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  Proteins

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

  •

  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

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  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.

  Types and Functions of Proteins

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  , 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.

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  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

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  Protein Types and Functions

  Type

  Examples

  Functions

  Digestive

  Enzymes

  Amylase, lipase, pepsin,

  trypsin

  Help in digestion of food by catabolizing

  nutrients into monomeric units

  Transport

  Hemoglobin, albumin

  Carry substances in the blood or lymph

  throughout the body

  Structural

  Actin, tubulin, keratin

  Construct different structures, like the

  cytoskeleton

  Hormones

  Insulin, thyroxine

  Coordinate the activity of different body systems

  Defense

  Immunoglobulins

  Protect the body from foreign pathogens

  Contractile

  Actin, myosin

  Effect muscle contraction

  Storage

  Legume storage proteins,

  egg white (albumin)

  Provide nourishment in early development of

  the embryo and the seedling

  Table 3.1

  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

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  . All proteins are

  made up of different arrangements of the same 20 types of amino acids.

  CHAPTER 3 | BIOLOGICAL MACROMOLECULES 91

  Amino Acids

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  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 (NH

  2

  ), 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 (

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  ).

  Figure 3.22

  Amino acids have a central asymmetric carbon to which an amino group, a carboxyl

  group, a hydrogen atom, and a side chain (R group) are attached.

  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 amino acids present in proteins. Ten 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 (

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  ).

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  Figure 3.23

  There are 20 common amino acids commonly found in proteins, each with a

  different R group (variant group) that determines its chemical nature.

  Which categories of amino acid would you expect to find on the surface of a soluble

  protein, 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 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 (

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  ).

  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

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  , 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

  (

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  ).

  CHAPTER 3 | BIOLOGICAL MACROMOLECULES 93

  Figure 3.24

  Peptide bond formation is a dehydration synthesis reaction. The carboxyl group of one

  amino acid is linked to the amino group of the incoming amino acid. In the process, a molecule of

  water is released.

  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,

  phosphorylation, or may require the addition of other chemical groups. Only after these modifications is

  the protein completely functional.

  Click through the steps of protein synthesis in this

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• 3.4 Proteins (CNX OpenStax)
• 3.5 Nucleic Acids (CNX OpenStax)

Learning Objectives

1. Draw the basic structure of an amino acid, and explain the relationships between amino acids, proteins, and peptide bonds.
2. Describe the levels of organization of protein in terms of its primary, secondary, tertiary, and quaternary structures.
3. Define the term nucleic acid, give the subunits of a nucleotide, and name the two main types of nucleic acids found in living organisms.
4. Explain why ATP is important and describe its general structure.

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.

Monomers bond together through a dehydration synthesis reaction between adjacent amino and carboxyl groups to yield a peptide bond.

How amino acids interact with each other and the environment

Use the following simulation to test how a polypeptide chain with fold based on the type of solution it is in and the composition of the amino acids.

• Protein Folding Simulation (CC BY 4.0 Concord Consortium)

Protein Structure

• Primary Structure (1°): The sequence of amino acids read from the Amino or N-terminal end of the molecule to the Carboxyl or C-terminal end
  • Tyr-Cys-Arg-Phe-Leu-Val-….
• Secondary Structure (2°): local three-dimensional structures that form from interactions of amino acids, like hydrogen bonding
  • Alpha Helix – coils  occurring from the H-bonds between N-H and C=O groups along the backbone of the protein
    • 

      Side view of α-helix illustrating H-bonds in magenta between carboxyl oxygen (red) and amine nitrogen (blue) Credit: WillowW [CC-BY-SA 3.0]

      

      Top-down view of an α-helix Credit: WillowW [CC-BY-SA 3.0]

    • 

      Side view of ribbon diagram of α-helices traversing a membrane. Credit: Andrei Lomize [CC-BY-SA 3.0]

  • Beta Sheets – laterally connected strands or sheets of amino acids occurring from the H-bonds between N-H and C=O groups along the backbone of the protein
    • 
    • 

      Ribbon diagram of β-sheets

• Tertiary structure (3°): overall 3-D structure of the peptide chain
• Quaternary structure(4°): multimeric protein structure from assembling multiple peptide subunits

Disruption to Structure

The weak interactions that govern the secondary and tertiary structure of proteins can be disrupted through the application of energy, removal of the water environment, alteration of salt content or changes in the pH. The unfolding or misfolding of proteins from these disruptions is called denaturation. Changes in salt and pH will disrupt the charges on amino acids to disrupt structure. Since eggs are mostly protein and water, it is understood how frying an egg can push the water out (as steam) to leave behind a a congealed gelatinous solid. Similarly, cooking generally works to denature proteins. As such, there are methods of cooking that rely , not only on heat, but on dehydration or curing (using salts) and changes in pH (using acids or bases).

Diversity of Proteins

 

Learn more about complexity of protein structures at the Protein Data Bank

Protein Function

Interactive Animation @ PDB :https://cdn.rcsb.org/pdb101/molecular-machinery/

1. Enzymes
   • Help “catalyze” chemical reactions
2. Structural Proteins
   • Give support, strength, flexibility
   • Examples: collagen, elastin, keratin
3. Storage Proteins
   • Storage of amino acids, for building proteins later or energy
   • Examples: egg albumin (ovalbumin), Casein (in milk)
4. Transport Proteins
   • Examples: Hemoglobin (O₂), H⁺ pump
5. Signaling Proteins
   • Hormonal Proteins and receptor proteins
   • Example: Insulin and Insulin receptor
6. Motor Proteins
   • Actin and myosin perform muscle contraction
7. Immune Defense Proteins
   • Antibodies help fight infection

Nucleic Acids

Nucleic acids are polymers that were named because they were first described in the nucleus. There are 2 types, deoxyribonucleic acid and ribonucleic acid (DNA & RNA). DNA is the storage vessel for genetic information and RNA largely plays a role in expressing this genetic information.

Their monomers are called nucleotides, which are made up of individual subunits. Nucleotides consist of a 5-Carbon sugar (a pentose), a charged phosphate and a nitrogenous base (Adenine, Guanine, Thymine, Cytosine or Uracil). Each carbon of the pentose has a position designation from 1 through 5. One major difference between DNA and RNA is that DNA contains deoxyribose, and RNA contains ribose. The discriminating feature between these pentoses is at the 2′ position where a hydroxyl group in ribose is substituted with a hydrogen.

The following video illustrates the structure and properties of DNA

DNA is a double helical molecule. Two anti-parallel strands are bound together by hydrogen bonds. Adenine forms 2 H-bonds with Thymine. Guanine forms 3 H-bonds with Cytosine. This AT & GC matching is referred to as complementarity. While the nitrogenous bases are found on the interior of the double helix (like rungs on a ladder), the repeating backbone of pentose sugar and phosphate form the backbone of the molecule. Notice that phosphate has a negative charge. This makes DNA and RNA, overall negatively charged.

ATP

• ATP (adenosine triphosphate) is composed of adenine, ribose, and three phosphates
• In cells, one phosphate bond is hydrolyzed – Yields:
  • The molecule ADP (adenosine diphosphate)
  • An inorganic phosphate molecule
  • Energy used for work in the cell

Additional Resources

• Fats and Proteins http://www.visionlearning.com/en/library/Biology/2/Fats-and-Proteins/62

Test Yourself

• Macromolecules Quiz
• Macromolecules Flashcards