Structural analysis of a dipeptide

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1. Amino acids

아미노산(amino acid)은 단백질의 기본 구성 단위로, 단백질을 완전히 가수분해하면 암모니아와 함께 생성된다. 화학적으로 아미노기와 카복실기를 포함한 모든 분자를 지칭하며 화학식은 NH2CHRnCOOH(n=1~20)이다. 생화학에서는 흔히 α-아미노산을 간단히 아미노산이라 부른다. α-아미노산은 아미노기와 카복실기가 하나의 탄소(알파 탄소라고 부른다)에 붙어있다. 아미노산의 일종인 프롤린(proline)은 실제로는 아미노기 대신 이차 아미노기를 포함한 2차 아민인데 생화학적으로 보통의 아미노산과 비슷한 기능을 수행하기 때문에 2차 아미노기를 가진 프롤린도 아미노산으로 분류한다.
2. Glycine

Glycine(Gly, G)은 HO2CCH2NH2의 화학식을 갖는 유기물이다. Glycine은 20개의 기본 아미노산 중의 하나로 동물 단백질에서 흔히 발견된다. Glycine의 측쇄는 수소(-H)이며, 이는 모든 아미노산 중에서 가장 작고 기본적이다. 이런 성질 때문에 Glycine은 다른 아미노산이 쉽게 들어갈 수 없는 작은 공간을 채울 수 있으며, 이런 성질 때문에Glycine이 다른 아미노산으로 바뀔 경우 다른 아미노산이 공간을 제대로 채우지 못해 단백질의 구조가 바뀌기 쉽다. 또한 Glycine은 아미노산 중에서 광학 활성을 띠지 않는 유일한 아미노산이다.
3. Alanine

Alanine(Ala, A)은 HO2CCH(NH2)CH3의 화학식을 갖는 α-아미노산으로, 단백질 합성에 쓰이는 단백질성 아미노산이다. 화학적으로는 아민기와 카복실기를 포함하며 두 작용기는 메틸 작용기를 가지는 중심 탄소 원자에 붙어있다. Alanine은 무극성인 지방족 아미노산이다.
4. Leucine

Leucine(Leu, L)은 C6H13NO2의 화학식을 갖는 α-아미노산으로, 백색 결정이 되는 것으로부터 그리스어로 "희다"를 의미하는 "leuco"에 연관되어 명명되었다. Leucine은 필수 아미노산이며, 단백질에서 분리해내기가 어렵다. 그 이유는 valine과 성질이 매우 비슷하며, isoleucine과는 이성질체 관계이기 때문이다.
5. Phenylalanine

Phenylalanine(Phe, F)는 화학식 C9H11NO2의 필수 α-아미노산으로, alanine의 메틸기로 치환된 벤질기(Benzyl group), 또는 alanine의 말단 수소 대신에서 페닐기로 볼 수 있다. 이 필수 아미노산은 벤질 측쇄의 비활성 및 소수성(hydrophobic) 특성인 비친수성으로 인해 중성 및 비극성으로 분류된다.
6. Histidine

Histidine(His, H)은 화학식 C6H9N3O2의 성장기 아동에게 필요한 조건부 필수 아미노산으로, α-아미노기를 가지고 있고(생물학적 환경에서는 -NH3로 나타나는) 카복실기도 가진다.(생물학적 환경에서는 CO2-로 존재하는) 그리고 부분적으로 양성자 첨가된 imidazole 작용기를 가지는데, 이 성질 덕에 histidine은 생리학적 PH(산성도)에서 양전하를 띠는 아미노산으로 분류된다.
7. NMR analysis

1H NMR은 1H을 사용하며, peak은 보통 0~10 ppm에서 나타난다. 1H NMR에서는 결과가 단순한 peak 하나로만나타나기도 하고, 여러 개의 peak이 겹쳐서 나오기도 한다. 이를 multiplet이라고 하며, 이는 이웃한 수소와의 상호작용과 coupling 때문에 발생한다. 13C NMR의 경우에는13C를 사용하며, peak은 0~200 ppm에서 나타난다. 동위원소 존재비가 낮은13C를 사용하기때문에 원래 자석의 강도의 1/4로 성능이 줄어든다.
8. HPLC analysis

HPLC(High performance liquid chromatography)는 고정상(분리관)과 시료 및 이동상(액체)과의 상호작용으로 혼합물을 단일성분으로 분리시키는 방법이다. Normal phase HPLC의 column은 극성 column이며, 이동상은 hexane, heptane과 같은 비극성 용액을 사용한다. Reverse phase HPLC의 경우 column은 비극성 column이며, 이동상은 H2O / ACN이나 H2O / MeOH와 같은 극성 용매를 사용한다.
9. TLC analysis

TLC(Thin-Layer Chromatography)는 지지체상 위의 미립자 운반체를 고정상으로 하고 용매를 이동상으로 하여 물질을 전개, 분리하는 판이다. 주로 비휘발성 화합물을 분리할 때 사용한다. Ninhydrin은 암모니아 또는 일차/이차 아민을 발견하기 위해 사용되는 화학 물질이다.
10. Fmoc protection

Fmoc(Fluorenylmethyloxycarbonyl protecting group)은 유기 합성에 사용되는 base-labile protecting group이다. Fmoc carbamate는 아민을 Fmoc-Cl(fluorenylmethyloxycarbonyl chloride)과 반응시켜 Fmoc기를 도입할 수 있는 아민의 보호기로 사용된다. Fmoc기는 일부 secondary base 뿐만 아니라 primary base에 의해 빠르게 제거된다.

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1. Amino acids

Amino acids are the fundamental building blocks of proteins, which are essential for the structure and function of all living organisms. They play a crucial role in various biological processes, including cell signaling, enzyme catalysis, and energy production. Understanding the properties and functions of different amino acids is crucial for fields such as biochemistry, molecular biology, and medicine. Amino acids can be classified into different categories based on their side chain characteristics, such as polarity, charge, and hydrophobicity. Studying the unique properties of each amino acid and how they interact with one another in protein structures can provide valuable insights into the complex mechanisms underlying biological systems.
2. Glycine

Glycine is the simplest and most abundant amino acid found in proteins. It is a non-polar, neutral amino acid with a hydrogen atom as its side chain. Glycine is known for its unique structural properties, as it is the only amino acid that does not have a chiral carbon atom. This allows glycine to adopt a more compact conformation in protein structures, often found in tight turns and bends. Glycine is particularly important in collagen, the most abundant protein in the human body, where it helps maintain the triple-helix structure. Additionally, glycine plays a role in various metabolic processes, such as the synthesis of heme, creatine, and glutathione. Understanding the importance of glycine in protein structure and function is crucial for understanding the fundamental principles of biochemistry and their applications in fields like structural biology and medicine.
3. Alanine

Alanine is a non-polar, neutral amino acid with a methyl group as its side chain. It is one of the most common amino acids found in proteins and is known for its high propensity to form alpha-helical structures. Alanine's small, non-reactive side chain makes it a versatile amino acid that can be easily accommodated in various protein conformations. Its prevalence in protein structures is often attributed to its ability to provide stability and flexibility to the overall protein fold. Alanine is also involved in several metabolic pathways, including gluconeogenesis and the citric acid cycle. Understanding the role of alanine in protein structure and function is essential for studying protein folding, enzyme catalysis, and the design of therapeutic proteins and peptides.
4. Leucine

Leucine is a branched-chain, non-polar amino acid that is essential for protein synthesis and muscle growth. It is one of the three branched-chain amino acids (along with isoleucine and valine) and is known for its hydrophobic nature and ability to form stable, compact structures within proteins. Leucine plays a crucial role in various physiological processes, such as protein synthesis, energy metabolism, and the regulation of gene expression. It is particularly important in the maintenance and repair of muscle tissue, making it a popular supplement among athletes and bodybuilders. Understanding the unique properties of leucine and its interactions with other amino acids in protein structures is essential for understanding the complex mechanisms underlying muscle growth, protein folding, and metabolic regulation. Studying the role of leucine in these processes can have important implications for fields like sports science, nutrition, and medicine.
5. Phenylalanine

Phenylalanine is an aromatic, non-polar amino acid with a benzene ring in its side chain. It is an essential amino acid, meaning it cannot be synthesized by the human body and must be obtained through dietary sources. Phenylalanine plays a crucial role in various physiological processes, including the synthesis of neurotransmitters like dopamine and norepinephrine, as well as the production of the hormone thyroxine. Its aromatic side chain also allows it to participate in important interactions, such as pi-stacking, within protein structures, contributing to the stability and function of proteins. Deficiencies in phenylalanine metabolism can lead to the genetic disorder phenylketonuria, highlighting the importance of understanding the role of this amino acid in human health and disease. Studying the unique properties and functions of phenylalanine can provide valuable insights into the complex biochemical pathways and protein structures that underpin various biological processes.
6. Histidine

Histidine is a polar, weakly basic amino acid with an imidazole ring in its side chain. It is considered a semi-essential amino acid, as it can be synthesized in the body but may need to be supplemented in certain situations, such as during periods of growth or illness. Histidine plays a crucial role in various biological processes, including pH regulation, enzyme catalysis, and metal ion binding. The imidazole ring in histidine's side chain allows it to act as a proton acceptor and donor, making it an important participant in acid-base reactions within proteins. Histidine is also a key component of the active sites of many enzymes, where it helps to facilitate catalytic reactions. Furthermore, histidine's ability to coordinate with metal ions, such as copper and zinc, is important for the proper functioning of various metalloproteins. Understanding the unique properties and functions of histidine is essential for studying protein structure, enzyme mechanisms, and the role of amino acids in biological systems.
7. NMR analysis

Nuclear Magnetic Resonance (NMR) analysis is a powerful analytical technique that has become indispensable in the study of biomolecules, including proteins, nucleic acids, and small molecules. NMR spectroscopy exploits the magnetic properties of atomic nuclei, such as hydrogen (1H) and carbon (13C), to provide detailed information about the structure, dynamics, and interactions of these molecules. In the context of amino acid analysis, NMR can be used to identify and characterize the individual amino acids within a protein, as well as to study their interactions and conformational changes. By analyzing the chemical shifts, coupling patterns, and relaxation properties of the nuclei, researchers can gain insights into the three-dimensional structure of proteins, the dynamics of their folding and unfolding, and the binding interactions with other molecules. NMR analysis has become a crucial tool in structural biology, drug discovery, and the study of complex biological systems, enabling a deeper understanding of the fundamental principles underlying the function and behavior of amino acids and proteins.
8. HPLC analysis

High-Performance Liquid Chromatography (HPLC) is a widely used analytical technique for the separation, identification, and quantification of amino acids and other biomolecules. HPLC is particularly useful for the analysis of amino acid composition and content in various samples, such as proteins, biological fluids, and food products. The technique relies on the differential partitioning of analytes between a stationary phase (the column) and a mobile phase (the liquid solvent) to achieve efficient separation. By carefully selecting the column, mobile phase, and detection method, researchers can accurately identify and quantify individual amino acids based on their unique physicochemical properties, such as polarity, charge, and size. HPLC analysis of amino acids is essential for applications in fields like biochemistry, nutrition, food science, and clinical diagnostics, where the accurate determination of amino acid profiles is crucial for understanding metabolic processes, assessing nutritional status, and detecting amino acid-related disorders. The versatility and high-resolution capabilities of HPLC make it an indispensable tool for the comprehensive analysis of amino acids and their role in biological systems.
9. TLC analysis

Thin-Layer Chromatography (TLC) is a simple, yet powerful analytical technique that can be used for the separation and identification of amino acids and other biomolecules. In the context of amino acid analysis, TLC offers a cost-effective and accessible method for separating and visualizing individual amino acids based on their relative polarity and affinity for the stationary phase (the TLC plate) and the mobile phase (the solvent system). By carefully selecting the appropriate TLC plates, solvents, and visualization techniques, researchers can effectively separate and identify amino acids in complex mixtures, such as protein hydrolysates or biological samples. TLC analysis of amino acids can provide valuable information about the composition and purity of samples, as well as serve as a complementary technique to more advanced analytical methods like HPLC and mass spectrometry. While TLC may not offer the same level of resolution and quantitative accuracy as these other techniques, it remains a useful tool for rapid screening, qualitative analysis, and educational purposes in the field of amino acid research and biochemistry. The simplicity, versatility, and accessibility of TLC make it an important analytical tool in various applications, from academic laboratories to industrial settings.
10. Fmoc protection

Fmoc (Fluorenylmethyloxycarbonyl) protection is a widely used strategy in solid-phase peptide synthesis (SPPS) for the temporary protection of amino groups during the stepwise assembly of peptide chains. The Fmoc group is a base-labile protecting group that can be selectively removed under mild conditions, allowing for the controlled deprotection and coupling of individual amino acids to the growing peptide sequence. The Fmoc protection strategy offers several advantages over alternative approaches, such as Boc (tert-butyloxycarbonyl) protection, including milder reaction conditions, compatibility with a broader range of functional groups, and the ability to monitor the progress of the synthesis using UV-Vis spectroscopy. The Fmoc protection method has become the predominant approach in modern SPPS, enabling the efficient and reliable synthesis of a wide range of peptides and proteins, including those with complex structures and post-translational modifications. Understanding the principles and applications of Fmoc protection is crucial for researchers working in the fields of peptide chemistry, protein engineering, and drug discovery, where the ability to precisely control the synthesis of peptides and proteins is essential for the development of novel therapeutic agents and the study of biological processes.