Midterm 2 Flashcards
(142 cards)
1
Q
What are essential amino acids?
A
Amino acids that cannot be synthesized by the organism at a rate sufficient to meet the normal requirements of growth, reproduction, and normal maintenance and therefore must be supplied in diet
2
Q
What are the essential amino acids?
A
Arginine Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Threonine Tryptophan Valine
3
Q
Which two amino acids are essential in the diets of kids but not adults?
A
Arginine
Histidine
4
Q
Why is tyrosine classified as nonessential?
A
Because it is readily formed from essential phenylalanine
5
Q
Describe the synthesis of alanine, aspartate, glutamate, asparagine, and glutamine
A
Pyruvate, oxaloacetate, and alpha ketoglutarate are all precursors for the first brews
First three are one step transamination reactions
Asparagine and glutamine are synthesized from aspartate and glutamate by atp dépendent amidation process
Synthesis of glutamine depends upon the formation of a gaba gaba glutamylphosphate intermediate
6
Q
Describe the synthesis of arginine, ornithine, and proline
A
Conversion of glutamate to proline involves the reduction of gaba carboxyl group to an aldehyde followed by formation of internal schiff base whose further reduction yields proline
Initated by phosphorylation of glutamate by gaba glutamyl kinase
Glutamate-5-semialdehyde cyclises spontaneously to form the internal schiff base pyrroline-5-carboxylate
Transamination of semialdehyde to produce ornithine
Ornithine converted to arginine via urea cycle
7
Q
Describe the synthesis of Serine, cysteine, and glycine
A
Synthesized from 3-phosphoglycerate
One transamination followed by a hydrolysis of a phosphate group
Homocysteine a breakdown produce of Met
Cysteine synthesized from serine and homocysteine
Serine + homocysteine -> cystathionine -> cysteine + alpha ketobutyrate
8
Q
Describe the synthesis of lysine, methionine, and threonine
A
Begin with aspartate
Methionine synthesis depends upon donation of a methyl group by N5-methyl-THF to homocysteine
Methionine synthase: coenzyme B12 associated enzyme
High levels of homocysteine in the blood = risk factors in cardio vascular disease
9
Q
What is homocysteinuria?
A
High levels of homocysteine in the blood giving high risk of cardiovascular disease
10
Q
Describe the synthesis of valine, leucine, and isoleucine
A
Pyruvate as the starting reactant
First step in isoleucine is thiamine pyrophosphate-dependant
Final steps of synthesis dependent upon glutamate
Valine aminotransferase catalyzes both valine and isoleucine biosynthesis while leucine depends upon leucine aminotransferase
11
Q
What are the precursors to the synthesis of tyrosine, phenylalanine, and tryptophan?
A
1) phosphoenolpyruvate (PEP): intermediate of glycolysis
2) erythose-4-phosphate: intermediate of the pentose phosphate pathway
12
Q
What is the use of substrate tunneling?
A
Increases rate of a metabolic pathway
1) prevents the loss of intermediate product
2) prevents side reactions or degradation of intermediate product
13
Q
Describe the synthesis of tyrosine, phenylalanine and tryptophan
A
2-keto-3-deoxy-D-arabinoheptulosonate-7-phosphate cyclizes to form chorismate
Last two steps of tryptophan synthesis catalyzed by alpha and beta subunits of tryptophan synthase respectively
Substrate tunneling
14
Q
Describe the synthesis of histidine
A
Histidine derived from 5-phosphoribosyl-alpha-pyrophosphate (PRPP) a phospho-sugar intermediate involved in the biosynthesis of purine and pyrimidique nucleotide
15
Q
What are the two types of protein digestion?
A
- Extracellular: gastrointestinal tract (pepsin, trypsin, carboxypeptidase)
- Intracellular: eg. enzyme systems retained in lysosomes (cathepsins)
16
Q
What is cathepsins?
A
Enzymes that degrade body tissue upon death
Broken down to constitutive amino acids
17
Q
Define glucogenjc
A
Capable of producing glucose precursors
Degraded to pyruvate, alpha ketoglutarate, succinyl CoA, fumarate, Or oxaloacetate
18
Q
Define ketogenic
A
Capable of producing fatty acids or ketone bodies degraded to acetyl coA and acetiacetate
19
Q
Describe amino acid oxidation
A
Amino acids -> carbon skeleton -> carb metabolism OR fatty acid metabolism -> acetyl coA -> CO2 and water
20
Q
What are the glucogenic amino acids?
A
Glucose precursors
Degraded to pyruvate, alpha ketoglutarate, succinyl-CoA, fumarate, or oxaloacetate
Asparagine, aspartate, phe, tyr, île, met, val, glutamate, glu, his, pro, ala, cys, gly, ser, thr, trp
21
Q
What was the ketogenic amino acid?
A
Can be converted to fatty acids or ketone bodies
Degraded to acetyl-CoA and acetoacetate
Ile, leu, lys, thr, phe, trp, tyr
22
Q
Describe the degradation of cysteine, glycine, alanine, serine, and threonine to pyruvate
A
Alanine: straight transamination breakdown to pyruvate
Serine converted to pyruvate by dehydration catalyzed to serine dehydratase (dépendant on PLP)
Cystine converted to pyruvate via several routes with release of sulfhydryl group
Glycine and tbreonine and converted to serine by serine hydroxymethyltransferase using N5-N10-methyl-tetrahydrofolate as a one carbon donor cofactor
Threonine is both glucogenic and ketogenic
23
Q
Describe the use of PLP as a cofactor
A
Capable of forming schiff bases with amino acids and proteins
- Can cleave Calpha-Cbeta bond in threonine
- Can remove OH group from serine to eventually form pyruvate
24
Q
Describe the use of tetrahydrofolate (THF)
A
Derived from folic acid
One-carbon carriers
25
Describe the degradation of asparagine and aspartate to oxaloacetate
Asparagine -> aspartate (aminotransferase) -> oxaloacetate (L-asparaginase)
Hydrolysis of asparagine give aspartate which is later transaminated to oxaloacetate
26
Describe degradation of arginine, glutamate, glutamine, histidine, and proline to alpha-ketoglutarate
Conversion of glutamine to glutamate involves a one step hydrolysis by glutaminase (amino group leaves)
Histidines imidiazole ring cleaved to form N-formiminoglutamate
Combines with THF to form N-formimino-THF -> catalyzed by glutamate formiminotransferase
Arginine and proline converted to glutamate through the intermediate glutamate-5-semialdehyde
27
Describe degradation of methionine to succinyl-CoA
First step involves methionine interaction with ATP to form S-adenosylmethionine (SAM)
SAM converted to homocysteine which can be back converted to met or combine with serine to form cystathionine and alpha ketoglutarate -> cysteine synthesis
Alpha ketoglutarate converted to propionyl-CoA which is then converted to succinyl-CoA by a series of reactions involving biotin and coenzyme B12
28
What are the 3 reactions that employ common enzymes in the degradation of Ile, Val, and leu?
1. Transamintion of their corresponding alpha Leto acid
2. Oxidative decarboxylation to the corresponding acyl-CoA
3. Dehydrogenation to FAD to form a double bond
29
What does branched-chain alpha dehydrogenase rely on?
TPP
Lipoic acid
FAD
NAD+
30
What is branched-chain alpha keto acid dehydrogenase?
Multienzyme complex that resembles pyruvate dehydrogenase and alpha ketaglutarate dehydrogenase
31
Describe degradation of lysine to acetoacetate
First step begins with a lysine-a-ketoglutarate adduct known as saccharopine
One enzyme in pathway is PLP dépendant
Defects in saccharopine dehydrogenase results in increases in lysine in the blood (hyperlysinemia) and urine (hyperlysinuria)
32
Describe degradation of tryptophan to acetoacetate
The enzyme kinureninase is a PLP dépendant enzyme that cleaved a C beta-gamma bond to release alanine
33
Describe degradation of phenylalanine and tyrosine to acetoacetate and fumarate
First reaction of Phe breakdown is its hydroxylation of tyrosine
Final products are fumarate (CAC) and acetoacetate (ketone body)
34
What is alkaptonuria?
Characterized by urinary excretion of large amounts of homogentisate
Genetic deficiency in homogentisate dioxygenase
Develop arthritis later in life
35
Describe phenylketonuria (PKU)
Urine contains excessive phenylpyruvate
Can suffer severe mental retardation if not recognized immediately after birth
Genetic deficiency in phenylalanine hydroxylase
Individuals with PKU must avoid aspartamate as it is broken down into phe and asp
36
What are the types of the removal of NH3?
1. Oxidative deamination
2. Non-oxidative deamination
3. Transamination
4. Transamination with oxidative deamination
37
What is the urea cycle?
Organisms must excrete excess nitrogen arising from amino acid catabolism
Convert ammonia to urea
Urea is synthesized in the liver by urea cycle enzymes
Secrètes into blood stream and brought into kidneys for excretion in urine
38
What are the mitochondrial reactions of the urea cycle?
1. Carbamoyl phosphate synthétase: usés first amino group of urea to form carbamoyl phosphate, committing step
2. Ornithine transcarbamoylase: transfers the carbamoyl group to ornithine to form citruline
39
What are the cytosolic reactions in the urea cycle?
1. Arginosuccinate synthatase: acquisition of the seconds nitrogen of urea from aspartate
2. Arginosuccinase: élimination of fumarate to leave arginine
3. Arginase: hydrolyses arginine to yield urea and regeneration of ornithine
40
What regulates the urea cycle?
N-acetylglutamate activation of carbamoyl phosphate synthétase
When amino acid breakdown increases, so does the flux through the urea cycle
41
Define carbohydrates
Contain carbon, hydrogen, and oxygen which can directly or indirectly after hydrolysis, reduce alkali solutions of heavy metal salts
Can yield aldehyde or ketone upon hydrolysis
42
What are the different types of carbs?
Monosacchrides: 2-9C
Oligosacchrides: 2-10 monosacchride units, joined by glycosidic link
Polysacchrides: >10 monosacchride units
Homopolysacchrides: contain the same unit
Heteropolysacchrides: contain different units
43
What are the biochemical importance of carbs?
1) energy provision and storage
2) structure and protection
3) conversion to other compounds eg. Carbs to fat
4) internal units of other compounds eg. Ribose in RNA
44
What are trioses and tétroses?
Trioses: 3 carbons, predominantly D-series sugars
Tetroses: 4 carbons:
Pentoses: aldose 4 D-series members, ketones 2 D-séries members
Hexoses: aldose 8 D-series members, kératoses 4-D series members
45
Describe pyranose and furanose
Pyranose: contains 5 to 6 carbon and 1 oxygen, oxygen between carbons C1 and C5
Furanose: contains 4 to 5 carbon and 1 oxygen, oxygen between C1 and C4
46
What is the difference between alpha and beta anomers?
OH down = alpha
| OH up = beta
47
Describe the reactivity of hemiacetals.
1. Potential reducing group: unreacted OH group is a potential reducing group, forming a straight chain molecule with an aldehyde group on the end
2. High capacity to rotate plane polarized light
3. Séparation by chromatography
4. High capacity to interact with water: hydrophilic
48
Describe detoxification
Makes sugar amino acids more water soluble so that can be excreted
Turn up in various polysacchrides
49
Describe oligosacchrides
Alpha: easily hydrolysed, susceptible to attack by alpha glucosidase
Bêta: less easily hydrolyzed, also attacked by beta-glucosidase
50
Describe alpha and bet glycosidic links
Alpha: involved in energy production, easily hydrolyzed and attacked by enzyme
Bêta: extremely hard to hydrolyze and very stable, biological importants to structure and protective compounds, OH group can be provided by another sugar
51
What are some naturally occurring disaccharides?
Maltose: alpha glycosidic linkage, degradation product of starch
Cellobiose: bêta glycosidic linkage, degradation product of cellulose
Lactose: bêta glycosidic linkage
Sucrose: non reducing
Trehalose: non reducing, invertebrates, plants, fungi, alpha,1,1-glucoside bond
Imomaltose: reducing, alpha,1,6-glycosidic linkage
52
What are polysacchrides used as energy in the cell?
1. Large molecular weight: large aggregates or colloid state
2. Protection of cells colligative properties: dépendant on # particles, larger molecules easier to store and protect against water loss, water balance,
53
What are the two classifications of polysacchrides?
1. Energy: alpha glycosidic link
| 2. Structure and protection: bêta glycosidic link
54
Describe plant starch
Occurs as granules in cell cytoplasm
Heterogeneous (1 part amylose, 3 parts amylopectin)
Amylose, amylopectin, glucogen, dextrans
55
Describe amylose
Composed of D-glucose units joined in 1-4 alpha glycosidic links
Polymer of maltose
56
Describe amylopectin
Not linear
Branches with chains of D-glucose units joined in a 1-4 alpha glycosidic link
Branch points of 1-6 a-glycosidic link always involving C1
Branching provided by OH on C6
25 units per chain
Compacts the space taken by many glucose units into a smaller volume
57
Describe glycogen
```
Animal product present in muscle and liver
Very large molecular weight
Similar structure to amylopectin
1,6 glycosidic links
Every 8 to 10 units is a D-glycose unit
```
58
Describe dextrans
Forms of energy storage in bacteria
| Composed of D-glucose joined via various glycosidic links
59
What are some structural polysaccharides?
Cellulose
- 50% of all natural organic material in biosphère contain cellulose
- linear chains of D-glucose units joined via 1,4-beta glycosidic links
- Polymer of cellobiose
- has same chemical component of amylose and involved in structure and rigidity of plants
-
60
What are mucopolysacchrides?
Generally occur in association with proteins
Glycoproteins <4% hexosamine
Mucoproteins >4% hexosamine
Wide range of activities: found in cell coats, joint lubricants, blood group factors and blood typing, reflects in surface of red blood cell, anticoagulant
Ex. Chitin
61
What are the two types of glycoprotein links?
Glycoproteins: carbs linked to proteins
1. O-linked glycosylation: beta-D-N-acetylglucosamine linked to the hydroxyl groups of serine, threonine, tyrosine, hydroxylysine, or hydroxyproline, hydroxyl groups linked to them
2. N-linked glycosylation: N-acetyleglucosamine linked to the anime group of asparagine, amino groups linked to them
62
What are glycoproteins used for?
Used for cell to cell communication
Sometimes are receptors
Stick out from cell membrane
Often have repeating amino acid units to which sugars are attached
Can form cell to cell junctions
Ex. Leukosialin, decay-accelerating factor (DAF), LDL receptor
63
Describe polysaccharide degradation
A. Polysacchrides undergoes dégénération to permit use of constituent monosacchrides (plant starch, glycogen)
B. Pathway of degradation varies with location
64
What are the two ways to achieve monosacchride release?
1. Extracellular hydrolysis
| 2. Intracellular phosphorolysis
65
Describe extracellular hydrolysis
Gastro-intestinal tract: cells secrète enzymes to outer body that conduct hydrolysis
Salivary amylase and pancreatic amylase: catalyze the hydrolysis of 1-4 alpha glycosidic links, amylo-1,5-a-glucosidase (hydrolysis of branch points, introduction of water), important to digestion
66
Describe intracellular phoohorolysis
Bind cleavage with phosphoric acid
Working from non reducing end of molecule
Nucleophilic attack of phosphate on C1
Phosphorilytic degradation of glycogen results in release of D-glucose-1-phosphate
Phosphorylase regulated and system is crutial in deriving energies from energy bank
67
Describe a phosphorylase phosphatase
Two phosphorylase forms: a (active) and b (inactive)
Conversion between forms
Inactive form in muscle
If using phosphate group from ATP, ADP and AMP accumulate = trouble
AMP + modified system (changes to make active)
ATP (-) and AMP (+) compete for allosteric sites
68
What turns phosphorylase kinase on?
Hormones: Adrenalin in muscle, glucagon in liver
Stimulates the release: ATP upon hormone stimulation releases 2 pyroP
cAMP stimulates enzyme system and turns the protein kinase inactive to a protein kinase active which stimulates the phosphorylase kinase
Release of glucose from glycogens creates instant release of energy
69
Define glucose oxidation (glycolysis)
The oxidation of glucose to 2 or 3 carbon compounds under anaerobic conditions
Shows a unity of mechanisms but different end products
70
What occurs in glycolysis with low oxygen?
Lead to little flux of electrons through the ETC and a dramatic decrease in the number of mitochondria
71
Describe the activation of glycolysis
D-glucose to G6P catalyzed by hexokinase consuming ATP
High energy level to low = irreversible
Glucose can diffuse from cell but G6P cannot
Thermodynamically favorable
Subject to product inhibition
72
Describe the isomérisation of G6P
G6P to fructose 6 phosphate catalyzed by phosphoglucose isomerase
Relatively irreversible
Produces another primary alcohol
Réaction favours G6P
73
Describe activation of fructose 6 phosphate
Fructose 6 phosphate to fructose 1,6 bisphosphate catalyzed by phosphofructokinase consuming ATP
Thermodynamically favourable
Allosteric enzyme system
74
What is hexokinase?
Catalyses first ATP utilization step
Transfers phospho group from ATP to glucose
Ubiquitous: phosphorylates hexoses
Glucokinase in liver cells does the same to maintain blood glucose level
Requires Mg2+ complexed with ATP
Competitively inhibited by uncomplexed ATP
75
What is phosphoglucose isomerase?
Isomérisation of an aldose to a ketose
| Ring opening, isomérisation, ring closure
76
What is phosphofructokinase?
Catalyzes second ATP utilization step
Bisphosphorylates F6P
Catalyzes one of the raté determining steps
Allosterically enhanced by ADP and AMP
Allosterically inhibited by ATP and citrate
77
Describe the split of fructose-1,6-bisphosphate
Splits to dinydroxyacetone phosphate and D-glyceraldehyde-3-phosphate catalyzed by aldolase
Strong thermodynamic break
Wants to go in reverse direction
Dihydroxyacetone cannot go through rest of glycolysis and must be made in D-G3P
78
Describe isomérisation of dihydroxyacetone phosphate
Dihydroxyacetone phosphate to G3P catalyzed by triose phosphate isomerase
Almost readily reversible
Cell pulls forward
79
Describe oxidation of G3P
G3P to G3P dehydrogenase to 1,3-bisphosphoglycerate with formation of NADH
80
What is aldolase?
Base catalyzed aldol cleavage of FBP to form two trioses
Forms an enolate intermediate
Two classes:
1) animal, plants: enolate stabilized by a schiff base
2) fungi, algae, bacteria: enolate stabilized by divalent cations (Zn2+)
81
What is triose phosphate isomerase?
DHAP cannot continue on to glycolysis and is isomerized to G3P
Forms an enediol intermediate
As GAP is removed, DHAP is rapidly converted to GAP
82
What is G3P dehydrogenase?
Catalyzes an oxidation and phosphorylation
Forms high energy intermediate 1,3-bisphosphoglycerate through formation of a phosphoanhydride bond
Energy is conserved through the reduction of NAD to NADH
83
Describe substrate phosphorylation of 1,3-bisphosphoglycerate
1,3-bisphosphoglycerate to 3-phosphoglycerate catalyzed by phosphoglycerate kinase (PKG) releasing ATP
In muscles, forms ATP in the absence of O2
84
Describe mutation of 3-phosphoglycerage
3-phosphoglycerate to 2-phosphoglycerate catalyzes by phospjoglycerate mutase
Somewhat readily reversible
Shift of phosphate group from C3 to C2
85
Describe dehydration of 2-phosphoglycerate
2-phosphoglycerate to phosphoenolpyruvate catalyzed by enolase releasing water
Forward is favoured
86
Describe the last step of glycolysis
Substrate phosphorylation of phosphoenolpyruvate to pyruvate catalyzed by pyruvate kinase releasing ATP
Forward direction is very highly favoured
87
What is enolase?
Phosphoenolpyruvate - enzyme system suceptible to fluoride ions
Shut the enzyme down with high concentration of fluoride ions
88
What phosphoglycerate kinase?
Generates the first ATP of glycolysis
Requires Mg+ complexes to ADP
Production of ATP in the absence of oxygen = substrate-level phosphorylation
Highly favourable consumption of 1,3-BPG pulls the GAPDH reaction forward
89
What is phosphoglycerate mutase (PGM)?
Mutase catalyzes the transfer of a functional group from one position in a molecule to a different position in the same molecule
Simple intramolecular phosphorus group transfer is energetically neutral but produces high energy grouping
90
What is pyruvate kinase?
Generates the second ATP of glycolysis
Requires K and Mg for catalytic activity
Hydrolysis followed by tautomerization from pyruvate (enol form) to pyruvate (keto form)
Highly exergonic
91
Describe pyruvate kinase with respect to cancer cells
In a normal cell it is a tetromer with 4 subunits and highly active
In cancer cell, PK is a diner and inactive which causes intermediates to build up on glycosidic pathway
Begin to go into alternate pathways
Will shit down and shuttle build up of intermediates into making NADH and ribonucleotide precursors
92
What is the Warburg effect?
Activation of LDH rather than shuttling pyruvate to the mitochondria
Shut down of PK forcing metabolites to go through pentose phosphate pathway
Relience on glutamine for synthesis of citrate and acetyl-coA and eventually fatty acids
93
What occurs in the muscle when NADH is reduced anaerobically?
Pyruvate to lactate catalyzed by lactate dehydrogenase producing NAD+
Smooth muscle = lower km, more dépendant upon LDH
Cardiac muscle = high Km, less dépendant upon LDH
Muscle cramps = more NAD+ produced
2 ATP in, 4 ATP out
30% efficiency
94
What occurs when NADH is reduced in yeast?
Pyruvate to acetaldehyde (pyruvate decarboxylase) to ethanol (alcohol dehydrogenase) producing CO2 and NAD+
Ethanol is toxic
2 ATP in, 4 ATP out
Break down of 2ATP result in energy generated as heat, could cause heat dénaturation of enzyme systems
95
What occurs in aerobic tissues with the reduction of NADH?
Access to O2 and ETC
Pyruvate to acetyl-CoA catalyzed by pyruvate decarboxylase, releasing CO2
40% efficient
Only 8% of total energy in glucose is released upon glycolysis
18X increase in amount of energy when oxygen is present
96
What is créatine phosphate?
Used for muscle contraction
| High energy phosphate reserve
97
What are some regulatory enzymes of glycolysis?
Hexokinase/glucokinase: glucose-6-phosphate, indicible by insulin
Phosphofructokinase: ATP and citrate, positive by AMP and b-D-fructose-2,6-bisphosphate
Pyruvate kinase: negative ATP, acetyl coA, alanine, glucagon, positive AMP and fructose-1,6-bisphosphate
98
Describe the pentose phosphate pathway
Present in highly differentiate tissues
Aerobic but not involved in ETC and involved in 1) NADPH formation, 2) Formation of pentoses, 3) photosynthesis
Can only use NADP+ as electron acceptor
Specific oxidation releases 2 NADPH and 6 pentoses and 6 CO2
99
What are the three stages of the pentose phosphate pathway?
1. Oxidative reactions: glucose dehydrogenase (commuting step), 6-phosphigluconolactonase, 6-phospholgluconate dehydrogenase
2. Isomérisation and epimerization réactions: ribulose-5-phosphate isomerase (important precursor in nucleotide sequence), ribulose-5-phosphate epimerase
3. Carbon-carbon cleavage and formation reactions: transketolase, transaldolase
100
What is gluconeogenesis?
New glucose formation (synthesis of glucose from non-carb sources)
Endergonic
Involves reversal of the steps of glycolysis except for 3 bypasses
Occurs in liver
Aerobic = 36 ATP
anaerobic = 2 ATP
101
What are the three large energy differences in glycolysis?
Pyruvate kinase step
Phosphofructokinase
Hexokinase
102
Describe pyruvate carboxylase
Catalyzes atp driven conversion of pyruvate to oxaloacetate
Biotin as prosthetic group
Oxaloacetate converted to malate before leaving the mitochondria and converted back into oxaloacetate in cytosol by malate dehydrogenase
103
Describe phosphoenolpyruvate.
Catalyzes the GTP-driven decarboxylation of oxaloacetate to PEP
104
Describe fructose bis-phosphatase
Inhibited by fructose-2,6-bisphophate
Decreased levels of F2,6P inhibits PFK and actives FBPase -> caused by low blood glucose and increased cAMP levels
Controlling point between glycolysis and gluconeogenesis
105
Describe glucose-6-phosphatase
Catalyses the final step leading to the release of glucose into the bloodstream from the liver
106
What is glycogenesis?
Synthesis of glycogen from glucose
Glucose-6-phosphate converted to glucose-1-phosphate by phosphoglucomutase
G1P combined to UTP by pyrophosphate uridyltransferase to form UDP-glucose
UDP-glucose converted to branches primer by glycogen synthase (negatively regulated by cAMP, positively by G6P)
Branching factor links branched primers to form glycogen
107
What is glycogenolysis?
Catabolism of glycogen to G1P
Glycogen broken down to a-1,4-glucosan by debranching steps
Converted to G1P by phosphorylase (negatively by cAMP and AMP, positively by ATP)
108
What are nucléoprotéines?
Consists of a protein component, generally rich in basic amino acids to which is attached a non-protein prosthetic group of nucleic acids
Prosthetic group: hemoglobin (blood carries oxygen), myoglobin (muscle stores oxygen)
109
What is an ester?
Interaction of alcohol with an acid forming nucleic acids
110
What are nucleotides?
Composed of a nitrogen base joined with a glycosidic link to a sugar unit to which is attached an estérified phosphate
111
What are nucleosides?
Nitrogenous bass joined with a glycosidic link to a sugar
112
What is the chemical composition of nucleic acids?
1. Phosphate (organic): 10% of nucleic acid molecule
2. Sugar: two pentose sugars each containing 5 carbon atoms
3. Purines and pyrimidines: pyrimidine (numbered clockwise, oxygen functions on C2 and C4) purines (numbered counterclockwise, heterocyclic)
113
Why is DNA negatively charged?
Negative charge in phosphodiester link on oxygen
114
Why does the number of G-C bonds drive up the melting point?
3 bonds to break instead of 2 (A-T)
115
Describe susceptibility of RNA and DNA to weak alpha hydrolysis
RNA (acid soluable) : breaks down to nucleotides
| DNA (acid insoluable) : does not break down, reflects presence of unreacted OH grouping in the sugar
116
Describe the double helix of DNA
Two right handed hélices similar but not identical, showing complementary running in opposite directions
Nitrogenous bases are perpendicular to acid and project onwards, nonpolar
Sugars are polar, project outwards
Major and minor grooves
117
What are the three structural forms of DNA?
A-DNA: more compact due to dehydration, in fungal or bacterial spores
B-DNA: normal
Z-DNA: Seen a lot in synthetic DNA, takes on this form when heavily methylated, left handed
118
What are some intercalating agents?
Ethidium bromide
Acridien orange
Actinomycin D
119
What stabilizes the double helix?
1. Hydrogen bonding
2. Apolar interactions between stacked N-bases
3. Ionic interactions nucleic acid, protein, and Mg+
120
What are some physico-chemical properties of DNA?
1. Very large molecular mass leads to the colloid state - imparts viscosity
2. Acid nature - DNA histones
3. DNA can undergo dénaturation
121
What denatures DNA?
Urea, pH, temperature
122
What are the biological properties of DNA?
1. Non-protein bound DNA in prokaryotes
2. Protein-associated DNA in eukaryotes
3. DNA packaged into chromosomes which contain genes and polycistrons
123
Describe mRNA
Single stranded - no conjugation with protein
Contains sequence complimentary to the DNA -> leads to the complementary triplet or codon
Serves as a template for translation
124
Describe tRNA
Basic composition
Structure - 60 to 70% helicity
Single stranged
125
Describe translation
3 different RNAs work in conjunction:
mRNA: provides template, each amino acid is encoded by one codon
tRNA: bring esterified amino acids to the ribosome
rRNA: scaffold for the ribosome, ribosome moves along the mRNA codon by codon, bringing in aminoacylated tRNAs and linking amino acids with peptide bonds
Many ribosomes can work on the same mRNA template at the same time
126
What is the difference between prokaryotic and eukaryotic ribosomes?
Subunit: 30S + 50S (pro) 40S + 60S (euk)
RNA:
- pro: 16S (30S), 23S, 5S(50S)
- euk: 18S (40S), 28S, 5S (60S)
127
Describe transcription and translation
Transcription: gènes to RNA
Translation: RNAs to Proteins
128
What are the different domains of the transcription factors?
```
Activation domain
Ligand binding domain
Dimerization domain
DNA-binding domain
Nuclear localization sequence
```
129
Describe the zinc finger
Amino acids at top of loops insert themselves in major and minor grooves
130
What is helix turn helix?
Comprised of 3 alpha helix
1 and 2 are 90 degrees to 3
1 and 2 are there to stabilize 3 which hydrogen bonds in the groove
131
What is a leucine zipper?
Proteins with leucine can dimerize
Often have a region of basic amino acids that are right next to DNA
Basic regions are termed beta zip proteins
Basic regions insert themselves into major and minor groups of DNA
132
What are the 1961 mRNA postulates based on?
1. DNA in nucleus, protein synthesis in cytosol
2. Base composition that reflects that of DNA
3. Heterogeneous with respect to molecular mass
4. Able to associate with ribosomes (protein synthesis)
5. High rate of turnover
133
Describe action if RNAP
Bacteria: single RNAP for cellular RNAs plus one for primers involved in DNA replication
Viruses: typically encode RNAP for viral-specific RNAs
Eukaryotes: multiple RNAPs dedicated to sunsets of RNAs
134
Describe core RNA polymerase
Synthesized RNA but unable to recognize promoters and accurately initiate transcription
135
Describe RNA polymerase holoenzyme
Association with omega confers DNA binding and transcription initiation capability but omega is not needed one polymerization process occurs
136
What are the phases of transcription?
1. Template binding by RNA polymerase (at promoter for accurate initiation of transcription)
2. RNA chain initiation (closed to open complex)
3. Chain elongation
4. Chain termination
137
Describe the binding of RNA polymerase to template DNA
Holoenzyme binds nonspecifically to DNA with low affinity and migrates along it, looking for promoter
Sigma subunit recognizes promoter sequence
Genetic mapping indicates promoter region about 40bp region upstream of +1
138
Describe initiation of polymerization
RNA polymerase has two binding sites for NTPs
Initiation site prefers to bind ATP and GTP
Elongation site binds the second incoming NTP
Initiation reaction: coupling of two nucleoside triphosphates
Eliminates PPi
139
Describe the steps of translation
1. Recognition of promoter by sigma, binding of holoenzyme to DNA, migration to promoter
2. Formation of an RNAP, closed promoter complex
3. Unwinding DNA at promoter formation of open promoter complex
4. RNA polymerase initiates mRNA synthesis, almost always with a purine
5. Holoenzyme-catalyzed elongation of mRNA to about 9-12 nucleotides
6. Release of sigma subunit as core RNAP proceeds down the template, elongating RNA transcript
140
What are rifamycins?
Rofamycins are a group of antibiotics that are synthesized either naturally by bacterium or synthesized artificially
Specifically inhibit transcription by prokaryotic but not eukaryotic, RNA polymerases, useful against gram positive bacteria and TB
Bind to prokaryotic RNAPs blocking further elongation
Permits experiments that involve the dissection of the ignition and elongation phases of transcription
141
What are the two mechanisms of chain termination?
1. Intrinsic termination: GC-rich palindromic region followed by A-T rich sequence, stem loop chases RNAP to stall
2. Rho termination: rho factor (ATP-dependent helicase unwinds RNA:DNA hybrid duplexes recognizes C-rich regions in RNA transcript
142
Why is it necessary to regulate transcription?
Organisms environment changes rapidly
Survival depends on ability to adapt
Organism must express the enzymes required to survive the environment
Enzyme synthesis is costly
Therefore want to make enzymes when required
