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The meaning of the $alpha$ helix and $eta$ sheets in proteins

The meaning of the $alpha$ helix and $eta$ sheets in proteins


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I asked this question to my Biology teacher and he, in collaboration with a Chemistry teacher, couldn't find the answer. My question is the following: "What does the $alpha$ and $eta$ represent in the secondary structure of a protein? I do reference to the $alpha$ helix and $eta$ sheets in proteins." I had a similar question with the glucose and we concluded that it was related to the Chemistry, the $alpha$ or $eta$, was related with the functional groups bonded to the carbon.


The answer is very simple. As described in the accepted answer to the related question about alpha-subunits vs alpha-helices the alpha- and beta- are arbitrary names. It could easily have been 1 and 2 or A and B based on ordering of letters or numbers; indeed, there are "type I" and "type II" turns.

The history, from the wikipedia page on alpha-helices says:

In the early 1930s,… William Astbury initially proposed a kinked-chain structure for the fibers. He later joined other researchers (notably the American chemist Maurice Huggins) in proposing that:

  • The unstretched protein molecules formed a helix (which he called the α-form)
  • The stretching caused the helix to uncoil, forming an extended state (which he called the β-form).

(Emphasis added). In other words, he named the "α-form" first, and considered the "β-form" to be an uncoiled form of the first one. These names later became "α-helix" and "β-sheet". It could easily have been the other way around.

Indeed there are other types of helix; the 310 helix and the π-helix. If either of these had been discovered first, perhaps they would be the alpha-helix. Of them all, the 310 helix has the most 'logical' name as:

the helix has three residues per turn, and… has 10 atoms in the ring formed by making the hydrogen bond

so if we followed a similar naming scheme, the alpha helix would be a 3.613 helix. Admittedly this is a bit of a cumbersome name.

As well there are the alpha sheet - a sheet made of helical strands - and the beta helix - a helix made of strands. For both of these, the "alpha" and "beta" part of the name has been chosen because of the naming of the original structures they are related to.


A protein's primary structure is the specific order of amino acids that have been linked together to form a polypeptide chain. But polypeptides do not simply stay straight as liniar sequences of amino acids. The fold back on themselves to create complex 3-dimensional shapes.

When examing different proteins, you will notice that there are two specifically recognizable shapes that are often repeated throughout a protein's 3-dimensional structure. One of these shapes looks like a curl and the other looks like rows or zig-zags.

The curls are called alpha helices and almost look like a spiral staircase or a spring. They exist when a protein's backbone curls up into a helical shape.

Click Here to display an alpha helix in the interactive display to the right.

The rows are called beta pleated sheets and almost look like a long line for a ride at an amusement park. They exist when a protein's backbone forms an extended zig-zag structure that passes back and forth.

Click Here to display a beta pleated sheet in the interactive display to the right.

The organization and frequency of these two structures in a protein's overall 3-dimensional shape is called the protein's secondary structure.

Secondary Structures in a Real Protein

One type of protein that clearly shows both an alpha helix and a beta pleated sheet is a zinc finger protein, which helps regulate DNA expression in a cell's nucleus. This relatively small protein is only 28 amino acids long but includes a four-turn alpha helix and a two strand beta pleated sheet.

Click Here to show a zinc finger protein in the interactive display to the right.

Visualizing Complex Protein Structures

Protein structures can become very visually overwhelming. This is especially true for large proteins, which can be thousands of amino acids long and include tens of thousands of atoms!

Because of this, proteins are often visually represented using different display formats and color schemes. Click on the buttons below to see the zinc finger protein in the interactive display to the far right shown in some of the most common display formats and color schemes.

Each of the different display formats and color schemes used in protein visualization has advantages and disadvantages.

For example, spacefill format is an excellent way to represent the overall globular shape of a protein, but may make it difficult to see details at the very center of the protein. Cartoon format is an excellent way to see the overall path of a protein's backbone, but may not shown the details of each individual amino acid's R-group.


Predicted alpha-helix/beta-sheet secondary structures for the zinc-binding motifs of human papillomavirus E7 and E6 proteins by consensus prediction averaging and spectroscopic studies of E7

The E7 and E6 proteins are the main oncoproteins of human papillomavirus types 16 and 18 (HPV-16 and HPV-18), and possess unknown protein structures. E7 interacts with the cellular tumour-suppressor protein pRB and contains a zinc-binding site with two Cys-Xaa2-Cys motifs spaced 29 or 30 residues apart. E6 interacts with another cellular tumour-suppressor protein p53 and contains two zinc-binding sites, each with two Cys-Xaa2-Cys motifs at a similar spacing of 29 or 30 residues. By using the GOR I/III, Chou-Fasman, SAPIENS and PHD methods, the effectiveness of consensus secondary structure predictions on zinc-finger proteins was first tested with sequences for 160 transcription factors and 72 nuclear hormone receptors. These contain Cys2His2 and Cys2Cys2 zinc-binding regions respectively, and possess known atomic structures. Despite the zinc- and DNA-binding properties of these protein folds, the major alpha-helix structures in both zinc-binding regions were correctly identified. Thus validated, the use of these prediction methods with 47 E7 sequences indicated four well-defined alpha-helix (alpha) and beta-sheet (beta) secondary structure elements in the order beta beta alpha beta in the zinc-binding region of E7 at its C-terminus. The prediction was tested by Fourier transform infrared spectroscopy of recombinant HPV-16 E7 in H2O and 2H2O buffers. Quantitative integration showed that E7 contained similar amounts of alpha-helix and beta-sheet structures, in good agreement with the averaged prediction of alpha-helix and beta-sheet structures in E7 and also with previous circular dichroism studies. Protein fold recognition analyses predicted that the structure of the zinc-binding region in E7 was similar to a beta beta alpha beta motif found in the structure of Protein G. This is consistent with the E7 structure predictions, despite the low sequence similarities with E7. This predicted motif is able to position four Cys residues in proximity to a zinc atom. A model for the zinc-binding motif of E7 was constructed by combining the Protein G coordinates with those for the zinc-binding site in transcription factor TFIIS. Similar analyses for the two zinc-binding motifs in E6 showed that they have different alpha/beta secondary structures from that in E7. When compared with 12 other zinc-binding proteins, these results show that E7 and E6 are predicted to possess novel types of zinc-binding structure.


Situations of gamma-turns in proteins : Their relation to alpha-helices, beta-sheets and ligand binding sites

Gamma-turns occur as one of two possible enantiomers with regard to their main-chain structure, called classic and inverse. Of these, inverse ones are more common. Unlike other hydrogen bonds, those in inverse gamma-turns include a large proportion that are weak. If such hydrogen bonds are included, these turns may be said to be abundant in proteins. A significant number of inverse gamma-turns, usually weak ones, exist as consecutive turns in a structural feature, now called the 2·27-helix, proposed for polypeptides as long ago as 1943 by Huggins. Most of these features occur within strands of beta-sheet. The less-weak inverse gamma-turns fall into several structural subgroups. They are frequently situated directly at either end of alpha-helices or of strands of beta-sheet, or adjacent to certain loop motifs. In general, they are well conserved during evolution and some are found at key positions in proteins. One occurs in the first hypervariable loop in the heavy chain of immunoglobulins.

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Lesson Worksheet: Proteins Biology

In this worksheet, we will practice describing the synthesis, structures, and functions of proteins.

Which of the following best explains the role of hydrogen bonds in protein structure?

  • A Hydrogen bonds form within amino acids to join the carboxyl group to the amino group.
  • B Hydrogen bonds form between amino acids to hold the protein in its secondary-structure shape (e.g., alpha-helix).
  • C Hydrogen bonds form between amino acids to hold them in a polypeptide chain.
  • D Hydrogen bonds form between amino acids and water molecules to contribute to the quaternary structure of the protein.

Proteins are complex macromolecules formed from polypeptide chains. What monomers join to form polypeptides?

  • A Glycerol
  • B Lipids
  • C Fatty acids
  • D Simple sugars
  • E Amino acids

Which of the following best describes the primary structure of a protein?

  • A The primary structure of a protein refers to the sequence of amino acids in its polypeptide chain.
  • B The primary structure of a protein is the complex 3D structure formed when multiple polypeptides interact and combine.
  • C The primary structure of a protein is the 3D structure that forms due to interactions between the R groups of amino acids.
  • D The primary structure of a protein is the folded structure (alpha-helix or beta-sheet) formed by additional bonds formed in the polypeptide chain.

Which of the following best describes the quaternary structure of a protein?

  • A The quaternary structure of a protein is the 3D structure that forms due to interactions between the R groups of amino acids.
  • B The quaternary structure of a protein is the folded structure (alpha-helix or beta-sheet) formed by additional bonds formed in the polypeptide chain.
  • C The quaternary structure of a protein is the complex 3D structure formed when multiple polypeptides interact and combine.
  • D The quaternary structure of a protein refers to the sequence of amino acids in its polypeptide chain.

Which of the following best describes the secondary structure of a protein?

  • A The secondary structure of a protein refers to the sequence of amino acids in its polypeptide chain.
  • B The secondary structure of a protein is the folded structure (alpha-helix or beta-sheet) formed by additional bonds that are formed in the polypeptide chain.
  • C The secondary structure of a protein is the 3D structure that forms due to interactions between the R groups of amino acids.
  • D The secondary structure of a protein is the complex 3D structure formed when multiple polypeptides interact and combine.

Which of the following best explains the structure of a polypeptide?

  • A A polypeptide is a protein formed by the joining of three amino acids to a glycerol molecule.
  • B A polypeptide is a chain of amino acids joined together by carboxyl bonds between the amino groups of each amino acid.
  • C A polypeptide is a chain of amino acids joined together by peptide bonds between the carboxyl group of one and the amino group of another.
  • D A polypeptide is a chain of proteins joined by peptide bonds between the hydrogens of each protein.

Which of the following best describes the tertiary structure of a protein?

  • A The tertiary structure of a protein is the folded structure (alpha-helix or beta-sheet) formed by additional bonds that are formed in the polypeptide chain.
  • B The tertiary structure of a protein is the complex 3D structure formed when multiple polypeptides interact and combine.
  • C The tertiary structure of a protein refers to the sequence of amino acids in its polypeptide chain.
  • D The tertiary structure of a protein is the 3D structure that forms due to interactions between the R groups of amino acids.

The following is a list of bonds found in biological molecules:

  1. Hydrogen
  2. Ionic
  3. Phosphodiester
  4. Disulfide bridges
  5. Glycosidic

What bonds are commonly present in the tertiary structure of proteins?

  • A I only
  • B I, II, and IV
  • C I and IV only
  • D II, III, and IV
  • E I, II, and III

Keratin is a long protein found in hair and nails, with many repeats of the sulfur-containing amino acid cysteine. Using the table provided, determine the group of proteins that keratin is most likely to belong to.

ProteinGlobularConjugatedFibrous
PropertiesCompact, roughly spherical, and water-soluble Proteins with a prosthetic groupLong and insoluble with a repetitive primary structure

Part of the basic structure of an amino acid is provided. Give the molecular formula of the functional group that is missing.


The meaning of the $alpha$ helix and $eta$ sheets in proteins - Biology

(for tutorials on the alpha helix and beta sheet secondary structures, see the Bio 13 tutorials)

Type I and Type II Reverse Turns

A Type I Turn:
In addition to the alpha helix and beta sheet secondary structures (see Bio 13 tutorials), another distinct structural motif has been recognized in which the the polypeptide chain reverses direction over the span of only a few amino acids. Such a structure is known as the Reverse turn or the beta turn (because it is found joining adjacent antiparallel sequences of beta sheet).

Three subclasses of reverse turns (Types I - III) have been recognized, All involve a four amino acid sequence in whch the carbonyl oxygen of AA-1 is H-bonded to the amino-H of AA-4 (rather than AA-5 as is found in the alpha helix). Type I and type II turns differ in the bond linking residue 2 and residue 3. The two types differ in a 180 degree rotation around the bond linking residues 2 and 3. Although various amino acids can make up the turn, frequently AA-2 is a proline since it does introduce a sharp bend in the polypeptide chain.

A Type II Turn:

Observe how the orientation of the carbonyl oxygen of residue 2 is flipped between type I and Type II. This can be seen easily if you make this oxygen spacefilling (button 2 above). Because B turns are always found at the surface of proteins, they contain hydrophilic amino cids mainly and almost 30% of them also contain a proline at the C-2 poition. 60% of all b turns have either asp, asn or gly at their third position

Glycine at position 3 of Type II Reverse Turns Minimizes Steric Interference

Because of this flip, Type II turns usually have glycine at residue 3 to avoid steric interactions between its R group and the carbonyl oxygen residue of residue 2.


Difference Between Alpha Helix and Beta Pleated Sheet

The motif positioned on the secondary building of proteins and turns into regular as a coiled like or spiral right-hand affirmation that gives it the excellence of a helix, due to this fact usually known as an alpha helix. On the alternative hand, the beta pleated sheet moreover often known as the b-sheet will get outlined as the standard motif of the attribute secondary building present throughout the proteins.

Comparison Chart

BasisAlpha HelixBeta Pleated Sheet
DefinitionThe motif positioned on the secondary building of proteins and turns into regular as a coiled like or spiral right-hand affirmation that gives it the excellence of a helix.The beta pleated sheet moreover often known as the b-sheet will get outlined as the standard motif of the attribute secondary building present throughout the proteins.
Amino AcidsThe -R groups of amino acids exist on the floor ground.The -R groups exist on the floor and inside ground of the sheet.
BondingThe hydrogen bonds get created all through the polypeptide chain for creating helical constructions.Exist by linking of two or better than two beta strands from hydrogen bonds.

What is Alpha Helix?

The motif positioned on the secondary building of proteins and turns into regular as a coiled like or spiral right-hand affirmation that gives it the excellence of a helix, due to this fact usually known as an alpha helix. Here, all through the development, the N-H group denotes a hydrogen bond to the C=O group often known as the backbone of amino acids which turns into present in four residues sooner than the protein sequence. Two key developments throughout the demonstrating of the present day α-helix had been: the becoming bond geometry, because of the expensive stone building judgments of amino acids and peptides and Pauling’s expectation of planar peptide bonds and his giving up of the suspicion of a vital number of deposits per flip of the helix. The crucial minute acquired right here throughout the early spring of 1948 when Pauling acquired right here down with a bug and went to mattress. Being exhausted, he drew a polypeptide chain of normally correct measurements on a bit of paper and collapsed it proper right into a helix, being acutely aware to take care of up the planar peptide bonds. The alpha helix is basically essentially the most well-known helix current in nature. It consists of of a wound polypeptide chain, throughout which the side chains of the amino acids broaden outward from the center, this permits it to take care of up its type. They could also be current in quite a lot of kinds of proteins, from globular proteins, as an illustration, myoglobin to keratin, which is a stringy protein. It can each be a privilege gave or left-hand helice but it surely has been demonstrated that the alpha helix loop is supported as a result of the side chains don’t battle. This knowledge gives the alpha-helix steadiness. There are three.6 amino corrosive deposits for each flip of the alpha-helix curl.

What is Beta Pleated Sheet?

The beta pleated sheet moreover often known as the b-sheet will get outlined as the standard motif of the attribute secondary building present throughout the proteins. The distinction it has over completely different proteins turns into the difficulty that it consists of strands which have a reference to not lower than two or three of the hydrogen atoms present all through the development that sort the pleated sheet. A β-strand is an extent of polypeptide anchor generally three to 10 amino acids prolonged with the spine in a broadened adaptation. The supramolecular relationship of β-sheets has embroiled throughout the affiliation of the protein totals and fibrils seen in fairly just a few human sicknesses, eminently the amyloidoses, as an illustration, Alzheimer’s sickness. This building happens when two components of a polypeptide chain cowl each other and type a line of hydrogen bonds with each other. This movement can occur in a parallel plan of motion or in hostile to parallel plan. Parallel and in the direction of the equivalent sport plan is the speedy consequence of the directionality of the polypeptide chain. A corresponding building to the beta-creased sheet is the α-creased sheet. This building is enthusiastically a lot much less final than the beta-creased sheet and is genuinely unprecedented in proteins. A α-creased sheet will get described by the affiliation of its carbonyl and amino gatherings the carbonyl groups are altogether adjusted in a single heading, whereas all the N-H gatherings are adjusted the alternative technique.


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Alpha Helix, Beta Sheet, and Beta Turn - Protein Structure

The existence of the alpha helix was predicted by Pauling and Cory from careful structural studies of amino acids and peptide bonds. This pre-diction came before identification of the alpha helix in X-ray diffraction patterns of proteins. Even though the data were all there, it was over-looked. The alpha helix is found in most proteins and is a fundamental structural element. In the alpha helix, hydrogen bonds are formed between the carbonyl oxygen of one peptide bond and the amide hydrogen of the amino acid located three and a third amino acids away.


The side chains of the amino acids extend outward from the helix, and the hydrogen bonds are nearly parallel to the helix axis (Fig. 6.12). If they were precisely parallel to the axis, the helix pitch would be 3.33 amino acids per turn, but due to steric constraints, the hydrogen bonds are somewhat skewed, and the average pitch is found to be 3.6 to 3.7 amino acids per turn.


If we look down the axis of an alpha helix, we see the amino acids winding around in a circle. Every third and then every fourth amino acid lies on one side of the helix (Fig. 6.13). This pattern follows from the fact that the alpha helix is nearly 3.5 amino acids per turn. If every third and then every fourth amino acid were hydrophobic, two such helices could bind together through their parallel strips of hydrophobic amino acids. This occurs in structures called coiled coils. These are found in structural proteins like myosin as well as in a class of transcrip-tional regulators that dimerize by these interactions. These activators are called leucine-zipper proteins. They possess leucine residues seven amino acids apart. Strips of hydrophobic amino acids along one face of alpha helices are frequently found in bundles containing two, three, or four alpha helices.


The beta-strand is a second important structural element of proteins. In it the polypeptide chains are quite extended (Fig. 6.14). From a top view the peptide backbone is relatively straight, but in a side view the peptide backbone is pleated. The side chains of the amino acids are relatively unconstrained since alternate groups are directed straight up and straight down. The amide hydrogens and the carboxyl groups are directed to either side and are available for hydrogen bonding to another beta-strand lying alongside to form a beta sheet. This second strand can be oriented either parallel or antiparallel to the first.


The third readily identified secondary structural element is the re-verse or beta bend (Fig. 6.15). A polypeptide chain must reverse direc-tion many times in a typical globular protein. The beta bend is an energy-effective method of accomplishing this goal. Three amino acids often are involved in a reverse bend.


Proteins

Proteins provide much of the structural and functional capacity of cells. Proteins are composed of monomers called amino acids. Amino Acids are hydrocarbons that have an amino group (-NH2) and an acidic carboxyl group (-COOH).The R group represents a hydrocarbon chain with a modification that alters the properties of the amino acid. 20 universal amino acids are used to construct proteins. The variation in functional groups along the amino acid chain gives rise to the functional diversity of proteins.

20 amino acids and their properties. A 21st amino acid on this table represents the non-universally found selenocysteine. Monomers bond together through a dehydration synthesis reaction between adjacent amino and carboxyl groups to yield a peptide bond .

Three amino acids bound into a tripeptide.


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