test 2 Flashcards
What is a heterocyclic compound?
- cyclic compound
- atoms of at least two different elements as members of its ring.
What is a heteroatom?
What are the most common heteroatoms?
Atoms other than carbon or hydrogen present in an organic compound.
- oxygen, nitrogen, sulfur
How is a heterocyclic compound formed?
One or more heteroatoms (oxygen, sulfur, or nitrogen) replaces carbon in a ring.
How can heterocyclic compounds be classified?
1) according to the number of atoms in a ring
2) according to the kind of heteroatoms
3) according to the number of rings
How are heteroatoms classified according to the number of atoms in a ring?
1) tri-members: eg. thiirane
2) four-members: eg. oxetane
3) five-members: eg. pyrole
4) six-members: eg. pyridine
How are heteroatoms classified according to the kind of heteroatoms?
same: imidazole, pyrimidine
different: thiazole
How are heteroatoms classified according to the number of rings?
- monocyclic (eg. pyrimidine)
- polycyclic (eg. purine)
How many rings does pyrimidine have? Purine?
pyrimidine: 1 ring
purine: 2 rings
pure: hetero
What do monomethyl pyridines undergo?
side chain oxidation to carboxylic acids
What are porphyrins? What structure? Shape?
Macrocyclic compounds containing pyrrole rings linked by one-carbon brindge.
- flat
- conjugated system (18 pi electrons) –> COLOUR
State examples of porphyrins. Do they exist in nature?
Only exist in analogous compounds with various side chains.
- heme (iron-porphyrin: red colour of arterial blood)
- indole (benzene ring fused to pyrrole)
Explain how red blood cells carry oxygen molecules. Other molecules?
Hb binds O2 (oxyhemoglobin), it attaches to Fe2+.
- same with: CO (carboxylhemoglobin), NO (nitrosylhemoglobin)
binding of CO is 230 times greater than O2 –> poisoning
What is the indole ring system biosynthesised from? What is its derivative?
tryptophan (amino acid)
derivative: serotonin (happiness hormone)
What are the most important derivatives of pyrimidine?
- cytosine
- thymine
- uracil
What pyrimidines are found in DNA? RNA?
DNA: cytosine, thymine
RNA: cytosine, uracil
What two pyrimidines are structurally similar?
uracil and thymine
Explain lactimic-lactamic tautomerization. How does it occur? Where does it occur? What is the lactam? What is the lactim?
- heterocyclic bases undergo tautomerization (keto-enolic)
LACTAM structure: keto tautomer (no -OH)
LACTIM structure: imidic acid (-OH present)
(vic)TIM = -OH
What of bases depends on the pH? Explain how it changes.
free pyrimidine and purine bases exist in 2+ tautomeric forms depending on pH.
lactam: no -OH
lactim: single -OH
double lactim: double -OH
What is a purine?
fused-ring heterocycle
(pyrimidine ring fused to an imidazole ring)
What are the two common purine bases?
- guanine
- adenine
What is uric acid? What are its lactam and lactim forms?
- present in urine
- product of nitrogen metabolism
uric acid (double lactim)–> sodium urate (lactim)–> disodium urate (lactam)
What are the functions of nucleotides?
- building block for DNA and RNA
- intracellular energy source (ATP)
- second messenger (cAMP)
- signalling switches (G-proteins)
Describe the structure of a nucleoside.
- carbon ring
- nitrogen + C1’ ribose/deoxyribose (5-C sugar)
- glycosidic bond
ribose: ribonucleotide
deoxyribose: deoxyribonucleotide
How are nucleosides named?
changing nitrogen base ending:
purine: -osine
pyrimidines: -idine
What is a nucleotide?
nucleoside + ribose/deoxyribose (C5’ -OH group)
- phosphate ester
What is a ‘ (prime) used for?
to differentiate the atoms of the carbohydrate from the base
- the position number
How are nucleosides formed? What bonds with what? What bond?
sugar (ribose/deoxyribose) + base (purine/pyrimidine)
bond: N-glycosidic bond
What are the differences b/w purine and pyrimidine nucleosides?
purine: C1’ carbon + N9 atom
pyrimidine: C1’ carbon + N1 atom
purine: chooses right one
pyr: goes for first
In simple terms, explain the formation of a nucleoside. (+ difference b/w ribose and deoxyribose)
carbohydrate + base ribonucleoside
carbohydrate + 2’-deoxyribonucleotide
What reaction occurs to form a nucleotide? (b/w phosphate groups)
nucleotides: nuscleoside + phosphate group
- esterification reaction b/w phosphate groups must occur
How are phosphoric acid anhydrides formed?
- esterification reaction
- condensation reaction
What makes a nuscleoside a nucleotide? What group is essential? For what?
phosphate groups!
- essential for polymerization
What determines nucleotide nomenlature? State examples of names
the number of phosphate groups!
1) Monophosphate (AMP):
free= inorganic phosphate (Pi)
2) Diphosphate (ADP)
free= pyro-phosphate (PPi)
3) Triphosphate (ATP)
free= no free form exists!
How are nucleotides formed?
1+ phosphates & nucleoside (5’ end)
- esterification
How are nucleotides named?
1) changing the nitrogen base ending:
- purines: to -osine
- pyrimidines: to -idine
2) name of nucleoside + “5’-monophosphate”
State the name of the nucleosides and nucleotides for RNA and DNA of (A).
1) RNA
Base: Adenine (A)
Nucleoside: Adenosine (A)
Nucleotide: Adenosine 5’-monophosphate (AMP)
2) DNA
Base: Adenine (A)
Nucleoside: Deoxyadenosine (A)
Nucleotide: Deoxyadenosine 5’-monophosphate (dAMP)
State the name of the nucleosides and nucleotides for RNA and DNA of (C).
1) RNA
Base: Cytosine (C)
Nucleoside: Cytidine (C)
Nucleotide: Cytidine 5’-monophosphate (CMP)
2) DNA
Base: Cytosine (C)
Nucleoside: Deoxycytidine (C)
Nucleotide: Deoxycytidine 5’-monophosphate (dCMP)
What are nucleic acids? Nucleotides or nucleosides? What bonds?
Polymers consisting of long chains of monomers (nucleotides).
- covalently bonded
string of nucleotides= sugar, phosphate, base
dna is like a tide
What are the two types of nucleic acids?
1) Ribonucleic acid (RNA):
- single stranded
- shorter
2) Deoxyribonucleic acid (DNA):
- double stranded
- very long
What do nucleic acids do?
Store information for cellular growth and reproduction.
What is the primary structure of DNA? What bonding?
BACKBONE (“sugar-phosphate” backbone):
- 2-deoxyribose and phosphate groups alternate
- 3’hydroxyl of ribose (1) unit + 5’hydroxyl unit of ribose (2) unit
- phosphodiester bonding
- heterocylic base is connected to the anomeric carbon of each deoxyribose by a B N glycosidic bond.
How are the two ribose molecules connected in the backbone of DNA? What parts? What bonding?
- 3’hydroxyl of ribose (1) unit + 5’hydroxyl unit of ribose (2) unit
- phosphodiester bonding
What bond is the heterocylic base connected to the anomeric carbon (deoxyribose) by?
B N glycosidic bond.
How should one read the primary structure of a nucleic acid polymer?
the free 5’-end –> the free 3’-end
- eg. “5’-A-C-G-T-3’”
Explain the secondary structure of DNA.
How many helixes?
What direction fo the strands run in?
Where and how are the different parts positioned?
What bonding is present?
How many base pairs for every turn of the helix?
How often does the structure repeat?
What grooves are present?
- two helical polynucleotide chains coiled around a common axis
- strands run in opposite direction (3’ and 5’ ends)
- purine and pyrimidine bases lie inside the helix (perpendicular to the axis)
- phosphate groups form the outside of the helix
- hydrogen bonds hold the bases together (A-T G-C)
- 10 base pairs for every helix turn
- structure repeats every 3,4nm
- there is no restriction on the sequence of bases. the exact sequence carries the genetic information.
- minor groove and major groove
What type of bonding holds the purine-pyrimidine base pairs together in DNA? How?
hydrogen bonding
- A with T (2 hydrogen bonds)
- G with C (3 hydrogen bonds)
What type of bonding holds the purine-pyrimidine base pairs together in RNA? How?
hydrogen bonding
- A with U (2 hydrogen bonds)
- G with C (3 hydrogen bonds)
What molecules are present in DNA? DNA nucleotides?
1) DNA- deoxyribonucleic acid
- 2 strands of covalently bonded nucleotides
2) DNA nucleotides:
- deoxyribose
- phosphate
- 1/4 nitrogenous bases (adenine, guanine, cytosine, thymine)
What molecules are present in RNA? RNA nucleotides?
1) DNA- deoxyribonucleic acid
- 1 strand of covalently bonded nucleotides
2) RNA nucleotides:
- ribose
- phosphate
- 1/4 nitrogenous bases (adenine, guanine, cytosine, uracil)
Explain the storage of DNA in eukaryotic cells.
- in nucleus
- seperated by a semipermeable membrane
- DNA –> chromosomes –> chromatin –> nucleosomes –> histones
What are the three types of RNA? What are their functions?
mRNA (messenger):
- makes proteins
- carries instructions for polypeptide synthesis from the nucleus to ribosomes
rRNA (ribosomal):
- makes up ribosomes
- forms both side of the ribosome
tRNA (transfer):
- carries amino acids to protein synthesis place (ribosome)
- matches amino acids to the code on the mRNA
What are enzymes? What type of molecule? Substrate specific or not? Used up in reaction or not?
Enzymes are mediators of metabolism that catalyze reactions responsible for the “dynamic” life.
- substrate-specific catalysts that enhance reaction rates without being used up in the process.
- most: proteins!
Where are enzymes found? What are they?
catalysts of common reactions: majority of cells
catalysts of unique reactions: particular form of cells
What is an active site? What structure is it formed by? What does it bind to? What does it form?
- a restricted region of an enzyme molecule which binds to the substrate.
- pockets formed by tertiary and quartenary structures
- forms the enzyme-substrate complex
When does an enzyme cause a reaction?
When all of its pockets (tertiary and quartenary structures) called active sites are occupied by substrates.
What are the two enzyme theories?
1) lock and key theory
2) induced fit theory
Explain the lock and key theory.
- the enzyme active site is complementary in conformation to the substrate
- enzyme is specific
- complementary geometric shapes
Explain the induced fit theory.
The enzyme changes shape on the binding of the substrate.
- cofirmation of the enzyme active site and substrate is complementary only after binding
How are enzymes named?
- name indicated function
- suffix “-ase” is used
- identified and named systematically with an EC number (1-6)
EC number= 4 digits
1- class of enzyme
2- subclass
3- sub-subclass
4- serial number of the enzyme in its subsub-class
State main group proteins, and explain their function.
Aminotransferases- transfer amino groups between substrates
Mutases- shift a phosphate group from one oxygen to another within the same molecule
Proteases- degrade proteins
State the function of:
1) oxidoreductases
2) transferases
3) hydrolases
4) lyases
5) isomerases
6) ligases
1) oxidoreductases- catalyse redox processes
2) transferases- transfer chemical groups from one molecule to another/another part of the molecule
3) hydrolases- clease a bond using water to produce two molecules from one
4) lyases- remove a group or add a group to double bonds
5) isomerases- interconvert isomeric structures by molecular arrangements
6) ligases- join two seperate molecules by the formation of a new bond using ATP
What are the different properties of enzymes?
- catalysts
- specific for substrates
- regulated by temperature, pH and some additives
Explain the work of an enzyme. Reaction rates? Transition state? Activation energy?
- Transition state: molecules pass through a high energy state
-** Activation energy**: energy required to achieve the reaction
- the higher the free energy change for the transition barrier, the slower the reaction rate.
- enzymes lower the energy barrier, by forcing molecules through a different transition state.
Explain the specificity of enzymes.
- complementary shape
- charge
- hydrophobic/hydrophillic characteristics
1) What are the properties of enzymes related to?
2) What affects the rate of reactions?
1) their tertiary structures
2)
- temperature
- pH
- substrate concentration (increases until the substrate concentration becomes the limiting factor)
- competative and non-competative inhibition
What molecules can enzymes activity be affected by?
- inhibitors
- activators
What are the two types of enzyme inhibition?
Reversable:
- non-covalent interaction
- no chemical changes
- reversable= no interactiosn b/w the inhibitor and substrate
Irreversable:
- covalent bonding
- inhibitor prevents catalytic activity of enzyme
- irreversable= strong covalent bonding
What are the two types of reversible enzyme inhibition? State examples. Explain process.
Competative:
- similar structure to substrate
- occupy active site temporarily
- higher rate of reaction when there is more ‘real’ substrate
eg. statin drugs
Noncompetative:
- bind to enzyme not at the active site
- binding doesnt change the shape of the enzyme
- reaction rate decreases
What are cofactors?
Inorganic ions or organic molecules that serve as enzyme helpers.
What are coenzymes?
Organic molecules that function as a cofactor.
- amino acids
- nitrogenous bases
- vitamins
must be organic
What do many enzymes require? What cofactors? Metal activated enzymes? metalloenzymes
inorganic cations!
- metal activated enzymes (stimulated by metal ions ie. K+, Ca2+, Mg2+)
- metalloenzymes (firmly bound metal ions at the enzymes active site ie. Fe, Zn, Cu, Co)
State examples of metalloenzymes. Explain their action.
carbonic anhydrase
- zinc ion promotes the ionization of H2O
- nucleophillic OH- attacks carbon of CO2
What happens to iron in metalloenzymes? What compounds contain iron?
undergoes reversible oxidation and reduction:
Fe3+ + e- –> Fe2+ + oxidized substrate
Iron containing enzymes:
- enzyme heme groups
- cytochromes
- non-heme iron: iron-sulfur clusters (Fe2+ = S2-)
State examples of metabolite coenzymes.
- nucleoside triphosphates
- ATP (donates: Pi, PPi, AMP, adenosil group)
What type of vitamins are coenzymes?
- soluble in water
- biological active forms
What vitamins must be supplied from food, fluids or microorganisms inhabiting the digestive tract? State the different types
water soluble vitamins:
- B
- C
Explain the function of Vitamin B.
- acts as a coenzyme
- specific reactions in glycolysis, the tricarboxylic acid cycle and lipid metabolism
What are enzyme molecules activated by?
- ions (Ca2+, Mg 2+)
- cofactors, coenzymes
- conversion of a proteoenzyme into an active molecule
What is vitamin B1? What is its coenzyme? Where is it found?
- Thyamin
- coenzyme thiamin pyrophosphate (TPP)
- coenzyme thiamin diphosphate
- produced by microbes, present in plant and animal tissue
What reactions does Thiamine Pyrophosphate (TPP) participate in?
- decarboxylation (pyruvate to acetyl CoA)
- oxidative decarboxylation
- transketolase enzyme reactions
What are the two groups of oxidation-reduction coenzymes?
- ribofalvin (vit. B2)
- nicotinamide (vit. B3)
What is riboflavin?
Vitamin B2
- alcohol ribotol, sugar flavin
- part of coenzyme: FAD (flavin adenine dinucleotide) and FMN (flavin mononucleate)
- coenzyme FAD and FMN are used in redox reactions involving carbohydrates, proteins and fats
What is Niacin?
- vitamin B3
- coenzyme: NAD+ (nicotineamide adenine dinucleotide), NADP+ (P=phosphate)
- coenzyme NAD+ and NADP+ are used in redox reactions involving carbohydrates, proteins and fats
What are the groups of transporting coenzymes?
- Pantothenic Acid (B5)
- Pyridoxine (B6)
- Folic Acid (B9)
- Cobalamin (B12)
What is Panthonetic Acid?
- part of coenzyme A
- Coenzyme A (involved in energy production, conversion of lipids and amino acids to glucose and synthesis of cholesterol and steroid hormones)
How does coenzyme A activate carboxylic acids?
- participates in acyl group transfer reactions (+ carboxylic acids / fatty acids)
- oxidation of fuel molecules
- biosynthesis of carboxylic acids
acetyl groups are covalently attached to the -SH of CoA to form thioesthers
What is Pyridoxine?
- Vitamin B6
- pyrodixine and pyridoxal (forms of B6)
- converted to PLP (coenzyme pyridoxal phosphate)
- PLP= transamination of amino acids and decarboxylation of carboxylic acids
What is PLP?
-
prosthetic group forenzyme catalysing reactions
involving amino acid metabolism: - isomerizations
- decarboxylations
- side chain elimination/replacement
What do biotin enzymes catalyse? What is biotin?
Biotin=prosthetic group
- carboxyl-group transfer reactions
- ATP dependent carboxylation reactions
What is folic acid?
- Folate (Vitamin B9)
- consists of: pyrimidine, p-aminobenzoic acid, glutamate
- forms coenzyme THFA used in synthesis of nucleic acids
What is cobalamin?
- 4 pyrole rings + Co2+
coenzyme involved in:
- the transfer of methyl groups
- acetyl choline synthesis
- red blood cell production
What is ascorbic acid? Ascorbate?
Vitamin C
- very polar hydroxy ester
- weak acid
- cosubstrate in the hydroxylation of dopamine to norepinephrine
Ascorbate: powerful reducing agent (antioxidant)
involved in:
- synthesis of hydroxyproline and hydroxylysine (2 modified amino acids required for collagen synthesis)
- biogenic amine biosynthesis
What are catecholamines?
associated with:
- animal ability to deal with stress,
- mobilize glycogen
- mobilize triglycerides for energy purpose
What plays a role of coenzymes and participates in an organisms metabolism?
derivatives of water soluble vitamins
