Name: peptide bond formation and shape
Uploaded: 2020-09-24T15:06:53.000Z
Duration: 2 min 43 s
Channel: JoVE

K12 Standards

Pennsylvania State Academic Standards

9-12

Life Science

matter-and-energy-in-organisms-and-ecosystems

Matter and Energy in Organisms and Ecosystems

3.1.9-12.F

Peptide Bonds

Les acides aminés se lient les uns aux autres de manière covalente par des liaisons peptidiques. Une liaison peptidique relie le groupe carboxyle d'un acide aminé au groupe amino de l'autre. Les peptides sont de petites chaînes d'acides aminés allant de deux à cinquante monomères.Une liaison peptidique se forme par une réaction de condensation qui libère une molécule d'eau. Lorsqu'un groupe amino et un groupe carboxyle se lient, il se traduit par la formation d'un groupe amide. La liaison peptidique a une structure plane rigide et présente certaines caractéristiques d'une double liaison.C'est parce que la double liaison sur le carbonyle peut agir comme une structure de résonance avec liaison de carbone-azote peptidique. Cette résonance conduit à la diminution dans la longueur de la liaison simple, une augmentation de la longueur de la double liaison, et inhibe la rotation des groupes autour de la liaison peptidique. Les liaisons peptidiques peuvent exister en conformations cis et trans.Dans la conformation cis, les carbones alpha sont du même côté de la liaison peptidique, et dans la conformation trans, ils sont sur les côtés opposés de l'obligation. Les liaisons peptidiques se produisent principalement dans la conformation trans sauf lorsque la proline contribue à la liaison de son groupe de formation amino. Les Acides aminés liés par des liaisons peptidiques ont un N-terminal et un C-terminal.Le N-terminal est l'extrémité où le groupe amino n'est pas impliqué dans la formation d'une liaison peptidique, et le C-terminal est l'extrémité où le groupe carboxyle n'est pas impliqué dans la formation d'une liaison peptidique. La séquence d'acides aminés dans un peptide ou une protéine commence toujours par le N-terminal et se termine par le C-terminal. Quand deux acides aminés se lient par une liaison peptidique, ils sont connus sous le nom de dipeptides.Quand trois et quatre acides aminés se lient par des liaisons peptidiques, ils sont connus sous forme de tripeptides et de tétrapeptides, respectivement. Et quand plusieurs acides aminés se lient par des liaisons peptidiques, ils sont connus sous le nom de polypeptides. Les liaisons peptidiques peuvent être rapidement décomposées par hydrolyse utilisant des catalyseurs chimiques, tels que des acides ou des enzymes connus sous forme de protéases.La rupture des liaisons peptidiques implique l'ajout d'une molécule d'eau. Alternativement, ces liens peuvent se rompre spontanément par un processus lent en présence d'eau.

liaisons peptidiques

Une liaison peptidique lie les acides aminés de façon covalente suivant une réaction de déshydratation. Le groupe carboxyle d'un acide aminé et le groupe aminé d'un autre acide aminé se combinent, libérant ainsi une molécule d'eau. La liaison résultante est la liaison peptidique. Les produits que ces liaisons forment sont des peptides. Comme de plus en plus d'acides aminés rejoignent cette chaîne grandissante, la chaîne qui en résulte est un polypeptide. Chaque polypeptide a un groupe aminé libre à une extrémité. Cette extrémité est le N-terminus, ou terminal aminé, et l'autre extrémité a un groupe carboxyle libre, le C-terminus ou terminal carboxylé. Alors que les termes polypeptide et protéine sont parfois utilisés de manière interchangeable, un polypeptide est techniquement un polymère d'acides aminés, alors que le terme protéine est utilisé pour un polypeptide ou des polypeptides qui se sont combinés et qui ont souvent des groupements prosthétiques non peptidiques liés, une forme distincte ainsi qu'une fonction unique. 
 Chimie des liaisons peptidiques 
 Une liaison peptidique a une structure plane rigide due à la résonance. Cette résonance implique le partage des électrons entre les doubles liaisons présentes dans le groupe carbonyle et la liaison peptidique entre le carbone et l'azote, qui est une liaison simple. Cela entraîne une augmentation de la longueur de la liaison double et une diminution de la longueur de la liaison simple par rapport à la longueur à laquelle on s'attend en l'absence de résonance. 
 Les liaisons peptidiques peuvent se produire dans deux conformations possibles : cis et trans. Dans la configuration cis, les carbones alpha des deux acides aminés reliés par la liaison peptidique sont du même côté de la liaison ; et dans la configuration trans, les carbones alpha des deux acides aminés reliés par la liaison peptidique se trouvent sur les côtés opposés de la liaison. La configuration cis se produit généralement lorsque la proline contribue à la formation de la liaison par son groupe aminé ; cependant, seulement environ 10 % des prolines sont précédées par des liaisons cis. 
 La rotation n'est pas possible autour des liaisons peptiques en raison de sa structure rigide. Cependant, la rotation peut se produire autour des liaisons qui relient le carbone alpha aux atomes d'azote et de carbone, respectivement. 
 Ce texte a été adapté de<a href="https://openstax.org/books/biology-2e/pages/3-4-proteins"> Openstax, Biologie 2e, Chapitre 3.4 : Protéines</a>.

Liaisons peptidiques

Une liaison peptidique attache de manière covalente les acides aminés par une réaction de déshydratation. Le groupe carboxyle d'un acide aminé et l'acide aminé d'un autre acide aminé ...

Education

Enseignement

JoVE Core

Chemistry

Chimie

Biochemistry

Biochimie

KEY TERMS AND CONCEPTS

TERMES ET CONCEPTS CLÉS

peptide bond formation and shape

Peptide bonds join amino acids into peptides and polypeptides. They form when the carboxyl group of one amino acid reacts with the amino group of another. This dehydration reaction releases a water molecule and creates a covalent link.

As more amino acids are added, the chain becomes a polypeptide. Each polypeptide has a free amino group at one end. This end is the N-terminal, or amino-terminal. The other end has a free carboxyl group. This end is the C-terminal, or carboxyl-terminal.

The terms polypeptide and protein are sometimes used as if they mean the same thing. Technically, a polypeptide is a polymer of amino acids. A protein is a polypeptide, or more than one polypeptide, that has joined together and often carries non-peptide prosthetic groups. Proteins also have a distinct shape and a unique function.

Peptide bonds have a rigid, planar shape because of resonance. Resonance is the sharing of electrons between the carbonyl group and the peptide bond between carbon and nitrogen. This changes bond lengths. The double bond becomes longer, and the single bond becomes shorter than expected without resonance.

Peptide bonds can exist in cis and trans forms. In the cis form, the alpha carbons of the two amino acids are on the same side of the bond. In the trans form, they are on opposite sides. The cis form usually appears when proline donates its amino group, but only about 10% of prolines are preceded by cis bonds.

Rotation does not occur around the peptide bond because of its rigid structure. Rotation can still happen around the bonds that connect the alpha carbon to the nitrogen and carbon atoms. This limited movement helps define the shape of peptides and proteins.

Peptide Bond Formation and Shape

functional groups

Functional Groups in Organic Chemistry

Functional groups in organic chemistry are groups of atoms that give molecules specific properties. When these groups attach to a carbon skeleton, they can change how the molecule behaves. Some functional groups make a molecule hydrophilic, or water-attracting. Others make it hydrophobic, or water-repelling. Functional groups are a key part of organic chemistry and are also found in major biological molecules. They appear in carbohydrates, proteins, lipids, and nucleic acids. Each functional...

structure of lipids

Lipids, Fats, and Cell Membranes

Lipids are nonpolar molecules that do not mix well with water. They are hydrophobic, which means “water fearing,” because they contain mostly nonpolar carbon-carbon and carbon-hydrogen bonds. In cells, lipids store long-term energy as fats, help insulate plants and animals, and form protective water-repellent layers on feathers and fur. They are also part of cell membranes and serve as building blocks for many hormones. Common lipids include fats, oils, waxes, phospholipids, and steroids. A...

chemistry of the cell

Cell Chemistry: Water and Macromolecules

Cell chemistry includes water, organic molecules, and inorganic ions. These materials shape how cells store energy, build structures, and carry out life processes. Most cellular chemistry and metabolism happen in the watery cytoplasm. Water is a key part of the cell because it has special properties tied to its polarity. In a water molecule, hydrogen and oxygen form polar covalent bonds, so the molecule has no net charge but does have a slightly positive end and a slightly negative end. Oxygen...

dna base pairing

Chargaff’s Rules and DNA Pairing

Chargaff’s rules and DNA base pairing explain how DNA strands match up. In double-stranded DNA, adenine (A) pairs with thymine (T), and guanine (G) pairs with cytosine (C). Chargaff also found that A equals T, G equals C, and the total amount of purines (A and G) equals the total amount of pyrimidines (C and T). Watson and Crick later showed why these matches matter. A forms two hydrogen bonds with T, while G forms three hydrogen bonds with C. These pairings keep the DNA double helix a...

chemistry of carbohydrates

Carbohydrates as Energy and Storage Molecules

Carbohydrates are important energy sources in human and animal diets. Grains, fruits, and vegetables are natural sources of carbohydrates. They help provide energy to the body, especially through glucose, a simple sugar found in starch and many staple foods. Carbohydrates are identified by the stoichiometric formula (CH2O)n, where n is the number of carbons in the molecule. This means the ratio of carbon to hydrogen to oxygen is usually 1:2:1. The name carbohydrate comes from this pattern,...

protein and protein structure

How Protein Shape Controls Function

Proteins are a major class of organic molecules in living systems, and their shape helps determine what they do. They can act as structural, regulatory, contractile, or protective molecules. They also take part in transport, storage, membranes, toxins, and enzymes. All proteins are polymers of amino acids arranged in a linear sequence. A protein’s function depends on its three-dimensional form. For example, an enzyme works when its active site can bind a specific substrate. If local changes or...

amino acids

Amino Acids and Protein Building

Amino acids are the building blocks of proteins. Each amino acid has the same basic structure. A central carbon atom, called the alpha carbon, is bonded to an amino group, a carboxyl group, and a hydrogen atom. Each amino acid also has an R group, or side chain, attached to the central carbon. The R group is different for every amino acid. It helps determine whether an amino acid is acidic, basic, polar, or nonpolar. Scientists call these molecules amino acids because they contain both amino...

peptide bonds

Peptide bonds join amino acids into peptides and polypeptides. They form when the carboxyl group of one amino acid reacts with the amino group of another. This dehydration reaction releases a water molecule and creates a covalent link. As more amino acids are added, the chain becomes a polypeptide. Each polypeptide has a free amino group at one end. This end is the N-terminal, or amino-terminal. The other end has a free carboxyl group. This end is the C-terminal, or carboxyl-terminal. The...

nucleic acids

DNA and RNA: Genetic Instructions

DNA and RNA are the nucleic acids that store genetic information and help direct cell activity. These macromolecules carry the cell’s genetic blueprint and the instructions it uses to function. DNA is the genetic material in all living organisms, from single-celled bacteria to multicellular mammals. In eukaryotic cells, DNA is found in the nucleus and also in organelles such as chloroplasts and mitochondria. In prokaryotes, DNA is not enclosed in a membrane. The full genetic content of a cell...

dna replication

DNA Copying: Leading and Lagging Strands

DNA replication copies genetic material before a cell divides. Each original DNA strand serves as a template for a new complementary strand. The result is semiconservative replication, which means each new DNA molecule contains one old strand and one new strand. The two daughter cells then receive DNA with the same sequence. Replication starts when helicase separates the two strands of the double helix. This creates a Y-shaped replication fork. Primase then adds short RNA primers that give DNA...

from dna to protein

The Genetic Code and Codons

The genetic code and codons explain how cells turn DNA information into proteins. Genes first direct the sequence of mRNA, and mRNA then directs the sequence of amino acids that make up proteins. Specific proteins and RNAs carry out this decoding. Cells copy DNA into mRNA so the original DNA stays protected while the cell uses the message for protein synthesis. Copying DNA to RNA is relatively simple. One nucleotide is added to the mRNA strand for every nucleotide read on the DNA strand.

polymers

Polymer Chains and How They Form

Polymers are long chains of molecules made from repeating units called monomers. The word polymer comes from the Greek words "poly," meaning many, and "mer," meaning parts. Polymers can be found in nature, such as DNA and proteins, or made synthetically, such as plastics. A polymer’s shape helps define its properties. Some polymers form linear chains, while others are branched or arranged in complex networks. Functional groups on a polymer also affect how it behaves. The repeating units in a...

key terms and concepts

Learn how peptide bonds form amino acid chains, create N- and C-terminals, and why resonance gives peptides a rigid cis and trans structure.

Peptide Bond Formation and Shape | JoVE K12

chemistry

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Louisiana Student Standards for Science

High School

Life Sciences

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

From Molecules To Organisms: Structures And Processes

HS-LS1-6

Next Generation Science Standards

From Molecules to Organisms: Structures and Processes

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

HS-LS1-6.

Light as Energy

The energy required to carry out photosynthesis is light&#8212; typically electromagnetic radiation from the sun. The range of all possible wavelengths is ...

What is Photosynthesis?

All living organisms on Earth are directly or indirectly dependent on photosynthesis. It is the only biological process that can capture energy from ...

The Anatomy of Chloroplasts

Green algae and plants, including green stems and unripe fruit, harbor specialized organelles called chloroplasts to carry out photosynthesis. They ...

Photosystems

Photosystems are multiprotein complexes that form the functional units of photosynthesis in plants, algae, and cyanobacteria. They are found embedded in ...

The Photochemical Reaction Center

Reaction centers are pigment-protein complexes that initiate energy conversion from photons to chemical entities. Therefore, photochemical reaction center ...

The Antenna Complex

Plants and other photosynthetic organisms comprise pigments capable of absorption of direct sunlight. These pigments are present in the reaction center - ...

the-z-scheme-of-electron-transport-in-photosynthesis

The Z-Scheme of Electron Transport in Photosynthesis

The light reactions of photosynthesis assume a linear flow of electrons from water to NADP+. During this process, light energy drives the splitting of ...

The Calvin Benson Cycle

Ribulose 1,5- bisphosphate carboxylase/oxygenase (RuBisCo) is a critical enzyme that catalyzes carbon dioxide assimilation during photosynthesis. However, ...

Photosynthesis

Autotrophs

Almost all living organisms on Earth depend on photosynthesis, which is the process that converts sunlight energy into a simple sugar called ...

Plant Pigment Chromatography and Floating Leaf Discs in a Vacuum
ExpandOn the day before the experiment, fill a container with water.
Place the spinach ...

Plant Pigment Chromatography
ExpandNOTE: In this experiment you will separate pigments from spinach leaves using chromatography paper. Individual pigments ...

Students who demonstrate understanding can use a model to illustrate how photosynthesis transforms light energy into stored chemical energy.  Assessment Boundary: Assessment does not include specific biochemical steps.

3.1.9-12.E

Compounds Essential to Human Function

The human body is composed of cells that are fundamentally made up of several different molecules. These molecules are essential to carry out all ...

Overview of Functional Groups

Functional groups are a group of atoms with characteristic properties, which when linked to the carbon skeleton of a molecule, alter the properties of ...

Introduction to Carbohydrates

Carbohydrates, proteins, and fats are the primary macronutrients in the human diet. However, carbohydrates are the most favored source of energy in the ...

Sugars as Energy Storage Molecules

What are Lipids?

lipid-derived-compounds-in-the-human-body

Lipid-derived Compounds in the Human Body

Fats and lipids are crucial components in the human body. Some lipid-derived compounds, such as fat-soluble vitamins, eicosanoids, lipoproteins, and ...

What are Proteins?

Protein Organization

Globular Proteins

In organisms, proteins are the most abundant macromolecules. They act as the building blocks of life and play various crucial roles in the body. Proteins ...

Fibrous Proteins

Fibrous proteins are either long and narrow proteins or assemble to form long and thin structures. They contain repetitive units and usually consist of ...

Protein Denaturation

The function of proteins depends on their native three-dimensional structure, which is dictated by the amino acid sequence of the specific protein. ...

Role of Proteins in the Human Body

Proteins are the building block of life. They are also&#160; the most abundant macromolecules with as many diverse roles in the body. They are part of ...

Amino acids

Amino acids are the monomers that comprise proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, or the ...

A peptide bond covalently attaches amino acids through a dehydration reaction. One amino acid&#39;s carboxyl group and another amino acid&#39;s amino ...

Nucleic Acids and Nucleotides

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell&#39;s genetic blueprint and have instructions for its ...

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group ...

What is Energy?

The universe is composed of matter in different forms, and all forms of matter contain energy. &#xA0;The different forms of energy on Earth originate from ...

Energy Budgets and Reproductive Strategies

Organisms must balance energy intake with the energy required for growth, maintenance, and reproduction. These trade-offs result in a variety of ...

Energy Dynamics

The Food Chain
Energy is one of the most important abiotic factors in an ecosystem and organisms in an ecosystem are connected by the flow of energy and ...

Production Efficiency

Net production efficiency (NPE) is the efficiency at which organisms assimilate energy into biomass for the next trophic level. Due to low metabolic rates ...

Trophic Efficiency

Trophic level transfer efficiency (TLTE) is a measure of the total energy transfer from one trophic level to the next. Due to extensive energy loss as ...

Students who demonstrate understanding can construct and revise an explanation based on evidence for how carbon, hydrogen, and oxygen from sugar molecules may combine with other elements to form amino acids and/or other large carbon-based molecules.  Assessment Boundary: Assessment does not include the details of specific chemical reactions or identification of macromolecules.

Introduction to Cellular Respiration

Organisms harvest energy from food, but this energy cannot be directly used by cells. Cells convert the energy stored in nutrients into a more usable ...

What is Glycolysis?

Overview
Cells make energy by breaking down macromolecules. Cellular respiration is the biochemical process that converts &#34;food energy&#34; (from the ...

Energy-requiring Steps of Glycolysis

Glucose is the source of nearly all energy used by organisms. The first step of converting glucose into usable energy is called glycolysis. Glycolysis ...

Energy-releasing Steps of Glycolysis

Glycolysis is divided into two phases based on whether energy is utilized or released. While the first phase consumes ATP, the second phase produces ...

Outcomes of Glycolysis

Nearly all the energy used by cells comes from the bonds that make up complex organic compounds. These organic compounds are broken down into simpler ...

Pyruvate Oxidation

After glycolysis, the charged pyruvate molecules enter the mitochondria via active transport and undergo three enzymatic reactions. These reactions ensure ...

Mitochondria

Mitochondria are eukaryotic cellular organelles that are known to produce energy through a process called oxidative phosphorylation. Besides their primary ...

Mitochondrial Membranes

A single mitochondrion is a bean-shaped organelle enclosed by a double-membrane system. The outer membrane of mitochondria is smooth and contains many ...

The Inner Mitochondrial Membrane

The inner mitochondrial membrane is the primary site of ATP synthesis. The inner membrane domain that forms a smooth layer adjacent to the outer membrane ...

The Citric Acid Cycle: Overview

In aerobic organisms, the citric acid cycle is the second stage of cellular respiration wherein molecules derived from the breakdown of carbohydrates, ...

The Citric Acid Cycle: Output

The citric acid cycle is termed an amphibolic pathway as it operates both anabolically and catabolically. The cyclic reactions balance the flux of the ...

electron-transport-chain-complex-i-and-ii

Electron Transport Chain: Complex I and II

The mitochondrial electron transport chain (ETC) is the main energy generation system in the eukaryotic cells. However, mitochondria also produce ...

electron-transport-chain-complex-iii-and-iv

Electron Transport Chain: Complex III and IV

During the electron transport chain, electrons from NADH and FADH2 are first transferred to complexes I and II, respectively. These two complexes then ...

The Electron Transport Chain

The electron transport chain or oxidative phosphorylation is an exothermic process in which free energy released during electron transfer reactions is ...

the-supercomplexes-in-the-crista-membrane

The Supercomplexes in the Crista Membrane

The mitochondrial cristae membrane is the primary site for the oxidative phosphorylation (OXPHOS) process of energy conversion mediated through ...

ATP Synthase: Structure

ATP synthase or ATPase is among the most conserved proteins found in bacteria, mammals, and plants. This enzyme can catalyze a forward reaction in ...

ATP Synthase: Mechanism

In animals, the mitochondrial F1F0 ATP synthase is the key protein that synthesizes ATP molecules through a complex catalytic mechanism. While the nuclear ...

The ADP/ATP Carrier Protein

ADP/ATP carrier or AAC protein is the most abundant carrier protein in the inner mitochondrial membrane. It transports large quantities of ADP and ATP, ...

Students who demonstrate understanding can use a model to illustrate that cellular respiration is a chemical process whereby the bonds of food molecules and oxygen molecules are broken and the bonds in new compounds are formed resulting in a net transfer of energy.  Assessment Boundary: Assessment should not include identification of the steps or specific processes involved in cellular respiration.

3.1.9-12.G

What is an Ecosystem?

Overview

An ecosystem is the interaction between all abiotic and biotic factors in an environment and can be classified as terrestrial or aquatic. ...

Trophic Levels

All organisms in an ecosystem occupy a trophic level in the food chain. The lowest level consists of primary producers, which synthesize their food from ...

Primary Production

The total amount of energy acquired by primary producers in an ecosystem is called gross primary production (GPP). However, of this energy, producers use ...

What are Biogeochemical Cycles?

The most common elements in organic molecules, carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorus, are only available in the ecosystem in limited ...

The Water Cycle

The Earth&rsquo;s hydrosphere includes all of the areas where the storage and movement of water occurs. Since water is the basis of all living processes, ...

The Carbon Cycle

Carbon is the basis of all organic matter on Earth, and is recycled through the ecosystem in two primary processes: one in which carbon is exchanged among ...

The Nitrogen Cycle

Nitrogen atoms, present in all proteins and DNA, are recycled between abiotic and biotic components of the ecosystem. However, the primary form of ...

The Phosphorus Cycle

Unlike carbon, water, and nitrogen, phosphorus is not present in the atmosphere as a gas. Instead, most phosphorus in the ecosystem exists as compounds, ...

The Sulfur Cycle

Sulfur, an important element in the chemical makeup of proteins, is recycled through the atmosphere and aquatic and terrestrial environments. Found in the ...

Students who demonstrate understanding can use mathematical representations to support claims for the cycling of matter and flow of energy among organisms in an ecosystem.  Assessment Boundary: Assessment is limited to proportional reasoning to describe the cycling of matter and flow of energy.

3.1.9-12.H

Peptide Bond Formation and Shape

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