CHEMISTRY Flashcards by Rommel Bautista

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)

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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)

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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

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Type of prodrugs

1.carrier
2.bioprecursor

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Type of carrier prodrugs

Bipartite
Tripartite
Codrugs

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Activation of carrier prodrug is cause by which reaction

Hydrolysis

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Activation of bioprecursor prodrugs is cause by?

Redox

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Chemical groups having similar physicochemical properties
Which give similar biological effects

Bioisosteres

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Phase 1 metebolism reactions:

HORD

Hydrolysis
Oxidation- CYP450
Reduction
Deamination

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In phase 2 glucoronidation metabolism, which enzyme facilitates the reaction?

UDP glucoronosyl transferase

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Metabolic pathway/conjugation present in neonates/ infants (Sanggol)

Sulfate conjugation

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Paracetamol is metabolized by which conjugation process?

Glutathione Conjugation

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Carbohydrates contains which functional groups

Carbonyl group:
Ketones R-C=O-R
Aldehydes R-C=O-H

+Polyalcohols -OH

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Suffix of monosaccharides containing ketone group

-ulose

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Disacharide MALTOSE composition

2 glucose

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Disacharide LACTOSE composition

Gluc/galactose

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Disacharide SUCROSE composition

Gluc/Fructose

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Trisaccharide RAFFINOSE composition

Gluc/fruc/galactose

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Tetrasaccharide STACHYOSE composition

Gluc/fruc/ 2-galactose

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Metabolic process which converts GLUCOSE into PYRUVATE

GLYCOLYSIS

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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

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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

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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

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No. Of ATP yeilded from GLYCOLYSIS

5 or 7

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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:

1. Pyruvate 2. Lactate 3. Glycerol (from triglycerides) 4. 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

1. GSD Type I (Von Gierke Disease): • Defective Enzyme:

Glucose-6-phosphatase

2. GSD Type II (Pompe Disease): • Defective Enzyme:

Acid alpha-glucosidase (GAA)

3. GSD Type III (Cori Disease): • Defective Enzyme:

Glycogen debranching enzyme (Amylo-1,6-glucosidase)

4. GSD Type IV (Andersen Disease): • Defective Enzyme:

Glycogen branching enzyme (GBE1)

5. GSD Type V (McArdle Disease): • Defective Enzyme:

Muscle glycogen phosphorylase

6. GSD Type VI (Hers Disease): • Defective Enzyme:

Liver glycogen phosphorylase

7. 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

6. Gln or Q 7. Glu or E 8. Gly or G 9. His 10. Ile

amino acids along with their three-letter codes: 11. Leucine 12. Lysine 13. Methionine 14. Phenylalanine 15. Proline

11. Leu 12. Lys 13. Met 14. Phe 15. Pro

amino acids along with their three-letter codes: 16. Serine 17. Threonine 18. Tryptophan 19. Tyrosine 20. Valine

16. Ser 17. Thr 18. Trp or W 19. Tyr 20. Val

The one letter code for tryptophan

The one letter code for glutamic acid

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

1. Isoelectric point/pH (Electrically neutral) 2. 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:

1. 5' CAP addition- stability, binding site of ribosomal subunit for protein synthesis 2. POLY-A tail addition- for motility 3. INTRONS deletion- non coding region 4. 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:

1. INITIATION- 3 bases (codons) -mRNA Start CODON- AUG (MET) -tRNA ANTICODON- UAC -Small ribosomal unit 2. ELONGATION- big ribosomal unit will attach, tRNA will bind to/release from the ribosome complex (repeatedly) until elongation is complete 3. 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

1. Degenerate 2. Unambigous 3. Non overlapping 4. Universal

DNA base pairing rule:

1. Adenine (A) always pairs with Thymine (T), forming two hydrogen bonds. 2. 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

CHEMISTRY Flashcards

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