Biochemistry- Amino Acids And Proteins

Front 1

Structure of proteins:

Back 1

1. Polymers of aminoacids
2. Macromolecules (Mr > 10 000)

Front 2

Amino acids in proteins:

Back 2

1. L-α-aminocarboxylic acids (Amino group on the left side)
2. There are 21 proteinogenic AAs
3. The rest of the AAs are formed by posttranslational modifications.

Front 3

Non-polar group of amino acids:
1. Characteristics
2. Names

Back 3

1. Hydrophobic
2. Ala, Val, Leu, Ile, Pro, Phe, Trp, Met

Front 4

Polar group of amino acids:
1. Characteristics
2. Names

Back 4

1. Hydrophilic (non- charged)
2. Gly, Ser, Thr, Cys, Tyr, Asn, Gln

Front 5

Acidic group of amino acids:
1. Characteristics
2. Names

Back 5

1. Negatively charged
2. Asp, Glu

Front 6

Basic group of amino acids:
1. Characteristics
2. Names

Back 6

1. Positively charged
2. Lys, Arg, His

Front 7

Modified amino acids:

Back 7

1. 4- Hydroxyproline
2. 3- Hydroxyproline
3. 5- Hydroxylysine
4. Allysine

Front 8

Essential amino acids (grouped);

Back 8

1. Branched chain AAs: Val, Leu, Ile
2. Aromatic AAs: Phe, Trp
3. Basic AAs: His, Arg, Lys
4. Sulfur- containing AAs: Met
5. Other: Thr

Front 9

What determines the final properties of amino acids:

Back 9

The side chains

Front 10

1. What is the Isoeletric point (pI):?
2. Formula:

Back 10

1.The pH value at which the net charge of the compound is zero
2. pI= pKCOOH+ pK NH3/ 2

Front 11

What are AA solution called called and what is the charge under physiological conditions?

Back 11

Ampholytes (amphoteric electrolytes). Are negatively charged under physiological conditions.

Front 12

Properties of AAs:

Back 12

1. UV radiation absorbtion
2. Ability to bind other compounds (phosphate or saccharide)
3. Can form disulfide bonds

Front 13

Important reactions of AAs:

Back 13

1. Dissociation--> salts
2. Decarboxylation--> bioenic amines
3. Transamination--> 2-oxoacids
4. Oxidative deamination--> 2- oxoacids
5. Formation of peptide bonds---> peptides/ proteins

Front 14

Nr. of AAs:
1. Oligopeptides
2. Polypeptides
3. Proteins

Back 14

1. 2-10AAs
2. >10 AAs
3. Proteins: About 50> AAs. Polypeptides of Mr > 10 000

Front 15

Peptide bond:

Back 15

Condensation of an N and C terminal from 2 AAs. Removal of H2O (O from COO- and H2 from NH3+)

Front 16

Bonds found in proteins:

Back 16

1. Covalent: Peptide bonds and disulfide bonds
2. Noncovalent interactons: Hydrogen bonds, hydrophobic interactions between nonpolar side chains and ionic interactions

Front 17

Primary structure of proteins:

Back 17

1. The order of amino acids
2. Read from N- to C-
3. Coded on a genetic level
4. Stabilized by peptide bonds

Front 18

Secondary structure of proteins:

Back 18

1. Spatial arrangement of the polypeptide chain given by rotation of the planar peptide bonds around α- carbons
2. Stabilized by hydrogen bonds between -CO- and -NH- of the peptide bonds
3. Different parts of the polypeptide chain exist in various secondary structure

Front 19

Helical structure:

Back 19

1. Various types of spiral: Different steepness, direction of rotation, and number of AAs per turn
2. Peptide bonds are parallel to the axis of the helix with R- perpendicular to it
3. H- bonds are formed between AAs found above and below themselves
4. α- helix is right handed, collagern helix is left handed and steaper

Front 20

β- plated sheet:

Back 20

1. Parallel or antiparallel
2. R- groups are placed above or below the sheet
3. H- bonds are formed between peptide bonds of the neighboring parts of the polypeptide chain
4. Function: brings strength to proteins

Front 21

Tertiary structure of proteins:

Back 21

1. Consists of spatial arrangement of secondary structure which are folded into domains
2. Stabilization between side chains of AAs:
- Hydrogen bonds
- Ionic interactions
- Hydrophobic interactions
- Disulfide bonds

Front 22

Classification of proteins according to their structure:

Back 22

1. Globular: Spheroidal shape, both secondary structures are abundant
2. Fibrous proteins: rod like shape, one secondary structure predominates, e.g. alfa- keratin, collagen

Front 23

Quaternary structure of proteins:

Back 23

1. Oligomeric structure (2 or more subunits)
2. Stabilized by noncovalent interactions
3. Proteins have an allosteric effect

Front 24

Classification of proteins:

Back 24

1. By localization in an organism: intra-/ extracellular
2. By function: structural/ biological active
3. By shape: globular/ fibrous
4. By chemical composition: simple/ complex (conjugated proteins)

Front 25

What does conjugated proteins contain:

Back 25

Polypeptide chain+ prosthetic group

Front 26

Physiochemical properties of proteins:

Back 26

1. Solubility depends on structure
2. Proteins form colloidal solutions= oncotic pressure
3. Can be denaturated by heat, radiation, strong pH changes, salts of heavy metals, organic solvents

Front 27

Protein determent in laboratory:

Back 27

1. Chemical reactions of peptide bonds with biuret reagent- spectophotometry
2. Complementary reaction with an antibody- immunochemistry
3. Separation in an electric field: electrophoresis

Front 28

Sources of AAs:

Back 28

1. Diet
2. Synthesis de novo
3. Protein degradation

Front 29

Conditionally essentiel AAs:

Back 29

Histidine and Arginine

Front 30

5 substrates for synthesis of AAs in a human body:

Back 30

1. Oxaloactetate--> Asp, Asn
2.α- ketoglutarate---> Glu, Gln, Pro, Arg
3. Pyruvate--> Ala
4. 3-phosphoglycerate---> Ser, Cys, Gly
5. Phe--->

Front 31

Transamination:

Back 31

1. A reversible exchange of - NH2 between amino acid and a α- ketoacid
2. Catalyzed by transaminases (most of the require α-ketoglutarate as an amino acceptor
3. Coenzyme of transaminases: pyroxidal phosphate

Front 32

Important aminotransfers:

Back 32

1.Glutamate+ α- keto acid--><---- α- ketoglutarate+ α- amino acid
2. Glutamate+ pyruvate= Alanine + α- ketoglutarate

Front 33

Amidation of glutamate:

Back 33

The side chain of carboxylic acid group is converted to amide group by adding of a ammonia group by the energy of ATP catalyzed by glutamine synthetase---> Glutamine ( the most important transport form of amino nitrogen in blood.

Front 34

Synthesis of aspargine:

Back 34

Aspartate+ Glutamine + ATP---> Aspargine+ Glutamate

Front 35

Synthesis of thyrosine:

Back 35

Phenylalanine is hydroxylated by Penylalanine hydroxylase while H2- biopterin is reduced by Dihydropteridine reductase to H4- biopterin while NADH is oxidized.

Front 36

Formation of activated methionine:

Back 36

Methionine + ATP (catalyzed by methionine adenosyltransferase)----> S- adenosylmethionine (SAM).

Front 37

What is the metabolic function of SAM (S-adenosylmethionine)?

Back 37

To function as a methyl group donor in metabolic methylations

Front 38

AAs used for synthesis of other N- compounds:

Back 38

1. Gln, Asp, Gly----> purines, pyrimidines
2. Gly---> porphyrines, creatine (+Arg and Met)
3. Arg--> NO
4. Cys--> taurine

Front 39

Decaroboxylation of AAs gives monoamines (biogenic amines):

Back 39

1. Tyr---> catecholamines
2. His---> histamine
3. Ser---> etanolamine---> choline -->acetylcholin
4. (Cys--> cysteamine, Asp--> β- alanine) ---> coenzyme A
5. Glu---> GABA

Front 40

3 main steps of catabolism of AAs:

Back 40

1. Removing of NH2 group form AAs
2. Detoxification of the amino group
3. Metabolism of carbon skeleton from AAs

Catalyzed by 20 different multi enzyme sequences

Front 41

All 20 AAs are converted to only 7 compounds:

Back 41

1. Pyruvate (both)
2. Acetyl- CoA (ketogenic)
3. Acetoacetyl- CoA (ketogenic)
4. α- ketoglutarate
5. Succinyl- CoA (both)
6. Fumarate (both)
7. Oxaloacetate

Front 42

Ketogenic AAs:

Back 42

1. Leucine
2. Lysine

Front 43

Both ketogenic and glucogenic AAs:

Back 43

1. Isoleucine
2. Threonine
3. Phenylalanine
4. Tyrosine
5. Tryptophan

Front 44

Deamination:

Back 44

1. E.g glutamate:
Glutamate is oxidated by glutamate dehydrogenase while NAD+ is reduced, releasing NH4+ and producing α- ketoglutarate.
NH4+ enter the urea cycle and α- ketoglutarate enter citric cycle or another transamination

Front 45

Examples of decarboxylation reactions:
(Product is amines!!)

Back 45

1. Histidine---> histamine by Histidine decarboxylase
2. Trp---> serotonin
3. Tyr----> adrenalin and noradrenalin
4. Glu---> GABA

Front 46

What process happen where:

Back 46

1. In extrahepatic tissue:
- Transamination
- Deamination
- Amidation
2. In the liver:
- Oxidative deamination

Front 47

Ammonia transport and detoxification:

Back 47

Ammonia is mainly transported by glutamine to liver mitochondria where glutaminase with the help of H2O cleaves and releases NH4 to the urea cycle and glutamate then glutamate can be oxidatively deaminated releasing the other ammonium to the urea cycle.

Front 48

Glucose- Alanine cycle:

Back 48

1. Glucose is degraded to pyruvate by glycolysis in extrahepatic tissues which undergoes transamination with glutamate from AAs----> α- ketoglutarate and Alanine. Catalyzed by "alanine transaminase"
2. Alanine is transported in blood to the liver where there is a transamination between alanine and α- ketoglutarate--> pyruvate and glutamate (alanine transaminase).
3. Pyruvate undergoes gluconeogenesis---> glucose which is transported back to extrahepatic tissues--> glycolysis
4. Glutamate undergoes oxidative deamination catalyzed bye "glutamate dehydrogenase"---> α- ketoglutarate and NH4+
5. NH4 + enters urea cycle and α- ketoglutarate can either enter citric acid cycle or undergo another transamination.

Front 49

1. Glutamine synthetase catalyze:
2. Glutaminase catalyze:

Back 49

1.Glutamate+ NH4+ + ATP---> glutamine+ ADP+ Pi
2. glutamine+ H2O---> glutamate+ NH4+ (in kidneys)

Front 50

Glutamate dehydrogenase:

Back 50

1. Removes amino group from glutamate in liver while NAD+ is reduced---> α- ketoglutarate and NH4+
2. The - NH2 from AAs was transferred by transamination

Front 51

Urea (ornithine cycle)
1. Why?
2. Location in body and cell:
3. Substartes and products:
4. Regulatory enzyme:
5: Negative consequence??
6. Energy requirements:

Back 51

1. NH3 exists as NH4+ which can change membrane potensials and inhibit action potensials
2. Mitochondria and cytosol of liver cells
3. Substrates: NH4+, CO2 and HCO3-. Product: urea---> urine
4. Carbamoyl phosphate synthase (allosteric activator: N- acetylglutamate)
5. Consumes HCO3- ---> decreased buffer capacity----> acidosis
6. 3 ATP and 4 energy rich bonds from fumarate

Front 52

Urea cycle gets NH4+ from:

Back 52

1. Glutamate by glutamate dehydrogenase
2. Glutamine by glutaminase

Front 53

Urea cylce:

Back 53

1. Matrix: CO2+ 2ATP+ NH3+ (Carbampyl phosphate synthetase 1)---> Carbamoyl phosphate+ 2ADP+ P
2. Carbamoyl gets transferred to Ornithine by Ornithine carbamoylase, releasing P----> L- Citrulline
3. Citrulline is transported to the cytosol where aspartate is added---> Argininosuccinate (argininosuccinate synthaze), consuming 1 more ATP (3total)
4. Argininosuccinate is cleaved by (argininosuccinate lyase)---> Fumarate + L- Arginine (containing the nitrogens)
5. Arginine is cleaved by (arginase with H2O)---> Urea + Ornithine (which can enter back into the matrix and undergo the cycle once again

Front 54

How is the urea cycle regulated?

Back 54

1. Allosteric regulation
2. Enzyme induction by protein rich diet or by metabolic changes during starvation

Front 55

Regulatory enzymes of urea cycle?

Back 55

1. Carbamoyl phosphate synthase 1 (mitochondrial) is activated by N- acetylglutamate.
2. N- acetylglutamate synthetase is activated by arginine

Front 56

What inhibits urea cycle?

Back 56

Acidosis inhibits urea cycle because HCO3- is saved to buffer the acidosis instead of being wasted in urea synthesis

Front 57

Important notes about synthesis of purines:

Back 57

1. Location: cytoplasm
2. PRPP (phosphoribosyl pyrophosphate) provides the ribose phosphate for purine synthesis. Derived from ribose-5-P----> a set of steps until --> IMP
3. IMP: inosine monophosphate common precursor of AMP and GMP
4. Glutamine, Glycine and Aspartate donate C and N atoms
5. CO2 donates C
6. C1 units are transferred via tetrahydrofolate
7. Regulatory enzyme: Glutamine: PRPP amidotransferase: activated by PRPP and inhibited by AMP and GMP

Front 58

Salvage pathway:

Back 58

Purines from normal turnover of cellular NA can be converted to nucleoside triphosphates
E.g: Hypoxanthine---> IMP, Guanine---> GMP, Adenine----> AMP
Substrates: purine bases, PRPP, ATP

Front 59

Important enzymes in synthesis of purine nucleotides:

Back 59

1. Glutamine- PRPP amidotransferase: catalyze first step where PRPP---> 5- phosphoribosylamine where glutamate donates NH2 and becomes glutamate
2. Adenylsuccinate lysase: hydrolyses and releases fumarate

Front 60

Degradation of purine nucleotides:

Back 60

1.Uric acid is formed by enzyme xanthine oxidase
2. GMP--> Guanosine--> Guanine--> (xanthine oxidase) Xanthine---> (xanthine oxidase)---> Urate
3. AMP---> (adenylate deaminase) IMP--> Inosine---> Hypoxanthine---> (xanthine oxisase) xanthine---> (xanthine oxidase) Urate

Front 61

Important notes about pyrimidine nucleotides synthesis:

Back 61

1. First step: Carbamoyl phosphate is formed from Glutamine, 2 ATP and CO2 (catalyzed by carbamoyl- P synthetase II)
2. Above mentioned enzyme is inhibited by UTP and activated by PRPP.
3. Carbamoyl phosphate + aspartate---> Carbamoyl aspartate---> Dihydroorotate---> Orotate---> OMP---> UMP---> UTP--> CTP.
4. dUMP can be converted to dTMP by thymidylate synthase

Front 62

Ribonucleotide reductase:
1. Function:
2. Structure:
3. Regulation:

Back 62

1. Conversion of ribonucleotides to deoxynucleotides
2. Composed of two nonidentical dimeric subunits: R1 and R2 and two sulfhydryl groups on the enzyme which are donors of Hydrogens needed for reduction of 2`hydroxyl groups. Form disulfide bonds
3. Activated by ATP, inhibited dATP.

Front 63

Degradation of pyrimidine bases:

Back 63

The pyrimidine rings are are reduced by NADPH oxidation and opened----> β- aminoacids are formed (β- alanine and β- aminoisobutyrate) and CO2 and NH4+ released

Front 64

Tetrapyrrols:

Back 64

1. Circular compounds binding a metal ion (most frequently Fe2+ or Fe3+)
2. Consists of 4 pyrrol rings interconnected via methenyl bridges (porphyrins)
3. Contain side chain attached to each of the 4 pyrrole rings
4. Examples:
- Heme (Fe2+)
- Chlorophyll (Mg2+)
- Vitamin B12 (Co2+)

Front 65

Where can we find heme?

Back 65

1. Hemoglobin
2. Myoglobin
3. Cytochrome C
4. Catalases

Front 66

Biosynthesis of heme:
1. Organ location:
2: Subcellular location
3. Substrates:
4. Important intermediates:
5: Key regulatory enzyme:

Back 66

1. 85% bone marrow, rest in liver
2. Mitochondria and cytosol
3. Succinyl- CoA and glycine
4. δ- aminolevulinic acid (ALA), porphobilinogen , uroporphyrinogen III, protoporphyrin IX
5. ALA synthase (inhibited by Heme and Iron)

Front 67

Heme synthesis:

Back 67

1. Mitochondria: Succinyl- CoA and glycine condensate----> δ- aminolevulinic acid (ALA) catalyzed by ALA synthase, releasing CO2 and CoA- SH
2. ALA leaves cytoplasm where 2 ALA molecules condense---> porhobilinogen (catalyzed by porhobilinogen synthase) releasing 2 H2O
3. 4 porphobilinogen molecules links and cleaves of 4 NH4+---> uroporphyrinogen III
4. 4 acetate residues are decarboxylated into methyl groups---> coproporphyrinogen III which returns to the mitochondria
5. Coproporphyrinogen--> Protoporphyrinogen IX
6. Oxidation of Protoporphyrinogen IX---> Protoporphyrin IX
7. Fe2+ is incorporated into protoporphyrin IX (catalyzed by ferrochelatase)---> Heme

Front 68

Regulation of heme synthesis:

Back 68

1. ALA synthase is an allosteric enzyme inhibited by heme by feedback inhibition
2. ALA synthase requires pyridoxal phosphate
3. Certain steroid hormones and drugs can increase heme synthesis
3. Porphobilinogen synthase and ferrochelatase is inhibited by lead ions (lead poisoning)

Front 69

Porphyrias:

Back 69

1. Hereditary disturbances of heme synthesis
2. Abnormality of enzymes in heme synthesis----> accumulation of intermediates and a deficiency of heme---> excretion of heme precursors in urine (dark red color)
3. Accumulation of porphyrinogens in skin---> photosensitivity
4. Neurological symptoms
5. Treatment: Injection of hemin: supplements heme and inhibits transcription of ALA- synthase

Front 70

Heme degradation:

Back 70

1. Erythrocytes are degraded in reticuloendothelial cells in spleen, liver and bone marrow.
2. Hb is degraded to:
- Globin--> AAs---> metabolism
- Heme---> Bilirubin
- Fe2+--> transported with transferrin and used in the next heme biosynthesis

Front 71

Conversion of heme to bilirubin:

Back 71

1. Heme is reduced and O2 is added while NADPH is oxidized. (Catalyzed by heme oxygenase) releases CO+ Fe3+ + NADP----->Biliverdin
2. Biliverdin is reduced to Bilirubin by "Biliverdin reductase" while NADPH is oxidized

Front 72

Fate of Bilirubin:

Back 72

1. Bilirubin is released by RES to blood and transported by albumin to liver.
2. In the hepatocytes bilirubin is conjugated with two molecules of glucuronic acid---> bilirubin diglucuronide which is soluble. (Catalyzed by UDP- glucuronosyltransferase)
3. Bilirubin diglucuronide---> bile---> intestine
4. Bacteria reduces Bilirubin diglucuronide---> urobilinogen.
5. Uribilinogen is oxidized by intestinal bacteria to stercobilin which is secreted by feces
6. Some urobilinogen is transported by blood to kidneys where it is oxidized to urobilin and excreted by urine

Front 73

Determation of bilirubin in serum:

Back 73

Conjugated bilirubin reacts directly with dyes, free bilirubin reacts only when there is methanol or caffeine in the solutine and are therefore indirect.
Total bilirubin: <20micromol/L

Front 74

Hyperbilirubinemias:

Back 74

1. > 10mg/L---> Bilirubin diffuses from blood to peripheral tissues---> jaundice

Front 75

Causes of jaundice:

Back 75

1. Hemolytic jaundice: Increased erythrocyte degradation
2. Hepatocellular jandice: Impaired conjugation in the liver (liver damage)
3. Obstructive jaundice: Disturbance of bile drainage (gallstones)
(Only conjugated bilirubin can be present in urine)

Front 76

Icterus
1. What?
2. Two types:

Back 76

1. Yellow coloration of skin and mucus due to jaundice
2. - Hemolytic icterus: Elevated levels of unconjugated bilirubin in blood
- Neonatal jaundice: Elevated hemolysis, decreased activity of UDP- glucuronsyltransferase--> Elevated unconjugated bilirubin (happens a few days after birth

Front 77

Kernicterus:

Back 77

Severe cases of jaundice where unconjugated bilirubin cross the blood brain barrier causing brain damage