Proteinlerin Yapısı ve İşlevi
Özet
Proteinler doğada en bol bulunan, canlı sistemlerde çok çeşitli görevler üstlenen, tüm hücrelerde ve hücrelerin bölümlerinde en fazla bulunan biyolojik makromoleküllerdir. Proteinler vücutta savunma sisteminden, taşıyıcı sistemine, hormonlardan enzimlere kadar çok değişik önemli sistemlerde görev alan muhteşem moleküllerdir. Bu moleküller amino asitlerin peptit adı verilen bağlar ile bağlanmasından oluşmaktadır. DNA’mız tarafından kodlanan L-a yirmi amino asitin dizilişi protein molekülünün üç boyutlu yapısı için gerekli olan bilgiyi taşımaktadır. Bu bölümde proteinlerin yapı taşları olan amino asitlerin, proteinlerin sınıflandırılmasından ve temel biyokimyasal özelliklerinden bahsedilmektedir.
Referanslar
Keha EE, Küfrevioğlu Öİ. Biyokimya. 6. baskı Erzurum: Aktif Yayınevi; 2009. p. 64-66.
Gürdöl F, Ademoğlu E. Biyokimya. In: Öner P (ed). Proteinler. Gözden Geçirilmiş 2. Baskı. İstanbul: Nobel Tıp Kitabevleri; 2013. p. 81-110.
Nelson DL, Cox MM, Hoskins AA. Lehninger Principles of Biochemstry. 8nd ed. NewYork: Macmillon Learning; 2021. p. 358-614.
Rodwell VW, Bender DA, Botham KM, Kennelly PJ, Weil PA. Harper’ Illustrated Biochemstry. In. Peter J, Kennelly PhD& Rodwel VW PhD. Amino Acids& Peptides and Proteins: Higher Orders of Structure. 31st (ed.) New York: Mc Grow Hill Education; 2018. p. 14-43.
Cooper GM. The Cell A Molecular Approach. 8th (ed.) NewYork: Oxford Universty Press; 2019. p. 55-62.
Ferrier DR. Lippincott Illustrated Reviews Biochemstry. 7th (ed.) Philadelphia: Wolters Kluwer; 2017. p. 12-88.
Nelson DL, Cox MM, Lehninger Principles of Biochemstry. 4th (ed.) NewYork: Macmillon Learning; 2005.p. 75-106
Whitford D. Proteins Structure and Function. England: John Wiley&Sons, Ltd; 2005. p. 1-102.
Berg JM, Tymoczko JL, Lubert S. Çeviri editörleri Denizli A, Özden AK. Biyokimya. In: Ersöz A, Yavuz SÖ. Proteinlerin Bileşimi ve Yapısı. 7. Baskıdan Çeviri. Ankara: Palme Yayıncılık; 2014. p. 25-60.
Rodwell VW, Bender DA, Botham KM, Kennelly PJ, Weil PA. Harper’ Illustrated Biochemstry. In. Rodwell WV PhD. Biosynthesis of the Nutritionally Nonessential Amino Acids. 31st (ed.) New York: Mc Grow Hill Education; 2018. p. 263-264.
Üstdal KM, Karaca M, Türköz L, Testereci H, Kuş S, Paşaoğlu H. Biyokimya. Malatya: Medipres; 2003.p. 207-227
Lopez MJ, Mohiuddin SS. Biochemistry, essential amino acids. In: StatPearls Publishing, Treasure Island FL; 2021.
Massey KA, Blakeslee, CH, Pitkow HS. A review of physiological and metabolic effects of essential amino acids. Amino acids. 1998;14(4), 271-300.
Ellis RJ, Minton AP. Protein aggregation in crowded environments. Biol. Chem.2006; 387:485–97
Kim YE, Hipp MS, Bracher A, Hayer-Hartl M, Hartl FU. Molecular chaperone functions in protein folding and proteastasis. Annu.Rev.Biochem.2013. 82:323-55
Hartl FU. Molecular chaperones in cellular protein folding. Nature. 1996. 381:571–79
Hartl FU, Hayer-Hartl M. 2002. Molecular chaperones in the cytosol: from nascent chain to folded protein. Science 295:1852–58
Chiti F, Dobson CM. Protein misfolding, functional amyloid, and human disease. Annu. Rev.Biochem. 2006. 75:333–66
Balch WE, Morimoto RI, Dillin A, Kelly JW. Adapting proteostasis for disease intervention. 2008. Science. 319:916–19
Morimoto RI. Proteotoxic stress and inducible chaperone network sin neuro degenerative disease and aging. Genes Dev. 2008. 22:1427–38
Henry N, Ginsberg MD. Lipid Disorder. In:Lipoprotein physiology.1998; 27: 503-518
Lin SH, Guidotti G. Purification of membrane proteins. Methods in Enzymology. 2009;463:619-629
Chung CZ, Krahn N. The selenocysteine toolbox: A guide to studying the 21 st amino acid. Archives of Biochemstry and Biophysics.2022; https://doi.org/10.1016/j.abb.2022.109421
Hames D, Hooper N. Çeviri editörleri Tutar Y, Geçkil H, Karataş M. BİOS Hazır Notlar Biyokimya. Amino asitler ve Proteinler. 3. Baskıdan Çeviri. Ankara: Nobel Yayın Dağıtım; 2010. P.29-75
. Chen, M.E. Hoover, X. Dang, A.A. Shomo, X. Guan, A.G. Marshall, M.A. Freitas, N.L. Young, Quantitative mass spectrometry reveals that intact histone H1 phosphorylations are variant specific and exhibit single molecule hierarchical dependence, Molecular & Cel- lular Proteomics, 15 (2016) 818-833.
G.P. Copenhaver, K. Nickel, T. Kuromori, M.-I. Benito, S. Kaul, X. Lin, M. Bevan, G. Murp- hy, B. Harris, L.D. Parnell, Genetic definition and sequence analysis of Arabidopsis centro- meres, Science, 286 (1999) 2468-2474.
A.R. Cutter, J.J. Hayes, A brief review of nucleosome structure, FEBS letters, 589 (2015) 2914-2922.
T. De Lange, Shelterin: the protein complex that shapes and safeguards human telomeres, Genes & development, 19 (2005) 2100-2110.
P.J. Robinson, D. Rhodes, Structure of the ‘30 nm’chromatin fibre: a key role for the linker histone, Current opinion in structural biology, 16 (2006) 336-343.
M.G. Schueler, A.W. Higgins, M.K. Rudd, K. Gustashaw, H.F. Willard, Genomic and gene- tic definition of a functional human centromere, Science, 294 (2001) 109-115.
A. Travers, The location of the linker histone on the nucleosome, Trends in biochemical sciences, 24 (1999) 4-7.
G. Bernardi, The isochore organization of the human genome, Annual review of genetics, 23 (1989) 637-659.
E. Elhaik, D. Graur, A comparative study and a phylogenetic exploration of the compo- sitional architectures of mammalian nuclear genomes, PLoS Computational Biology, 10 (2014) e1003925.
I. Ovcharenko, G.G. Loots, M.A. Nobrega, R.C. Hardison, W. Miller, L. Stubbs, Evolution and functional classification of vertebrate gene deserts, Genome research, 15 (2005) 137- 145.
M. Costantini, O. Clay, F. Auletta, G. Bernardi, An isochore map of human chromosomes, Genome research, 16 (2006) 536-541.
A.G.I.g.t.o.g.g. de, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana, nature, 408 (2000) 796-815.
M. Ashburner, C.M. Bergman, Drosophila melanogaster: a case study of a model genomic sequence and its consequences, Genome research, 15 (2005) 1661-1667.
S. Istrail, G.G. Sutton, L. Florea, A.L. Halpern, C.M. Mobarry, R. Lippert, B. Walenz, H. Shatkay, I. Dew, J.R. Miller, Whole-genome shotgun assembly and comparison of human genome assemblies, Proceedings of the National Academy of Sciences, 101 (2004) 1916- 1921.
N. Naidoo, Y. Pawitan, R. Soong, D.N. Cooper, C.-S. Ku, Human genetics and genomics a decade after the release of the draft sequence of the human genome, Human genomics, 5 (2011) 1-46.
Iniative, A. G. (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408(6814), 796-815.
Project management: Fulton Lucinda A. 1 Mardis Elaine R. 1 Wilson Richard K. 1. (2004). Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432(7018), 695-716.
B. Dujon, The yeast genome project: what did we learn?, Trends in Genetics, 12 (1996) 263-270.
L. Duret, tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes, Trends in Genetics, 16 (2000) 287-289.
J. Xu, J. Zhang, Are human translated pseudogenes functional? Molecular Biology and Evo- lution, 33 (2015) 755-760.
Y. Tutar, Pseudogenes, International Journal of Genomics, 2012 (2012).
L. Poliseno, L. Salmena, J. Zhang, B. Carver, W.J. Haveman, P.P. Pandolfi, A coding-inde- pendent function of gene and pseudogene mRNAs regulates tumour biology, Nature, 465 (2010) 1033-1038.
D.A. Petrov, Evolution of genome size: new approaches to an old problem, TRENDS in Genetics, 17 (2001) 23-28.
B.A. Payseur, P. Jing, R.J. Haasl, A genomic portrait of human microsatellite variation, Mo- lecular biology and evolution, 28 (2011) 303-312.
A.K. Csink, S. Henikoff, Something from nothing: the evolution and utility of satellite re- peats, Trends in Genetics, 14 (1998) 200-204.
P.J. Keeling, J.M. Archibald, Organelle evolution: what’s in a name? Current biology, 18 (2008) R345-R347.
L. Margulis, Origin of eukaryotic cells: evidence and research implications for a theory of the origin and evolution of microbial, plant, and animal cells on the Precambrian earth, (No Title), (1970).
B.F. Lang, M.W. Gray, G. Burger, Mitochondrial genome evolution and the origin of eukar- yotes, Annual review of genetics, 33 (1999) 351-397.
J.D. Palmer, Comparative organization of chloroplast genomes, Annual review of genetics, 19 (1985) 325-354.
Takahashi, T., Nishida, T., Tuji, A. et al. Delineation of six species of the primitive algal genus Glaucocystis based on in situ ultrastructural characteristics. Sci Rep 6, 29209 (2016).
Muñoz-López M, García-Pérez JL. DNA transposons: nature and applications in genomics. Curr Genomics. 2010 Apr;11(2):115-28.
Frazer K A, Chen X, Hinds D A, Pant P V, Patil N, Cox D R. Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates. Genome Res. 2003;13(3):341–346.
Nekrutenko A, Li W H. Transposable elements are found in a large number of human protein-coding genes. Trends Genet. 2001;17(11):619–621.
Referanslar
Keha EE, Küfrevioğlu Öİ. Biyokimya. 6. baskı Erzurum: Aktif Yayınevi; 2009. p. 64-66.
Gürdöl F, Ademoğlu E. Biyokimya. In: Öner P (ed). Proteinler. Gözden Geçirilmiş 2. Baskı. İstanbul: Nobel Tıp Kitabevleri; 2013. p. 81-110.
Nelson DL, Cox MM, Hoskins AA. Lehninger Principles of Biochemstry. 8nd ed. NewYork: Macmillon Learning; 2021. p. 358-614.
Rodwell VW, Bender DA, Botham KM, Kennelly PJ, Weil PA. Harper’ Illustrated Biochemstry. In. Peter J, Kennelly PhD& Rodwel VW PhD. Amino Acids& Peptides and Proteins: Higher Orders of Structure. 31st (ed.) New York: Mc Grow Hill Education; 2018. p. 14-43.
Cooper GM. The Cell A Molecular Approach. 8th (ed.) NewYork: Oxford Universty Press; 2019. p. 55-62.
Ferrier DR. Lippincott Illustrated Reviews Biochemstry. 7th (ed.) Philadelphia: Wolters Kluwer; 2017. p. 12-88.
Nelson DL, Cox MM, Lehninger Principles of Biochemstry. 4th (ed.) NewYork: Macmillon Learning; 2005.p. 75-106
Whitford D. Proteins Structure and Function. England: John Wiley&Sons, Ltd; 2005. p. 1-102.
Berg JM, Tymoczko JL, Lubert S. Çeviri editörleri Denizli A, Özden AK. Biyokimya. In: Ersöz A, Yavuz SÖ. Proteinlerin Bileşimi ve Yapısı. 7. Baskıdan Çeviri. Ankara: Palme Yayıncılık; 2014. p. 25-60.
Rodwell VW, Bender DA, Botham KM, Kennelly PJ, Weil PA. Harper’ Illustrated Biochemstry. In. Rodwell WV PhD. Biosynthesis of the Nutritionally Nonessential Amino Acids. 31st (ed.) New York: Mc Grow Hill Education; 2018. p. 263-264.
Üstdal KM, Karaca M, Türköz L, Testereci H, Kuş S, Paşaoğlu H. Biyokimya. Malatya: Medipres; 2003.p. 207-227
Lopez MJ, Mohiuddin SS. Biochemistry, essential amino acids. In: StatPearls Publishing, Treasure Island FL; 2021.
Massey KA, Blakeslee, CH, Pitkow HS. A review of physiological and metabolic effects of essential amino acids. Amino acids. 1998;14(4), 271-300.
Ellis RJ, Minton AP. Protein aggregation in crowded environments. Biol. Chem.2006; 387:485–97
Kim YE, Hipp MS, Bracher A, Hayer-Hartl M, Hartl FU. Molecular chaperone functions in protein folding and proteastasis. Annu.Rev.Biochem.2013. 82:323-55
Hartl FU. Molecular chaperones in cellular protein folding. Nature. 1996. 381:571–79
Hartl FU, Hayer-Hartl M. 2002. Molecular chaperones in the cytosol: from nascent chain to folded protein. Science 295:1852–58
Chiti F, Dobson CM. Protein misfolding, functional amyloid, and human disease. Annu. Rev.Biochem. 2006. 75:333–66
Balch WE, Morimoto RI, Dillin A, Kelly JW. Adapting proteostasis for disease intervention. 2008. Science. 319:916–19
Morimoto RI. Proteotoxic stress and inducible chaperone network sin neuro degenerative disease and aging. Genes Dev. 2008. 22:1427–38
Henry N, Ginsberg MD. Lipid Disorder. In:Lipoprotein physiology.1998; 27: 503-518
Lin SH, Guidotti G. Purification of membrane proteins. Methods in Enzymology. 2009;463:619-629
Chung CZ, Krahn N. The selenocysteine toolbox: A guide to studying the 21 st amino acid. Archives of Biochemstry and Biophysics.2022; https://doi.org/10.1016/j.abb.2022.109421
Hames D, Hooper N. Çeviri editörleri Tutar Y, Geçkil H, Karataş M. BİOS Hazır Notlar Biyokimya. Amino asitler ve Proteinler. 3. Baskıdan Çeviri. Ankara: Nobel Yayın Dağıtım; 2010. P.29-75
. Chen, M.E. Hoover, X. Dang, A.A. Shomo, X. Guan, A.G. Marshall, M.A. Freitas, N.L. Young, Quantitative mass spectrometry reveals that intact histone H1 phosphorylations are variant specific and exhibit single molecule hierarchical dependence, Molecular & Cel- lular Proteomics, 15 (2016) 818-833.
G.P. Copenhaver, K. Nickel, T. Kuromori, M.-I. Benito, S. Kaul, X. Lin, M. Bevan, G. Murp- hy, B. Harris, L.D. Parnell, Genetic definition and sequence analysis of Arabidopsis centro- meres, Science, 286 (1999) 2468-2474.
A.R. Cutter, J.J. Hayes, A brief review of nucleosome structure, FEBS letters, 589 (2015) 2914-2922.
T. De Lange, Shelterin: the protein complex that shapes and safeguards human telomeres, Genes & development, 19 (2005) 2100-2110.
P.J. Robinson, D. Rhodes, Structure of the ‘30 nm’chromatin fibre: a key role for the linker histone, Current opinion in structural biology, 16 (2006) 336-343.
M.G. Schueler, A.W. Higgins, M.K. Rudd, K. Gustashaw, H.F. Willard, Genomic and gene- tic definition of a functional human centromere, Science, 294 (2001) 109-115.
A. Travers, The location of the linker histone on the nucleosome, Trends in biochemical sciences, 24 (1999) 4-7.
G. Bernardi, The isochore organization of the human genome, Annual review of genetics, 23 (1989) 637-659.
E. Elhaik, D. Graur, A comparative study and a phylogenetic exploration of the compo- sitional architectures of mammalian nuclear genomes, PLoS Computational Biology, 10 (2014) e1003925.
I. Ovcharenko, G.G. Loots, M.A. Nobrega, R.C. Hardison, W. Miller, L. Stubbs, Evolution and functional classification of vertebrate gene deserts, Genome research, 15 (2005) 137- 145.
M. Costantini, O. Clay, F. Auletta, G. Bernardi, An isochore map of human chromosomes, Genome research, 16 (2006) 536-541.
A.G.I.g.t.o.g.g. de, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana, nature, 408 (2000) 796-815.
M. Ashburner, C.M. Bergman, Drosophila melanogaster: a case study of a model genomic sequence and its consequences, Genome research, 15 (2005) 1661-1667.
S. Istrail, G.G. Sutton, L. Florea, A.L. Halpern, C.M. Mobarry, R. Lippert, B. Walenz, H. Shatkay, I. Dew, J.R. Miller, Whole-genome shotgun assembly and comparison of human genome assemblies, Proceedings of the National Academy of Sciences, 101 (2004) 1916- 1921.
N. Naidoo, Y. Pawitan, R. Soong, D.N. Cooper, C.-S. Ku, Human genetics and genomics a decade after the release of the draft sequence of the human genome, Human genomics, 5 (2011) 1-46.
Iniative, A. G. (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408(6814), 796-815.
Project management: Fulton Lucinda A. 1 Mardis Elaine R. 1 Wilson Richard K. 1. (2004). Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432(7018), 695-716.
B. Dujon, The yeast genome project: what did we learn?, Trends in Genetics, 12 (1996) 263-270.
L. Duret, tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes, Trends in Genetics, 16 (2000) 287-289.
J. Xu, J. Zhang, Are human translated pseudogenes functional? Molecular Biology and Evo- lution, 33 (2015) 755-760.
Y. Tutar, Pseudogenes, International Journal of Genomics, 2012 (2012).
L. Poliseno, L. Salmena, J. Zhang, B. Carver, W.J. Haveman, P.P. Pandolfi, A coding-inde- pendent function of gene and pseudogene mRNAs regulates tumour biology, Nature, 465 (2010) 1033-1038.
D.A. Petrov, Evolution of genome size: new approaches to an old problem, TRENDS in Genetics, 17 (2001) 23-28.
B.A. Payseur, P. Jing, R.J. Haasl, A genomic portrait of human microsatellite variation, Mo- lecular biology and evolution, 28 (2011) 303-312.
A.K. Csink, S. Henikoff, Something from nothing: the evolution and utility of satellite re- peats, Trends in Genetics, 14 (1998) 200-204.
P.J. Keeling, J.M. Archibald, Organelle evolution: what’s in a name? Current biology, 18 (2008) R345-R347.
L. Margulis, Origin of eukaryotic cells: evidence and research implications for a theory of the origin and evolution of microbial, plant, and animal cells on the Precambrian earth, (No Title), (1970).
B.F. Lang, M.W. Gray, G. Burger, Mitochondrial genome evolution and the origin of eukar- yotes, Annual review of genetics, 33 (1999) 351-397.
J.D. Palmer, Comparative organization of chloroplast genomes, Annual review of genetics, 19 (1985) 325-354.
Takahashi, T., Nishida, T., Tuji, A. et al. Delineation of six species of the primitive algal genus Glaucocystis based on in situ ultrastructural characteristics. Sci Rep 6, 29209 (2016).
Muñoz-López M, García-Pérez JL. DNA transposons: nature and applications in genomics. Curr Genomics. 2010 Apr;11(2):115-28.
Frazer K A, Chen X, Hinds D A, Pant P V, Patil N, Cox D R. Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates. Genome Res. 2003;13(3):341–346.
Nekrutenko A, Li W H. Transposable elements are found in a large number of human protein-coding genes. Trends Genet. 2001;17(11):619–621.
