SATUAN ACARA DAN JADUAL KULIAH BIOKIMIA

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1 SATUAN ACARA DAN JADUAL KULIAH BIOKIMIA
No. Topik Perkuliahan Tanggal Pengajar 1. Pendahuluan Konsep dasar biokimia Reaksi-reaksi biokimia Drs. Winarto Hariadi, M.Si. 2. Air dan Buffer 3. Karbohidrat I Tinjauan umum Monosakarida Disakarida Polisakarida Dr. Ir. Arman Wijonarko, M.Sc. 4. Karbohidrat II Reaksi monosakarida Ikatan glikosida Fungsi karbohidrat

2 SATUAN ACARA DAN JADUAL KULIAH BIOKIMIA
No. Topik Perkuliahan Tanggal Pengajar 5. Asam Amino dan Protein I Tinjauan umum Asam amino Biosintesis asam amino Dr. Ir. Arman Wijonarko, M.Sc. 6. Asam Amino dan Protein II Peptida Struktur protein Fungsi asam amino dan protein Biosintesis protein 7. Lipida I Asam lemak jenuh dan tak jenuh Reaksi asam lemak Drs. Winarto Hariadi, M.Si. 8. Lipida II Fungsi asam lemak dan lipida Biosintesis asam lemak 9. UJIAN SISIPAN Topik 1 s/d 8

3 SATUAN ACARA DAN JADUAL KULIAH BIOKIMIA
No. Topik Perkuliahan Tanggal Pengajar 10. Asam nukleat I Tinjauan umum Nukleosida dan nukleotida Ir. Sedyo Hartono, M.P., Ph.D. 11. Asam nukleat II Struktur DNA dan RNA 12. Enzim I Klasifikasi enzim Koenzim dan kofaktor Ir. Irfan D. Prijambada, M.Eng., Ph.D. 13. Enzim II Mekanisme dan kinetika kerja enzim Penghambatan kerja enzim

4 SATUAN ACARA DAN JADUAL KULIAH BIOKIMIA
No. Topik Perkuliahan Tanggal Pengajar 14. Metabolisme I Tinjauan umum Jalur metabolisme Ir. Irfan D. Prijambada, M.Eng., Ph.D. 15. Metabolisme II Bioenergetika Pengendalian metabolisme 16. UJIAN AKHIR Mengikuti jadual Fakultas Topik 10 s/d 15

5 KARBOHIDRAT II. Reaksi monosakarida. Ikatan glikosida
KARBOHIDRAT II * Reaksi monosakarida * Ikatan glikosida * Fungsi karbohidrat Irfan D. Prijambada, Ph.D. Lab. Mikrobiologi Tanah dan Lingkungan, Fakultas Pertanian UGM

6 Monosakarida Memiliki atom karbon 3 sampai 7
Setiap atom karbon memiliki gugus hidroksil, keton atau aldehida. Setiap molekul monosakarida memiliki 1 gugus keton atau 1 gugus aldehida Gugus aldehida selalu berada di atom C pertama Gugus keton selalu berada di atom C kedua

7 Monosakarida Aldosa (mis: glukosa) memiliki gugus aldehida pada salah satu ujungnya. Ketosas (mis: fruktosa) biasanya memiliki gugus keto pada atom C2.

8 Notasi D vs L D - g l y c e r a d h Notasi D & L dilakukan karena adanya atom C dengan konfigurasi asimetris seperti pada gliseraldehida. C H O 2 D - g l i s e r a d h C H O 2 L - g l i s e r a d h C H O 2 C H O 2 L - g l i s e r a d h Penampilan dalam bentuk gambar bagian bawah disebut Proyeksi Fischer.

9 Penamaan Gula Untuk gula dengan atom C asimetrik lebih dari 1, notasi D atau L ditentukan oleh atom C asimetrik terjauh dari gugus aldehida atau keto. Gula yang ditemui di alam adalah dalam bentuk isomer D. O H O H C H – C – OH HO – C – H HO – C – H – C – OH OH HO – C – H HO – C – H CH 2 D - glukosa L -glukosa

10 Stereoisomers lainnya memiliki names yang unik,
O H O H C H – C – OH HO – C – H HO – C – H – C – OH OH HO – C – H HO – C – H CH 2 D - glukosa L -glukosa Gula dalam bentuk D merupakan bayangan cermin dari gula dalam bentuk L. Kedua gula tersebut memiliki nama yang sama, misalnya D-glukosa & L-glukosa. Stereoisomers lainnya memiliki names yang unik, misalnya glukosa, manosa, galaktosa, dll. Jumlah stereoisomer adalah 2n, dengan n adalah jumlah pusat asimetrik. Aldosa dengan 6-C memiliki 4 pusat asimetrik, oleh karenanya memiliki 16 stereoisomer (8 gula berbentuk D dan 8 gula berbentuk L).

11 Pembentukan hemiasetal & hemiketal
Aldehida dapat bereaksi dengan alkohol membentuk hemiasetal. Keton dapat bereaksi dengan alkohol membentuk hemiketal. + aldehida C H R O hemiasetal O C H R ' alkohol R ' O H C R ' O keton hemiketal O C R ' H " " R O H alkohol

12 Penampilan dalam bentuk gula siklik disebut proyeksi Haworth.
C 2 a - D glukosa b 3 4 5 6 1 (bentuk linier) Pentosa dan heksosa dapat membentuk struktur siklik melalui reaksi gugus keton atau aldehida dengan gugus OH dari atom C asimetrik terjauh. Glukosa membentuk hemiasetal intra-molekular sebagai hasil reaksi aldehida dari C1 & OH dari atom C5, dinamakan cincin piranosa. Penampilan dalam bentuk gula siklik disebut proyeksi Haworth.

13 Fruktosa dapat membentuk
C H 2 O 1 6 5 4 3 D - fruktosa ( l i n e a r ) fruktofuranosa Fruktosa dapat membentuk Cincin piranosa, melalui reaksi antara gugus keto atom C2 dengan OH dari C6. Cincin furanosa, melalui reaksi antara gugus keto atom C2 dengan OH dari C5.

14 a (OH di bawah struktur cincin) b (OH di atas struktur cincin).
2 a - D glukosa b 3 4 5 6 1 Pembentukan cincin siklik glukosa menghasilkan pusat asimetrik baru pada atom C1. Kedua stereoisomer disebut anomer, a & b. Proyeksi Haworth menunjukkan bentuk cincin dari gula dengan perbedaan pada posisi OH di C1 anomerik : a (OH di bawah struktur cincin) b (OH di atas struktur cincin).

15 O H a - D glukopiranosa b 1 6 5 4 3 2 Karena sifat ikatan karbon yang berbentuk tetrahedral, gula piranosa membentuk konfigurasi “kursi" atau “perahu", tergantung dari gulanya. Penggambaran konfigurasi kursi dari glukopiranosa di atas lebih tepat dibandingkan dengan proyeksi Haworth.

16 Turunan gula C O H Asam D-glukonat Asam D-glukuronat 2 Gula alkohol – tidak memiliki gugus aldehida atau ketone; misalnya ribitol. Gula asam –gugus aldehida pada atom C1, atau OH pada atom C6, dioksidasi membentuk asam karboksilat; misalnya asam glukonat, asam glukuronat.

17 Oksidasi gula aldehida
C O H 2 D - g l u c o s e Asam D-glukonat C O H 2 Oksidator

18 Oksidasi gula aldehida
Gula yang dapat dioksidasi adalah senyawa pereduksi. Gula yang demikian disebut sebagai gula pereduksi. Senyawa yang sering digunakan sebagai pengoksidasi adalah ion Cu+2, yang berwarna biru cerah, yang akan tereduksi menjadi ion Cu+, yang berwarna merah kusam. Hal ini menjadi dasar bagi pengujian Benedict yang digunakan untuk menentukan keberadaan glukosa dalam urin, suatu pengujian bagi diagnosa diabetes.

19 Oksidasi gula aldehida
panas & alk . pH Glukosa + Cu++ Gluconic acid + Cu2O (Cu2O is insol ppt) glukosa oksidase Glukosa + O2 Asam glukonat + H2O2 (H2O2 nya diukur) heksokinase Glukosa + ATP Glukosa-6-P + ADP (G-6-Pnya diukur)

20 Turunan gula C H O H C H O H 2 2 O H O H H H H H O H H O H H O H O H O H O H O H N H H N C C H 2 3 H a - - glukosamina a D - D - N - asetilglukosamina Gula amino - gugus amino menggantikan gugus hidroksil. Sebagai contoh glukosamina. Gugus amino dapat mengalami asetilasi, seperti pada N-asetilglukosamina.

21 Ikatan Glikosida Gugus hidroksil anomerik dan gugus hidroksil gula atau senyawa yang lain dapat membentuk ikatan yang disebut ikatan glikosida dengan membebaskan air : R-OH + HO-R'  R-O-R' + H2O Misalnya methanol bereaksi dengan gugus OH anomerik dari glukosa membentuk metil glukosida (metil-glukopiranosa). O H a - D glukopiranosa C 3 Metil-a-D-glukopiranosa + metanol 2

22 Disaccharides: Maltose, a cleavage product of starch (e.g., amylose), is a disaccharide with an a(1® 4) glycosidic link between C1 - C4 OH of 2 glucoses. It is the a anomer (C1 O points down). Cellobiose, a product of cellulose breakdown, is the otherwise equivalent b anomer (O on C1 points up). The b(1® 4) glycosidic linkage is represented as a zig-zag, but one glucose is actually flipped over relative to the other.

23 Other disaccharides include:
Sucrose, common table sugar, has a glycosidic bond linking the anomeric hydroxyls of glucose & fructose. Because the configuration at the anomeric C of glucose is a (O points down from ring), the linkage is a(12). The full name of sucrose is a-D-glucopyranosyl-(12)-b-D-fructopyranose.) Lactose, milk sugar, is composed of galactose & glucose, with b(14) linkage from the anomeric OH of galactose. Its full name is b-D-galactopyranosyl-(1 4)-a-D-glucopyranose

24 Polysaccharides Plants store glucose as amylose or amylopectin, glucose polymers collectively called starch. Glucose storage in polymeric form minimizes osmotic effects. Amylose is a glucose polymer with a(14) linkages. It adopts a helical conformation. The end of the polysaccharide with an anomeric C1 not involved in a glycosidic bond is called the reducing end.

25 Amylopectin is a glucose polymer with mainly a(14) linkages, but it also has branches formed by a(16) linkages. Branches are generally longer than shown above. The branches produce a compact structure & provide multiple chain ends at which enzymatic cleavage can occur.

26 Glycogen, the glucose storage polymer in animals, is similar in structure to amylopectin. But glycogen has more a(16) branches. The highly branched structure permits rapid release of glucose from glycogen stores, e.g., in muscle during exercise. The ability to rapidly mobilize glucose is more essential to animals than to plants.

27 Cellulose, a major constituent of plant cell walls, consists of long linear chains of glucose with b(1®4) linkages. Every other glucose is flipped over, due to the b linkages. This promotes intra-chain and inter-chain H-bonds and van der Waals interactions, that cause cellulose chains to be straight & rigid, and pack with a crystalline arrangement in thick bundles called microfibrils. Botany online website

28 Multisubunit Cellulose Synthase complexes in the plasma membrane spin out from the cell surface microfibrils consisting of 36 parallel, interacting cellulose chains. These microfibrils are very strong. The role of cellulose is to impart strength and rigidity to plant cell walls, which can withstand high hydrostatic pressure gradients. Osmotic swelling is prevented. Explore and compare structures of amylose & cellulose using Chime.

29 Glycosaminoglycans (mucopolysaccharides) are polymers of repeating disaccharides.
Within the disaccharides, the sugars tend to be modified, with acidic groups, amino groups, sulfated hydroxyl and amino groups, etc. Glycosaminoglycans tend to be negatively charged, because of the prevalence of acidic groups.

30 Hyaluronate is a glycosaminoglycan with a repeating disaccharide consisting of 2 glucose derivatives, glucuronate (glucuronic acid) & N-acetyl-glucosamine. The glycosidic linkages are b(1®3) & b(1®4).

31 Proteoglycans are glycosaminoglycans that are covalently linked to specific core proteins. 
Some proteoglycans of the extracellular matrix in turn link non-covalently to hyaluronate via protein domains called link modules.

32 For example, in cartilage multiple copies of the aggrecan proteoglycan bind to an extended hyaluronate backbone to form a large complex. Versican, another proteoglycan that binds to hyaluronate, is in the extracellular matrix of loose connective tissues. See web sites on aggrecan and aggrecan plus versican.

33 Heparan sulfate is initially synthesized on a membrane-embedded core protein as a polymer of alternating N-acetylglucosamine and glucuronate residues. Later, in segments of the polymer, glucuronate residues may be converted to the sulfated sugar iduronic acid, while N-acetylglucosamine residues may be deacetylated and/or sulfated.

34 Heparin has an extended helical conformation.
Heparin, a soluble glycosaminoglycan found in granules of mast cells, has a structure similar to that of heparan sulfates, but is more highly sulfated. When released into the blood, it inhibits clot formation by interacting with the protein antithrombin. Heparin has an extended helical conformation. C  O  N  S Charge repulsion by the many negatively charged groups may contribute to this conformation. Heparin shown has 10 residues, alternating IDS (iduronate-2-sulfate) & SGN (N-sulfo-glucosamine-6-sulfate).

35 Some cell surface heparan sulfate glycosaminoglycans remain covalently linked to core proteins embedded in the plasma membrane. Proteins involved in signaling & adhesion at the cell surface recognize and bind segments of heparan sulfate chains having particular patterns of sulfation.

36 Oligosaccharides that are covalently attached to proteins or to membrane lipids may be linear or branched chains. O-linked oligosaccharide chains of glycoproteins vary in complexity. They link to a protein via a glycosidic bond between a sugar residue & a serine or threonine OH.  O-linked oligosaccharides have roles in recognition, interaction, and enzyme regulation.

37 N-acetylglucosamine (GlcNAc) is a common O-linked glycosylation of protein serine or threonine residues. Many cellular proteins, including enzymes & transcription factors, are regulated by reversible GlcNAc attachment. Often attachment of GlcNAc to a protein OH alternates with phosphorylation, with these 2 modifications having opposite regulatory effects (stimulation or inhibition).

38 N-linked oligosaccharides of glycoproteins tend to be complex and branched. First N-acetylglucosamine is linked to a protein via the side-chain N of an asparagine residue in a particular 3-amino acid sequence.

39 Additional monosaccharides are added, and the N-linked oligosaccharide chain is modified by removal and addition of residues, to yield a characteristic branched structure.

40 Many proteins secreted by cells have attached N-linked oligosaccharide chains.
Genetic diseases have been attributed to deficiency of particular enzymes involved in synthesizing or modifying oligosaccharide chains of these glycoproteins. Such diseases, and gene knockout studies in mice, have been used to define pathways of modification of oligosaccharide chains of glycoproteins and glycolipids. Carbohydrate chains of plasma membrane glycoproteins and glycolipids usually face the outside of the cell. They have roles in cell-cell interaction and signaling, and in forming a protective layer on the surface of some cells.

41 Lectins are glycoproteins that recognize and bind to specific oligosaccharides. A few examples:
Concanavalin A and wheat germ agglutinin are plant lectins that have been useful research tools.  Mannan-binding lectin (MBL) is a glycoprotein found in blood plasma. It associates with cell surface carbohydrates of disease-causing microorganisms, promoting phagocytosis of these organisms as part of the immune response.

42 Selectins are integral proteins of mammalian cell plasma membranes with roles in cell-cell recognition & binding. A lectin-like domain is at the end of an extracellular segment that extends out from the cell surface. A cleavage site just outside the transmembrane a-helix provides a mechanism for regulated release of some lectins from the cell surface. A cytosolic domain participates in regulated interaction with the actin cytoskeleton.