Name: how protein shape determines function
Uploaded: 2023-04-30T18:28:47.000Z
Duration: 2 min 15 s
Channel: JoVE

K12 Standards

Next Generation Science Standards

High School

Life Science

from-molecules-to-organisms-structures-and-processes

From Molecules to Organisms: Structures and Processes

HS-LS1-1

Protein and Protein Structures

Proteinler, peptit bağlarıyla birbirine bağlanan amino asitlerin polimerleridir. Çoğu protein, işlevlerini yerine getirmek için belirli üç boyutlu yapılara katlanır. Protein yapısı dört kategoriye ayrılır:birincil, ikincil, üçüncül ve dördüncül.Proteindeki amino asitlerin doğrusal dizisi, birincil yapısıdır. Bu diziler polimer sentez sırasına göre, N-terminalinden, serbest amino ucundan, C-terminaline, serbest karboksil ucuna kadar okunur. İkincil yapılar, bir amino asidin karbonil grubundan gelen oksijen ile diğerinin amino grubundan gelen hidrojen arasında hidrojen bağıyla oluşur.Yaygın ikincil yapılar, α-sarmalları ve β-kıvrımlı tabakaları içerir. Bunlar ve β dönüşleri gibi diğer bağlantı yapıları, proteinin üçüncül yapı olarak bilinen üç boyutlu yapısını oluşturmak için daha fazla etkileşime girer. Üçüncül yapının oluşumu, amino asitlerin R grupları arasındaki etkileşimler nedeniyle oluşur.Zıt yüklü R grupları iyonik bağlar oluşturabilir ve iki sisteindeki kükürt bir kovalent disülfür köprüsü oluşturabilir. Diğer katkıda bulunanlar, hidrofobik yan zincirler arasındaki hidrofobik etkileşimleri ve polar yan zincirler arasındaki hidrojen bağlarını içerir. Ek olarak, bazı proteinler, iki veya daha fazla polipeptit zincirinin düzenekleri olan dörtlü yapılar oluşturur.Örneğin, hemoglobin, iki α ve iki β olmak üzere dört alt birimden oluşan bir proteindir. Bilim adamları, bir hücredeki işlevini ve konumunu tahmin etmek için bir proteinin yapısını kullanabilir. Hücre sitoplazmasındaki proteinler, yüzeylerinde sitoplazmadaki suyla etkileşime giren ve hidrofobik çekirdeklere sahip hidrofilik amino asitlere sahiptir.Bunun tersine, hücre zarlarında bulunan proteinlerin yüzeyinde genellikle zardaki gliserofosfolipidlerle etkileşime giren ve hidrofilik çekirdeklere sahip hidrofobik amino asitler bulunur.

<ol>
	<li>Nelson, D. L. ve Cox, M. M. (2008). Lehninger biyokimya ilkeleri (5. baskı). W.H. Freeman. Sayfa 113-140</li>
	<li>Dört Haem'de de Oksijene Bağlı T Durumu Hemoglobinin Kristal Yapısı.Paoli, M., Liddington, R., Tame, J., Wilkinson, A., Dodson, G. (1996) J Mol Biol 256: 775</li>
</ol>

protein ve protein yapıları

Proteinler, canlı sistemlerde en bol bulunan organik moleküllerden biridir ve tüm makromoleküller arasında en çeşitli işlevlere sahiptir. Proteinler yapısal, düzenleyici, kontraktil veya koruyucu olabilir. Taşımada, depolamada veya membranlarda hizmet edebilirler; veya toksin ya da enzim olabilirler. İşlevleri gibi yapıları da büyük ölçüde değişir. Ancak hepsi lineer bir dizilimde düzenlenmiş amino asit polimerleridir.
 
 Bir proteinin şekli, işlevi için kritik öneme sahiptir. Örneğin, bir enzim, aktif bölgesinde spesifik bir substratı bağlayabilir. Bu aktif bölge, lokal değişiklikler veya genel protein yapısındaki değişiklikler nedeniyle değiştirilirse, enzim substrata bağlanamayabilir. Proteinin son şeklini veya konformasyonunu nasıl aldığını anlamak için, protein yapısının dört seviyesini anlamamız gerekir: birincil, ikincil, üçüncül ve dördüncül.
 
 Birincil Yapı
 
 Amino asitlerin bir polipeptit zincirindeki benzersiz dizisi, birincil yapısıdır. Örneğin, pankreas hormonu insülini, A ve B olmak üzere iki polipeptit zincirine sahiptir ve bunlar disülfid bağlarıyla birbirine bağlanır. A zincirinin N terminali amino asidi glisindir; oysa C terminali amino asit asparajindir.  A ve B zincirlerindeki amino asit dizileri insüline özgüdür.
 
 Proteini kodlayan gen, sonuçta her protein için benzersiz diziyi belirler. Genin kodlama bölgesinin nükleotid dizisindeki bir değişiklik, büyüyen polipeptit zincirine farklı bir amino asit eklenmesine yol açarak protein yapısında ve işlevinde bir değişikliğe neden olabilir. Orak hücreli anemide, hemoglobin β zinciri, protein yapısında ve işlevinde bir değişikliğe neden olan tek bir amino asit ikamesine sahiptir. Spesifik olarak, β zincirindeki valin amino asidi glutamik asidin yerini alır. Zincirdeki bir amino asidin bu değişikliği nedeniyle, hemoglobin molekülleri, bikonkav veya disk şeklindeki kırmızı kan hücrelerini bozan ve kan damarlarını tıkayan hilal veya “orak” bir şekil almalarına neden olan uzun lifler oluştururlar. Bu, bu hastalıktan etkilenenler için nefes darlığı, baş dönmesi, baş ağrısı ve karın ağrısı gibi sayısız ciddi sağlık sorunlarına yol açabilir.
 
 İkincil Yapı
 
 Polipeptidin bazı bölgelerde lokal olarak katlanması, proteinin ikincil yapısına yol açar. En yaygın olanları α-sarmal ve β-yaprak tabaka yapılarıdır. Her iki yapı da hidrojen bağları ile şekillenir. Hidrojen bağları, bir amino asitteki karbonil grubundaki oksijen atomu ile zincir boyunca dört amino asit daha uzak olan başka bir amino asit arasında oluşur.
 
 Bir alfa sarmalındaki her sarmal dönüş, 3.6 amino asit kalıntısına sahiptir. Polipeptidin R grupları (varyant grupları) α-sarmal zincirinden dışarı çıkar. β yaprak tabakada, polipeptit zincirinin omurgasındaki atomlar arasındaki hidrojen bağı "kıvrımları" oluşturur. R grupları karbonlara bağlıdır ve yaprak kıvrımlarının üstünde ve altında uzanır. Kıvrımlı bölümler birbirine paralel veya antiparalel olarak hizalanır ve amino grubundaki kısmen pozitif hidrojen atomu ile peptit omurgasının karbonil grubundaki kısmen negatif oksijen atomu arasında hidrojen bağları oluşur. α-sarmal ve β-yaprak tabaka yapıları, globüler ve fibröz proteinlerin çoğunda bulunur ve önemli bir yapısal rol oynarlar.
 
 Üçüncül Yapı
 
 Polipeptidin benzersiz üç boyutlu yapısı, üçüncül yapısıdır. Bu yapı kısmen polipeptit zinciri üzerindeki kimyasal etkileşimlerden kaynaklanmaktadır. Öncelikle, R grupları arasındaki etkileşimler, proteinin karmaşık üç boyutlu üçüncül yapısını oluşturur. İlgili amino asitlerdeki R gruplarının doğası, standart ikincil yapılar için tanımladığımız hidrojen bağlarının oluşumunu engelleyebilir. Örneğin, benzer yüklere sahip R grupları birbirini iter ve farklı yüklere sahip olanlar birbirini çeker (iyonik bağlar). Protein katlanması gerçekleştiğinde, polar olmayan amino asitlerin hidrofobik R grupları proteinin içinde bulunur; hidrofilik R grupları ise dışarıdadır. Sistein yan zincirleri arasındaki etkileşimler, protein katlanması sırasında oluşan tek kovalent bağ olan oksijen varlığında disülfid bağları oluşturur.
 
 Zayıf ve güçlü tüm bu etkileşimler, proteinin son üç boyutlu şeklini belirler. Bir protein üç boyutlu şeklini kaybettiğinde artık işlevsel olmayabilir.
 
 Dördüncül Yapı
 
 Doğada, bazı proteinler birkaç polipeptit veya alt birimden oluşur ve bu alt birimlerin etkileşimi dördüncül yapıyı oluşturur. Alt birimler arasındaki zayıf etkileşimler, genel yapıyı stabilize etmeye yardımcı olur. Örneğin, insülin (küresel bir protein) hidrojen ve disülfid bağlarının bir kombinasyonuna sahiptir ve bu da onun çoğunlukla bir top şeklinde kümelenmesine neden olur. İnsülin tek bir polipeptit olarak başlar ve kalan zincirleri bir arada tutan disülfid bağlarını oluşturduktan sonra translasyon sonrası modifikasyonun varlığında bazı iç dizileri kaybeder. Bununla birlikte ipek (fibröz bir protein), farklı zincirler arasındaki hidrojen bağının sonucu olan β-yaprak tabaka yapısına sahiptir.
 
 Bu metin bu kaynaktan uyarlanmıştır: <a href="https://openstax.org/books/biology-2e/pages/3-4-proteins">Openstax, Biology 2e, Chapter 3.4: Proteins</a>.

Protein ve Protein Yapıları

Proteinler, canlı sistemlerde en bol bulunan organik moleküllerden biridir ve tüm makromoleküller arasında en çeşitli işlevlere sahiptir. Proteinler ...

Education

JoVE Core

Cell Biology

Hücre Biyolojisi

Unit 1

Ünite 1

Biochemistry of the Cell

Hücre Biyokimyası

KEY TERMS AND CONCEPTS

TEMEL TERİMLER VE KAVRAMLAR

how protein shape determines function

Proteins are essential molecules in living things, and their shape affects how they work. Protein structure is described at several levels, including primary, secondary, tertiary, and quaternary structure. These levels help explain how a protein is built and how its final form supports its job.

Primary structure is the sequence of amino acids in a protein. Secondary structure forms when parts of the chain fold into regular patterns. Tertiary structure is the overall three-dimensional shape of one protein chain. Quaternary structure appears when more than one protein chain joins together to make a working protein.

The video also shows how protein structure can be represented in different ways. A simple line drawing can show the amino acid sequence. Other models can show folding and the full 3D shape. These visual forms help students compare levels of structure and see why protein shape matters.

How Protein Shape Determines Function

the periodic table and organismal elements

the-periodic-table-and-organismal-elements

Elements in the Human Body and Periodic Table

Elements are the smallest units of matter that cannot be broken down further by chemical processes. Scientists know 118 elements, but not all of them occur naturally. Only a small number are essential for life, and living matter depends mostly on carbon, nitrogen, hydrogen, and oxygen. The periodic table organizes elements by their physical and chemical properties. Each square shows the element name, chemical symbol, atomic number, and atomic weight. The atomic number is the number of protons...

functional groups

Functional Groups in Organic Molecules

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types of chemical bonds

Chemical Bonds and How Atoms Join

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noncovalent attractions in biomolecules

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chemistry of carbohydrates

Carbohydrate Structure and Bonding

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protein and protein structures

Proteins are essential molecules in living things, and their shape affects how they work. Protein structure is described at several levels, including primary, secondary, tertiary, and quaternary structure. These levels help explain how a protein is built and how its final form supports its job. Primary structure is the sequence of amino acids in a protein. Secondary structure forms when parts of the chain fold into regular patterns. Tertiary structure is the overall three-dimensional shape of...

ph regulation in cells

Cell pH and Organelle Balance

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chemistry of the cell

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Cell chemistry explains the substances that make cells work. Water is the main component of cells, and it supports the chemical reactions that keep life going. Cells also contain organic molecules, which are carbon-based compounds, and inorganic ions, which are charged particles needed for cell function. Organic molecules in cells include carbohydrates, lipids, proteins, and nucleic acids. These molecules have different roles, but together they build cell structures, store energy, and carry...

key terms and concepts

Learn how proteins are built and folded through primary, secondary, tertiary, and quaternary structure, and how protein shape affects function.

How Protein Shape Determines Function | JoVE K12

cell biology

JoVE Core Hücre Biyolojisi, anlaşılması kolay ancak kapsamlı animasyonlu video derslerde karmaşık hücresel süreçleri gösterir. Bu koleksiyon, organeller ve zarlar, hücresel taşıma ve hücre enerjileri dahil olmak üzere hücrelerin temel bileşenlerine ve işlevlerine odaklanır. Gerçek dünya araştırma deneylerinde hücre biyolojisinin uygulanmasını gösteren bilim insanı eylem videoları ile tamamlanmaktadır.

Florida Department of Education

SC.912.L.18

SC.912.L.18.1

SC.912.L.18.4

new-york-state-science-learning-standards

New York State Science Learning Standards

Structure and Function

HS-LS1-1.

Georgia Standards of Excellence

9-12

Biology

SB6.c

Characteristics of Life

Biology is a natural science that studies life and living organisms, including their structure, function, development, interactions, evolution, ...

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GTPases and their Regulation

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protein-complexes-with-interchangeable-parts

Protein Complexes with Interchangeable Parts

Mechanical Protein Function

Structural Protein Function

Protein Networks

Construct an explanation based on evidence for how the structure of DNA determines the structure of proteins, which carry out the essential functions of life through systems of specialized cells. [Assessment Boundary: Assessment does not include identification of specific cell or tissue types, whole body systems, specific protein structures and functions, or the biochemistry of protein synthesis.]

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The Parasympathetic Nervous System

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Develop and use a model to illustrate the hierarchical organization of interacting systems that provide specific functions within multicellular organisms. [Clarification Statement: Emphasis is on functions at the organism system level such as nutrient uptake, water delivery, and organism movement in response to neural stimuli. An example of an interacting system could be an artery depending on the proper function of elastic tissue and smooth muscle to regulate and deliver the proper amount of blood within the circulatory system.] [Assessment Boundary: Assessment does not include interactions and functions at the molecular or chemical reaction level.]

HS-LS1-2

How Protein Shape Determines Function

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