1. Cellular & Molecular Structure & Function Flashcards

Question

What are the charged amino acids?

Answer 1

Basic (positively charged): * Lysine * Histidine * Arginine Acidic (negatively charged): * Aspartic acid * Glutamic acid

Answer 2

* Serine * Threonine * Asparagine * Glutamine

Answer 3

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

Answer 4

* Cysteine * Selenocysteine * Glycine * Proline

Answer 5

* 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).

Answer 6

* 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

Answer 7

Glycine, because it is so small and flexible.

Answer 8

* 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.

Answer 9

* 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.

Answer 10

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

Answer 11

* 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)

Answer 12

On syllabus: * Disulfide bonding * Cross-linking * Peptidolysis * Glycosylation * Phosphorylation * Adenylation * Farnesylation Others: * Methylation * Acetylation * Hydroxylation * Isoprenylation * Ubiquitination * Deamidation

Answer 13

Do it, using Miffy's essay.

Answer 14

Alpha-carbon

Answer 15

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

Answer 16

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

Answer 17

Enantiomers: * D-(Dextro) * L-(Laevo)

Answer 18

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

Answer 19

* 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

Answer 20

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).

Answer 21

* 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\*.

Answer 22

* 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

Answer 23

* The psi bond has the **PS**ame atoms on each side of the bond, and the symbol is like **PS**oidon's trident * The phi bond has di**PHI**rent atoms on each side of the bond, and the symbol looks like a pie being cut in half (pie rhymes with phi)

Answer 24

Ramachandran plot

Answer 25

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

Answer 26

* 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

Answer 27

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

Answer 28

* 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

Answer 29

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

Answer 30

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

Answer 31

* 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

Answer 32

* 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

Answer 33

The standard is the n+4 helix, but rarely there may also be: * 3₁₀ helix -\> n+3 * π helix -\> n+5

Answer 34

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

Answer 35

* 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

Answer 36

Globular proteins

Answer 37

* 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

Answer 38

* 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

Answer 39

Usually on the surface of proteins, so they often act as: * Binding sites * Enzyme active sites

Answer 40

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.

Answer 41

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

Answer 42

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

Answer 43

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

Answer 44

Supersecondary structure

Answer 45

* 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

Answer 46

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

Answer 47

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

Answer 48

* 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.

Answer 49

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

Answer 50

* 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

Answer 51

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

Answer 52

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

Answer 53

* Charge-charge * Charge-dipole * Dipole-dipole E = q₁q₂/εRⁿ

Answer 54

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.

Answer 55

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

Answer 56

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

Answer 57

* 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^-13seconds, then it would take ~ 10¹⁰ years... * Therefore it was decided that proteins must have evolved mechanisms of efficient, guided folding pathways.

Answer 58

* 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.

Answer 59

* 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.

Answer 60

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

Answer 61

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.

Answer 62

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

Answer 63

* 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)

Answer 64

Electron transfer

Answer 65

* Alpha structures * Beta structures * Alpha-beta structures -\> Including alpha/beta and alpha+beta structures

Answer 66

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

Answer 67

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

Answer 68

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.

Answer 69

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

Answer 70

Ligand-gated ion channels

Answer 71

**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

Answer 72

* 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).

Answer 73

* Active proteins * Passive structural proteins

Answer 74

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

Answer 75

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

Answer 76

* 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

Answer 77

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

Answer 78

* Immature = Procollagen * Mature = Tropocollagen

Answer 79

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

Answer 80

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

Answer 81

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

Answer 82

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

Answer 83

A catalyst that is produced by a biological organism.

Answer 84

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

Answer 85

* 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

Answer 86

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

Answer 87

* 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.

Answer 88

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

Answer 89

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

Answer 90

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

Answer 91

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

Answer 92

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

Answer 93

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

Answer 94

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

Answer 95

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

Answer 96

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

Answer 97

Enzymes that contain more than one polypeptide chain.

Answer 98

* 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

Answer 99

* 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

Answer 100

* 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.

Answer 101

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.

Answer 102

* 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

Answer 103

* Co-enzymes -\> Organic * Inorganic ions

Answer 104

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

Answer 105

* Enzyme concentration * Substrate concentration

Answer 106

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

Answer 107

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

Answer 108

Rectangular hyperbola

Answer 109

* 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)

Answer 110

A high affinity.

Answer 111

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

Answer 112

* Turnover number * The number of substrate molecules each enzyme site converts to product per unit time * Units: s^-1 Note: K_cat = k₂

Answer 113

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

Answer 114

V_max does, but K_mand K_catdo not, since they are properties of each enzyme molecule.

Answer 115

By increasing K_cat.

Answer 116

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

Answer 117

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

Answer 118

* 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]

Answer 119

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

Answer 120

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

Answer 121

* 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_maxstays the same

Answer 122

* 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_maxis reduced, but K_mis unchanged

Answer 123

* 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.

Answer 124

* 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

Answer 125

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

Answer 126

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

Answer 127

Non-competitive inhibition is a type of allosteric control.

Answer 128

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.

Answer 129

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

Answer 130

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).

Answer 131

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.

Answer 132

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

Answer 133

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

Answer 134

* 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.

Answer 135

* 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

Answer 136

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

Answer 137

* 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.

Answer 138

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.

Answer 139

* Concerted (MWC) * Sequential (KNF)

Answer 140

* 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.

Answer 141

* 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.

Answer 142

* 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).

Answer 143

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

Answer 144

* 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

Answer 145

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

Answer 146

* 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)

Answer 147

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

Answer 148

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

Answer 149

* 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

Answer 150

* 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.

Answer 151

* 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

Answer 152

* 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

Answer 153

* 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

Answer 154

* 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

Answer 155

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

Answer 156

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

Answer 157

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

Answer 158

* 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)

Answer 159

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

Answer 160

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

Answer 161

* 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

Answer 162

* Hydrophilic carboxyl head * Saturated or unsaturated hydrophobic tail

Answer 163

* 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)

Answer 164

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!).

Answer 165

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

Answer 166

C20:5 (ω-3)

Answer 167

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

Answer 168

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

Answer 169

* 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.

Answer 170

* 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).

Answer 171

An even number.

Answer 172

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).

Answer 173

* Dietary * De Novo synthesis

Answer 174

* 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

Answer 175

* Signalling molecules * Synthesis of triglycerides

Answer 176

* Storage * Transport

Answer 177

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

Answer 178

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

Answer 179

Boiling in NaOH or KOH.

Answer 180

Glycerophospholipids

Answer 181

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

Answer 182

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

Answer 183

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

Answer 184

* 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

Answer 185

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

Answer 186

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

Answer 187

* 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

Answer 188

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

Answer 189

* 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.

Answer 190

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

Answer 191

* 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

Answer 192

* Sphingomyelin * Gangliosides * Cerebrosides

Answer 193

* 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

Answer 194

* 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.

Answer 195

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

Answer 196

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.

Answer 197

Cholesterol

Answer 198

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

Answer 199

Cholesterol is composed of: * Three 6-membered rings * One 5-carbon ring * Short aliphatic chain * Single hydroxyl group

Answer 200

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

Answer 201

* 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

Answer 202

Regulate transcription.

Answer 203

* 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.

Answer 204

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

Answer 205

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

Answer 206

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

Answer 207

The sugars WITHIN glycoproteins, glycolipids and proteoglycans.

Answer 208

Proteins that bind specifically to carbohydrates.

Answer 209

* 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)

Answer 210

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

Answer 211

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

Answer 212

* 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

Answer 213

They are usually monosaccharides, most commonly hexoses.

Answer 214

C_n(H₂O)_n

Answer 215

* Glucose * Fructose * Galactose

Answer 216

Aldose - it contains an aldehyde group.

Answer 217

Ketose - it contains a ketone.

Answer 218

* 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

Answer 219

D-galactose

Answer 220

D-fructose

Answer 221

* Pyranose * Furanose

Answer 222

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

Answer 223

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

Answer 224

* 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

Answer 225

* 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

Answer 226

* 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

Answer 227

* 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

Answer 228

* 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

Answer 229

* Structural * Energy sources * Biosynthetic precursors * Signalling molecules

Answer 230

1,4 and 1,6

Answer 231

All are homopolyers of glucose: * Glycogen -\> α-1,4 glycosidic bonds * Starch -\> α-1,4 glycosidic bonds * Cellulose -\> β-1,4 glycosidic bonds.

Answer 232

* 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

Answer 233

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

Answer 234

* 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

Answer 235

* 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

Answer 236

They do not affect osmotic potential.

Answer 237

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

Answer 238

* Sucrose * Maltose * Lactose

Answer 239

* 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.

Answer 240

* 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

Answer 241

They are named after where they were first isolated: * Hyaluronic acid -\> Hyaline membranes * Chondroitin sulphate -\> Cartilage * Dermatan sulphate -\> Skin * Keratin sulphate -\> Skin

Answer 242

* 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)

Answer 243

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

Answer 244

* 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

Answer 245

* Aggrecan -\> Cartilage * Neurocan -\> Brain * Versican -\> Blood vessels + Skin

Answer 246

* N-linked glycosylation -\> Asparagine * O-linked glycosylation -\> Serine/threonine

Answer 247

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

Answer 248

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.

Answer 249

* 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.

Answer 250

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

Answer 251

* 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.

Answer 252

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).

Answer 253

* 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.

Answer 254

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

Answer 255

* Nucleotides * Fatty acids * Amino acids (Add some more flashcards on this?)

Answer 256

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

Answer 257

* 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

Answer 258

* 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

Answer 259

Complex networks of protein filaments extending throughout the cytoplasm.

Answer 260

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

Answer 261

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

Answer 262

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

Answer 263

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

Answer 264

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

Answer 265

* 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.

Answer 266

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

Answer 267

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.

Answer 268

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.

Answer 269

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

Answer 270

DNA replication

Answer 271

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

Answer 272

* Prophase * Metaphase * Anaphase * Telophase * Cytokinesis

Answer 273

Appearance of the chromosomes and separation of the chromatids

Answer 274

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

Answer 275

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

Answer 276

Cloning by functional complementation

Answer 277

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

Answer 278

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

Answer 279

Haploid gametes

Answer 280

Reductive division

Answer 281

Primary gametocytes

Answer 282

Prophase I

Answer 283

Anaphase I

Answer 284

* 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

Answer 285

Two secondary gametocytes

Answer 286

It essentially resembles mitosis.

Answer 287

It increases with age.

Answer 288

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

Answer 289

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

Answer 290

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

Answer 291

* Regulation * Targeting * Turnover * Structural

Answer 292

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

Answer 293

* Threonine * Serine * Tyrosine

Answer 294

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

Answer 295

* Tyrosine * Threonine * Serine

Answer 296

Affects various protein properties, including: * Stability * Enzymatic activity * Co-factor binding

Answer 297

Addition of an isoprenyl group to an amino acid.

Answer 298

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

1. Cellular & Molecular Structure & Function Flashcards

(359 cards)