CHEMISTRY Flashcards
DICARBOXYLIC ACIDS
OH MY SUCH GOOD APPLE PIE, SWEET AS SUGAR:
Oxalic acid (HOOC-COOH)
Malonic acid (HOOC-CH2-COOH)
Succinic acid (HOOC-CH2-CH2-COOH)
Glutaric acid (HOOC-(CH2)3-COOH)
Adipic acid (HOOC-(CH2)4-COOH)
Pimelic acid (HOOC-(CH2)5-COOH)
Suberic acid (HOOC-(CH2)6-COOH)
Azelaic acid (HOOC-(CH2)7-COOH)
Sebacic acid (HOOC-(CH2)8-COOH)
monocarboxylic acids
THE FLIGHT ATTENDANT OF THE PLANE BUY A VALERIAN CAP TO ENTERTAIN CAPRIL AND PELARGO
Formic acid (HCOOH)
Acetic acid (CH3COOH)
Propionic acid (CH3CH2COOH)
Butyric acid (CH3CH2CH2COOH)
Valeric acid (CH3(CH2)3COOH)
Caproic acid (CH3(CH2)4COOH)
Enanthic acid (CH3(CH2)5COOH)
Caprylic acid (CH3(CH2)6COOH)
Pelargonic acid (CH3(CH2)7COOH)
ARRANGEMENT ACCORDING TO ACIDITY
ELEMENT
most electronegative
BCNOF flourine most
heaviest
FClBrI Iodine most
RESONANCE- aromatic rings
CONDUCTIVITY- no of electronegative atoms
HYBRIDIZATION- sp or triple bond most acidic
Type of prodrugs
1.carrier
2.bioprecursor
Type of carrier prodrugs
- Bipartite
- Tripartite
- Codrugs
Activation of carrier prodrug is cause by which reaction
Hydrolysis
Activation of bioprecursor prodrugs is cause by?
Redox
Chemical groups having similar physicochemical properties
Which give similar biological effects
Bioisosteres
Phase 1 metebolism reactions:
HORD
Hydrolysis
Oxidation- CYP450
Reduction
Deamination
In phase 2 glucoronidation metabolism, which enzyme facilitates the reaction?
UDP glucoronosyl transferase
Metabolic pathway/conjugation present in neonates/ infants (Sanggol)
Sulfate conjugation
Paracetamol is metabolized by which conjugation process?
Glutathione Conjugation
Carbohydrates contains which functional groups
Carbonyl group:
Ketones R-C=O-R
Aldehydes R-C=O-H
+Polyalcohols -OH
Suffix of monosaccharides containing ketone group
-ulose
Disacharide MALTOSE composition
2 glucose
Disacharide LACTOSE composition
Gluc/galactose
Disacharide SUCROSE composition
Gluc/Fructose
Trisaccharide RAFFINOSE composition
Gluc/fruc/galactose
Tetrasaccharide STACHYOSE composition
Gluc/fruc/ 2-galactose
Metabolic process which converts GLUCOSE into PYRUVATE
GLYCOLYSIS
10 steps of glycolisis
Great grandmother throws fresh fruit dish & go by picking pumpkins to prepare pies
1. Glucose phosphorylation
2. Isomerization of glucose-6-phosphate
3. Second phosphorylation
4. Cleavage of fructose-1,6-bisphosphate
5. Isomerization of dihydroxyacetone phosphate
6. Phosphorylation of 3-phosphoglycerate
7. Conversion of 3-phosphoglycerate to 2-phosphoglycerate
8. Enolase-mediated dehydration
9. Phosphorylation of 2-phosphoglycerate
10. Substrate-level phosphorylation to generate pyruvate
Meaning of Mnemonics DGB
In great grandma throws fresh fruits DISH & GO BY picking pumpkins to prepare pies
-10 steps of glycolysis
DihydroxyAcetone Phosphate
GlycerAldehyde 3-Phosphate
1,3- BiphosphoGlycerate
Enzymes involved in glycolysis metabolism
He Put the Phone And Tried to Get the Plastic Plate to Eat Pie
Hexokinase
PhosphoFructo Isomerase
PhosphoFructoKinase
Aldolase
Trios Phosphate Isomerase
Glyceraldehyde 3-Phosphate Dehydrogenase
PhosphoGlyceroKinase
PhosphoGlyceroMutase
Enolase
Pyruvate Kinase
No. Of ATP yeilded from GLYCOLYSIS
5 or 7
End product of ANAEROBIC glycolysis in vertebrates
L-lactate
Total ATP yield = 2
By enzyme LACTATE DEHYDROGENASE
End product of ANAEROBIC glycolysis in microorganisms
Ethanol
By enzyme- PYRUVATE DECARBOXYLASE
Gluconeogenesis will covert pyruvate to oxaloacetate- G6P by the enzyme
PYRUVATE CARBOXYLASE
End product of AEROBIC glycolysis
Acetyl-CoA
Major pathway for formation of ATP. Also provides substrate for gluconeogenesis, AA & FA synthesis
TCA/ CITRIC ACID/ KREB’s cycle
Occuring in mitochondria
End products of KREB’s CYCLE
2 CO2
1 GTP
3 NADH
1 FADH2
RLS (rate limiting step) of KREB’s CYCLE
Conversion of
Isocitrate to
alpha-ketoglutarate
By enzyme isocitrate dehydrogenase
RLS (rate limiting step) of glycolysis
conversion of
fructose-6-phosphate
to fructose-1,6-bisphosphate
4 fates of PYRUVATE
Ethanol- microorganisms ANAErobic
Lactate- vertebrates ANAErobic
G6P- gluconeogenis
Acetyl-CoA- AEROBIC
Substrates (steps) of Kreb’s cycle/citric Ac/ TCA
On Campus Areas, I Kiss Sexy Seductive Fair Maidens
Oxaloacetate
Citrate
Aconitate
Isocitrate
α-Ketoglutarate
Succinyl-CoA
Succinate
Fumarate
Malate
Total ATP yeild from TCA
10 ATP
Total ATP yeild of complete glucose oxidation
30/32 ATP
The substrates for gluconeogenesis, which is the process of synthesizing glucose from non-carbohydrate precursors, include:
- Pyruvate
- Lactate
- Glycerol (from triglycerides)
- Glucogenic amino acids (amino acids that can be converted to intermediates of the Kreb cycle)
Reverse of glycolysis
A metabolic pathway in which lactate produced by anaerobic glycolysis in muscles is transported to the liver and converted back to glucose.
CORI CYCLE
- GSD Type I (Von Gierke Disease):
• Defective Enzyme:
Glucose-6-phosphatase
- GSD Type II (Pompe Disease):
• Defective Enzyme:
Acid alpha-glucosidase (GAA)
- GSD Type III (Cori Disease):
• Defective Enzyme:
Glycogen debranching enzyme (Amylo-1,6-glucosidase)
- GSD Type IV (Andersen Disease):
• Defective Enzyme:
Glycogen branching enzyme (GBE1)
- GSD Type V (McArdle Disease):
• Defective Enzyme:
Muscle glycogen phosphorylase
- GSD Type VI (Hers Disease):
• Defective Enzyme:
Liver glycogen phosphorylase
- GSD Type IX:
• Various subtypes with defects in different enzymes like
phosphorylase kinase, phosphoglucomutase, and others depending on the subtype.
Glycogen storage diseases (GSDs)
VPCAMHT
Viagra Pills Cause A Major Hard Turnon
1. GSD Type I: Von Gierke Disease 2. GSD Type II: Pompe Disease 3. GSD Type III: Cori Disease 4. GSD Type IV: Andersen Disease 5. GSD Type V: McArdle Disease 6. GSD Type VI: Hers Disease 7. GSD Type VII: Tarui
The biochemical process through which glycogen, a polysaccharide composed of glucose units, is broken down into glucose molecules
Glycogenolysis
also known as the pentose phosphate pathway (PPP) or phosphogluconate pathway, is a series of biochemical reactions that occur in the cytoplasm of cells.
Hexose Monophosphate (HMP) shunt
G6PD- RLS
Amino Acid chemical structure
.
H O
| ||
NH2—-C—-C–OH
|
R
Side chain
Amino acid not optically active
GLYSINE
amino acids along with their three-letter codes:
1. Alanine 2. Arginine 3. Asparagine 4. Aspartic acid 5. Cysteine
amino acids along with their three-letter codes:
1. Ala 2. Arg 3. Asn 4. Asp 5. Cys
amino acids along with their three-letter codes:
6. Glutamine
7. Glutamic acid
8. Glycine
9. Histidine
10. Isoleucine
- Gln or Q
- Glu or E
- Gly or G
- His
- Ile
amino acids along with their three-letter codes:
11. Leucine
12. Lysine
13. Methionine
14. Phenylalanine
15. Proline
- Leu
- Lys
- Met
- Phe
- Pro
amino acids along with their three-letter codes:
16. Serine
17. Threonine
18. Tryptophan
19. Tyrosine
20. Valine
- Ser
- Thr
- Trp or W
- Tyr
- Val
The one letter code for tryptophan
W
The one letter code for glutamic acid
E
Amino acids which are not synthesized by the body
Essential amino acids
10 essential amino acids
PVT TIM HALL
always ARGues never TYRes
1. Phenylalanine (Phe)
2. Valine (Val)
3. Threonine (Thr)
4. Tryptophan (Trp)
5. Isoleucine (Ile)
6. Methionine (Met)
7. Histidine (His)
8. Arginine (Arg)
9. Leucine (Leu)
10. Lysine (Lys)
Semi essential amino acids
HArg
HISTIDINE
ARGININE
Amino acids that undergoes glucogenic/ketogenic metabolism
WIFY
Tryptophan- W
Isoliucine- I
Phenylalanine- F
Tyrosine- Y
Amino acids metabolic products
Glucogenic Metabolism - glucose
Ketogenic Metabolism- Acetyl CoA
Amino acids that undergo ketogenic metabolism
Leu Ly
Leucine
Lysine
Amino acids: Non polar alipathic R groups
Glycine
Alanine
Valine
Leucine
Isoleucine
Methionine
.
COOH-
|
H3N+—-C—–H
|
H
Glycine
.
COOH-
|
H3N+—-C—–H
|
CH3
Alanine
.
COOH-
|
H3N+—-C—–H
|
CH
^
CH3 CH3
Valine
.
COOH-
|
H3N+—-C—–H
|
CH2
|
CH
^
CH3 CH3
Leucine
.
COOH-
|
H3N+—-C—–H
|
CH2
|
CH2
|
S
|
CH3
Methionine
.
COOH-
|
H3N+—-C—–H
|
H—-C—-CH3
|
CH2
|
CH3
Isoleucine
Amino acids: Non polar AROMATIC R groups
Phenylalanin
Tyrosine
Tryptophan
.
COOH-
|
H3N+—-C—–H
|
CH2
|
^
|o|
v
Phenylalanine
.
COOH-
|
H3N+—-C—–H
|
CH2
|
^
|o|
v
|
OH
Tyrosine
.
COOH-
|
H3N+—-C—–H
|
CH2
|_
|_>NH
<__>
Indole ring
Tryptophan
Amino acids: Polar uncharged R groups
ASP PRO SER THRE GLUT CYST
Asparagine
Proline
Serine
Threonine
Glutamine
Cysteine
.
COOH-
|
H3N+—-C—–H
|
CH2OH
Serine
.
COOH-
|
H3N+—-C—–H
|
H—-C—OH
|
CH3
Threonine
.
COOH-
|
H3N+—-C—–H
|
CH2
|
SH
Cysteine
.
COOH-
|
C—–H
^
H2N CH2
| |
H2C—–CH2
Proline
.
COOH-
|
H3N+—-C—–H
|
CH2
|
C
^
H2N =O
Asparagus na naglutathione
Asparagine
.
COOH-
|
H3N+—-C—–H
|
CH2
|
CH2
|
C
^
H2N =O
Glutamine
Asparagus na naglutathione
Amino acids: Positively charged R groups
Basic/alkaline in nature
HIS ARGuments are LYS
Histidine
Arginine
Lysine
.
COOH-
|
H3N+—-C—–H
|
CH2
|
CH2
|
CH2
|
CH2
|
+NH3
Lysine
.
COOH-
|
H3N+—-C—–H
|
CH2
|
CH2
|
CH2
|
NH
|
C=NH2
|
+NH2
Arginine
.
COOH-
|
H3N+—-C—–H
|
CH2
|
C—–NH+
| >CH
C—–N
H
Histidine
Amino acids: negatively charged R groups
Acidic nature
Glutasp
Aspartate
Glutamate
.
COOH-
|
H3N+—-C—–H
|
CH2
|
COO-
Aspartate
.
COOH-
|
H3N+—-C—–H
|
CH2
|
CH2
|
COO-
Glutamate
How to determine net charge of AA in an environment with Ph given
- Isoelectric point/pH (Electrically neutral)
- IP is less than PH(given)
= net charge is positive
3.IP is more than PH(given)
= net charge is negative
More is less, Less is more
AA which is electrically neutral
Zwitterion
For neutral AA:
To compute isolectic point (pI)
given pka1 and pka2
Average of pka’s
For ACIDIC AA:
To compute isolectic point(pI)
given pka1, pka2 and Pka3
Average of 2 lowest pka’s
For BASIC AA:
To compute isolectic point(pI)
given pka1, pka2 and Pka3
Average of the 2 highest pka
Tryptophan codes
Trp/ W
Glutamine codes
Gln/ Q
Codes for Asparagin
Asn/ N
End product of glycogenolysis
GLUCOSE- liver
GLUCOSE-6-PHOSPHATE- muscle
End product of pentose phosphate pathway/ HMP SHUNT
NADH
RIBOSE-5-phosphate
AA structure not affected by denaturation process
Primary structure
Only destroyed by hydrolysis
Stabilized by peptide bonds
Alpha helix 3.6 no of amino acids per turn
ex. Keratin
Beta pleeted sheet helix ex. Amiloid
Stabilized by Hydrogen bond
Secondary structure enzyme
3D structure or DOMAIN: AA
Ex. Fibrous
Globular
Tertiary Structure
AA structure with Spatial arrangement
Stabilized by COVALENT interactions
Quaternary
Are proteins that act as catalysts, are not consumed in the reaction and has specificity
ENZYMES
Dehydrogenase is an example of enzyme(category) that TRANSFER electrons, which also result in change of oxidation state
OXIDOREDUCTASE
Phosphorylase and kinase is an example of enzyme(category) that transfer FUNCTIONAL GROUP from one molecule to another
TRANSFERASE
Protease, phosphatase is an example of enzyme(category) that BREAKDOWN covalent bond using water
HYDROLASE
Decarboxylase is an example of enzyme(category) that BREAKDOWN covalent bond WITHOUT water or oxidation
LYASE
Mutase is an example of enzyme(category) that REARRANGEMENT of bond within a molecule
ISOMERASE
An enzyme(category) that cause FORMATION of COVALENT BETWEEN 2 large molecule
LIGASE
Plot used in enzyme kinetics
MICHAELIS-MENTEN PLOT
MICHAELIS-MENTEN PLOT
Enzyme velocity increase as (V1)
Substrate concentration increases (S)
1st order kinetics
MICHAELIS-MENTEN PLOT- (order kinetics)
Enzyme velocity increase as (V1)
Substrate concentration (S) remains CONSTANT at Vmax
Zero order kinetics
MICHAELIS-MENTEN PLOT
Km or MICHAELIS-MENTEN constant= Affinity
Point where 1/2 of Vmax meet S
Relationship between Km & Affinity
⬆️Km= ⬇️ Affinity
⬇️Km= ⬆️ Affinity
Plot used to determine
Vmax & Km
(Enzyme kinetics- Inhibition)
LINEWEAVER-BURK Plot
LINEWEAVER-BURK Plot
Which type of inhibition is described as enzyme binding on ACTIVE site
Vmax= NA
Km= ⬆️
Competitive inhibition
LINEWEAVER-BURK Plot
Which type of inhibition is described as enzyme binding on ALOSTERIC site
Vmax= ⬇️
Km= NA
Non competitive inhibition
LINEWEAVER-BURK Plot
Which type of inhibition is described as enzyme binding on ENZYME SUBSTRATE site
Vmax= ⬇️
Km= ⬇️
Uncompetitive inhibition
In enzyme structure apoenzyme(protein) + cofactor(non protein) will yeild
HOLOENZYME
Cofactor composed of organic compounds is called
COENZYME
Loosely/temporarily attached to APOenzyme
Coenzyme composed of inorganic compounds is called
PROSTHETIC GROUP
Permanently attached to APOenzyme
Coenzyme Derived from Pantothenic Acid (Vitamin B5)
Coenzyme A (CoA)
Coenzyme Derived from Niacin (Vitamin B3)
Nicotinamide Adenine Dinucleotide (NAD):
Coenzyme Derived from Niacin (Vitamin B3)
Nicotinamide Adenine Dinucleotide Phosphate (NADP)
Coenzyme Derived from Riboflavin (Vitamin B2)
Flavin Mononucleotide (FMN)
Coenzyme Derived from Pyridoxine (Vitamin B6)
Pyridoxal Phosphate (PLP)
Coenzyme Derived from Folate (Vitamin B9)
Tetrahydrofolate (THF)
Coenzyme that Acts as a coenzyme in various reactions
Cobalamin (B12)
Coenzyme that Acts as a coenzyme in carboxylation reactions
Biotin
Coenzyme that Plays a role in some enzymatic reactions, acting as a cofactor rather than a coenzyme.
Ascorbic Acid (Vitamin C)
In gycolysis, the conversion of dihydroxyacetone phophate to glyceraldehyd 3-phophate is facilitated by which enzyme?
TRIOSE phosphate ISOMERASE
Yielding 2 molecules
In Kreb’s cycle, the Starting point on which the pyruvate join the cycle is at the conversion of ______ to citrate by the enzyme citrate synthase
OXALOACETATE
In Kreb’s cycle, What is the substrate which is converted from Citrate?
ACONITATE
These are polymers of NUCLEOTIDES joined by phosphodiester bonds
NUCLEIC ACIDS
Nucleotide composition
Phosphate- Pentose sugar- Nitrogenous Base
NucleoSIDE composition
Pentose sugar- Nitrogenous Base
Nitrogenous base in Nucleotides could be either
PYRIMIDINE ^\N
|| |
V/
N
PURINE
N_ ^\N
// || |
\ N / \N//
H
Pentose sugar in Nuceleotide could be either
RIBOSE
DEOXYRIBOSE
Difference point between RIBOSE and DEOXYRIBOSE is on Carbon 2 functional group
Ribose- OH
Deoxyribose- H
In nucleotides, what is the bond connecting Nitrogenous base to sugar
GLYCOSIDIC BOND
In nucleotides, what is the bond connecting phosphate to sugar
ESTER BOND
In nucleotides, what is the bond connecting a nucleotide subunit to another nucleotide subunit
PHOSPHODIESTER BOND
In nucleotides, what is the bond connecting 2 nitrogen bases together (base pairing)
HYDROGEN bonds
In DNA, How many Hydrogen bonds are there in A-T and C-G pairing
Adenine-thymine 2 H-bonds
Cytosine- Guanine 3 H-bonds
What are the Pyrimidine Nitrogen Bases
CUT the Pyramid
CYTOSINE
URACIL
THYMINE
What are the Purine Nitrogen Bases
PurGA
GUANINE
ADENINE
Composition of pyrimidine nitrogen base CYTOSINE
Pyrimidine- NH2
cy2sine
Composition of pyrimidine nitrogen base URACIL
Pyrimidine- O
Oracil
Composition of pyrimidine nitrogen base THYMINE
Pyrimidine- O + CH3
OCHymine
Composition of PURINE nitrogen base ADENINE
Purine - NH2
adeNHine
Composition of PURINE nitrogen base GUANINE
Purine- O + NH2
gOaNHine
What PYRIMIDINE bases are exclusively found in DNA & RNA respectively
DNA- Thymine
RNA- Uracil
Both PURINES A&G are found in D/RNA
What type of DNA 🧬 is left Handed
Z DNA
A/B are right handed
Number of turns/twists in DNA types A,B,Z
A has 11 (Aleven) ALANG tubig DEHYDRATED
B has 10 BASA HYDRATED
Z has 12 (Zuelve)
RNA that Carries genetic information from the DNA in the cell nucleus to the ribosomes in the cytoplasm. It serves as a template for protein synthesis during translation.
Messenger RNA (mRNA)
RNA that Transfers amino acids to the ribosome during protein synthesis
Transfer RNA (tRNA):
RNA that Forms a major part of the ribosomes, where protein synthesis occurs. It helps in the binding of mRNA and tRNA during translation.
Ribosomal RNA (rRNA
RNA structure consisiting of:
5’ CAP
POLY (A)tail
Also contains CODON
🧢
mRNA🪡
Clover shape RNA structure, consisiting of:
5’
D arm loop
Anticodon arm
3’CCA Acceptor arm
tRNA
Support or hold together tRNA & mRNA
SUPPORTING ACTORS
rRNA
Process by which DNA is transformed to RNA
Transcription
Process by which RNA is transformed to PROTEIN
TRANSLATION
Enzymes in DNA replication
Helicase- unwind the strand from inside the bubble
Topoisomerase- relieves tension on parent chain to allow unwinding
DNA polymerase- assembles new DNA
DNA Ligase- connects okazaki fragments from lagging strand
DNA Transcription steps
INITIATION
ELONGATION
TERMINATION
Enzymes in RNA transcription (mRNA)
RNA polymerase- binds to TATA box (promoter region of DNA) then unwind the strand - INITIATION of mRNA
mRNA- transcription/ ELONGATION
AAAAAA- TERMINATION point
PROCESSING occur after mRNA transcription before releasing into CYTOSOL for translation.
The following are the modifications:
- 5’ CAP addition- stability, binding site of ribosomal subunit for protein synthesis
- POLY-A tail addition- for motility
- INTRONS deletion- non coding region
- EXONS connection- coding region
TRANSLATION or protein synthesis
tRNA will start in the Attachment of AA to 3’ = aminoacyl-tRNA (powered by GTP). The translation processes are:
- INITIATION- 3 bases (codons)
-mRNA Start CODON- AUG (MET)
-tRNA ANTICODON- UAC
-Small ribosomal unit - ELONGATION- big ribosomal unit will attach, tRNA will bind to/release from the ribosome complex (repeatedly) until elongation is complete
- TERMINATION- STOP codon
UGA
UAG
UAA
Final modification of Protein synthesis occurs in
Golgi appratus
The rules stating:
DNA contains
Adinine = Thymine
Cytosine=Guanine
Purine=pyrimidine
CHARGAFF’s rule
Generic code characteristics
- Degenerate
- Unambigous
- Non overlapping
- Universal
DNA base pairing rule:
- Adenine (A) always pairs with Thymine (T), forming two hydrogen bonds.
- Guanine (G) always pairs with Cytosine (C), forming three hydrogen bonds.
Esters of fatty acids and alcohol
Fats/ Oils
Bond that stabilize triacylglycerol (triglycerides)
Ester bond
Reaction that combine fatty acids and glycerol
DEHYDRATION
Triacylglycerol (triglycerides) are derived ( liver/ adipose glycolysis) from DHAP(Dihydroxyacetone phosphate) to?
Glycerol phosphate
TAG (triacylglycerol) is produced from glycerol phosphate by
Linking of FA to glycerol by ACETYLTRANSFERASE
X3
Hydrolysis of stored fat is
LIPOLYSIS
By TAG-lipase releasing FREE FA
- Beta oxidation - producing 106/131 ATP
Rate limiting step in LIPOLYSIS
Carnitine palmitoyl transferase
What is the complex lipid consisting of:
Glycerol backbone
3 fatty acids
(Breakdown products)
TRIACYLGLYCEROL
Complex lipid consisting of:
Glycerol backbone
2 fatty acids
1 phosphate head group
(Breakdown products)
GLYCEROPHOSPHOLIPIDS
Ex. Phosphatidylcholine, serine, ethanolamine, etc
Complex lipid consisting of:
GlyceroEther backbone
1 fatty acids
1 phosphate head group
(Breakdown products)
Ether glycerolipids
Ex. Plasmalogens
Complex lipid consisting of:
Sphingosine backbone
1 fatty acids
1 phosphate head group
(Breakdown products)
SPHINGOPHOSPHOLIPIDS
Ex. Sphingomyelin
Complex lipid consisting of:
Sphingosine backbone
1 fatty acids
1 CARBOHYDRATE
(Breakdown products)
GLYCOLIPIDS
Ex. Cerebrosides, Sulfatides, Globosides, Gangliosides