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Which is the correct statement on proteins?

Which is the correct statement on proteins?



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I need help with one of the questions on my biochemistry assignment

Choose the correct statement on proteins: a) proteins are folded by alpha-helix b) proteins can preserve their function even if they only partially change their shapes c) proteins are composed of amino acids d) all of the above

Thanks in advance! :)


Do you have a textbook? That will definitely have the answer early on in the chapter. Also, have you tried reading the protein Wikipedia article, in particular the structure subsection. You will find the information you want there.


MCAT Biology : Protein Structure

Which of the following statements is NOT true regarding the comparison of the alpha-helix structure to the beta-sheet structure in proteins?

All possible hydrogen bonds between the peptide carbonyl oxygen (C=O) and the amide hydrogen (N-H) are formed in each

The peptide bond in each is planar and trans

Each may occur in typical globular proteins

Each is stabilized by inter-chain hydrogen bonds

Each is an example of secondary structure

Each is stabilized by inter-chain hydrogen bonds

Alpha-helices and beta-sheets are secondary structure motifs that occur when sequences of amino acids are linked by hydrogen bonds. These secondary structures are an integral part of globular proteins, such as hemoglobin. Alpha-helices resemble a coiled spring, with hydrogen bonding occurring in an intra-chain arrangement between carbonyl oxygens and amide hydrogens that is parallel to the central axis. Beta sheets, on the other hand, may have either inter- or intra-chain hydrogen bonding between carbonyl oxygens and amide hydrogens. Thus, the correct answer (and false statement) is that each is stabilized by interchain hydrogen bonds.

Example Question #1581 : Mcat Biological Sciences

Which of the following describes the folding of soluble globular proteins?

Most hydrophilic amino acid residues are protected from water

The energy of the system (protein + water) is at a maximum

Most hydrophobic amino acids are internal, away from solvent water

None of the answers are true

Two of the answers are true

Most hydrophobic amino acids are internal, away from solvent water

Globular proteins are representative of the quaternary structure of a class of proteins, an example of which is hemoglobin. In a soluble molecule the surface of the molecule must interact with water. Any hydrophobic portions of the molecule must remain internal and away from water, while hydrophilic portions will remain on the exterior portion interacting with water molecules. A soluble globular protein is folded so as to minimize the energy of the system. Thus, the correct answer is that most hydrophobic amino acids are internal, away from solvent water.

Example Question #1 : Protein Structure

Hemoglobin is the principal oxygen-carrying protein in humans. It exists within erythrocytes, and binds up to four diatomic oxygen molecules simultaneously. Hemoglobin functions to maximize oxygen delivery to tissues, while simultaneously maximizing oxygen absorption in the lungs. Hemoglobin thus has a fundamentally contradictory set of goals. It must at once be opitimized to absorb oxygen, and to offload oxygen. Natural selection has overcome this apparent contradiction by making hemoglobin exquisitely sensitive to conditions in its microenvironment.

One way in which hemoglobin accomplishes its goals is through the phenomenon of cooperativity. Cooperativity refers to the ability of hemoglobin to change its oxygen binding behavior as a function of how many other oxygen atoms are bound to the molecule.

Fetal hemoglobin shows a similar pattern of cooperativity, but has unique binding characteristics relative to adult hemoglobin. Fetal hemoglobin reaches higher saturation at lower oxygen partial pressure.

Because of cooperativity, adult and fetal oxygen-hemoglobin dissociation curves appear as follows.

Beyond its ability to carry oxygen, hemoglobin is also effective as a blood buffer. The general reaction for the blood buffer system of hemoglobin is given below.


Can you answer these Multiple Choice Questions on Biology?

71. Which of the following has the longest small intestine?

(a) carnivore (b) omnivore (c) herbivore (d) autotroph

72. The process of obtaining food by Amoeba is known as:

(a) dialysis (b) cytokinesis (c) phagocytosis (d) amoebiasis

73. The organism having parasitic mode of nutrition is:

(a) Penicillium (b) Plasmodium (c) Paramecium (d) Parrot

74. One of the following organisms has a saprophytic mode of nutrition. This organism is:

(a) mushroom (b) malarial parasite (c) leech (d) lice

75. The length of small intestine in a human adult is about

(a) 4.5 m (b) 1.5 m (c) 3.5 m (d) 6.5 m

76. The process of digestion of food in humans begins in:

(a) stomach (b) food pipe (c) mouth (d) small intestine

77. The process of digestion in humans is completed in:

(a) oesophagus (b) small intestine (c) stomach (d) large intestine

78. In human digestive system, bile is secreted by:

(a) pancreas (b) liver (c) kidneys (d) stomach

79. Two of the following organisms have a holozoic mode of nutrition. These organisms are:

(a) Paramecium and Plasmodium (b) Plasmodium and Parakeet

(c) Parakeet and Paramecium (d) Paramecium and Parasite

80. The autotrophic mode of nutrition requires:

(a) carbon dioxide and water (b) chlorophyll

(c) sunlight (d) all of the above

81. The correct order of steps occurring in nutrition in animals is:

(a) Ingestion —- > Absorption — > Digestion — > Assimilation

(b) Ingestion —- > Digestion — > Assimilation —- > Absorption

(c) Ingestion —- > Digestion — > Absorption— > Assimilation

(d) Ingestion —- > Assimilation — > Digestion —- > Absorption

82. In human digestive system, the enzymes pepsin and trypsin are secreted respectively by:

(a) pancreas and liver (b) stomach and salivary glands

(c) pancreas and gall bladder (d) stomach and pancreas

83. When carrying out the starch test on a leaf, why is it important to boil the leaf in alcohol?

(a) to dissolve the waxy cuticle (b) to make the cells more permeable to iodine solution

(c) to remove the chlorophyll (d) to stop chemical reactions in the cells.

84. Pancreatic juice contains enzymes which digest:

(a) proteins and carbohydrates only (b) proteins and fats only

(c) fats and carbohydrates only (d) proteins, fats and carbohydrates

85. Which of the following is the correct statement regarding bile?

(a) secreted by bile duct and stored in liver (b) secreted by gall bladder and stored in liver

(c) secreted by liver and stored in bile duct (d) secreted by liver and stored in gall bladder

86. Where are proteins first digested in the alimentary canal?

(a) small intestine (b) oesophagus

87. The inner lining of stomach is protected by one of the following from the harmful effect of hydrochloric acid. This is:

88. Which part of alimentary canal receives bile from the liver?

(a) oesophagus (b) small intestine

(c) stomach (d) large intestine

89. Which of the following component of our food is digested by an enzyme which is present in saliva as well as in pancreatic juice?

(c) minerals (d) carbohydrate

90. If the saliva is lacking in salivary amylase, then which of the following processes taking place in the buccal cavity will be affected?

(a) proteins breaking down into amino acids

(b) starch breaking down into sugars

(c) fats breaking down into fatty acids and glycerol

(d) intestinal layer breaking down leading to ulcers

91. Which of the following are the correct functions of two components of pancreatic juice trypsin and lipase?

(a) trypsin digests proteins and lipase carbohydrates

(b) trypsin digests emulsified fats and lipase proteins

(c) trypsin digests starch and lipase fats

(d) trypsin digests proteins and lipase emulsified fats

92. The oxygen liberated during photosynthesis by green plants comes from:

(c) carbon dioxide (d) chlorophyll

93. Which of the following is an incorrect statement?

(a) energy is essential for life processes

(b) organisms grow with time

(c) movement of molecules does not take place among cells

(d) organisms must repair and maintain their body

94. The internal energy (cellular energy) reserve in autotrophs is:

95. Which of the following events does not occur in photosynthesis?

(a) conversion of light energy into chemical energy

(b) reduction of carbon dioxide to carbohydrates

(c) oxidation of carbon to carbon dioxide

(d) absorption of light energy by chlorophyll

96. The opening and closing of the stomatal pores depends upon:

(a) oxygen (b) water in guard cells

(c) temperature (d) concentration of C02 in stomata

97. Most of the plants absorb nitrogen in one of the following forms. This is:

(a) proteins (b) nitrates and nitrites

(c) urea (d) atmospheric nitrogen

98. The first enzyme to mix with food in the digestive tract is:

99. Which of the following is the correct statement?

(a) heterotrophs synthesise their own food

(b) heterotrophs utilize solar energy for photosynthesis

(c) heterotrophs do not synthesise their own food

(d) heterotrophs are capable of converting carbon dioxide and water into carbohydrates

100. In which of the following groups of organisms the food material is broken down outside the body and then absorbed?

(a) Mushroom, Green plants, Amoeba

(b) Yeast, Mushroom, Bread mould

(c) Paramecium, Amoeba, Cuscuta

101. Which of the following is the correct sequence of parts as they occur in the human alimentary canal?

(a) Mouth->Stomach Small intestine -> Oesophagus ->Large intestine

(b) Mouth -> Oesophagus -> Stomach -> Large intestine -> Small intestine

(c) Mouth -> Stomach -> Oesophagus -> Small intestine -> Large intestine

(d) Mouth -> Oesophagus -> Stomach -> Small intestine –> Large intestine

71. (c) 72. (c) 73. (b) 74. (a) 75. (d) 76. (c) 77. (b) 78. (b) 79. (c) 80. (d) 81. (c) 82. (d) 83. (c) 84 (d) 85. (d) 86. (d) 87. (b) 88. (b) 89. (d) 90. (b) 91. (d) 92. (b) 93. (c) 94. (d) 95. (c) 96. (b) 97. (b) 98. (c) 99. (c) 100. (b) 101. (d)


What do proteins do for the body?

Our bodies are made up of thousands of different proteins, each with a specific function. They make up the structural components of our cells and tissues as well as many enzymes, hormones and the active proteins secreted from immune cells (figure 1).

These body proteins are continually being repaired and replaced throughout our lives. This process (known as &lsquoprotein synthesis&rsquo) requires a continuous supply of amino acids. Although some amino acids can be recycled from the breakdown of old body proteins, this process is imperfect. This means we must eat dietary protein to keep up with our body&rsquos amino acid demand.

As protein is essential for cell and tissue growth, adequate intake of protein is particularly important during periods of rapid growth or increased demand, such as childhood, adolescence, pregnancy, and breastfeeding. 1

Figure 1. Functions of proteins in the body.


Types of Proteins

There is a total of seven different protein types under which all proteins fall. These include antibodies, contractile proteins, enzymes, hormonal proteins, structural proteins, storage proteins, and transport proteins.

Antibodies

Antibodies are specialized proteins that defend the body against antigens or foreign invaders. Their ability to travel through the bloodstream enables them to be utilized by the immune system to identify and defend against bacteria, viruses, and other foreign intruders in blood. One way antibodies counteract antigens is by immobilizing them so that they can be destroyed by white blood cells.

Contractile Proteins

Contractile proteins are responsible for muscle contraction and movement. Examples of these proteins include actin and myosin. Eukaryotes tend to possess copious amounts of actin, which controls muscle contraction as well as cellular movement and division processes. Myosin powers the tasks carried out by actin by supplying it with energy.

Enzymes

Enzymes are proteins that facilitate and speed up biochemical reactions, which is why they are often referred to as catalysts. Notable enzymes include lactase and pepsin, proteins that are familiar for their roles in digestive medical conditions and specialty diets. Lactose intolerance is caused by a lactase deficiency, an enzyme that breaks down the sugar lactose found in milk. Pepsin is a digestive enzyme that works in the stomach to break down proteins in food—a shortage of this enzyme leads to indigestion.

Other examples of digestive enzymes are those present in saliva: salivary amylase, salivary kallikrein, and lingual lipase all perform important biological functions. Salivary amylase is the primary enzyme found in saliva and it breaks down starch into sugar.

Hormonal Proteins

Hormonal proteins are messenger proteins that help coordinate certain bodily functions. Examples include insulin, oxytocin, and somatotropin.

Insulin regulates glucose metabolism by controlling blood-sugar concentrations in the body, oxytocin stimulates contractions during childbirth, and somatotropin is a growth hormone that incites protein production in muscle cells.

Structural Proteins

Structural proteins are fibrous and stringy, this formation making them ideal for supporting various other proteins such as keratin, collagen, and elastin.

Keratins strengthen protective coverings such as skin, hair, quills, feathers, horns, and beaks. Collagen and elastin provide support to connective tissues like tendons and ligaments.

Storage Proteins

Storage proteins reserve amino acids for the body until ready for use. Examples of storage proteins include ovalbumin, which is found in egg whites, and casein, a milk-based protein. Ferritin is another protein that stores iron in the transport protein, hemoglobin.

Transport Proteins

Transport proteins are carrier proteins that move molecules from one place to another in the body. Hemoglobin is one of these and is responsible for transporting oxygen through the blood via red blood cells. Cytochromes, another type of transport protein, operate in the electron transport chain as electron carrier proteins.


3.4 Proteins

In this section, you will investigate the following questions:

  • What are functions of proteins in cells and tissues?
  • What is the relationship between amino acids and proteins?
  • What are the four levels of protein organization?
  • What is the relationship between protein shape and function?

Connection for AP ® Courses

Proteins are long chains of different sequences of the 20 amino acids that each contain an amino group (-NH2), a carboxyl group (-COOH), and a variable group. (Think of how many protein “words” can be made with 20 amino acid “letters”). Each amino acid is linked to its neighbor by a peptide bond formed by a dehydration reaction. A long chain of amino acids is known as a polypeptide. Proteins serve many functions in cells. They act as enzymes that catalyze chemical reactions, provide structural support, regulate the passage of substances across the cell membrane, protect against disease, and coordinate cell signaling pathways. Protein structure is organized at four levels: primary, secondary, tertiary, and quaternary. The primary structure is the unique sequence of amino acids. A change in just one amino acid can change protein structure and function. For example, sickle cell anemia results from just one amino acid substitution in a hemoglobin molecule consisting of 574 amino acids. The secondary structure consists of the local folding of the polypeptide by hydrogen bond formation leading to the α helix and β pleated sheet conformations. In the tertiary structure, various interactions, e.g., hydrogen bonds, ionic bonds, disulfide linkages, and hydrophobic interactions between R groups, contribute to the folding of the polypeptide into different three-dimensional configurations. Most enzymes are of tertiary configuration. If a protein is denatured, loses its three-dimensional shape, it may no longer be functional. Environmental conditions such as temperature and pH can denature proteins. Some proteins, such as hemoglobin, are formed from several polypeptides, and the interactions of these subunits form the quaternary structure of proteins.

Information presented and the examples highlighted in the section, support concepts and Learning Objectives outlined in Big Idea 4 of the AP ® Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP ® Biology course, an inquiry-based laboratory experience, instructional activities, and AP ® exam questions. A Learning Objective merges required content with one or more of the seven science practices.

Big Idea 4 Biological systems interact, and these systems and their interactions possess complex properties.
Enduring Understanding 4.A Interactions within biological systems lead to complex properties.
Essential Knowledge 4.A.1 The subcomponents of biological molecules and their sequence determine the properties of that molecule.
Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales.
Learning Objective 4.1 The student is able to explain the connection between the sequence and the subcomponents of a biological polymer and its properties.
Essential Knowledge 4.A.1 The subcomponents of biological molecules and their sequence determine the properties of that molecule.
Science Practice 1.3 The student can refine representations and models of natural or man-made phenomena and systems in the domain.
Learning Objective 4.2 The student is able to refine representations and models to explain how the subcomponents of a biological polymer and their sequence determine the properties of that polymer.
Essential Knowledge 4.A.1 The subcomponents of biological molecules and their sequence determine the properties of that molecule.
Science Practice 6.1 The student can justify claims with evidence.
Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models.
Learning Objective 4.3 The student is able to use models to predict and justify that changes in the subcomponents of a biological polymer affect the functionality of the molecules.

Teacher Support

Twenty amino acids can be formed into a nearly limitless number of different proteins. The sequence of the amino acids ultimately determines the final configuration of the protein chain, giving the molecule its specific function.

Teacher Support

Emphasize that proteins have a variety of functions in the body. Table 3.1 contains some examples of these functions. Note that not all enzymes work under the same conditions. Amylase only works in an alkaline medium, such as in saliva, while pepsin works in the acid environment of the stomach. Discuss other materials that can be carried by protein in body fluids in addition to the substances listed for transport in the text. Proteins also carry insoluble lipids in the body and transport charged ions, such as calcium, magnesium, and zinc. Discuss another important structural protein, collagen, as it is found throughout the body, including in most connective tissues. Emphasize that not all hormones are proteins and that steroid based hormones were discussed in the previous section.

The amino group of an amino acid loses an electron and becomes positively charged. The carboxyl group easily gains an electron, becoming negatively charged. This results in the amphipathic characteristic of amino acids and gives the compounds solubility in water. The presence of both functional groups also allows dehydration synthesis to join the individual amino acids into a peptide chain.

Protein structure is explained as though it occurs in three to four discrete steps. In reality, the structural changes that result in a functional protein occur on a continuum. As the primary structure is formed off the ribosomes, the polypeptide chain goes through changes until the final configuration is achieved. Have the students imagine a strand of spaghetti as it cooks in a clear pot. Initially, the strand is straight (ignore the stiffness for this example). While it cooks, the strand will bend and twist and (again, for this example), fold itself into a loose ball made up of the strand of pasta. The resulting strand has a particular shape. Ask the students what types of chemical bonds or forces might affect protein structure. These shapes are dictated by the position of amino acids along the strand. Other forces will complete the folding and maintain the structure.

The Science Practice Challenge Questions contain additional test questions for this section that will help you prepare for the AP exam. These questions address the following standards:
[APLO 1.14] [APLO 2.12] [APLO 4.1] [APLO 4.3][APLO 4.15][APLO 4.22]

Types and Functions of Proteins

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective they may serve in transport, storage, or membranes or they may be toxins or enzymes. Each cell in a living system may contain thousands of proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, polymers of amino acids, arranged in a linear sequence.

Enzymes , which are produced by living cells, are catalysts in biochemical reactions (like digestion) and are usually complex or conjugated proteins. Each enzyme is specific for the substrate (a reactant that binds to an enzyme) it acts on. The enzyme may help in breakdown, rearrangement, or synthesis reactions. Enzymes that break down their substrates are called catabolic enzymes, enzymes that build more complex molecules from their substrates are called anabolic enzymes, and enzymes that affect the rate of reaction are called catalytic enzymes. It should be noted that all enzymes increase the rate of reaction and, therefore, are considered to be organic catalysts. An example of an enzyme is salivary amylase, which hydrolyzes its substrate amylose, a component of starch.

Hormones are chemical-signaling molecules, usually small proteins or steroids, secreted by endocrine cells that act to control or regulate specific physiological processes, including growth, development, metabolism, and reproduction. For example, insulin is a protein hormone that helps to regulate the blood glucose level. The primary types and functions of proteins are listed in Table 3.1.

TypeExamplesFunctions
Digestive EnzymesAmylase, lipase, pepsin, trypsinHelp in digestion of food by catabolizing nutrients into monomeric units
TransportHemoglobin, albuminCarry substances in the blood or lymph throughout the body
StructuralActin, tubulin, keratinConstruct different structures, like the cytoskeleton
HormonesInsulin, thyroxineCoordinate the activity of different body systems
DefenseImmunoglobulinsProtect the body from foreign pathogens
ContractileActin, myosinEffect muscle contraction
StorageLegume storage proteins, egg white (albumin)Provide nourishment in early development of the embryo and the seedling

Proteins have different shapes and molecular weights some proteins are globular in shape whereas others are fibrous in nature. For example, hemoglobin is a globular protein, but collagen, found in our skin, is a fibrous protein. Protein shape is critical to its function, and this shape is maintained by many different types of chemical bonds. Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the shape of the protein, leading to loss of function, known as denaturation . All proteins are made up of different arrangements of the most common 20 types of amino acids.

Amino Acids

Amino acids are the monomers that make up proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group (Figure 3.24).

The name "amino acid" is derived from the fact that they contain both amino group and carboxyl-acid-group in their basic structure. As mentioned, there are 20 common amino acids present in proteins. Nine of these are considered essential amino acids in humans because the human body cannot produce them and they are obtained from the diet. For each amino acid, the R group (or side chain) is different (Figure 3.25).

Visual Connection

  1. Polar and charged amino acids will be found on the surface. Non-polar amino acids will be found in the interior.
  2. Polar and charged amino acids will be found in the interior. Non-polar amino acids will be found on the surface.
  3. Non-polar and uncharged proteins will be found on the surface as well as in the interior.

The chemical nature of the side chain determines the nature of the amino acid (that is, whether it is acidic, basic, polar, or nonpolar). For example, the amino acid glycine has a hydrogen atom as the R group. Amino acids such as valine, methionine, and alanine are nonpolar or hydrophobic in nature, while amino acids such as serine, threonine, and cysteine are polar and have hydrophilic side chains. The side chains of lysine and arginine are positively charged, and therefore these amino acids are also known as basic amino acids. Proline has an R group that is linked to the amino group, forming a ring-like structure. Proline is an exception to the standard structure of an animo acid since its amino group is not separate from the side chain (Figure 3.25).

Amino acids are represented by a single upper case letter or a three-letter abbreviation. For example, valine is known by the letter V or the three-letter symbol val. Just as some fatty acids are essential to a diet, some amino acids are necessary as well. They are known as essential amino acids, and in humans they include isoleucine, leucine, and cysteine. Essential amino acids refer to those necessary for construction of proteins in the body, although not produced by the body which amino acids are essential varies from organism to organism.

The sequence and the number of amino acids ultimately determine the protein's shape, size, and function. Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond , which is formed by a dehydration reaction. The carboxyl group of one amino acid and the amino group of the incoming amino acid combine, releasing a molecule of water. The resulting bond is the peptide bond (Figure 3.26).

The products formed by such linkages are called peptides. As more amino acids join to this growing chain, the resulting chain is known as a polypeptide. Each polypeptide has a free amino group at one end. This end is called the N terminal, or the amino terminal, and the other end has a free carboxyl group, also known as the C or carboxyl terminal. While the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically a polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have combined together, often have bound non-peptide prosthetic groups, have a distinct shape, and have a unique function. After protein synthesis (translation), most proteins are modified. These are known as post-translational modifications. They may undergo cleavage or phosphorylation, or may require the addition of other chemical groups. Only after these modifications is the protein completely functional.

Link to Learning

Click through the steps of protein synthesis in this interactive tutorial.


3.4 Proteins

By the end of this section, you will be able to do the following:

  • Describe the functions proteins perform in the cell and in tissues
  • Discuss the relationship between amino acids and proteins
  • Explain the four levels of protein organization
  • Describe the ways in which protein shape and function are linked

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes or they may be toxins or enzymes. Each cell in a living system may contain thousands of proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.

Types and Functions of Proteins

Enzymes , which living cells produce, are catalysts in biochemical reactions (like digestion) and are usually complex or conjugated proteins. Each enzyme is specific for the substrate (a reactant that binds to an enzyme) upon which it acts. The enzyme may help in breakdown, rearrangement, or synthesis reactions. We call enzymes that break down their substrates catabolic enzymes. Those that build more complex molecules from their substrates are anabolic enzymes, and enzymes that affect the rate of reaction are catalytic enzymes. Note that all enzymes increase the reaction rate and, therefore, are organic catalysts. An example of an enzyme is salivary amylase, which hydrolyzes its substrate amylose, a component of starch.

Hormones are chemical-signaling molecules, usually small proteins or steroids, secreted by endocrine cells that act to control or regulate specific physiological processes, including growth, development, metabolism, and reproduction. For example, insulin is a protein hormone that helps regulate the blood glucose level. Table 3.1 lists the primary types and functions of proteins.

TypeExamplesFunctions
Digestive EnzymesAmylase, lipase, pepsin, trypsinHelp in food by catabolizing nutrients into monomeric units
TransportHemoglobin, albuminCarry substances in the blood or lymph throughout the body
StructuralActin, tubulin, keratinConstruct different structures, like the cytoskeleton
HormonesInsulin, thyroxineCoordinate different body systems' activity
DefenseImmunoglobulinsProtect the body from foreign pathogens
ContractileActin, myosinEffect muscle contraction
StorageLegume storage proteins, egg white (albumin)Provide nourishment in early embryo development and the seedling

Proteins have different shapes and molecular weights. Some proteins are globular in shape whereas, others are fibrous in nature. For example, hemoglobin is a globular protein, but collagen, located in our skin, is a fibrous protein. Protein shape is critical to its function, and many different types of chemical bonds maintain this shape. Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the protein's shape, leading to loss of function, or denaturation . Different arrangements of the same 20 types of amino acids comprise all proteins. Two rare new amino acids were discovered recently (selenocystein and pirrolysine), and additional new discoveries may be added to the list.

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 alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group (Figure 3.22).

Scientists use the name "amino acid" because these acids contain both amino group and carboxyl-acid-group in their basic structure. As we mentioned, there are 20 common amino acids present in proteins. Nine of these are essential amino acids in humans because the human body cannot produce them and we obtain them from our diet. For each amino acid, the R group (or side chain) is different (Figure 3.23).

Visual Connection

Which categories of amino acid would you expect to find on a soluble protein's surface and which would you expect to find in the interior? What distribution of amino acids would you expect to find in a protein embedded in a lipid bilayer?

The chemical nature of the side chain determines the amino acid's nature (that is, whether it is acidic, basic, polar, or nonpolar). For example, the amino acid glycine has a hydrogen atom as the R group. Amino acids such as valine, methionine, and alanine are nonpolar or hydrophobic in nature, while amino acids such as serine, threonine, and cysteine are polar and have hydrophilic side chains. The side chains of lysine and arginine are positively charged, and therefore these amino acids are also basic amino acids. Proline has an R group that is linked to the amino group, forming a ring-like structure. Proline is an exception to the amino acid's standard structure since its amino group is not separate from the side chain (Figure 3.23).

A single upper case letter or a three-letter abbreviation represents amino acids. For example, the letter V or the three-letter symbol val represent valine. Just as some fatty acids are essential to a diet, some amino acids also are necessary. These essential amino acids in humans include isoleucine, leucine, and cysteine. Essential amino acids refer to those necessary to build proteins in the body, but not those that the body produces. Which amino acids are essential varies from organism to organism.

The sequence and the number of amino acids ultimately determine the protein's shape, size, and function. A covalent bond, or peptide bond , attaches to each amino acid, which a dehydration reaction forms. One amino acid's carboxyl group and the incoming amino acid's amino group combine, releasing a water molecule. The resulting bond is the peptide bond (Figure 3.24).

The products that such linkages form are peptides. As more amino acids join to this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end the N terminal, or the amino terminal, and the other end has a free carboxyl group, also the C or carboxyl terminal. While the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically a polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have combined together, often have bound non-peptide prosthetic groups, have a distinct shape, and have a unique function. After protein synthesis (translation), most proteins are modified. These are known as post-translational modifications. They may undergo cleavage, phosphorylation, or may require adding other chemical groups. Only after these modifications is the protein completely functional.

Link to Learning

Click through the steps of protein synthesis in this interactive tutorial.

Evolution Connection

The Evolutionary Significance of Cytochrome c

Cytochrome c is an important component of the electron transport chain, a part of cellular respiration, and it is normally located in the cellular organelle, the mitochondrion. This protein has a heme prosthetic group, and the heme's central ion alternately reduces and oxidizes during electron transfer. Because this essential protein’s role in producing cellular energy is crucial, it has changed very little over millions of years. Protein sequencing has shown that there is a considerable amount of cytochrome c amino acid sequence homology among different species. In other words, we can assess evolutionary kinship by measuring the similarities or differences among various species’ DNA or protein sequences.

Scientists have determined that human cytochrome c contains 104 amino acids. For each cytochrome c molecule from different organisms that scientists have sequenced to date, 37 of these amino acids appear in the same position in all cytochrome c samples. This indicates that there may have been a common ancestor. On comparing the human and chimpanzee protein sequences, scientists did not find a sequence difference. When researchers compared human and rhesus monkey sequences, the single difference was in one amino acid. In another comparison, human to yeast sequencing shows a difference in the 44th position.

Protein Structure

As we discussed earlier, a protein's shape is critical to its function. For example, an enzyme can bind to a specific substrate at an active site. If this active site is altered because of local changes or changes in overall protein structure, the enzyme may be unable to bind to the substrate. To understand how the protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary.

Primary Structure

Amino acids' unique sequence in a polypeptide chain is its primary structure . For example, the pancreatic hormone insulin has two polypeptide chains, A and B, and they are linked together by disulfide bonds. The N terminal amino acid of the A chain is glycine whereas, the C terminal amino acid is asparagine (Figure 3.25). The amino acid sequences in the A and B chains are unique to insulin.

The gene encoding the protein ultimately determines the unique sequence for every protein. A change in nucleotide sequence of the gene’s coding region may lead to adding a different amino acid to the growing polypeptide chain, causing a change in protein structure and function. In sickle cell anemia, the hemoglobin β chain (a small portion of which we show in Figure 3.26) has a single amino acid substitution, causing a change in protein structure and function. Specifically, valine in the β chain substitutes the amino acid glutamic. What is most remarkable to consider is that a hemoglobin molecule is comprised of two alpha and two beta chains that each consist of about 150 amino acids. The molecule, therefore, has about 600 amino acids. The structural difference between a normal hemoglobin molecule and a sickle cell molecule—which dramatically decreases life expectancy—is a single amino acid of the 600. What is even more remarkable is that three nucleotides each encode those 600 amino acids, and a single base change (point mutation), 1 in 1800 bases causes the mutation.

Because of this change of one amino acid in the chain, hemoglobin molecules form long fibers that distort the biconcave, or disc-shaped, red blood cells and causes them to assume a crescent or “sickle” shape, which clogs blood vessels (Figure 3.27). This can lead to myriad serious health problems such as breathlessness, dizziness, headaches, and abdominal pain for those affected by this disease.

Secondary Structure

The local folding of the polypeptide in some regions gives rise to the secondary structure of the protein. The most common are the α-helix and β-pleated sheet structures (Figure 3.28). Both structures are held in shape by hydrogen bonds. The hydrogen bonds form between the oxygen atom in the carbonyl group in one amino acid and another amino acid that is four amino acids farther along the chain.

Every helical turn in an alpha helix has 3.6 amino acid residues. The polypeptide's R groups (the variant groups) protrude out from the α-helix chain. In the β-pleated sheet, hydrogen bonding between atoms on the polypeptide chain's backbone form the "pleats". The R groups are attached to the carbons and extend above and below the pleat's folds. The pleated segments align parallel or antiparallel to each other, and hydrogen bonds form between the partially positive hydrogen atom in the amino group and the partially negative oxygen atom in the peptide backbone's carbonyl group. The α-helix and β-pleated sheet structures are in most globular and fibrous proteins and they play an important structural role.

Tertiary Structure

The polypeptide's unique three-dimensional structure is its tertiary structure (Figure 3.29). This structure is in part due to chemical interactions at work on the polypeptide chain. Primarily, the interactions among R groups create the protein's complex three-dimensional tertiary structure. The nature of the R groups in the amino acids involved can counteract forming the hydrogen bonds we described for standard secondary structures. For example, R groups with like charges repel each other and those with unlike charges are attracted to each other (ionic bonds). When protein folding takes place, the nonpolar amino acids' hydrophobic R groups lie in the protein's interior whereas, the hydrophilic R groups lie on the outside. Scientists also call the former interaction types hydrophobic interactions. Interaction between cysteine side chains forms disulfide linkages in the presence of oxygen, the only covalent bond that forms during protein folding.

All of these interactions, weak and strong, determine the protein's final three-dimensional shape. When a protein loses its three-dimensional shape, it may no longer be functional.

Quaternary Structure

In nature, some proteins form from several polypeptides, or subunits, and the interaction of these subunits forms the quaternary structure . Weak interactions between the subunits help to stabilize the overall structure. For example, insulin (a globular protein) has a combination of hydrogen and disulfide bonds that cause it to mostly clump into a ball shape. Insulin starts out as a single polypeptide and loses some internal sequences in the presence of post-translational modification after forming the disulfide linkages that hold the remaining chains together. Silk (a fibrous protein), however, has a β-pleated sheet structure that is the result of hydrogen bonding between different chains.

Figure 3.30 illustrates the four levels of protein structure (primary, secondary, tertiary, and quaternary).

Denaturation and Protein Folding

Each protein has its own unique sequence and shape that chemical interactions hold together. If the protein is subject to changes in temperature, pH, or exposure to chemicals, the protein structure may change, losing its shape without losing its primary sequence in what scientists call denaturation. Denaturation is often reversible because the polypeptide's primary structure is conserved in the process if the denaturing agent is removed, allowing the protein to resume its function. Sometimes denaturation is irreversible, leading to loss of function. One example of irreversible protein denaturation is frying an egg. The albumin protein in the liquid egg white denatures when placed in a hot pan. Not all proteins denature at high temperatures. For instance, bacteria that survive in hot springs have proteins that function at temperatures close to boiling. The stomach is also very acidic, has a low pH, and denatures proteins as part of the digestion process however, the stomach's digestive enzymes retain their activity under these conditions.

Protein folding is critical to its function. Scientists originally thought that the proteins themselves were responsible for the folding process. Only recently researchers discovered that often they receive assistance in the folding process from protein helpers, or chaperones (or chaperonins) that associate with the target protein during the folding process. They act by preventing polypeptide aggregation that comprise the complete protein structure, and they disassociate from the protein once the target protein is folded.

Link to Learning

For an additional perspective on proteins, view this animation called “Biomolecules: The Proteins.”


Contents

The first signaling scaffold protein discovered was the Ste5 protein from the yeast Saccharomyces cerevisiae. Three distinct domains of Ste5 were shown to associate with the protein kinases Ste11, Ste7, and Fus3 to form a multikinase complex. [2]

Scaffold proteins act in at least four ways: tethering signaling components, localizing these components to specific areas of the cell, regulating signal transduction by coordinating positive and negative feedback signals, and insulating correct signaling proteins from competing proteins. [1]

Tethering signaling components Edit

This particular function is considered a scaffold's most basic function. Scaffolds assemble signaling components of a cascade into complexes. This assembly may be able to enhance signaling specificity by preventing unnecessary interactions between signaling proteins, and enhance signaling efficiency by increasing the proximity and effective concentration of components in the scaffold complex. A common example of how scaffolds enhance specificity is a scaffold that binds a protein kinase and its substrate, thereby ensuring specific kinase phosphorylation. Additionally, some signaling proteins require multiple interactions for activation and scaffold tethering may be able to convert these interactions into one interaction that results in multiple modifications. [3] [4] Scaffolds may also be catalytic as interaction with signaling proteins may result in allosteric changes of these signaling components. [5] Such changes may be able to enhance or inhibit the activation of these signaling proteins. An example is the Ste5 scaffold in the mitogen-activated protein kinase (MAPK) pathway. Ste5 has been proposed to direct mating signaling through the Fus3 MAPK by catalytically unlocking this particular kinase for activation by its MAPKK Ste7. [6]

Localization of signaling components in the cell Edit

Scaffolds localize the signaling reaction to a specific area in the cell, a process that could be important for the local production of signaling intermediates. A particular example of this process is the scaffold, A-kinase anchor proteins (AKAPs), which target cyclic AMP-dependent protein kinase (PKA) to various sites in the cell. [7] This localization is able to locally regulate PKA and results in the local phosphorylation by PKA of its substrates.

Coordinating positive and negative feedback Edit

Many hypotheses about how scaffolds coordinate positive and negative feedback come from engineered scaffolds and mathematical modeling. In three-kinase signaling cascades, scaffolds bind all three kinases, enhancing kinase specificity and restricting signal amplification by limiting kinase phosphorylation to only one downstream target. [3] [8] [9] These abilities may be related to stability of the interaction between the scaffold and the kinases, the basal phosphatase activity in the cell, scaffold location, and expression levels of the signaling components. [3] [8]

Insulating correct signaling proteins from inactivation Edit

Signaling pathways are often inactivated by enzymes that reverse the activation state and/or induce the degradation of signaling components. Scaffolds have been proposed to protect activated signaling molecules from inactivation and/or degradation. Mathematical modeling has shown that kinases in a cascade without scaffolds have a higher probability of being dephosphorylated by phosphatases before they are even able to phosphorylate downstream targets. [8] Furthermore, scaffolds have been shown to insulate kinases from substrate- and ATP-competitive inhibitors. [10]

Scaffold Proteins Pathway Potential Functions Description
KSR MAPK Assembly and localization of the RAS-ERK pathway One of the best studied signaling pathways in biology is the RAS-ERK pathway in which the RAS G-protein activates the MAPKKK RAF, which activates the MAPKK MEK1 (MAPK/ERK kinase 1), which then activates the MAPK ERK. Several scaffold proteins have been identified to be involved in this pathway and other similar MAPK pathways. One such scaffold protein is KSR, which is the most probable equivalent of the well-studied yeast MAPK scaffold protein Ste5. [11] It is a positive regulator of the pathway and binds many proteins in the pathway, including all three kinases in the cascade. [6] KSR has been shown to be localized to the plasma membrane during cell activation, thereby playing a role in assembling the components of the ERK pathway and in localizing activated ERK to the plasma membrane. [12]
MEKK1 MAPK Assembly and localization of the death receptor signalosome Other scaffold proteins include B-cell lymphoma 10 (BCL-10) and MEK kinase 1 (MEKK1), which have roles in the JUN N-terminal kinase (JNK) pathway.
BCL-10 MAPK Assembly and specificity of JNK
AKAP PKA Pathways Coordination of phosphorylation by PKA onto downstream targets This family of proteins is only structurally related in their ability to bind the regulatory subunit of PKA but can otherwise bind a very diverse set of enzymes and substrates
AHNAK-1 Calcium signaling Assembly and localization of calcium channels Calcium signaling is essential for the proper function of immune cells. Recent studies have shown that the scaffold protein, AHNAK1, is important for efficient calcium signaling and NFAT activation in T cells through its ability to properly localize calcium channels at the plasma membrane [14]. In non-immune cells, AHNAK1 has also been shown to bind calcium channels with phospholipase Cγ (PLC-γ) and PKC. [1] Calcium binding proteins often quench much of the entering calcium, so linking these calcium effectors may be especially important when signals are induced by a weak calcium influx.
HOMER Calcium signaling Inhibition of NFAT activation Another example of a scaffold protein that modulates calcium signaling is proteins of the HOMER family. The HOMER proteins have been shown to compete with calcineurin to bind to the N terminus of NFAT in activated T cells. [13] Through this competition, the HOMER proteins are able to reduce NFAT activation, which also reduces the production of the IL-2 cytokine. [13] In contrast, HOMER proteins have also been shown to positively regulate calcium signaling in neurons by linking the glutamate receptor with triphosphate receptors in the endoplasmic reticulum. [14]
Pellino Innate Immune Signaling Assembly of the TLR signalosome Evidence exists that Pellino proteins function as scaffold proteins in the important innate immune signaling pathway, the Toll-like receptor (TLR) pathway. Much Pellino function is speculation however, Pellino proteins can associate with IRAK1, TRAF6, and TAK1 following IL-1R activation, indicating that they may assemble and localize components of the TLR pathway near its receptor. [15] [16]
NLRP Innate Immune Signaling Assembly of the inflammasome The NLR family is a highly conserved and large family of receptors involved in innate immunity. The NLRP (NLR family, pyrine domain-containing) family of receptors function as scaffolds by assembling the inflammasome, a complex that leads to the secretion of pro-inflammatory cytokines such as IL-18 and IL-1β. [17]
DLG1 T-cell receptor signaling Assembly and localization of TCR signaling molecules, activation of p38 DLG1 is highly conserved in immune cells and is important for T-cell activation in the periphery. It is recruited to the immunological synapse and links the ζ-chain of the T-cell receptor (TCR) to CBL, WASP, p38, LCK, VAV1, and ZAP70. [18] [19] [20] [21] This data suggests that DLG1 plays a role in linking TCR signaling machinery with cytoskeleton regulators and also suggests a role in alternatively activating the p38 pathway. However, it is unclear to whether DLG1 positively or negatively regulates T-cell activation.
Spinophilin Dendritic cell signaling Assembly of DC immunological-synapse proteins Spinophilin is involved in dendritic cell function specifically in the formation of immunological synapses. Spinophilin is recruited to the synapse following dendritic cell contact with a T cell. This recruitment seems to be important because without spinophilin, dendritic cells cannot activate T cells in vitro or in vivo. [22] How spinophilin facilitates antigen presentation in this case is still unknown though it is possible that spinophilin regulates the duration of cell contact in the synapse or regulates the recycling of co-stimulatory molecules in the cell like MHC molecules. [1]
Plant FLU regulatory protein [23] Coordination of negative feedback during protochlorophyllide biosynthesis. Assembly and localization of the pathway that turns the synthesis of highly toxic protochlorophyllide, a precursor of chlorophyll. Synthesis of protochlorophyllide must be strictly regulated as its conversion into chlorophyll requires light. FLU regulatory protein is located in thylakoid membrane and only contains several protein-protein interaction sites without catalytic activity. Mutants lacking this protein overaccumulate protochlorophyllide in the darkness. The interaction partners are unknown. The protein underwent simplification during evolution.

Huntingtin protein co-localizes with ATM repair protein at sites of DNA damage. [24] Huntingtin is a scaffolding protein in the ATM oxidative DNA damage response complex. [24] Huntington’s disease patients with aberrant huntingtin protein are deficient in repair of oxidative DNA damage. Oxidative DNA damage appears to underlie Huntington’s disease pathogenesis. [25] Huntington’s disease is likely caused by the dysfunction of mutant huntingtin scaffold protein in DNA repair leading to increased oxidative DNA damage in metabolically active cells. [24]

On some other instances in biology (not necessarily about cell signaling), the term "Scaffold protein" is used in a broader sense, where a protein holds several things together for any purpose.

In chromosome folding Chromosome scaffold has important role to hold the chromatin into compact chromosome. Chromosome scaffold is made of proteins including condensin, topoisomerase IIα and kinesin family member 4 (KIF4) [26] Chromosome scaffold constituent proteins are also called scaffold protein. In enzymatic reaction Large multifunctional enzymes that performs a series or chain of reaction in a common pathway, sometimes called scaffold proteins. [27] such as Pyruvate dehydrogenase. In molecule shape formation An enzyme or structural protein that holds several molecules together to hold them in proper spatial arrangement, such as Iron sulphur cluster scaffold proteins. [28] [29] Structural scaffold In cytoskeleton and ECM, the molecules provide mechanical scaffold. Such as type 4 collagen [30]


Protein Structure

Each successive level of protein folding ultimately contributes to its shape and therefore its function.

Learning Objectives

Summarize the four levels of protein structure

Key Takeaways

Key Points

  • Protein structure depends on its amino acid sequence and local, low-energy chemical bonds between atoms in both the polypeptide backbone and in amino acid side chains.
  • Protein structure plays a key role in its function if a protein loses its shape at any structural level, it may no longer be functional.
  • Primary structure is the amino acid sequence.
  • Secondary structure is local interactions between stretches of a polypeptide chain and includes α-helix and β-pleated sheet structures.
  • Tertiary structure is the overall the three-dimension folding driven largely by interactions between R groups.
  • Quarternary structures is the orientation and arrangement of subunits in a multi-subunit protein.

Key Terms

  • antiparallel: The nature of the opposite orientations of the two strands of DNA or two beta strands that comprise a protein’s secondary structure
  • disulfide bond: A bond, consisting of a covalent bond between two sulfur atoms, formed by the reaction of two thiol groups, especially between the thiol groups of two proteins
  • β-pleated sheet: secondary structure of proteins where N-H groups in the backbone of one fully-extended strand establish hydrogen bonds with C=O groups in the backbone of an adjacent fully-extended strand
  • α-helix: secondary structure of proteins where every backbone N-H creates a hydrogen bond with the C=O group of the amino acid four residues earlier in the same helix.

The shape of a protein is critical to its function because it determines whether the protein can interact with other molecules. Protein structures are very complex, and researchers have only very recently been able to easily and quickly determine the structure of complete proteins down to the atomic level. (The techniques used date back to the 1950s, but until recently they were very slow and laborious to use, so complete protein structures were very slow to be solved.) Early structural biochemists conceptually divided protein structures into four “levels” to make it easier to get a handle on the complexity of the overall structures. To determine how the protein gets its final shape or conformation, we need to understand these four levels of protein structure: primary, secondary, tertiary, and quaternary.

Primary Structure

A protein’s primary structure is the unique sequence of amino acids in each polypeptide chain that makes up the protein. Really, this is just a list of which amino acids appear in which order in a polypeptide chain, not really a structure. But, because the final protein structure ultimately depends on this sequence, this was called the primary structure of the polypeptide chain. For example, the pancreatic hormone insulin has two polypeptide chains, A and B.

Primary structure: The A chain of insulin is 21 amino acids long and the B chain is 30 amino acids long, and each sequence is unique to the insulin protein.

The gene, or sequence of DNA, ultimately determines the unique sequence of amino acids in each peptide chain. A change in nucleotide sequence of the gene’s coding region may lead to a different amino acid being added to the growing polypeptide chain, causing a change in protein structure and therefore function.

The oxygen-transport protein hemoglobin consists of four polypeptide chains, two identical α chains and two identical β chains. In sickle cell anemia, a single amino substitution in the hemoglobin β chain causes a change the structure of the entire protein. When the amino acid glutamic acid is replaced by valine in the β chain, the polypeptide folds into an slightly-different shape that creates a dysfunctional hemoglobin protein. So, just one amino acid substitution can cause dramatic changes. These dysfunctional hemoglobin proteins, under low-oxygen conditions, start associating with one another, forming long fibers made from millions of aggregated hemoglobins that distort the red blood cells into crescent or “sickle” shapes, which clog arteries. People affected by the disease often experience breathlessness, dizziness, headaches, and abdominal pain.

Sickle cell disease: Sickle cells are crescent shaped, while normal cells are disc-shaped.

Secondary Structure

A protein’s secondary structure is whatever regular structures arise from interactions between neighboring or near-by amino acids as the polypeptide starts to fold into its functional three-dimensional form. Secondary structures arise as H bonds form between local groups of amino acids in a region of the polypeptide chain. Rarely does a single secondary structure extend throughout the polypeptide chain. It is usually just in a section of the chain. The most common forms of secondary structure are the α-helix and β-pleated sheet structures and they play an important structural role in most globular and fibrous proteins.

Secondary structure: The α-helix and β-pleated sheet form because of hydrogen bonding between carbonyl and amino groups in the peptide backbone. Certain amino acids have a propensity to form an α-helix, while others have a propensity to form a β-pleated sheet.

In the α-helix chain, the hydrogen bond forms between the oxygen atom in the polypeptide backbone carbonyl group in one amino acid and the hydrogen atom in the polypeptide backbone amino group of another amino acid that is four amino acids farther along the chain. This holds the stretch of amino acids in a right-handed coil. Every helical turn in an alpha helix has 3.6 amino acid residues. The R groups (the side chains) of the polypeptide protrude out from the α-helix chain and are not involved in the H bonds that maintain the α-helix structure.

In β-pleated sheets, stretches of amino acids are held in an almost fully-extended conformation that “pleats” or zig-zags due to the non-linear nature of single C-C and C-N covalent bonds. β-pleated sheets never occur alone. They have to held in place by other β-pleated sheets. The stretches of amino acids in β-pleated sheets are held in their pleated sheet structure because hydrogen bonds form between the oxygen atom in a polypeptide backbone carbonyl group of one β-pleated sheet and the hydrogen atom in a polypeptide backbone amino group of another β-pleated sheet. The β-pleated sheets which hold each other together align parallel or antiparallel to each other. The R groups of the amino acids in a β-pleated sheet point out perpendicular to the hydrogen bonds holding the β-pleated sheets together, and are not involved in maintaining the β-pleated sheet structure.

Tertiary Structure

The tertiary structure of a polypeptide chain is its overall three-dimensional shape, once all the secondary structure elements have folded together among each other. Interactions between polar, nonpolar, acidic, and basic R group within the polypeptide chain create the complex three-dimensional tertiary structure of a protein. When protein folding takes place in the aqueous environment of the body, the hydrophobic R groups of nonpolar amino acids mostly lie in the interior of the protein, while the hydrophilic R groups lie mostly on the outside. Cysteine side chains form disulfide linkages in the presence of oxygen, the only covalent bond forming during protein folding. All of these interactions, weak and strong, determine the final three-dimensional shape of the protein. When a protein loses its three-dimensional shape, it will no longer be functional.

Tertiary structure: The tertiary structure of proteins is determined by hydrophobic interactions, ionic bonding, hydrogen bonding, and disulfide linkages.

Quaternary Structure

The quaternary structure of a protein is how its subunits are oriented and arranged with respect to one another. As a result, quaternary structure only applies to multi-subunit proteins that is, proteins made from more than one polypeptide chain. Proteins made from a single polypeptide will not have a quaternary structure.

In proteins with more than one subunit, weak interactions between the subunits help to stabilize the overall structure. Enzymes often play key roles in bonding subunits to form the final, functioning protein.

For example, insulin is a ball-shaped, globular protein that contains both hydrogen bonds and disulfide bonds that hold its two polypeptide chains together. Silk is a fibrous protein that results from hydrogen bonding between different β-pleated chains.

Four levels of protein structure: The four levels of protein structure can be observed in these illustrations.


The Production of a Protein

Proteins are one of the most abundant organic molecules in living systems and have an incredibly diverse range of functions. Proteins are used to:

  • Build structures within the cell (such as the cytoskeleton)
  • Regulate the production of other proteins by controlling protein synthesis
  • Slide along the cytoskeleton to cause muscle contraction
  • Transport molecules across the cell membrane
  • Speed up chemical reactions (enzymes)
  • Act as toxins

Each cell in a living system may contain thousands of different proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, polymers of amino acids, arranged in a linear sequence (Figure 1).

The functions of proteins are very diverse because they are made up of are 20 different chemically distinct amino acids that form long chains, and the amino acids can be in any order. The function of the protein is dependent on the protein’s shape. The shape of a protein is determined by the order of the amino acids. Proteins are often hundreds of amino acids long and they can have very complex shapes because there are so many different possible orders for the 20 amino acids!

Figure 1 Protein structure. The colored balls at the top of this diagram represent different amino acids. Amino acids are the subunits that are joined together by the ribosome to form a protein. This chain of amino acids then folds to form a complex 3D structure. (Credit: Lady of Hats from Wikipedia public domain)

Contrary to what you may believe, proteins are not typically used as a source of energy by cells. Protein from your diet is broken down into individual amino acids which are reassembled by your ribosomes into proteins that your cells need. Ribosomes do not produce energy.

Figure 2 Examples of foods that contain high levels of protein. (“Protein” by National Cancer Institute is in the Public Domain)

The information to produce a protein is encoded in the cell’s DNA. When a protein is produced, a copy of the DNA is made (called mRNA) and this copy is transported to a ribosome. Ribosomes read the information in the mRNA and use that information to assemble amino acids into a protein. If the protein is going to be used within the cytoplasm of the cell, the ribosome creating the protein will be free-floating in the cytoplasm. If the protein is going to be targeted to the lysosome, become a component of the plasma membrane, or be secreted outside of the cell, the protein will be synthesized by a ribosome located on the rough endoplasmic reticulum (RER). After being synthesized, the protein will be carried in a vesicle from the RER to the cis face of the Golgi (the side facing the inside of the cell). As the protein moves through the Golgi, it can be modified. Once the final modified protein has been completed, it exits the Golgi in a vesicle that buds from the trans face. From there, the vesicle can be targeted to a lysosome or targeted to the plasma membrane. If the vesicle fuses with the plasma membrane, the protein will become part of the membrane or be ejected from the cell.

Figure 3 Diagram of a eukaryotic cell. (Photo credit: Mediran, Wikimedia. 14 Aug 2002)

Insulin

Insulin is a protein hormone that is made by specific cells inside the pancreas called beta cells. When the beta cells sense that glucose (sugar) levels in the bloodstream are high, they produce insulin protein and secrete it outside of the cells into the bloodstream. Insulin signals cells to absorb sugar from the bloodstream. Cells can’t absorb sugar without insulin. Insulin protein is first produced as an immature, inactive chain of amino acids (preproinsulin – See Figure 4). It contains a signal sequence that targets the immature protein to the rough endoplasmic reticulum, where it folds into the correct shape. The targeting sequence is then cut off of the amino acid chain to form proinsulin. This trimmed, folded protein is then shipped to the Golgi inside a vesicle. In the Golgi, more amino acids (chain C) are trimmed off of the protein to produce the final mature insulin. Mature insulin is stored inside special vesicles until a signal is received for it to be released into the bloodstream.

Figure 4 Insulin maturation. (Photo credit: Beta Cell Biology Consortium, Wikimedia. 2004. This picture is in the public domain.


Watch the video: Νεφρά: βλάπτει η ζωική πρωτεΐνη; (August 2022).