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

חומצות אמינו קשורות זו לזו באמצעות קשרים פפטידיים. קשר פפטידי מקשר את קבוצת הקרבוקסיל של חומצת אמינו אחת לקבוצת האמינו של החומצה האחרת. פפטידים הם שרשראות קצרות של חומצות אמינו, הנעות בין שניים ל-50 מונומרים.קשר פפטידי נוצר באמצעות תגובת דחיסה המשחררת מולקולת מים. כשקבוצת אמינו וקבוצת קרבוקסיל נקשרות זו לזו, התוצאה היא היווצרות של קבוצת אמיד. לקשר הפפטידי יש מבנה מישורי נוקשה ומציג כמה מהתכונות של קשר כפול.זאת משום שהקשר הכפול בקרבוניל יכול ליצור מבנה רזוננס עם הקשר הפפטידי פחמן-חנקן. מבנה רזונסס זה מוביל לירידה באורך הקשר היחיד, לגידול באורך הקשר הכפול ולמניעת ההסיבוב של הקבוצות סביב הקשר הפפטידי. קשרים פפטידיים יכולים להתקיים בתצורות ציס וטרנס.בתצורת ציס, פחמני אלפא נמצאים באותו צד של הקשר הפפטידי, ובתצורה טרנס הם בצדדים נגדיים של הקשר. קשרים פפטידיים מתרחשים בדרך כלל בתצורת טרנס, מלבד כשפרולין תורם את קבוצת האמינו שלו ליצירת קשר. לחומצות אמינו הקשורות באמצעות קשרים פפטידיים יש קצה-N קצה-C.קצה-N הוא הקצה שבו קבוצת האמינו אינה מעורבת ביצירה של קשר פפטידי, וקצה-C הוא הקצה שבו קבוצת הקרבוקסיל אינה מעורבת ביצירה של קשר פפטידי. רצף חומצות האמינו בפפטיד או בחלבון תמיד מתחיל בקצה-N ומסתיים בקצה-C. כששתי חומצות אמינו נקשרות זו לזו באמצעות קשר פפטידי, הן נקראות דיפפטידים.כששלוש וארבע חומצות אמינו נקשרות זו לזו באמצעות קשרים פפטידיים, הן מכונות טריפפטידים וטטרפפטידים, בהתאמה. וכשכמה חומצות אמינו נקשרות זו לזו בקשרים פפטידיים, הן מכונות פוליפפטידים. קשרים פפטידיים ניתנים לפירוק במהירות באמצעות הידרוליזה המבוצעת על ידי זרזים כימיים כגון חומצות או אנזימים הנקראים פרוטאזות.ניתוק קשרים פפטידיים מערב הוספה של מולקולת מים. לחלופין, קשרים אלה יכולים להתנתק באופן ספונטני באמצעות תהליך איטי, בנוכחות מים.

קשרי פפטיד

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 קשר פפטיד מחבר באופן קוולנטי חומצות אמינו באמצעות תגובת התייבשות. קבוצת הקרבוקסיל של חומצת אמינו אחת וקבוצת האמינו של חומצת אמינו אחרת מתחברים ומשחררים מולקולת מים. הקשר שנוצר הוא הקשר הפפטיד. התוצרים שיוצרים קשרים כאלה הם פפטידים. ככל שחומצות אמינו נוספות מצטרפות לשרשרת ההולכת וגדלה זו, השרשרת המתקבלת היא פוליפפטיד. לכל פוליפפטיד יש קבוצת אמינו חופשית בקצה אחד. לקצה זה יש את ה-N-טרמינל, או את האמינו-טרמינל, ולקצה השני יש קבוצת קרבוקסיל חופשית - ה-C- או הקרבוקסיל-טרמינל. בעוד שהמונחים פוליפפטיד וחלבון משמשים לעתים להחלפה, פוליפפטיד הוא מבחינה טכנית פולימר של חומצות אמינו, בעוד שהמונח חלבון משמש לפוליפפטיד או לפוליפפטידים שהתחברו יחד ולעיתים קרובות קשרו קבוצות תותבות לא-פפטידיות, צורה מובחנת, ופונקציה ייחודית. 

 כימיה של קשרי פפטיד 

 לקשר פפטיד יש מבנה מישורי נוקשה עקב תהודה. תהודה זו כוללת שיתוף אלקטרונים בין הקשרים הכפולים הקיימים בקבוצת הקרבוניל לבין הקשר הפפטיד בין פחמן לחנקן, שהוא קשר יחיד. כתוצאה מכך אורך הקשר הכפול גדל ואורך הקשר היחיד יורד מהאורך הצפוי בהיעדר לתהודה. 

 קשרי פפטיד יכולים להתרחש בשתי קונפורמציות אפשריות: ציס ו טראנס . בתצורת ציס , פחמי האלפא של שתי חומצות האמינו המחוברות בקשר הפפטיד נמצאים באותו צד של הקשר; ובתצורת ה טראנס , פחמי האלפא של שתי חומצות האמינו המחוברות בקשר הפפטיד נמצאים בצדדים המנוגדים של הקשר. תצורת ה ציס מתרחשת בדרך כלל כאשר פרולין תורם את קבוצת האמינו שלו ליצירת הקשר; עם זאת, רק כ-10% מהפרולינים קדמו להם קשרי ציס .

 סיבוב אינו אפשרי סביב קשרי פפטיד בשל המבנה הנוקשה שלו. עם זאת, סיבוב יכול להתרחש סביב הקשרים המקשרים את פחמן האלפא לאטומי החנקן והפחמן, בהתאמה. 

 טקסט זה מותאם מ<a href="https://openstax.org/books/biology-2e/pages/3-4-proteins">Openstax, Biology 2e, Chapter 3.4: Proteins</a>.

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קשר פפטידי מחבר באופן קוולנטי חומצות אמינו באמצעות תגובת התייבשות. קבוצת קרבוקסיל של חומצת אמינו אחת וחומצת אמינו אחרת ...

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Chemistry

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אחד

Biochemistry

ביוכימיה

KEY TERMS AND CONCEPTS

מונחים ומושגים מרכזיים

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

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chemistry of the cell

Cell Chemistry: Water and Macromolecules

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protein and protein structure

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amino acids

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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

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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

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from dna to protein

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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

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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 ...

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The Photochemical Reaction Center

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The Antenna Complex

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

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The Calvin Benson Cycle

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Photosynthesis

Autotrophs

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Plant Pigment Chromatography and Floating Leaf Discs in a Vacuum
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Place the spinach ...

Plant Pigment Chromatography
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3.1.9-12.E

Compounds Essential to Human Function

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Overview of Functional Groups

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

Lipid-derived Compounds in the Human Body

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What are Proteins?

Protein Organization

Globular Proteins

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Fibrous Proteins

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Protein Denaturation

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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

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Nucleic Acid Structure

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What is Energy?

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Energy Budgets and Reproductive Strategies

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Energy Dynamics

The Food Chain
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Production Efficiency

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Trophic Efficiency

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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

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What is Glycolysis?

Overview
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Energy-requiring Steps of Glycolysis

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Energy-releasing Steps of Glycolysis

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Outcomes of Glycolysis

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Pyruvate Oxidation

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Mitochondria

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Mitochondrial Membranes

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The Inner Mitochondrial Membrane

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The Citric Acid Cycle: Overview

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The Citric Acid Cycle: Output

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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

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The Electron Transport Chain

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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

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Primary Production

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What are Biogeochemical Cycles?

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The Water Cycle

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The Carbon Cycle

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The Nitrogen Cycle

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The Phosphorus Cycle

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The Sulfur Cycle

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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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