BIOKIMIA

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BIOCHEMISTRY

1. Alfia Rayhan Nurjanah(4301419032)

2. Ade Noorliza Niyamae (4301419052)

3. Maiko Haris Dwi Cahya (4301419071)

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PROTEIN 1

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3 Proteins are giant

molecules with

molecular masses (6,000 -1,000,000) In the body of proteins

in the form of hormones:

like insulin, a chemical messenger to regulate biochemical activities that regulate blood

sugar levels Protein

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4 forming long fibers as

constituents of muscle tissue As myosin

serves oxygen transport from the lungs

throughout the cells As hemoglobin

to fight disease As an antibody

arranges nail, hair and skin tissue

As a keratin

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Amino Acid

Protein is a polymer with a monomer consisting of various amino acids.

Amino acids: organic acids which have two functional groups namely

carboxyl groups (-COOH) which are acidic and amine groups (-NH₃) which are alkaline

.

Therefore neutral amino acids are amphoteric.

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Because the acid group is the donor proton while the base group is the proton acceptor, the amino acid can transfer protons from the carboxyl group to the amine group, forming a cationic and anionic molecule commonly

called the zwitter ion.

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There are 20 kinds of amino acids that become protein monomers, in the form of a α

amino carboxylic acids

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• The incorporation of amino acids produces a condensation polymer by removing the H₂O molecule.

• How to form it as follows:

• Peptide bonds: bonds between carbonyl groups and amines

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Protein Structure

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• The dipeptide end has a carboxyl group and a free amine group, so that this combination still has the chance to form new peptide bonds, thus successively forming polypeptides.

• The combination of amino acids to form polypeptides is done in a certain order, so that certain proteins are formed.

• So, for a protein there is a specific amino acid sequence.

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• This amino acid sequence initially forms the primary structure.

• Furthermore, due to hydrogen bonding between groups in the chain, the chain is twisted into forming a spiral (α helix) called a secondary structure.

• If in addition to bending, folds will also occur, tertiary structures will form which form a ball (globular) as in myoglobin.

• If tertiary structures interact with one another, more complex quarterly structures such as hemoglobin are formed.

• Heme group: atomic groups found in the tertiary structure of hemoglobin and

become the center of the tertiary structure. This heme cluster provides a place to bind oxygen.

• The quarterly structure of this hemoglobin 4 heme groups are arranged tetrahedrally.

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Bonding Styles in Protein Structure

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between a carbonyl group (-CO) and an amino group (-NH)

Hydrogen bonding

disulfide bonds as oxidation of cysteine molecules in a chain

Covalent bonds

between the -COOH ion and the NH₃⁺ ion

Salt bond (ion)

In hemoglobin and myoglobin Fe (II)

form complex ions which have a planar quadrilateral structure bound by

coordination bonds with histidine from the polypeptide chain

Coordination coordination by

heme clusters

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Enzyme

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• Enzymes: proteins that catalyze biochemical reactions whose effectiveness is astounding

• Enzymes can increase the reaction rate up to

• With enzymes can be obtained by the reaction without side effects.

• The rate of biochemical reaction depends on the production of enzymes.

• The mechanism of action of enzymes depends on enzymes being able to bind to reactant molecules called substrates.

• Some enzymes are very specific activity, meaning that it can only catalyze certain molecules, while some enzymes can catalyze compounds that have similar

structures.

• The mechanism of action of an enzyme is like a lock and a padlock, that is, the part of the substrate molecule that goes right into the fold of globular protein from the enzyme. If this happens then the substrate becomes tense or the energy rises so that it is easily attacked by reactants.

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• The part of the enzyme in the form of benzene which is hydrophobic, will be compressed in a suitable part of the enzyme. Furthermore, the carbonyl group will interact in more parts of the enzyme so that the bond with the group ... XR is easily attacked.

• The function of the enzyme depends only on the hydrophobic part and

the position of the CO group, so other substrates that have the same

hydrophic group and the CO group can be catalyzed by the enzyme

chemotrypsin.

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• If there are substances that are not substrates of an enzyme but have groups that can be bound by the active side of the enzyme, then this substance will immobilize the work of enzymes called inhibitors.

• Inhibitors can bind the enzyme so tightly that the enzyme cannot be tried to

reactivate (irreversible) because of the formation of covalent bonds between the enzyme and the inhibitor.

• Example: diisopropylfluorophosphate compound that reacts with the enzyme aceticolin esterase.

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• Another type of inhibitor is that the bond can be removed again (reversible) if more substrate is added, resulting in competitive inhibition. The inhibitor will compete with the substrate to bind to the active side. So there are two competing equilibrium

which take place simultaneously.

• If S is excessive, the equilibrium shifts towards ES and E will be pulled upward, and the equilibrium below will shift to the left so that the enzyme raises the inhibitor.

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 Example: the action of sulfanilamide

 The structure of sulfanilamide is very similar to the p-amino- benzoic acid (PABA) which is processed by enzymes to be converted into coenzymes needed by bacteria.

 Sulfanilamide compounds will occupy the active side of the

enzyme that will convert p-amino-benzoic acid, thus blocking the production of coenzymes so that bacteria will die.

Sulfanilamid a

P-amino-benzoat

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Effect of Temperature and pH

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Enzyme activity is influenced by temperature and pH which will change the shape and charge of the globular enzyme structure, is change the exact

active center for the formation of enzyme-substrate bonds to obtain the

expected catalyst activity.

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Carbohydrates B

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Carbohydrate function

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Energy sources

Sources of carbon elements for the formation of

biomolecules Cell and tissue constituent

materials

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The literal meaning of carbohydrate is hydrate of carbon. Because this assumption is not correct, it is replaced by the Saccharide. Thus, sucrose, or cane sugar, is

equivalent to Amore useful definition is that carbohydrates are polyhydroxy

aldehydes, polyhydroxy ketones, their derivatives, and substances that yield them on hydrolysis. Carbohydrates that are aldehydes are called aldoses; those that are

ketones are called ketoses. A five-carbon carbohydrate is a pentose, a six-carbon one, a hexose, and so on. The structures in the margin are those of two familiar

hexoses glucose and fructose, an aldose and a ketose, respectively

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Glyceraldehid

The types of saccharides found in nature (starch, cellulose) are giant molecules (forms of condensation of monomer) or monosaccharides.

Monosaccharides include Polyhidroxyaldehyde and ketone. The simplest example of this group is glyceraldehyde. One of the compounds of

glyceraldehyde is glucose (hexsosa, with 6 carbon)

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Glucose

In a solution, glucose forms the cyclical

and forms a rectangle called a piranous

ring. There are two kinds of isomer,

namely α-D-glucose and β-D-glucose,

due to the difference in the location of

OH group.

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Fructose

Fructose also forms a cyclical

structure forming a Pentagons

(furanous ring).

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Monosaccharides with others can form a

chain of pilisaccharide through the

Glycosidic bond (C-O-C). In an acidic

solution or containing amylase enzyme, the

Glycosidic bond of sucrose can be

hydrolyzed to glucose and frucrose.

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C Lipids

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Lipids are those constituents of plant and animal tissue that are soluble in low- polarity solvents, such as chloroform, carbon tetrachloride, diethyl ether, benzene

and and not soluble in polar solvent like water.

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Lipids are divided into

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Glycerol Ester of fatty acids

Steroid

Terpenes

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Glycerol Ester of fatty acids

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Glycerol Ester of fatty acids is carboxylic acid which the number of C atoms is between 12-28.

Divided into

1.Nertral lipid, an ester of glycerol and fatty acids.

Example: Triglycerides

2.Polar lipid, formed from the glycerol paa ester atom C1 and C2 with fatty acids, is not a C3 atom with

phosphate group.

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Some Common Fatty Acids

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Common Name IUPAC Name Formula

Saturated Acids Lauric acid

Myristic acid

Hexadecanoic acid Stearic acid

Dodecanoic acid

Tetradecanoic acid Palmitic acid

Octadecanoic acid

C

₁₁

H

₂₃

CO

₂

H C

₁₃

H

₂₇

CO

₂

H C

₁₅

H

₃₁

CO

₂

H C

₁₇

H

₃₅

CO

₂

H Unsaturated Acids

Oleic acid

Linoleic acid Linolenic acid Eleostearic acid

9-Octadecenoic acid

9,12-Octadecadienoic acid

9,12,15-Octadecatrienoic acid 9,11,13-Octadecatrienoic acid

C

₁₇

H

₃₃

CO

₂

H

C

₁₇

H

₃₁

CO

₂

H

C

₁₇

H

₂₉

CO

₂

H

C

₁₇

H

₂₉

CO

₂

H

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Triglycerides can apply a saponification reaction in a base

solution

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NUCLEID ACID D

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NUCLEID ACID

DNA plays a role in controlling the transmission of genetic information of a living thing from one generation to the next. Together RNA plays a role in protein synthesis

The smallest unit of nucleic acid formation is called nucleotide. Nucleotides are built by three molecules: nitrogenous bases, pentoses, and phosphoric acids.

Nucleic acid is the result of condensation polymerization of nucleotides, formed through ester bonds between phosphoric acid residues from one nucleotide and OH groups from C3 atoms from pentose from other nucleotides.

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Nitrogen Base Pentosa Phosphoric Acid

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PROTEIN E

SYNTHESIS

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PROTEIN SYNTHESIS

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In the process of translating amino acids will be coupled with other amino acids to form polypeptide chains or proteins. the type of amino acids arranged is determined by the sequence of the nucleotides in the mRNA. So, mRNA is used as a template for protein synthesis.

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PROTEIN SYNTHESIS

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1. Dicalis by the aminoacyl-tRNA synthetase enzyme 2. This enzyme is specific for each amino acid: 20

aminoacyl-tRNA synthetase enzymes

3. In this process the tRNA produced in the nucleus is paired with the corresponding amino acids

4. tRNA which has become called aminoacyl tRNA

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GENETIC CODE TABLE

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Thank you!

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