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    ________________ bonds form between amino acids to make a polypeptide, and then the amino acid side chains of the polypeptide attract and repel each other bending the protein into a _______________ shape.

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    Chapter 6 Flashcards by Briana white

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    Because it's 4 substituents are distinct, except for glycine, the alpha carbon is a ___. Amino acids that occur in ordinary proteins all have ___ configuration at that center.

    0

    D amino acids are present in other kinds of molecules, such as

    chiral center. L configuration

    Small protein like polypeptides in microorganisms

    The alpha carbon amino acid has four substituents, distinct from each other except in the case of the simplest amino acid, ___.

    1

    An amino group, a carboxyl group, and a proton are three of the substituents on all of the naturally occurring amino acids. The fourth, is the R group, which is the only______.

    Glycine

    Distinguishable feature.

    The R group is responsible for determining the amino acid's ____& ___.

    2

    Amino acids are put into 3 categories:

    The size of the sidechain is important for ___ amino acids because these side chains ____ and therefore, the functional roles in proteins such as glycine and alanine are quite different from those of phenylalanine and tryptophan.

    Polarity (which correlates with its solubility in water) and it's size.

    1. Neutral (uncharged) and nonpolar

    2. Neutral and polar

    3.charged

    Nonpolar, pack into the compact interior of a protein

    The ___ bonds are the covalent links between amino acids in a protein. One forms by a ___ reaction, with elimination of a water molecule.

    3

    Polypeptide chain is successive links of multiple ___ into a linear chain.

    The components of the chain are called amino acid ___.

    Peptide The peptide bond has partial double-character (the length of the bond is intermediate relative to single and double carbon-nitrogen bond).

    Condensation Amino acids Residues 4

    The amide and carboxyl components are nearly coplanar and in a ___ configuration.

    The peptide bond presents a significant barrier to rotation, and thus is central to a roughly planar, rigid group of __ atoms.

    The peptide bond has partial double-character (the length of the bond is intermediate relative to single and double carbon- nitrogen bond).

    The amide and carboxyl components are nearly coplanar and in a TRANS configuration.

    The peptide bond presents a significant barrier to rotation, and thus is central to a roughly planar, rigid group of SIX atoms.

    The φ torsion angle corresponds to the rotation about the __ bond; in the conformation here φ=180°.

    5

    (c) The ψ torsionangle corresponds to the rotation about the ___ bond. In the conformation here ψ=0°.

    So there are ___ bonds per amino acid residue in a peptides. The peptide bond is rigid, the other two have relative free rotation ability.

    N-Cα bond, Cα-C,

    Three, 6

    If the two negatively charged oxygen atoms of a peptide bond are too close together they will repel one another. This clash is called ____ and it further limits the ____.

    This clash is called STERIC HINDRANCE and it further limits the number of possible conformations of the polypeptide chain.

    Because its R group is just a proton, glycine is not ___, and it has more conformational freedom than any other amino acids.

    7

    Proline: in which the side chain has a ____, has less conformational freedom than many other amino acids.

    Chiral

    covalent bond with N as well as Cα

    8

    Cysteine, with a sulfhydryl (-SH) group on its side chain, is one amino acid that is sensitive to ___under roughly physiological conditions. Two cysteines can form___

    oxidation-reduction

    A disulfide bond by oxidation of the two – SH groups to S—S.

    Proteins on the cell surface or which are secreted into extracellular space are exposed to an environment with ___ that favors ___ formation; most such proteins have disulfide bonds and no ____.

    9

    Living cells maintain a more reducing internal environment, and intracellular protein very rarely have _____

    .

    Disulfide bonds enhance the stability of a folded protein by adding ____.

    Proteins on the cell surface or which are secreted into extracellular space are exposed to an environment with REDOX POTENTIAL that favors DISULFIDE formation; most such proteins have disulfide bonds and no UNOXIDIZED cysteines. Living cells maintain a more reducing internal environment, and intracellular protein very rarely have DISULFIDE BONDS.

    covalent cross-links

    10

    Hydrophobic molecules avoid the network of hydrogen bonds; hydrophilic molecules participate in it. It is therefore favorable for hydrophobic molecules to ___

    remain adjacent to each other than to disperse into a aqueous medium.

    Some amino acid side chains are hydrophilic (I.e___), some are hydrophobic (ie ____).

    11

    Some hydrophilic side chains can have hydrophobic parts (ie ___)

    The hydrophobic character of many amino acid side chains makes it favorable to ____, and the hydrophilic character of others allows them to ___.

    aspartic acid

    Phenylalanine

    methylene groups in lysine

    The hydrophobic character of many amino acid side chains makes it favorable to cluster away from water, and the hydrophilic character of others allows them to project into water.

    Source : www.brainscape.com

    The Shape and Structure of Proteins

    From a chemical point of view, proteins are by far the most structurally complex and functionally sophisticated molecules known. This is perhaps not surprising, once one realizes that the structure and chemistry of each protein has been developed and fine-tuned over billions of years of evolutionary history. We start this chapter by considering how the location of each amino acid in the long string of amino acids that forms a protein determines its three-dimensional shape. We will then use this understanding of protein structure at the atomic level to describe how the precise shape of each protein molecule determines its function in a cell.

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    Molecular Biology of the Cell. 4th edition.

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    The Shape and Structure of Proteins

    From a chemical point of view, proteins are by far the most structurally complex and functionally sophisticated molecules known. This is perhaps not surprising, once one realizes that the structure and chemistry of each protein has been developed and fine-tuned over billions of years of evolutionary history. We start this chapter by considering how the location of each amino acid in the long string of amino acids that forms a protein determines its three-dimensional shape. We will then use this understanding of protein structure at the atomic level to describe how the precise shape of each protein molecule determines its function in a cell.

    Go to:

    The Shape of a Protein Is Specified by Its Amino Acid Sequence

    Recall from Chapter 2 that there are 20 types of amino acids in proteins, each with different chemical properties. A protein molecule is made from a long chain of these amino acids, each linked to its neighbor through a covalent peptide bond (Figure 3-1). Proteins are therefore also known as . Each type of protein has a unique sequence of amino acids, exactly the same from one molecule to the next. Many thousands of different proteins are known, each with its own particular amino acid sequence.

    Figure 3-1

    A peptide bond. This covalent bond forms when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid. As indicated, a molecule of water is lost in this condensation (more...)

    The repeating sequence of atoms along the core of the polypeptide chain is referred to as the polypeptide backbone. Attached to this repetitive chain are those portions of the amino acids that are not involved in making a peptide bond and which give each amino acid its unique properties: the 20 different amino acid side chains (Figure 3-2). Some of these side chains are nonpolar and hydrophobic (“water-fearing”), others are negatively or positively charged, some are reactive, and so on. Their atomic structures are presented in Panel 3-1, and a brief list with abbreviations is provided in Figure 3-3.

    Figure 3-2

    The structural components of a protein. A protein consists of a polypeptide backbone with attached side chains. Each type of protein differs in its sequence and number of amino acids; therefore, it is the sequence of the chemically different side chains (more...)

    Panel 3-1

    The 20 Amino Acids Found in Proteins.

    Figure 3-3

    The 20 amino acids found in proteins. Both three-letter and one-letter abbreviations are listed. As shown, there are equal numbers of polar and nonpolar side chains. For their atomic structures, see Panel 3-1 (pp. 132–133).

    As discussed in Chapter 2, atoms behave almost as if they were hard spheres with a definite radius (their ). The requirement that no two atoms overlap limits greatly the possible bond angles in a polypeptide chain (Figure 3-4). This constraint and other steric interactions severely restrict the variety of three-dimensional arrangements of atoms (or that are possible. Nevertheless, a long flexible chain, such as a protein, can still fold in an enormous number of ways.

    Figure 3-4

    Steric limitations on the bond angles in a polypeptide chain. (A) Each amino acid contributes three bonds to the backbone of the chain. The peptide bond is planar and does not permit rotation. By contrast, rotation can occur about (more...)

    The folding of a protein chain is, however, further constrained by many different sets of weak that form between one part of the chain and another. These involve atoms in the polypeptide backbone, as well as atoms in the amino acid side chains. The weak bonds are of three types: , , and , as explained in Chapter 2 (see p. 57). Individual noncovalent bonds are 30–300 times weaker than the typical covalent bonds that create biological molecules. But many weak bonds can act in parallel to hold two regions of a polypeptide chain tightly together. The stability of each folded shape is therefore determined by the combined strength of large numbers of such noncovalent bonds (Figure 3-5).

    Figure 3-5

    Three types of noncovalent bonds that help proteins fold. Although a single one of these bonds is quite weak, many of them often form together to create a strong bonding arrangement, as in the example shown. As in the previous figure, R is used as a general (more...)

    A fourth weak force also has a central role in determining the shape of a protein. As described in Chapter 2, hydrophobic molecules, including the nonpolar side chains of particular amino acids, tend to be forced together in an aqueous environment in order to minimize their disruptive effect on the hydrogen-bonded network of water molecules (see p. 58 and Panel 2-2, pp. 112–113). Therefore, an important factor governing the folding of any protein is the distribution of its polar and nonpolar amino acids. The nonpolar (hydrophobic) side chains in a protein—belonging to such amino acids as phenylalanine, leucine, valine, and tryptophan—tend to cluster in the interior of the molecule (just as hydrophobic oil droplets coalesce in water to form one large droplet). This enables them to avoid contact with the water that surrounds them inside a cell. In contrast, polar side chains—such as those belonging to arginine, glutamine, and histidine—tend to arrange themselves near the outside of the molecule, where they can form hydrogen bonds with water and with other polar molecules (Figure 3-6). When polar amino acids are buried within the protein, they are usually hydrogen-bonded to other polar amino acids or to the polypeptide backbone (Figure 3-7).

    Source : www.ncbi.nlm.nih.gov

    Protein structure: Primary, secondary, tertiary & quatrenary (article)

    Orders of protein structure: primary, secondary, tertiary, and quaternary. Alpha helix and beta pleated sheet.

    Proteins

    Orders of protein structure

    Orders of protein structure: primary, secondary, tertiary, and quaternary. Alpha helix and beta pleated sheet.

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    Introduction

    Have you ever wondered why egg whites go from clear to opaque when you fry an egg? If so, this section is for you!

    Egg whites contain large amounts of proteins called albumins, and the albumins normally have a specific 3D shape, thanks to bonds formed between different amino acids in the protein. Heating causes these bonds to break and exposes hydrophobic (water-hating) amino acids usually kept on the inside of the protein

    ^{1,2} 1,2

    start superscript, 1, comma, 2, end superscript

    . The hydrophobic amino acids, trying to get away from the water surrounding them in the egg white, will stick to one another, forming a protein network that gives the egg white structure while turning it white and opaque. Ta-da! Thank you, protein denaturation, for another delicious breakfast.

    As we mentioned in the last article on proteins and amino acids, the shape of a protein is very important to its function. To understand how a protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary.

    Primary structure

    The simplest level of protein structure, primary structure, is simply the sequence of amino acids in a polypeptide chain. For example, the hormone insulin has two polypeptide chains, A and B, shown in diagram below. (The insulin molecule shown here is cow insulin, although its structure is similar to that of human insulin.) Each chain has its own set of amino acids, assembled in a particular order. For instance, the sequence of the A chain starts with glycine at the N-terminus and ends with asparagine at the C-terminus, and is different from the sequence of the B chain. [What's up with those S-S bonds?]

    Image of insulin. Insulin consists of an A chain and a B chain. They are connected to one another by disulfide bonds (sulfur-sulfur bonds between cysteines). The A chain also contains an internal disulfide bond. The amino acids that make up each chain of insulin are represented as connected circles, each with the three-letter abbreviation of the amino acid's name.

    image credit: OpenStax Biology.

    The sequence of a protein is determined by the DNA of the gene that encodes the protein (or that encodes a portion of the protein, for multi-subunit proteins). A change in the gene's DNA sequence may lead to a change in the amino acid sequence of the protein. Even changing just one amino acid in a protein’s sequence can affect the protein’s overall structure and function.

    For instance, a single amino acid change is associated with sickle cell anemia, an inherited disease that affects red blood cells. In sickle cell anemia, one of the polypeptide chains that make up hemoglobin, the protein that carries oxygen in the blood, has a slight sequence change. The glutamic acid that is normally the sixth amino acid of the hemoglobin β chain (one of two types of protein chains that make up hemoglobin) is replaced by a valine. This substitution is shown for a fragment of the β chain in the diagram below.

    Image of normal and sickle cell mutant hemoglobin chains, showing substitution of valine for glutamic acid in the sickle cell version.

    Image modified from OpenStax Biology.

    What is most remarkable to consider is that a hemoglobin molecule is made up of two α chains and two β chains, each consisting of about 150 amino acids, for a total of about 600 amino acids in the whole protein. The difference between a normal hemoglobin molecule and a sickle cell molecule is just 2 amino acids out of the approximately 600.

    A person whose body makes only sickle cell hemoglobin will suffer symptoms of sickle cell anemia. These occur because the glutamic acid-to-valine amino acid change makes the hemoglobin molecules assemble into long fibers. The fibers distort disc-shaped red blood cells into crescent shapes. Examples of “sickled” cells can be seen mixed with normal, disc-like cells in the blood sample below.

    Image credit: OpenStax Biology modification of work by Ed Uthman; scale-bar data from Matt Russell.

    The sickled cells get stuck as they try to pass through blood vessels. The stuck cells impair blood flow and can cause serious health problems for people with sickle cell anemia, including breathlessness, dizziness, headaches, and abdominal pain.

    Secondary structure

    The next level of protein structure, secondary structure, refers to local folded structures that form within a polypeptide due to interactions between atoms of the backbone. (The backbone just refers to the polypeptide chain apart from the R groups – so all we mean here is that secondary structure does not involve R group atoms.) The most common types of secondary structures are the α helix and the β pleated sheet. Both structures are held in shape by hydrogen bonds, which form between the carbonyl O of one amino acid and the amino H of another.

    Source : www.khanacademy.org

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