer 137

Pyruvate dehydrogenase complex -> A complex of three enzymes that converts pyruvate into acetyl-CoA by a process called pyruvate decarboxylation. The acetyl-CoA may then be used in the Krebs cycle, so this multienzyme complex is important in linking glycolysis to the Krebs cycle.

Question 138

Describe an enzyme activated by subunit dissociation.

Answer 138

• cAMP-dependent protein kinases
• These are made out of a regulatory and catalytic subunit
• When cAMP binds to the regulatory subunit, the catalytic subunit dissociates and becomes uninhibited, so that it can perform its normal function

Question 139

What are the two types of co-factor?

Answer 139

• Co-enzymes -> Organic
• Inorganic ions

Question 140

What are co-enzymes derived from?

Answer 140

Vitamins

(Check if you need to know specific vitamins and exampels)

Question 141

What two concentrations does the rate of an enzyme catalysed reaction depend on?

Answer 141

• Enzyme concentration
• Substrate concentration

Question 142

Describe the equation that can be used to model an enzyme-catalysed reaction.

Answer 142

Question 143

What is Michaelis-Menten behaviour?

Answer 143

Michaelis-Menten behaviour is a kinetic model commonly exhibited by enzymes that catalyse a single-substrate equation and which do not feature co-operativity, resulting in a rate-substrate concentration graph of a rectangular hyperbolic shape

Question 144

What are some important variables in Michaelis-Menten kinetics?

Answer 144

• K_m (Michaelis constant)
• V_max (Maximal velocity)
• K_cat (Turnover number)
• K_cat/K_m (Specificity constant)

Question 145

What shape graph is characteristic of Michaelis Menten kinetics?

Answer 145

Rectangular hyperbola

Question 146

What is K_m, what does it indicate and what are the units?

Answer 146

• Michaelis constant
• It is the substrate concentration that produces half the maximal reaction rate (V_max) -> Therefore it is a measure of affinity
• It is a property of each enzyme molecule
• Units: M (or mol/dm³)

Question 147

What does a low K_m value indicate?

Answer 147

A high affinity.

Question 148

What is V_max, what does it indicate and what are the units?

Answer 148

• Maximal velocity
• The maximal rate of reaction possible with a given enzyme amount
• Units: mol/sec (Check this!)

Question 149

What is K_cat, what does it indicate and what are the units?

Answer 149

• Turnover number
• The number of substrate molecules each enzyme site converts to product per unit time
• Units: s^-1

Note: K_cat = k₂

Question 150

What is K_cat/K_m, what does it indicate and what are the units?

Answer 150

• Specificity constant
• It is a measure of how efficiently an enzyme converts substrates into products
• Unit: M^-1s^-1

Question 151

Do V_max, K_m and K_cat vary with enzyme concentration?

Answer 151

V_max does, but K_m and K_cat do not, since they are properties of each enzyme molecule.

Question 152

In terms of reaction variables, how can V_max be increased?

Answer 152

By increasing K_cat.

Question 153

What is Ki?

Answer 153

The concentration of inhibitor at which the reaction rate is half of V_max (assuming that the substrate is saturating).

Question 154

What is the Michaelis-Menten equation?

Answer 154

v = V_max[S] / (K_m + [S])

Question 155

Draw the graph showing Michaelis-Menten behaviour, with all of the variables labelled.

Answer 155

Question 156

What two assumptions can be made in order to derive the Michaelis-Menten?

Answer 156

• Equilibrium assumption
  
  • Makes use of the idea that k₁ and k_-1 sometimes differ to a negligible extent, so that E + S <-> ES is an equilibrium that is not greatly affected by the ES -> E + P reaction
  • However, this assumption only weakly applies in situations where [S] is very low (so that k₁ is too low) or where k₂ is large enough for ES to be near instantly converted to the product
• Steady state assumption
  
  • Assumes that ES is in steady state and so [ES] does not change as the reaction progresses.

Both assumptions lead to a derivation that results in the equation V = (Vmax[S]) / (K_m + [S]), where V is the initial reaction rate at a given [S]

Question 157

How can a normal velocity-substrate conentration curve be changed to enable identification of kinetic parameters?

Answer 157

• A Lineweaver Burk plot (a.k.a. double reciprocal plot) can be plotted
• This is a plot of 1/v against 1/[S]

Question 158

What does a Lineweaver Burk (double reciprocal plot) allow to be determined?

Answer 158

• y-intercept = 1/V_max
• x-intercept = -1/K_m
• Gradient = K_m/V_max

Question 159

Describe competitive inhibition. What is the effect on the rate-substrate concentration graph?

Answer 159

• An inhibitor can compete for the same binding site at the substrate – often the active site
• But this means that inhibition can be overcome by increased substrate concentration
• K_m is increased, but V_max stays the same

Question 160

Describe non-competitive inhibition. What is the effect on the rate-substrate concentration graph?

Answer 160

• Allosteric interaction represent ‘long distance’ interactions between binding sites on the protein.
• These sites, located in distinct domains of the protein, interact via conformational changes.
• Unaffected by changes in substrate concentration
• V_max is reduced, but K_m is unchanged

Question 161

What is irreversible inhibition?

Answer 161

• Reversible inhibitors usually covalently modify an enzyme, and inhibition can therefore not be reversed.
• Irreversible inhibitors often contain reactive functional groups that react with amino acid side chains to form covalent adducts.

Question 162

Describe how competitive inhibition appears on a double reciprocal graph (Lineweaver Burk)?

Answer 162

Question 163

Describe how non-competitive inhibition appears on a double reciprocal graph (Lineweaver Burk)?

Answer 163

Question 164

What are the two models of enzyme catalysis and how do they differ?

Answer 164

• Induced fit model -> Substrate induces the conformational change
• Selected fit model -> Selects and stabilizes a complementary conformation from a pre-existing equilibrium of ground and excited states of the protein

Question 165

What are the two points at which an enzyme’s functioning can be inhibited?

Answer 165

• Inhibiting or promoting substrate binding (affect KM)
• Inhibiting or promoting formation/release of products (affect Kcat)

Question 166

What is allosteric control?

Answer 166

The regulation of an enzyme by binding an effector molecule at a site other than the enzyme’s active site.

Question 167

What is the difference between allosteric control and non-competitive inhibition?

Answer 167

Non-competitive inhibition is a type of allosteric control.

Question 168

What is co-operativity?

Answer 168

The process when the binding of one ligand to a protein causes the affinity for the binding of another molecule of the same ligand to either increase or decrease.

Question 169

What are the different types of co-operativity?

Answer 169

• Positive -> Binding of one ligand increases the affinity for the second
• Negative -> Binding of one ligand decreases the affinity for the second

Question 170

What is the shape of the rate-substrate concentration graph for positive co-operativity?

Answer 170

Sigmoidal

Question 171

What is the shape of the rate-substrate concentration graph for negative co-operativity?

Answer 171

Hyperbolic like that of an enzyme without co-operativity, except Vmax is typically lower and is reached at a lower substrate concentration (lower K_m).

Question 172

What are allosteric enzymes?

Answer 172

Allosteric enzymes are enzymes that undergo a conformational change upon the binding of a ligand (known as the effector) at a site other than the active site, which changes the enzyme’s catalytic rate. The effector may be an activator if it increases the enzyme’s normal activity or an inhibitor if it decreases it.

Question 173

What are the two types of allosteric control?

Answer 173

• Homotropic regulation -> Where the effector is the same molecule as the substrate.
• Heterotropic regulation -> Where the effector is a different molecule to the substrate.

Question 174

Describe why allosteric enzymes do not follow Michaelis-Menten kinetics.

Answer 174

• Allosteric enzymes have multiple active sites
• These sites exhibit cooperativity
• Therefore this results in a sigmoidal curve (or hyperbolic if negative cooperativity)

Question 175

Describe the structure of allosteric enzymes.

Answer 175

• Most allosteric proteins are made up of many similar subunits (known as oligomers).
• As oppose to this, monomeric enzymes are usually Michaelis-Menten-abiding enzymes.
• This said, there is increasing evidence that not all allosteric enzymes are oligomeric, or even composed of multiple subunits, which means that a small number of allosteric proteins are monomeric. It has been postulated that this is as a result of evolution driving the “stitching” of separate genes into a single gene that encodes a protein responsible for multiple functions. Such an enzyme would contain more than one binding site per subunit, an example being the enzyme glutamate dehydrogenase. However, there also exist examples of allosteric proteins that are monomeric and contain only a single ligand binding site, such as glucokinase, which has a single binding site for glucose and yet displays a sigmoidal curve that is indicative of positive co-operativity. Currently, the mechanism explaining this phenomenon is not fully clear.

Question 176

Describe the effect of allosteric ligands on rate-substrate concentration graph.

Answer 176

• Positive effectors give rise to activation
  
  • Decreasing the KM, increasing the Vmax
  • Therefore curve shifts left and/or up
• Negative effectors give rise to inhibition
  
  • Increasing the KM, or decreasing the Vmax
  • Therefore curve shifts right and/or up

Question 177

Can cooperativity be homotropic and heterotropic?

Answer 177

Yes, but we usually consider positive homotropic cooperativity in sigmoidal curves.

Question 178

Give an example of a enzyme that demonstrates the importance of cooperativity and allostery.

Answer 178

• Phosphofructokinase (PKF) shows a strong positive co-operativity (and can be regulated by other allosteric inhibitors and activators)
• It is used to catalyse the ATP-dependent conversion of fructose 6-phosphate to fructose 1,6-bisphosphate (and ADP), which is a step that commits to the process of glycolysis, so the control of the rate of respiration is highly dependent on PKF activity.
• At low-to-medium substrate concentrations, the rate of glycolysis is low, but at medium-to-high substrate concentrations, the rate of glycolysis is high.
• The importance of this is that glycolysis becomes an almost binary process (either very fast or very slow), with only a narrow range of substrate concentrations that lead to average reaction rates, so that the system can very quickly revert to a set substrate concentration when deviation occurs.

Question 179

Suggest why negative cooperativity may be important.

Answer 179

It has been proposed that the importance of negative co-operativity pertains to the increased range of substrate concentrations at which the enzyme can convert the substrate, which comes at the cost of a weaker response. This is exemplified by some G-protein coupled receptors that exhibit negative co-operativity.

Question 180

What are the two main models of cooperativity?

Answer 180

• Concerted (MWC)
• Sequential (KNF)

Question 181

Describe the concerted (MWC) model of cooperativity.

Answer 181

• All of the subunits of the protein show functional symmetry, and each can take on either the R (relaxed) or T (tense) conformational states.
• The T state is the inactive form, while the R state is the active form.
• The R and T states are in an equilibrium at all times, and since all of the subunits are functionally symmetrical, all of the subunits shift simultaneously between T and R states.
• Co-operativity is explained by the idea that the binding of a substrate molecule shifts the equilibrium, so that in positive co-operativity binding results in a higher probability of the enzyme existing in the relaxed active form.
• Additionally, heterotropic inhibitors induce the T form, while activators induce the R form.

Question 182

Describe the sequential (KNF) model of cooperativity.

Answer 182

• All of the protein subunits each can take on either the R (relaxed) or T (tense) conformational states
• The T state is the inactive form, while the R state is the active form.
• Subunits do not need to maintain functional symmetry.
• The binding of a ligand to a subunit only directly causes that one subunit to change between the R and T states, but the co-operative effect occurs because this binding increases (or decreases in negative co-operativity) the affinity at other sites, until all of the sites are occupied.

Question 183

Compare simply how the two models of cooperativity work.

Answer 183

• The concerted model states that binding of the substrate causes the affinity of the protein to change due to a change in the quaternary structure of the protein
• The sequential model implies it is due to tertiary level changes (which also affect the quaternary structure).

Question 184

Which out of the relaxed and tense states is active in cooperativity?

Answer 184

Relaxed

Question 185

What is the importance of positive cooperativity?

Answer 185

It increases sensitivity to the substrate over a short substrate concentration window.

Question 186

Compare haemoglobin and myoglobin in terms of where they are found and their cooperativity.

Answer 186

• Haemoglobin
  
  • Supplies oxygen all over the body
  • Has multiple subunits and therefore shows cooperativity
  • Lower affinity for oxygen
• Myoglobin
  
  • Supplies muscle with oxygen
  • Has only one subunit and therefore no cooperativity
  • Higher affinity for oxygen

Question 187

What is ATCase?

Answer 187

• Aspartate transcarbamylase
• It catalyses the first step of the pyrimidine synthesis pathway, forming N-carbamoyl aspartate from carbamoyl phosphate and aspartate

Question 188

Describe allostery in ATCase.

Answer 188

• Aspartate transcarbamylase is involved in the first step of the pyrimidine synthesis pathway, forming N-carbamoyl aspartate from carbamoyl phosphate and aspartate.
• The composition of the subunits is C₆R₆, forming 2 trimers of catalytic subunits and 3 dimers of regulatory subunits.
• ATCase can be inhibited by CTP, the end product of the whole pathway (binds to REGULATORY subunits)
• ATCase can be activated by the substrate (binds to CATALYTIC subunits)

Question 189

What is the importance of drugs as allosteric ligands?

Answer 189

Drugs that are allosteric ligands are useful for the selective regulation of enzymes/receptors that have similar active or receptor sites to each other.

Question 190

What are the main mechanisms of enzyme regulation?

Answer 190

• Covalent (via chemical modification)
  
  • Proteolysis
  • Phosphorylation
• Non-covalent (via allosteric control)

Question 191

Draw a table showing all of the ways of controlling enzyme action.

Answer 191

Question 192

Describe how proteolysis can be used to regulate enzyme activity.

Answer 192

• Many proteins are synthesised in a ‘pro’ or inactive form (zymogen)
• Usually the ’pro-protein’ form contains an additional sequence of amino acids
• The active or functional form of the protein is only liberated following proteolytic cleavage of the additional sequence -> Ensures that it is activated at the right time and in the right place

Question 193

Describe how digestive enzymes are activated.

Answer 193

• Proteolytic enzymes such as trypsin and chymotrypsin (small intestine) and pepsin (stomach) are synthesised as zymogens.
• Proteolysis of these in their respective areas of action is used to expose the active site.

Question 194

Describe how covalent modification is involved in the blood clotting mechanism.

Answer 194

• Blood clotting involves two main pathways, called the intrinsic (damaged surface) and extrinsic (trauma) pathways, which converge into a final common pathway
• They converge in the activation of factor X, which is an endopeptidase used to cleave prothrombin into thrombin in to places
• Thrombin then cleaves fibrinogen (secreted by fibroblast cells) into fibrin
• Fibrin has two domains, D and E, which aggregate into proteofibrils.
• FIbrin also activates factor XIII, which cross links the fibrin protein together, forming a stable mesh

Question 195

Describe which proteins can be phosphorylated and how they can be phosphorylated and dephosphorylated.

Answer 195

• Phosphorylation tends to occur on OH groups, which are found on serine, threonine and tyrosine
• Phosphorylated by protein kinases using phosphates from ATP (or AMP)
• Dephosphorylated by phosphatases

Question 196

Why is phosphorylation so common?

Answer 196

• Serine, tyrosine and threonine are uncharged
• Transfer of phosphate from ATP to an OH group is very energetically favourable (i.e. all target converted)
• Phosphorylation of these residues introduces a bulky and negatively charged moiety
• Phosphorylation will introduce large conformational changes due to electrostatic repulsion/attraction
• These conformational changes can alter substrate binding or intra-protein communication

Question 197

What is a phosphorylation cascade?

Answer 197

• A sequence of events where one enzyme phosphorylates another, causing a chain reaction leading to the phosphorylation of thousands of proteins
• It can be seen with the singal transduction of hormone messages

Question 198

What is the importance of phosphorylation cascades?

Answer 198

They can be used to rapidly amplify a signal transmitted to a cell inside the cell.

Examples of signal transduction:

• Cell cycle
• Glycogen breakdown
• Transcriptional regulation
• Cell growth and development

Question 199

What is mevanolin?

Answer 199

• It is a HMG-CoA reductase inhibitor (a.k.a. a statin)
• It is used to lower blood cholesterol

Question 200

What makes lipids insoluble in water?

Answer 200

Large regions of the surface composed of hydrocarbons with very few polar groups.

Question 201

Give some of the roles of lipids.

Answer 201

• Energy storage
• Membranes
• Insulation
• Chaperones for protein folding
• Light absorber (chlorophyll, retinal)
• Energy transduction (retinyl component attached to rhodopsin)
• Electron transfer (coenzyme Q)
• Hormone (testosterone, progesterone)
• Vitamins (vitamin A, E, D and K)
• Antioxidants (vitamin E)
• Signaling molecules (ceramides)

Question 202

What are the two major divisions of lipids?

Answer 202

• Simple -> Esters of fatty acids and glycerols or alcohols
• Complex -> Contain other groups, such as phosphate groups

Question 203

What are the 8 types of lipid?

Answer 203

• Fatty acid
• Glycerolipid (including triglycerides)
• Glycerophospholipid (a type of phospholipid)
• Sphingolipid (a type of phospholipid)
• Sterol lipid
• Prenol lipid
• Saccharolipid
• Polyketide

Question 204

What is a fatty acid?

Answer 204

• A monocarboxylic acid, usually with a long unbranched aliphatic tail that may either by saturated or unsaturated
• It is the fundamental building block of lipids

Question 205

Describe the general structure of fatty acids.

Answer 205

• Hydrophilic carboxyl head
• Saturated or unsaturated hydrophobic tail

Question 206

What are the different types of fatty acid depending on their length?

Answer 206

• Short-chain fatty acids (5 or fewer carbons)
• Medium-chain fatty acids (6 to 12 carbons)
• Long-chain fatty acids (13 to 21 carbons)
• Very long-chain fatty acids (22 or more carbons)

Question 207

What is the difference between fats and lipids?

Answer 207

Lipids are the general group of molecules that are soluble in non-polar solvents. Fats are a subdivision of lipids and are esentially triglycerides (double-check this!).

Question 208

Describe the naming of the carbons on a fatty acid molecule.

Answer 208

Question 209

What is the maximal number of double bonds a fatty acid chain can have?

Answer 209

6

Question 210

Describe fatty acid nomenclature.

Answer 210

e.g. 18:2 ∆^{9, 12} or 18:2 (ω-6) or 18:2 (n-6)

• The first number (18) indicates the number of carbons
• The second number (2) indicates the number of double bonds
• 18:2 ∆^{9, 12} ->The delta numbers indicate the position of the double bonds, with the first double bond being counted from the alpha (carboxyl) end
  
  • It is assumed that the bonds as cis, unless a ‘t’ is put after a number
• 18:2 (ω-6) or 18:2 (n-6) -> The omega or n numbers indicate the number of the double bond closest to the omega (non-carboxyl) end

Question 211

Give the omega name for this fatty acid.

Answer 211

C20:5 (ω-3)

Question 212

What are essential fatty acids?

Answer 212

Fatty acids that are necessary for human health but which cannot be synthesised by the body and must therefore be ingested.

Question 213

What are two essential fatty acids?

Answer 213

• Alpha-linolenic acid (an omega-3 fatty acid)
• Linoleic acid (an omega-6 fatty acid)

Question 214

What is the importance of trans fatty acids?

Answer 214

• TFAs enter the diet through dairy products, meat and partially hydrogenated plant oils that are commonly found in processed food.
• TFAs are suspected of disrupting the membrane bilayer, thus its function, and are linked to heart disease.

Question 215

What are isoprenoid fatty acids and what is their importance?

Answer 215

• Branched fatty acids containing repeating methyl branches called isoprenoids.
• Appear to be made of long polymers of a 5-carbon branched compound called Isoprene.
• Their role is to disrupt lipid packing and anchoring important biochemicals to the membrane (Vitamin A and Coenzyme Q).

Question 216

How many carbons do fatty acids in humans tend to contain?

Answer 216

An even number.

Question 217

What is the function of double bonds in fatty acids?

Answer 217

Induces a kink, which disrupts tight lipid packing in membranes, thus increasing the packing free volume ‘breathing space’ for normal membrane protein function (channels, receptors and transporters to function).

Question 218

What are the sources of fatty acids?

Answer 218

• Dietary
• De Novo synthesis

Question 219

Describe how diglycerides and triglycerides are synthesised.

Answer 219

• Carboxyl groups of fatty acids are made more reactive by the addition of coenzyme A, which contains a highly reactive thiol group
• These are they used along with glycerol to make diglycerides and triglycerides

Question 220

Describe the function of diglycerides.

Answer 220

• Signalling molecules
• Synthesis of triglycerides

Question 221

Describe the function of triglycerides.

Answer 221

• Storage
• Transport

Question 222

Describe the structure of diglycerides and triglycerides.

Answer 222

2 or 3 fatty acid molecules joined by ester bonds to a glycerol molecule.

Question 223

How are fatty acids joined to the rest of the molecule in lipids?

Answer 223

• Oxygen ester bond (e.g. in triglycerides)
• Amide bond (e.g. in sphingolipids) (Note: This can be thought of as a ‘nitrogen ester’)
• Thioesters

Question 224

How can ester bonds in a lipid be hydrolysed?

Answer 224

Boiling in NaOH or KOH.

Question 225

What is the more correct term for phospholipids?

Answer 225

Glycerophospholipids

Question 226

Describe the structure of a phospholipid.

Answer 226

• One glycerol
• Two fatty acids
• One phosphate
• One alcohol -> This is attached to the phosphate and varies between phospholipids

Question 227

What phospholipid classes do you need to know about and what is the alcohol group of each?

Answer 227

• PA -> Phosphatidic acid -> No alcohol
• PE -> Phosphatidylethanolamine -> Ethanolamine
• PC -> Phosphatidylcholine -> Choline
• PS -> Phosphatidylserine -> Serine
• PI -> Phosphatidylinositol
• CL -> Cardiolipin (a.k.a. diphosphatidylglycerol) -> Phosphatidylglycerol

Question 228

Name the different head groups in phospholipids and their charges.

Answer 228

Question 229

What is the role of phosphatidic acid in the cell?

Answer 229

• Smallest phospholipid
• Gives curvature to membranes
• Ca²⁺ can be used to aggregate several PAs and create a patch sensitive to temperature and pH

Question 230

What is the role of phosphatidylethanolamine in the cell?

Answer 230

• Found in cell membranes -> Particularly prevalent in nerve tissue
• Contains primary amine and therefore has a highly reactive chemical handle that can be easily modified

Question 231

What is the role of phosphatidylcholine in the cell?

Answer 231

• Major structural protein in membranes
• This is because it allows tight packing, partly due to the zwitterionic nature that means no charge disruption

Question 232

What is the role of phosphatidylserine in the cell?

Answer 232

• Enriched in brain tissue -> Suggests an important role in cognition -> Also declines with age
• Involved in many functions, including anchoring proteins in the membrane

Question 233

What is the role of phosphatidylinositol in the cell?

Answer 233

• Plays only a minor role in the membrane
• Mostly involved in signalling -> Particularly abundant in the brain
• Can be phosphorylated in 3 places, producing phosphatidylinositol phosphates
  
  • e.g. PIP₂ can be converted into DAG and IP₃ by phospholipase C

Question 234

What is the role of cardiolipin in the cell?

Answer 234

• Found predominantly in the mitochondrial inner membrane
• Stabilises proteins in the electron transport chain

Question 235

Describe infant respiratory distress syndrome.

Answer 235

• Pulmonary surfactant is a mixture of phospholipids and lipoproteins secreted by type II pneumocytes.
• It diminishes the surface tension of the water film that lines alveoli, thereby decreasing the tendency of alveoli to collapse and the work required to inflate them.
• If there are problems with these molecules, then the lungs have trouble inflating and the infant may need to be placed on a ventilator.

Question 236

What enzymes are used to degrade phospholipids?

Answer 236

• Phospholipases A1 and A2 are used to remove the acyl chains
• Phospholipase C is used to remove the head group

Question 237

Describe the structure of sphingolipids.

Answer 237

• Sphingosine backbone (an 18 carbon amino alcohol)
• Acyl group (fatty acid chain) is amide-linked to the carbon-2 of the backbone
• Variable group is attached to carbon-1 of backbone

Question 238

What are the different classes of sphingomyelin you need to need to know about?

Answer 238

• Sphingomyelin
• Gangliosides
• Cerebrosides

Question 239

Describe the variable group of sphingomyelin (as a sphingolipid) and its role.

Answer 239

• Variable group = Phosphocholine (or less commonly phosphoethanolamine) (meaning that sphingomyelins may also be classified as sphingophospholipids)
• Role:
  
  • Electrical insulation in nerve fibres
  • Used in signal transduction
  • Apoptosis

Question 240

Describe the variable group of gangliosides (as a sphingolipid) and its role.

Answer 240

• Variable group: Complex saccharides
• Role:
  
  • Oligosaccharide groups on gangliosides act as markers in cellular recognition and cell-to-cell communication.
  • Also act as specific receptors for pituitary glycoprotein hormones and bacterial protein toxins.

Question 241

Describe the variable group of cerebrosides (as a sphingolipid) and its role.

Answer 241

• Variable group: Glucose or galactose
• Role:
  
  • Need to be turned over properly or may result in Gauchers

Question 242

What is the clinical relevance of sphingolipids?

Answer 242

The absence of specific sphingolipid degrading enzymes are know to cause a number of deadly, incurable genetic lysosomal storage diseases:

• Tay-Sachs disease
• Gaucher’s disease
• Niemann-Pick disease.

Question 243

What is the major sterol in animals?

Answer 243

Cholesterol

Question 244

Describe the difference between cholesterol, sterols, steroids and steroid hormones.

Answer 244

• Cholesterol is a type of sterol
• Sterols are alcohol steroids
• Steroid hormones are steroids that act as hormones

Question 245

Describe the structure of cholesterol.

Answer 245

Cholesterol is composed of:

• Three 6-membered rings
• One 5-carbon ring
• Short aliphatic chain
• Single hydroxyl group

Question 246

Describe the structure of bile acids and steroid hormones.

Answer 246

They are derivates of cholesterol, so they have a similar basic structure:

• Three 6-membered rings
• One 5-carbon ring
• Short aliphatic chain
• Single hydroxyl group

Question 247

Describe some of the important structural features of cholesterol.

Answer 247

• The amphiphilic nature is conferred by the hydroxyl group
• The hydroxyl group can be esterified in cholesteryl esters, leading to a highly nonpolar structure.
• The molecules display a planar configuration which is rigid.
• The compactness of sterols confer an important role for packing in membranes

Question 248

What can steroid hormones do?

Answer 248

Regulate transcription.

Question 249

Describe cholesterol synthesis and how it can be inhibited.

Answer 249

• Acetyl CoA is converted to HMG CoA
• HMG CoA is then converted to mevalonate by HMG CoA reductase
• Mevalonate is then converted to cholesterol

Statins are often HMG CoA reductase inhibitors an therefore lower cholesterol levels.

Question 250

Give two examples of bile salts and their function.

Answer 250

• Cholic acid and chenodeoxycholate
• Bile salts & acids have higher hydrophilicity than cholesterol and are excreted into the intestine to emulsify lipids to aid digestion

Question 251

Name the 3 main roles of lipids in the cell and give an example of each.

Answer 251

• Structural components of membranes -> Phospholipids, sphingolipids
• Signaling molecules -> Phosphoinositides, arachidonic acid and steroid hormones
• Fuels -> Triglycerides as high density energy sources

Question 252

What are glycoconjugates?

Answer 252

• Mono-, oligo-, or polysaccharides attached to proteins or lipids.
• i.e. Glycoproteins and glycolipids

Question 253

What are glycans?

Answer 253

The sugars WITHIN glycoproteins, glycolipids and proteoglycans.

Question 254

What are lectins?

Answer 254

Proteins that bind specifically to carbohydrates.

Question 255

Name the different types of glycoconjugates.

Answer 255

• Those attached to lipids
• Those attached to proteins through a nitrogen atom (N-linked glycan)
• Those attached to proteins through an oxygen atom (O-linked glycan)

Question 256

Where are glycoconjugates (glycoproteins and glycolipids) found?

Answer 256

• At the cell surface membrane.
• Glycoproteins are also secreted into biological fluids and make up the insoluble ECM

Question 257

What is the difference in structure between a proteoglycan and a glycoprotein?

Answer 257

• Proteoglycans have long chains with disaccharide as repeating structures.
• Glycoproteins have short highly branched glycan chains with no repeating unit.

Question 258

What are some functions of glycoconjugates (glycoproteins and glycolipids)?

Answer 258

• Intrinsic
  
  • Structural components, Cell walls -> ECM
  • Modifying protein properties -> Solubility and stability
• Extrinsic
  
  • Directing trafficking of glycoconjugates
  • Mediating and modulating cell adhesion
  • Mediating and modulating signaling

Question 259

What type of sugar are glycans (the sugars in glycolipids and glycoproteins) usually?

Answer 259

They are usually monosaccharides, most commonly hexoses.

Question 260

What is the general formula for simple sugars?

Answer 260

C_n(H₂O)_n

Question 261

Give some examples of monosaccharides.

Answer 261

• Glucose
• Fructose
• Galactose

Question 262

What type of hexose is glucose?

Answer 262

Aldose - it contains an aldehyde group.

Question 263

What type of hexose is fructose?

Answer 263

Ketose - it contains a ketone.

Question 264

What is the relevance of stereochemistry in hexoses?

Answer 264

• Hexoses contain 4 chiral carbons
• This means that there are 16 possible configurations for aldoses (with the aldehyde at the top) and 16 possible ketoses
• There are 8 different aldosose, each with a D and L configuration, which depends on the OH on the final carbon
• This means that D-glucose and D-galactose are very similar, differing only by the carbon-4 orientation -> This makes them epimers
• On the other hand, D-glucose and L-glucose are enantiomers, since they are mirror images

Question 265

Name this a sugar.

Answer 265

D-galactose

Question 266

Name this sugar.

Answer 266

D-fructose

Question 267

Name this sugar.

Answer 267

D-glucose

Question 268

Name the two types of ring that a sugar can form.

Answer 268

• Pyranose
• Furanose

Question 269

Describe a pyranose ring and how it forms.

Answer 269

• A hexagonal ring containing 5 carbons and 1 oxygen
• Formed when the alcohol group on an aldose reacts with the aldehyde group

Question 270

Describe a furanose ring and how it forms.

Answer 270

• A pentagonal ring containing 4 carbons and 1 oxygen
• Formed when the alcohol group on an ketose reacts with the ketone group

Question 271

Describe anomeric carbons and the numbering of carbons in a pyranose and furanose ring.

Answer 271

• The anomeric carbon is the one that is next to the O in the ring and that has an OH on it
• In pyranose rings, it is C1, while it furanose rings it is C2
• The carbons are numbered from the end of the carbon chain so that the anomeric carbon has the lower possible number

Question 272

Describe the importance of the atoms attached to the anomeric carbon.

Answer 272

• If the OH points down (when the O is at the top of the ring), then the sugar is alpha
• If the OH points up (when the O is at the top of the ring), then the sugar is beta

Question 273

Describe how sugars can acts as reducing sugars and which ones can do this.

Answer 273

• Sugars that are open-chain with a free aldehyde group can act as reducing agents
• This includes aldoses and ketoses that can easily convert to aldoses
• The sugar reduces something while being oxidised -> Its carbonyl group is converted to a carboxyl group
• This includes all monosaccharides

Question 274

Describe how blood sugar tests work.

Answer 274

• They rely on the reducing properties of reducing sugars
• Classically, Fehling’s solution:
  
  • Copper(II) ions of the complex are reduced to copper(I) ions
  • Red copper(I) oxide then precipitates out of the reaction mixture, which indicates a positive result i.e. that redox has taken place.
• Modern tests involve either an electronic meters or colourimetric strips
  
  • Use glucose oxidase, that catalyses the oxidation of glucose to hydrogen peroxide and D-gluconolactone
  • Electronic meters measure the transfer of electrons
  • Colourimetric strips measure the hydrogen peroxide produced

Question 275

Draw the formation of a glycosidic bond.

Answer 275

Question 276

Describe the difference between an alpha and beta 1,4 glycosidic bond.

Answer 276

• In alpha bonds, the two OH groups forming the bond are on the same side
• In beta bonds, the two OH groups forming the bond are on different sides

Question 277

What are the main roles of carbohydrates?

Answer 277

• Structural
• Energy sources
• Biosynthetic precursors
• Signalling molecules

Question 278

When naming glycosidic bonds by the numbering of the carbons they link to, what two types do you need to know about?

Answer 278

1,4 and 1,6

Question 279

What sugars and bonds are found in glycogen, starch and cellulose?

Answer 279

All are homopolyers of glucose:

• Glycogen -> α-1,4 glycosidic bonds
• Starch -> α-1,4 glycosidic bonds
• Cellulose -> β-1,4 glycosidic bonds.

Question 280

Where is cellulose found, what is its structure and what is its function?

Answer 280

• It is found in the cell walls of plants
• It is a linear polymer of glucose, joined by β-1,4 glycosidic bonds -> There are hydrogen bonds between fibres, giving strength against osmotic expansion

Question 281

What are the two types of starch and what are their structures?

Answer 281

• Amylose -> Unbranched
• Amylopectin -> Branched, but less than glycogen and longer branches

Question 282

Where is starch found, what is its structure and what is its function?

Answer 282

• It is found in plant cells
• It forms unbranched (amylose) or branched (amylopectin) homopolymers of glucose
  
  • Within branches there are α-1,4 glycosidic bonds
  • Branches are formed by α-1,6 glycosidic bonds
• It is used for energy storage

Question 283

Where is glycogen found, what is its structure and what is its function?

Answer 283

• It is found in animal cells
• It forms unbranched homopolymers of glucose
  
  • Within branches there are α-1,4 glycosidic bonds
  • Branches are formed by α-1,6 glycosidic bonds
• It is used for energy storage

Question 284

Why are homopolymers useful for energy storage?

Answer 284

They do not affect osmotic potential.

Question 285

Describe how glycogen and starch are broken down in the cell.

Answer 285

Broken down from the (4)-end via phosphorylase: more branches, the faster the breakdown.

Question 286

What are some examples of disaccharides?

Answer 286

• Sucrose
• Maltose
• Lactose

Question 287

Give an example of the structural role of carbohydrates.

Answer 287

• Glycosaminoglycans (GAGs) are carbohydrate polymers that are attached to ECM proteins to form proteoglycans.
• These molecules have a net negative charge, which attract sodium ions and water, thus keeping the cells hydrated.
• This also gives compression strength to tissues.

Question 288

Describe the structure and role of proteoglycans.

Answer 288

• Proteoglycans are proteins that are heavily glycosylated.
• The basic proteoglycan unit consists of a “core protein” with one or more covalently attached glycosaminoglycan (GAG) chains
• Each GAG chain consists of alternating amino sugar derivatives and hexose derivatives
• Several proteoglycan units can be arranged along a hyaluronic acid backbone, which acts as scaffold
• The negative charge of the proteoglycan and the long carbohydrate chains help with stability and compression strength since they attract water to the ECM

Question 289

What are the different GAGs and what are they named after?

Answer 289

They are named after where they were first isolated:

• Hyaluronic acid -> Hyaline membranes
• Chondroitin sulphate -> Cartilage
• Dermatan sulphate -> Skin
• Keratin sulphate -> Skin

Question 290

What is the one unusual GAG and what makes it unusual?

Answer 290

• Hyaluronic acid
• It doesn’t form a proteoglycan with a core protein, but it acts as the very long backbone for the attachment of all of the other proteoglycans (non-covalently)

Question 291

What is the major proteoglycan in ECMs?

Answer 291

Aggrecan

Question 292

Describe the linkages in proteoglycan structures.

Answer 292

• Hyaluronic does not form proteoglycans (only acts as backbone)
• Chondroitin sulfate, dermatan sulfate -> O-linked glycosylation
• Keratan sulfate -> N-linked glycosylation

Question 293

Where is each GAG found:

• Hyaluronic acid
• Chondroitin sulphate
• Dermatan sulphate
• Keratin sulphate

Answer 293

• Hyaluronic acid -> Connective tissues, Skin, Cartilage, Synovial fluid
• Chondroitin sulphate -> Cartilage, Cornea, Bone, Skin, Arteries
• Dermatan sulphate -> Skin, Blood vessels, Heart valves
• Keratin sulphate -> Cartilage, Cornea

Question 294

Give some examples of different proteoglycans in different parts of the body.

Answer 294

• Aggrecan -> Cartilage
• Neurocan -> Brain
• Versican -> Blood vessels + Skin

Question 295

What amino acids allow for N-linked glycosylation and O-linked glycosylation?

Answer 295

• N-linked glycosylation -> Asparagine
• O-linked glycosylation -> Serine/threonine

Question 296

For N-linked glycosylation, what amino acid and sugar is typically involved? Is the link alpha or beta?

Answer 296

• Amino acid = Asparagine
• Sugar = N-acetylglucosamine (GlcNAc) (usually)
• 𝛽 configuration

Question 297

Describe the synthesis of an N-linked glycan structure.

Answer 297

1. Synthesis of dolichol-linked precursor oligosaccharide
   
   • Occurs in the cytoplasm
   • Dolichol is found on the outside of the ER membrane
   • Oligosaccharide is built up on dolichol phosphate (which is a long lipid made of repeating isoprene groups and an alcohol functional group) -> Dolichol phosphate acts as an anchor
   • Part of the synthesis occurs on the outside and part occurs on the inside of the ER
2. En bloc transfer of precursor oligosaccharide to protein
   
   • Occurs inside the ER during translation
   • Oligosaccharyl transferase transfers the oligosaccharide to the asparagine residue of the target protein at a target sequence
3. Processing of the oligosaccharide
   
   • Occurs inside the ER and then inside the Golgi apparatus
   • Exoglycosidases (cleave sugars from non-reducing end)
   • Glycosidase I removes terminal 𝛼1-2 linked glucose, whereas glucosidase II cleaves 𝛼1-3
   • Followed by a series of mannosidases, that remove mannose linked 𝛼1-2
   • Glycans containing between 5 and 9 mannose sugars are called high mannose oligosaccharides.
   • Finally, complex glycans are just built on this core that consists of just three mannose residues and two GlcNAc residues.

Question 298

Describe how blood type is determined and what the Bombay phenotype is.

Answer 298

• Blood type depends on the sugars in N-linked glycans attached to cell-surface proteins
• The antigenic glycans are built up on the ends of polylactosamine chains by fucosyltransferase -> This generates an H antigen.
• Individuals with the O blood group only contain this sugar.
• In A type individuals, a GalNAc residue is added to the terminal galactose, while in B type individuals, a Gal residue is appended.
• In AB type both modifications are present.
• Bombay phenotype -> Individuals lacking the genes for the fucosyltransferase make antibodies to the H antigen -> This means that they cannot receive any ABO blood groups.

Question 299

What are the main types of O-linked proteins?

Answer 299

• Proteoglycans
• Mucins
• Antibodies have small amounts of O-linked sugars at their hinges

Question 300

What are mucins and what is their function?

Answer 300

• Heavily O-glycosylated proteins
• Their role is to retain water and form gels, which is useful as a barrier and for lubrication
• Aside from this, transmembrane mucins have a receptor-like structure that is similar to immune receptors. The highly glycosylated extracellular domain of transmembrane mucins has a barrier function whereas the intracellular domain can be phosphorylated and activate signal transduction pathways. The extracellular domain of transmembrane mucins can bind bacteria and can be shed from the epithelial surface. Shedding of the extracellular domain could be an activation signal that leads to phosphorylation of the intracellular domain and activation of mucin-specific signaling pathways that alter inflammatory responses, epithelial cell adhesion, differentiation, and apoptosis.

Question 301

How does the process of O-linked glycosylation differ from N-linked glycosylation?

Answer 301

Similarities:

• Utilises glycosyltransferases analagous to those in N-linked pathways

Differences:

• All sugars are added sequentially, starting with the first GalNAc residue attached to the Ser/Thr. (there is no preferred or en bloc transfer event).
• There are no simple target sequences for O-linked glycosylation analagous to the Asn-X-S/T sequence.
• Specificity comes from recognition of the target protein by the oligosaccaharide transferase.
• O-linked glycosylation takes place in the Golgi apparatus post-translationally (i.e. not linked to protein translation).

Question 302

Name some of the roles of glycoproteins.

Answer 302

Question 303

Describe how glycolipids function as anchors.

Answer 303

• Anchoring proteins to lipid membranes by covalent attachment to fatty acids and lipids is an important alternative to anchoring through transmembrane helices
• In mammalian cells >100 proteins are known to be attached to the membrane through the use of membrane anchors
• Glycolipids attached to proteins are usually known as glycosylphosphatidyl inositol (GPI) anchors
• The glycan that bridges between the protein and the lipid is attached to the inositol head group of the lipid.
• For example, in humans AChE is tethered using a GPI anchor.
• The linkage may be cut to release the protein.

Question 304

What are lectins and what are the different types?

Answer 304

They are proteins that bind to sugar molecules:

• C-type lectins (sometimes referred to as selectins) -> Participate cell adhesion
• L-selectins on the surface of lymphocytes -> Binds to counter receptors on endothelial cells
• P and E selectins -> Involved in the migration of neutrophils to sites of inflammation

Question 305

Give some examples of molecules that carbohydrates are involved in the synthesis of.

Answer 305

• Nucleotides
• Fatty acids
• Amino acids

(Add some more flashcards on this?)

Question 306

What are some of the functions of biological membranes?

Answer 306

• Barrier
• Selective permeability
• Response to external stimuli
• Electrical excitability
• Energy conversion processes
• Signalling to external environment

Question 307

What are some common features of biological membranes?

Answer 307

• Membranes are sheet-like structure only a few molecules thick (50 - 70 Angstroms; 5-7nm)
• Membranes form self-repairing closed boundaries between compartments
• Membranes contain proteins embedded in a phospholipid bilayer
• Distinctive functions of membranes are mediated by the membrane proteins
• Membranes exist as non-covalent assemblies, held together by co-operative non-covalent forces
• Membranes are asymmetric - the two faces of the membrane differ in composition both for protein (absolute asymmetry) and lipid (relative asymmetry)
• Membranes form a highly fluid structure - “a two-dimensional solution of oriented proteins and lipids”
• Phospholipids may cluster to form patches or ‘rafts’ with distinct protein composition and properties

Question 308

Describe compartmentation within the cell.

Answer 308

• There is the classic form of compartmentation within organelles in the cell
• There is also dynamic membrane-free compartmentalisation by phase separation -> Examples include lipid droplets, stress granules and the nucleolus within the nucleus

Question 309

What is the cytoskeleton?

Answer 309

Complex networks of protein filaments extending throughout the cytoplasm.

Question 310

See flashcards on the cytoskeleton in the OB deck 1.

Answer 310

Do it.

Question 311

By what process is communication between organelles enabled?

Answer 311

Vesicular trafficking -> It prevents loss of organelle identity of leakage into the cytoplasm.

Question 312

What are the main vesicle trafficking route you need to know about?

Answer 312

From endoplasmic reticulum to Golgi apparatus, then to the plasmalemma or to lysosomes.

Question 313

Describe the vesicle trafficking route that comes from the endoplasmic reticulum.

Answer 313

• Endoplasmic reticulum passes vesicles to the Golgi apparatus
• From the Golgi, the vesicles can go to the cell membrane or to lysosomes (for degradation)

Question 314

What are the two functions of vesicular trafficking to the cell membrane?

Answer 314

1. Adds material to the plasmalemma
2. Allows secretion into the extracellular space

Question 315

What are the two forms of vesicular secretion from a cell?

Answer 315

• Constitutive -> When secretion is continuous, regardless of external factors or signals
• Regulated

Question 316

What is receptor-mediated endocytosis?

Answer 316

• A process by which cells absorb metabolites, hormones, proteins by the inward budding of the plasma membrane (invagination).
• This process forms vesicles containing the absorbed substances and is strictly mediated by receptors on the surface of the cell.
• Only the receptor-specific substances can enter the cell through this process.

Question 317

Describe the pathway of materials endocytosed into vesicles.

Answer 317

• Join early endosomes
• These become late endosomes and fuse with lysosomes
• This is where the material is processed

Question 318

What is transcytosis?

Answer 318

A type of transcellular transport in which various macromolecules are transported across the interior of a cell. Macromolecules are captured in vesicles on one side of the cell, drawn across the cell, and ejected on the other side.

Question 319

What is used to direct the secretion of a newly synthesised protein in vesicles?

Answer 319

Signal sequence -> A short peptide (usually 16-30 amino acids long) present at the N-terminus of the majority of newly synthesized proteins that are destined towards the secretory pathway.

Question 320

Draw the cell cycle.

Answer 320

NOTE: The arrow out of the cycle points to G₀, for non-cycling cells.

Question 321

What happens in the S phase of the cell cycle?

Answer 321

DNA replication

Question 322

What happens in the M phase of the cell cycle?

Answer 322

Mitosis

Question 323

Do G₁ and G₂ phases of the cell cycle involve an specific events?

Answer 323

No, they tend to involve growth, but no specific events must happen in them.

Question 324

What are the stages of mitosis you need to know about?

Answer 324

• Prophase
• Metaphase
• Anaphase
• Telophase
• Cytokinesis

Question 325

What happens at the start of mitosis?

Answer 325

Appearance of the chromosomes and separation of the chromatids

Question 326

Draw the stages of mitosis.

Answer 326

NOTE: Don’t think you need to know about prometaphase.

Question 327

What organism is very good for studying the cell cycle?

Answer 327

Yeast

Question 328

What are cdc genes?

Answer 328

Genes that code for proteins that regulate the cell division cycle. They regulate the movement between mitosis, interphase, etc.

Question 329

How can cdc genes be identified? [EXTRA?]

Answer 329

Cloning by functional complementation

Question 330

What is an example of an important cdc gene?

Answer 330

cdc2

Question 331

What does the cdc2 gene encode and what does it do?

Answer 331

Encodes a cyclin-dependent protein kinase (CDK):

• Activity totally dependent on association with a cyclin partner protein
• Phosphorylates numerous protein substrates to drive cell cycle transitions

Question 332

Draw the cell cycle showing the involvement of CDK proteins. [EXTRA?]

Answer 332

Question 333

Draw the main checkpoints in the cell cycle.

Answer 333

Question 334

What is ataxia-telangiectasia (A-T)?

[EXTRA?]

Answer 334

A condition characterised by no cell cycle response to the chromosomal breakages.

Question 335

Draw the stages of meiosis.

Answer 335

Question 336

What does meiosis produce?

Answer 336

Haploid gametes

Question 337

What is another name for meiosis I?

Answer 337

Reductive division

Question 338

What cells undergo meiosis I?

Answer 338

Primary gametocytes

Question 339

When does crossing over of chromatids (exchange of maternal and paternal genes) occur in meiosis?

Answer 339

Prophase I

Question 340

When does independent segregation occur in meiosis?

Answer 340

Anaphase I

Question 341

Describe the stages of meiosis I.

Answer 341

• Follows normal S phase in primary gametocyte
• Prophase I:
  
  • Pairing of homologous chromosomes
  • Chromatids cross-over (exchange of maternal and paternal genes)
• Metaphase I
• Anaphase I:
  
  • Maternal and paternal chromosomes separate at random to form daughter nuclei
• Telophase I

Question 342

What is the product of meiosis I?

Answer 342

Two secondary gametocytes

Question 343

Describe what happens in meiosis II.

Answer 343

It essentially resembles mitosis.

Question 344

Is there an S phase between meiosis I and II?

Answer 344

No

Question 345

How many gametes can be produced from a primary gametocyte?

Answer 345

4

Question 346

Draw the process of oogenesis, including where the cell cycle is arrested.

Answer 346

Question 347

How does the likelihood of meiotic segregation errors vary with maternal age?

Answer 347

It increases with age.

Question 348

Name the 3 ways in which meiosis and sexual behaviour generates diversity.

Answer 348

• Crossing-over during prophase I
• Independent assortment during meiosis I
• Different male and female gametes fuse on fertilization

Question 349

What are constitutive and facultative heterochromatin?

Answer 349

• Facultative heterochromatin -> The result of genes that are silenced through a mechanism such as histone deacetylation
• Constitutive heterochromatin -> Active DNA

Question 350

What are the main PTMs mentioned in the spec?

Answer 350

• Disulfide bonding
• Cross-linking
• Peptidolysis
• Glycosylation
• Phosphorylation
• Adenylation
• Farnesylation

Question 351

What are the main roles of PTMs?

Answer 351

• Regulation
• Targeting
• Turnover
• Structural

Question 352

Which amino acids can be glycosylated?

Answer 352

• N-linked:
  
  • Asparagine
  • Arginine side-chains
• O-linked:
  
  • Serine
  • Threonine
  • Tyrosine
  • Hydroxylysine
  • Hydroxyproline

Question 353

What amino acids can be phosphorylated?

Answer 353

• Threonine
• Serine
• Tyrosine

Question 354

What is adenylation?

Answer 354

• The process of attaching an AMP molecule to a protein side chain by covalent bonding.
• a.k.a. AMPylation

Question 355

Which amino acids can be adenylated?

Answer 355

• Tyrosine
• Threonine
• Serine

Question 356

What does adenylation do?

Answer 356

Affects various protein properties, including:

• Stability
• Enzymatic activity
• Co-factor binding

Question 357

What is farnesylation?

Answer 357

Addition of an isoprenyl group to an amino acid.

Question 358

What does farnesylation do?

Answer 358

Important to mediate protein–protein interactions and protein–membrane interactions

Question 359

Which amino acids can be farnesylated?

Answer 359

Cysteine