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How long does it take to form a peptide bond?

How long does it take to form a peptide bond?


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What is the time taken to form a peptide bond in vivo or in vitro? It isn't mentioned in my course on protein structures. I was just curious to find out if any time scale is known?

Given that prokaryotic and eukaryotic cells have difference ribosome structures, is there any chance that the time might vary between species or even within species?


Alberts et al, Molecular Biology of the Cell, say that eukaryotic ribosomes add about 2 amino acids per second, and bacterial about 20 per second (5th edition, p 275). These should be taken only as ballpark estimates: the rate certainly will vary from species to species, from cell to cell, from protein to protein. Some cells (reticulocytes, for instance) are professional protein synthesizers. Others, for instance bacterial endospores, do almost no protein synthesis at all.

These authors estimate the translation rate in mouse embryonic stem cells at around 5.5 amino acids/second. There is a lot of variation from gene to gene, even within this one cell type. They even see systematic variation depending on where you are in the gene.


Problem: When is a peptide bond formed during the process of translation?a. During the elongation phase just after a tRNA charged with an amino acid binds to the A site on the ribosomeb. During the termination phase just after a release factor binds to the A site on the ribosomec. During the elongation phase just after a tRNA that has lost its amino acid exits the E site on the ribosome

When is a peptide bond formed during the process of translation?

a. During the elongation phase just after a tRNA charged with an amino acid binds to the A site on the ribosome

b. During the termination phase just after a release factor binds to the A site on the ribosome

c. During the elongation phase just after a tRNA that has lost its amino acid exits the E site on the ribosome

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What to know about peptides for health

Peptides are smaller versions of proteins. Many health and cosmetic products contain different peptides for many uses, such as their potential anti-aging, anti-inflammatory, or muscle building properties.

Recent research indicates that some types of peptides could have a beneficial role in slowing down the aging process, reducing inflammation, and destroying microbes.

People may confuse peptides with proteins. Both proteins and peptides are made up of amino acids, but peptides contain far fewer amino acids than proteins. Like proteins, peptides are naturally present in foods.

Due to the potential health benefits of peptides, many supplements are available that contain peptides that manufacturers have derived either from food or made synthetically.

Some of the most popular peptides include collagen peptides for anti-aging and skin health, and creatine peptide supplements for building muscle and enhancing athletic performance.

In this article, we discuss the potential benefits and side effects of peptide supplements.

Share on Pinterest Peptides may help build strength and muscle mass.

Peptides are short strings of amino acids, typically comprising 2–50 amino acids. Amino acids are also the building blocks of proteins, but proteins contain more.

Peptides may be easier for the body to absorb than proteins because they are smaller and more broken down than proteins. They can more easily penetrate the skin and intestines, which helps them to enter the bloodstream more quickly.

The peptides in supplements may come from plant or animal sources of protein, including:

  • eggs
  • milk
  • meat
  • fish and shellfish
  • beans and lentils
  • soy
  • oats
  • flaxseed
  • hemp seeds
  • wheat

Scientists are most interested in bioactive peptides, or those that have a beneficial effect on the body and may positively impact human health.

Different bioactive peptides have different properties. The effects they have on the body depend on the sequence of amino acids they contain.

Some of the most common peptide supplements available are:

  • Collagen peptides, which may benefit skin health and reverse the effects of aging.
  • Creatine peptides, which may build strength and muscle mass.

Some people may take other peptides and peptide hormones to enhance athletic activity. However, the World Anti-Doping Agency have banned many of these, including follistatin, a peptide that increases muscle growth.

Research indicates that bioactive peptides may :

  • lower high blood pressure
  • kill microbes
  • reduce inflammation
  • prevent the formation of blood clots
  • improve immune function
  • act as antioxidants

People often use peptides to try to achieve the following effects:

Slow down the aging process

Collagen is a protein in the skin, hair, and nails. Collagen peptides are broken down collagen proteins that the body can absorb more easily. Taking collagen peptides may improve skin health and slow the aging process.

Some studies indicate that dietary food supplements that contain collagen peptides can treat skin wrinkles. Other research indicates that these supplements may also improve skin elasticity and hydration.

Peptides may stimulate the production of melanin, a skin pigment, which may improve the skin’s protection against sun damage.

Topical anti-aging cosmetics can also contain peptides, which manufacturers claim can reduce wrinkles, help skin firming, and increase blood flow.

Improve wound healing

As collagen is a vital component of healthy skin, collagen peptides may facilitate faster wound healing.

Bioactive peptides can also reduce inflammation and act as antioxidants, which can improve the body’s ability to heal.

Research is currently ongoing into antimicrobial peptides, which may also improve wound healing. Having very high or very low levels of some antimicrobial peptides may contribute to skin disorders, such as psoriasis, rosacea, and eczema.

Prevent age-related bone loss

Animal research links a moderate intake of collagen peptides with an increase in bone mass in growing rats who also did running exercise.

The study may point to collagen peptides being a useful way to counteract age-related bone loss. However, more research is necessary, especially on humans.

Build strength and muscle mass

Some research on older adults indicates that collagen peptide supplements can increase muscle mass and strength. In the study, participants combined supplement use with resistance training.

Creatine peptides may also improve strength and help to build muscle.

While fitness enthusiasts have been using creatine protein powders for many years, creatine peptides are increasing in popularity.

These particular peptides may be easier for the body to digest, which means they may cause fewer digestive problems than creatine proteins.


Peptides are compounds where two or more amino acids have joined together, with the carboxyl group of one joining together with the amino group of the other. When a molecule of water is eliminated from this bond, it leads to a peptide bond.

If you’ve forgotten your high school chemistry: here’s a more basic definition: peptides are basically just small proteins.

In general, anything with 50 or fewer amino acids is considered a peptide. However, that’s not a strict definition.

There are dipeptides, for example, which consists of two amino acids joined by a single peptide bond. And there are tripeptides, which are three amino acids with two peptide bonds. This naming system goes on and on and on.

In general, peptides with more than two peptide bonds are called polypeptides. A polypeptide can be defined as a long, un-branched chain of amino acids joined by peptide bonds. At the same time, this polypeptide is not complex enough to be referred to as a protein.

Proteins, you see, are made of multiple polypeptides.

Our Bodies Make Peptides from Amino Acids

Have you ever wondered why you take amino acid supplements?

The reason, as you probably know, is because amino acids are the building blocks for protein.

But in order to become protein, those amino acids first need to form into peptides.

With that in mind, your body needs to take in or produce amino acids in order to form the peptides your body needs to work efficiently.

As your body ages, and as it experiences different levels of stress, amino acids and peptide production can drop. This is one reason why the body starts to become weaker as we get older, why we gain fat instead of muscle, and why our skin starts to sag. It’s similar to the reason why our insulin-like growth factor (IGF-1) production naturally drops as we age and experience more environmental stressors.

What Do Peptides Do?

Peptides play a variety of roles throughout the body. You can’t just say “peptides always build muscle” or “peptides always fight against wrinkles” because that’s not true: they perform all sorts of different roles.

Some peptides act like neurotransmitters, for example, while others act like hormones.

Some peptides will change the way your body reacts to diet and physical exercise. Some amino acids will also contribute to your body’s natural production of human growth hormone (HGH).

Put simply, when your body isn’t absorbing or producing enough of these amino acids, it can’t produce enough peptides. And when it can’t produce enough peptides, your production of vital compounds like HGH will be lowered.

So Should I Take an Amino Acid Supplement or a Peptide Supplement?

We’ve learned so far that amino acids link up and turn into peptides within the body. That’s why taking an amino acid supplement is so important.

So why are so many bodybuilders and fitness enthusiasts beginning to take peptide supplements?

The idea is that peptides are digested and used more immediately by the body. Your body doesn’t have to take the time and effort to form up amino acids. It also doesn’t have to spend energy breaking down larger protein molecules.

Basically, peptides are small enough to be easily utilized throughout the body, but not so small they’re not utilized effectively.

Peptides are also thought to be more stable than amino acids after they enter the body. Amino acids are un-bonded and thought to be unstable, which means many of them break down before reaching their intended destination.

So while amino acids might break down within the body, peptides retain their chemical structure, which means you get better “bang for your buck” with peptide supplements – or at least that’s the idea.

Glutamine and Creatine Peptide Supplements

Today, you can find a variety of peptide supplements on the market.

Two types of peptide supplements, however, are particularly popular. Those supplements are glutamine and creatine peptide supplements.

These supplements promise to offer faster absorption, fewer side effects, and better efficiency than the standard (non-peptide) version of creatine or glutamine.

Injectable Peptides

There’s also a darker side to the world of peptide supplements in the athletic community: some peptides come in injectable form. These peptides are banned by most athletic government bodies.

Injectable peptide supplements promise powerful benefits. Many of them center around your body’s production of HGH.

You’ve probably noticed that human growth hormone has been in the news a lot lately. Peyton Manning allegedly took HGH to speed up his recovery from injury, for example. Other athletes have also been rumored to use HGH for all sorts of different purposes because they offer benefits like:

— Faster Recovery
— Greater Lean Muscle Mass Growth
— Stronger Injury Recovery

Of course, human growth hormone isn’t some crazy synthetic substance: it’s a compound naturally produced by the body. Certain peptides just encourage the body’s production of HGH more than others.

Nevertheless, by raising levels of HGH in your body, you can enjoy an unfair athletic advantage over your competitors, which is why peptides that raise levels of HGH are banned.

IGF-1, GHRP,-6, and Ipamorelin are three popular examples of these injectable peptides.

There are also injectable peptides like Melanotan, which actually tans the skin (I told you that different peptides have different effects on the body, didn’t I?).

There’s also SNAP-8, which is a popular anti-aging peptide used to fight back against wrinkles in the skin. We’ll talk about using peptides for anti-aging below.

These peptides aren’t strictly illegal in most countries. They’re just illegal if you’re involved in most collegiate or professional sports. Many of the above peptides can legally be ordered online “for research purposes”. Of course, you don’t have to prove your research purposes when you buy the supplements, so it’s a bit of an honor system.

Peptides for Anti-Aging

We mentioned that peptides can play a variety of roles within the body. Some peptides can help you build muscle, for example, while others raise melanin levels within the skin.

But there are a certain group of peptides purported to reduce the effects of aging on the skin. These peptides fight back against the effects of aging, making your skin appear less wrinkled and lined.

Peptides like SNAP-8, for example, are popular formulas for reducing the effects of aging.

When you see peptides used in anti-aging formulas, it’s typically one of the following five types of peptides:

— Pentapeptides: Your skin begins to lose its powers of regeneration as it grows older. One popular pentapeptide, palmitoyl pentapeptide-3, is trademarked under the name Matrixyl and can be found in a variety of anti-aging supplements on the market today. This peptide purportedly stimulates collagen production in the lower layers of the skin, increasing skin firmness.

— Hexapeptides: Hexapeptides are chains of six amino acids. This chain, especially one chain called acetyl hexapeptide-3, has been marketed for its ability to relax facial muscles. This can lead to a diminished appearance of fine lines. Some advertisements even claim that the results are similar to Botox. In anti-aging supplements, acetyl hexapeptide-3 is marketed under the name Argireline.

— Pamitoyl Oligopeptide: Palmitoyl oligopeptide promotes the production of collagen and hyaluronic acid in the deepest layers of your skin. It works in a slightly superior way to other peptides listed here because it also purportedly protects the skin from the damaging effects of UV radiation.

— Palmitoyl Tetrapeptide-7: Previously referred to as palmitoyl tetrapeptide-3, this compound consists of a chain of four amino acids bonded with palmitic acid. Palmitic acid is a fatty acid that binds with the skin, allowing the peptides in the formula to easily slip past the skin’s defenses. This is thought to reduce inflammation and stimulate the regeneration of new skin molecules.

— Copper Peptides: The most unique member of this list is the copper peptide. Copper peptides are small fragments of protein bonded with copper. They’re thought to expedite wound healing in the skin and enhance skin regeneration. The weird thing about copper is that it’s a toxic metal: the only safe way to use it on your skin is to combine it with a peptide chain. You’ll also see copper peptides sometimes marketed as copper gluconate.

Conclusion: The Bottom Line on Peptides

Ultimately, peptides are another buzzword in the fitness community that few people seem to understand. Peptides are simply a chain of two or more amino acids linked together. You get peptides from the foods you eat. You get them from your BCAA supplements. You get them from red meat, dairy, and other common ingredients. And you get them in anti-aging skin creams.

With all of these things in mind, peptides are just a generic term for a bunch of amino acids that aren’t big enough to be labeled as protein. They’re certainly nothing you should be worried about.


Protein Detection (Activity)

Protein Detection Theory:

Proteins can be detected through the use of the Biuret test. Specifically, peptide bonds (C-N bonds) in proteins complex with Cu 2+ in Biuret reagent and produce a violet color. A Cu 2+ must complex with four to six peptide bonds to produce a color therefore, free amino acids do not positively react. Long polypeptides (proteins) have many peptide bonds and produce a positive reaction to the reagent. Biuret reagent is an alkaline solution of 1% CuSO4, copper sulfate. The violet color is a positive test for the presence of protein, and the intensity of the color is proportional to the number of peptide bonds in the solution.

Biuret Test

  1. Examine the table below. Indicate if the sample is a negative control, positive control or an experimental.
  2. Predict the color change of the solution.
    • Formulate a hypothesis about the components of the experimentals.
  3. Obtain 6 test tubes and number them 1-6.
  4. Add the materials listed in the table.
  5. Add 3 drops of Biuret reagent (1.0% CuSO4 with NaOH) to each tube and mix.
  6. Record the color of the tubes&rsquo contents in Table.

Conclusions about the Urine Samples

Based on the results of the Benedict&rsquos test and the Biuret test, can we make any conclusions?


1.5 Structure and Function of Biological Macromolecules Overview

This section of the AP Biology curriculum takes a closer look at how biological macromolecules are synthesized, and how their structure determines their function. It also discusses the importance of directionality in biological macromolecules, and how this trait allows DNA to store information, create proteins, and keep order within a cell.

Let’s start with nucleic acids. Nucleic acids are directional molecules. This means that they can only be formed one way – with a hydroxyl group exposed on one end and a phosphate group exposed on the other. Each strand of DNA is a separate molecule, and each strand has a hydroxyl group exposed on one end and a phosphate group exposed on the other. We call these ends the 5’ end and the 3’ end. You can remember the difference because hydroxyl groups at the 3’ end are much smaller than the phosphate groups at the 5’ end.

DNA polymerase, the molecule responsible for attaching new nucleotides to a growing sequence, can only function in the 3’ to 5’ direction. When it is time to duplicate the DNA within cells, the two old strands of DNA are separated and DNA polymerase moves in to start adding new nucleotides. DNA polymerase builds a new strand that corresponds to the template by adding new nucleotides that are complementary to the template strand. Multiple DNA polymerase molecules work at the same time, moving in opposite directions on the two template strands.

The double-helix structure of DNA is formed through a relatively simple mechanism – hydrogen bonding. Let’s take a look at how this works. If we consider the complementary nucleotides Adenine and Thymine, we can see that two hydrogen bonds are formed between the nucleotides. Adenine has a slightly positive amino group, which easily forms a hydrogen bond with thymine’s slightly negative oxygen. The nitrogen on adenosine is slightly negative, allowing a hydrogen bond to form with thymines slightly positive nitrogen.

If we look at the complementary relationship between guanine and cytosine, we see a similar relationship. Everywhere that guanine has a slightly positive charge, cytosine has a corresponding negative charge. In this case, 3 hydrogen bonds can be formed. If guanine tried to form hydrogen bonds with thymine, positive charges would meet other positive charges. This would cause the two nucleotides to be repelled, disrupting the structure of the DNA double helix. This is how DNA repair enzymes can easily find and replace nucleotides that are incorrect in the sequence.

Between the sugar-phosphate backbone and these hydrogen bonds, DNA takes on a double-helix structure within the cell. The two strands run antiparallel to each other. In other words, one strand runs in the 3’ to 5’ direction, while the opposite strand runs in the 5’ to 3’ direction. This double helix typically has a major groove and a minor groove as it wraps around itself. This structure protects the nucleotide sequence, and allows DNA to be stored in massive units known as chromosomes.

Similar to the directionality of DNA molecules, proteins are also directional molecules. Each amino acid has a carboxyl group on one end and an amino group on the other end. This directionality makes it possible for ribosomes to create a chain of amino acids. Let’s see how this process works, in detail!

First, the ribosome grabs onto a piece of messenger RNA (mRNA for short). Floating around the ribosome are many loose transfer RNA (tRNA) molecules. These tRNAs have 3 nucleotides exposed, and hold specific amino acids on the opposite end. The tRNAs move into the E site of the ribosome. If the codons in the mRNA molecule form hydrogen bonds with the nucleotides exposed on the tRNA, they can move into the P site. As they transfer from the P site to the A site, a dehydration reaction is encouraged and a new peptide bond is formed.

The new covalent bond is formed between the carboxyl group on the growing peptide chain and the amino group of the new amino acid. This leaves another carboxyl group exposed, allowing another amino acid to be added in the same direction. This is important because it means that amino acids can only be added in one direction. The amino terminus on the first amino acid cannot be added to, meaning that peptides can only be made in the order that the mRNA dictates. This ensures that the DNA code can be perfectly translated into functional protein molecules!

Proteins are very complex molecules, thanks to the 20+ amino acids that can be used to construct them. Each amino acid has a different R-group, which confers both physical and chemical properties to a molecule.

The primary structure of a molecule is simply the order of amino acids within the molecule. This order is dictated by the codons in mRNA, which were transcribed directly from the codon sequence in DNA. Therefore, the primary structure of a protein is determined solely by the order of nucleotides in a DNA molecule.

However, as soon as this primary structure is created, interactions between amino acids in the chain start to create secondary structure. Secondary structure is the simplest level of 3-dimensional structure in a protein. There are several common motifs in secondary structure. The two most common motifs are beta-sheets and alpha-helices. A beta sheet is formed when a protein strand folds back on itself and creates hydrogen bonds. This creates a flat structure, much like a ribbon. By contrast, an alpha-helix is formed when peptides next to each other in the chain form hydrogen bonds, creating a helix structure that creates a rod-like 3D shape.

The tertiary structure of proteins is formed by interactions between different secondary structures. In a typical protein, both alpha-helices and beta-sheets interact to fold the molecule into a specific shape. In general, tertiary structures are formed by hydrogen bonding, polar interactions, and attractions between hydrophobic parts of the molecule. This also means that these interactions can be disrupted when conditions in the cell are not right.

For instance, if the temperature rises or pH is changed, this can lead to denaturation of a protein. The protein will lose its tertiary structure and unfold. Though the primary and secondary structure is unchanged, the protein will not be functional in these conditions. However, if the conditions are changed back (by lowering the temperature or buffering the pH) the protein will renature and become functional once again. This is a major reason why cells and organisms have mechanisms for controlling the physical and chemical conditions within cells.


Introduction

Carboxyl-reactive crosslinker reactive groups

Very few chemical groups are known to provide specific and practical conjugation to carboxylic acids (–COOH), such as occur in proteins and many other biomolecules. Certain diazomethane and diazoacetyl reagents have been used to derivatize small compounds for analysis by HPLC or for fluorescent labeling. Carbonyldiimidazole (CDI) can be used in non-aqueous conditions to activate carboxylic acids for direct conjugation to primary amines (–NH2) via amide bonds.

Carbodiimide compounds provide the most popular and versatile method for labeling or crosslinking to carboxylic acids. The most readily available and commonly used carbodiimides are the water-soluble EDC for aqueous crosslinking and the water-insoluble DCC for non-aqueous organic synthesis methods.

Chemical structures of carbodiimides EDC and DCC. EDC (also called EDAC) is 1-ethyl-3-(-3-dimethylaminopropyl) carbodiimide hydrochloride, MW 191.70. DCC is N', N’-dicyclohexyl carbodiimide, MW 206.32.

Carbodiimide conjugation, as with CDI-mediated conjugation, works by activating carboxyl groups for direct reaction with primary amines via amide bond formation. Because no portion of their chemical structure becomes part of the final bond between conjugated molecules, carbodiimides are considered zero-length carboxyl-to-amine crosslinkers.

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What Is a Polypeptide? (with picture)

Proteins are made up of building blocks called amino acids. When two or more amino acids stick together in a chain, they can be called a polypeptide. Each link between the amino acids, where energy attraction holds the blocks together, is a peptide bond. Polypeptides perform many functions in the body.

Amino acids are small molecules that are essential building blocks in biology. Many biological functions rely on the action of a protein or polypeptide. Generally, very short polypeptides are usually called peptides, and very long ones, with more than about 100 amino acids, are called proteins. All proteins fall into the polypeptide group, but some polypeptides do not fit the criteria to be a protein.

The peptide portion of the name originates from the type of bond between two amino acid building blocks. Each amino acid has one end called an alpha-carboxyl group and another end called an alpha-amino group. These two groups have different chemical properties.

An alpha-carboxyl tends to bond to an alpha-amino and vice versa. A single amino acid, therefore, tends to become attached to another amino acid in a specific way, kind of like one person holding hands with another person. One uses his right hand and the other uses her left hand to complete the bond. This form of bond is a peptide bond, and when the two molecules stick together, they produce one molecule.

Sticking together two amino acids requires energy. The body furnishes this energy when it needs to make new polypeptides for biological use. After the two amino acids are stuck together, the bond is quite stable and does not break down easily.

Polypeptides contain many of these amino acids stuck together in a straight line, in the same manner as a line of people holding hands between them. Typically, a polypeptide chain also has chains sticking off to the side at certain points. One polypeptide can contain as many as 2,000 individual amino acids.

In the body, polypeptides can perform functions as they are. They may also need to join up with another to form a new protein with a biological function. Sometimes, a single polypeptide is created as a large cell product, and then the cell uses an enzyme to chop it up into functional portions.

Polypeptides are first made when a cell reads its genetic instructions and translates that information into the sequence of amino acids. Each gene codes for a particular product, and the necessary amino acids are collected and stuck together in the correct order. The sequence is essential for the polypeptide to function properly, as otherwise, it cannot interact properly with its targets.


Why peptides are the ‘next big thing’ in medical research

Biochemists are excited by the possibilities presented by peptides and proteins as pharmaceuticals because they so often mimic exactly the behaviour of a natural ligand – the substance that interacts with the receptor on an enzyme or cell to cause a biological process.

This gives peptide drugs the potential to be more precisely targeted, with fewer side effects than small-molecule drugs.

Within the body, there are lot of different hormones that react with cells and trigger different biological processes. Often these are peptides, either cyclic versions or straight, linear ones.

And then there’s the matter of how fast that peptide breaks down, which causes some stability issues, but in terms of safety, can be a positive.

“We think peptides are the future of drugs for reasons of being more selective, more potent and potentially safer, because when a peptide eventually breaks down it just breaks down into amino acids, and amino acids are food, basically,” says Professor David Craik, who leads IMB’s Clive and Vera Ramaciotti Facility for Producing Pharmaceuticals in Plants.

There are also manufacturing considerations that make peptides attractive – their length allows them to be chemically synthesised, as opposed to proteins that are generally expressed in yeast or mammalian cells.


Engineering Perspectives in Biotechnology

2.58.2.4 Disulfide Bond Formation

Proteins containing disulfide bonds need to be reoxidized to form the correct disulfide bonds. 32,47 Generally, reducing agents such as β-mercaptoethanol or DTT are added to the lysis buffer to maintain the protein in a reduced state. Correct disulfide bonds are usually reformed during the renaturation step. Although air provides a suitable environment for disulfide bond formation, usually a redox system containing reduced and oxidized forms is added to the refolding buffer. Common redox systems include glutathionie (/GSSG), the combination of cysteine and cystine, or DTT and oxidized glutathione. Typically, buffers include a 1–3 mM concentration of reduced thiol and between a 10:1 and 5:1 ratio of reduced to oxidized forms although some reports suggest lower ratios provide more optimal yields. Studies suggest that hydrophobic interactions rather than disulfide bonding are the major cause of aggregation. However, intermolecular disulfide bonds can cross-link aggregates together and impact aggregate growth rates leading to larger aggregates, although the total amount of aggregate remains constant. 48



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