MCB Unit 2 Chapter 6: Proteins

Proteins control metabolism, transport, communication, structure, division and more

  • proteins begin as polymers called amino acids. A polymer of amino acids is called a polypeptide. Once the polypeptide is folded, it becomes a protein.

  • each polypeptide is carefully folded, creating unique sections that are tailored for their particular job. If the protein unfolds, or denatures, it will no longer function. Protein structure = conformation

The central carbon atom is flanked by an amino group (H2N) and a carboxyl group (COOH)—which of the 20 side chain groups is R determines the name of the amino acid

Structure

Primary structure of a protein is the sequence of amino acids in the polypeptide chain—20 amino acids total

Amino Acids: contain central carbon atom and is bonded to four different chemical groups

  • nitrogen-containing amino group (-NH2 or -NH3+)

  • A carboxyl group (-COOH or -COO-)

  • a hydrogen atom (-H)

  • a side chain (-R) that varies between the 20 amino acids

*the letter R or X represents the variable side chain of the 20 amino acids. The side chain can be as simple as a hydrogen atom, as in the amino acid glycine , or it can be more complex, containing various functional groups such as hydroxyl, sulfur, or aromatic rings, greatly influencing the properties and behavior of the amino acid in proteins.

*look for NCC backbone to tell if protein or not

Amino acids connect to each other by condensation, which removes water molecule as a covalent bond forms between the two amino acids. The boned between amino acids is called a peptide bond. These are extremely strong bonds.

Secondary Structure

-regular patterns as polypeptide folds into final structure, folded areas represent secondary structure

Alpha Helix: twists around like a spiral staircase

Pleated sheets: wind back and forth

*the type and number of secondary structures found in a protein depend on the protein. The structure depends on the protein and the protein’s function. Unique shape of each protein depends on what it binds to as part of its job

  • secondary structures held together with hydrogen bones that form between atoms of the backbone polypeptide chain

    • The nitrogen and hydrogen atoms in the amino groups of the amino acids are joined together with polar covalent bonds—nitrogen more electronegative

    • bond between the carbon and oxygen of carboxyl group is also polar covalent

      • oxygen more electronegative

***secondary structures are determined by amino and carboxyl

3D: Tertiary structure

  • globular proteins: have overall rounded or irregular shape. Many enzymes are globular proteins

  • fibrous proteins: long and cable like. Important to structure of the cell—cytoskeletal proteins

more extensive:

Globular Proteins

  • Globular proteins are typically round / spherical in shape and have an irregular amino acid sequence

  • They have functional roles within an organism or cell (they usually carry out a specific biological activity)

  • These proteins are typically soluble in water and are usually more sensitive to changes in temperature and pH

  • An example of a globular protein is insulin (a protein hormone responsible for blood sugar regulation)

    • Insulin is composed of two polypeptide chains connected by disulphide bridges (between cysteine residues)

    • The two chains associate via non-polar surfaces (hydrophobic) while the exterior of the dimer remains hydrophilic

    • The hydrophilic exterior allows insulin to travel freely within the bloodstream to distant target sites

Fibrous Proteins

  • Fibrous proteins are typically long / narrow in shape due to a repetitive amino acid sequence

  • They have structural roles within an organism or cell (help to maintain shape by providing a scaffold)

  • These proteins are typically insoluble in water and are usually less sensitive to changes in temperature and pH

  • An example of a fibrous protein is collagen (a component of the extracellular matrix ; found in connective tissues)

    • Collagen is composed of amino acid chains bound together to form a triple helix (with covalent cross-linking)

    • It is the most abundant protein in mammals and is found in blood vessels, bones, cartilage, tendons, ligaments and skin

    • The outer surface of the collagen helix is typically non-polar (hydrophobic), allowing collagen to maintain its structure in aqueous solution

TERTIARY STRUCTURE happens between atoms in R groups

chaperone proteins: help other proteins fold correctly

Bonds between R Groups

  • covalent bonds: amino acid cysteine has a suflhydryl group (-SH) in its R group. When the R groups from two cysteines come near each other in a folded polypeptide chain, they form a covalent bond called a disulfide bridge. Strong bonds.

  • ionic bonds: Some R groups ionize in the watery environment of the cell. When ionized R groups come near each other in a folded polypeptide chain, an ionic bond forms between them. In watery environment, these bonds are very weak. Lost when a protein denatures.

  • Hydrogen bonds: some R groups contain polar covalent bonds. Weak hydrogen bones formed, dissolve when protein denatures

  • Hydrophobic interactions: some R groups are hydrophobic. In the watery environment of the cell, these R groups can get pushed together in little pockets inside the folded polypeptide chain, forming hydrophobic interaction. Weak bonds fall apart with denature

Quarternary Structure

some proteins are large and complex: many polypeptide chains. Have a quarternary structure.

  • ex hemoglobin, which carries around oxygen in blood, has 4 joined polypeptide chains, two alpha chains and two beta chains

  • collagen

held together by same bonds as tertiary structures

Protein Function

  • enzymes—make chemical reactions faster

  • reinforce structures: plasma membranes, cytoskeleton, extracellular matrix

  • transport: help molecules enter and exit the cell

  • cellular identity: glycoprotiens on cell surfaces act as marker that identifies the cell

  • motor proteins: cytoskeletal proteins power movement of flagella and allow cells to crawl

  • communication: receptors for signals sent to cell (insuln)

  • defense: antibodies: key players in immune system

  • organize within cell: chaperone proteins

  • Regulate how DNA is used by cell. DNA binding proteins control which sections of DNA are used by the cell

Enzymes

  • enzymes are catalysts that speed up chemical reactions. Cells can regulate chemistry by regulating enzymes

Enzymes are very specific. Folding of enzyme leaves a pocked called an active site, that fits only certain molecules. Molecules that fit are called substrates.

  • enzymes slightly change in response to substrate

    • bonds form between substrate and R groups of the enzyme, interaction called induced fit.

Cofactors and Coenzymes

  • cofactors are inorganic molecules such as iron or zinc.

    • iron containing heme group for example, essential part of structure.

  • coenzymes are organic molecules, often derived from vitamins.

    • in order to transfer energy from food to your cells, enzymes need transfer electrons from one molecule to another. Many of the enzymes in metabolism require a coenzyme called NAD+ to help make this transfer happen—makes this from niacin (vitamin B3)

*deficiency of vitamins and minerals lead to disease. Chronic deficiency of Vitamin B1, thiamine, impacts metabolic enzymes—leads to disease beri beri—weak muscles and neurological symptoms

Inhibiting Enyzmes

  • cells can fine tune their metabolism by controlling the enzymes that catalyze the chemical reactions in the cell

  • regulatory molecules control enzymes by binding to them and trigger slight changes in the enzyme’s shape

    • competitive inhibition: occurs when a molecule that is similar in shape to the substrate enters in the active site and gets in the way of catalysis. Regulatory molecule, called a competitive inhibitor, isn’t the right shape for the reaction to occur: just prevents real substrate from entering

    • noncompetitive or allosteric inhibition: occurs when a regulatory molecules bings to a site other than the active site of the enzyme. When enzymes fold up in their 3 dimensional structure, have more than one pocket into which their molecules can bind. Binding sights others than the active sites are called allosteric sites. Molecules that bind to allosteric sites are called noncompetitive inhibitors. Cause slight changes in shape of membrane. Changes the active site as well—substrates can no longer bind to the enzyme

  • most common way that cells regulate their metabolic pathways is through feedback inhibition or end product inhibition

    • during feedback inhibition, end product of a pathway acts as the noncompetitive inhibitor of an enzyme in that pathway. If the cell has made enough of a product, then lots of those molecules will be floating around in the cell. The simplest way to entact a slowdown in production is for that product itself to bind the allosteric site on an enzyme and shut it down. When cell uses up the product, there won’t be any excess to bind to the enzyme, and production will start up again

Membrane proteins

  • make up 50% of the plasma membrane—coordinate activity

    • transport proteins: help molecules cross the membrane—some provide open channels for small molecules to pass through, while others bind specifically to certain molecules and move them across

    • receptor proteins: receive signals on the outside of the cell and relay message to inside of the of the cell. Chemical signals that bind to receptors are called ligands

    • Adhesion proteins: form connections between the outside and the inside of the cell. On the outside of the cell, they bind to molecules in the extracellular matrix, while on the inside of the cell, they bind to cytoskeletal proteins

    • identity proteins: glycoproteins that stick out of the cell and label the cell with its function and identity

    • enzymes: associated with membranes. Catalyze reactions that are a part of processes occurring within the membrane or they be involved in passing signals from receptor proteins to the inside of the cell

DNA binding proteins

  • genetic code that contains instructions for all the structures and functions of the cell is in the form of DNA

    • DNA binding proteins can actually control which parts of the DNA are being read and which are silenced

  • like enzymes, DNA binding proteins have binding sites, called DNA-binding domains, that are shaped to fit DNA

    • alpha helices and pleated sheets within DNA-binding domains fit into the grooves of the DNA molecules. Like other proteins, DNA-binding proteins are very specific—must recognize a specific target sequence

Types/Motifs:

  • helix turn helix motifs: two alpha helices connected by a short stretch of amino acids that forms a turn between the two helices. Most common in prokaryotic DNA-binding proteins

  • zinc finger motifs: have an alpha helix and two pleated sheets held together with a zinc atom. The zinc finger motif is common in eukaryotic DNA-binding proteins that regulate transcription

  • Leucine zipper motifs: have two alpha helices that cross over each other. The two helices are held together by hydrophobic interactions between the R groups on the amino acid leucine. Common in eukaryotic DNA-binding proteins that regulates transcription