From carbon compounds to macromolecules II

Question 1

Catalysts

Answer 1

Life would not be possible without enzymes, most of which are proteins. Enzymatic proteins regulate metabolism by acting as catalysts, chemical agents that selectively speed up chemical reactions without being consumed in the reaction. Because an enzyme can perform its function over and over again , these molecules keep the cells running by carrying out the processes of life.

Question 2

Enzymatic proteins

Answer 2

Selective acceleration of chemical reactions, e.g. digestive enzymes catalyze the hydrolysis of bonds in food molecules.

Question 3

Defensive proteins

Answer 3

They protect against diseases, e.g. antibodies inactivate and help destroy viruses and bacteria.

Question 4

Storage proteins

Answer 4

They store amino acids, e.g. casein, the protein of milk, is the major source of amino acids for baby mammals. Plants have storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo.

Question 5

Transport proteins

Answer 5

They transport substances, e.g. hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body. Other proteins transport molecules across membranes, (those are typically imbedded into the membrane).

Question 6

Hormonal proteins

Answer 6

They coordinate an organisms activates, e.g. insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration.

Question 7

Receptor proteins

Answer 7

They carry out the response of cell to chemical stimuli, e.g. receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells.

Question 8

Contractile and motor proteins

Answer 8

They are responsible for movement, e.g. motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin proteins are responsible for the contractions of muscles.

Question 9

Structural proteins

Answer 9

They are there for support, e.g. keratin is the protein of hair, horns, feathers, and other skin appendages. Insects and spiders use silk fibers to make their cocoons and webs, respectively. Collagen and elastin proteins provide a fibrous framework in animal connective tissue.

Question 10

Polypeptide

Answer 10

The bond between amino acids is called a peptide bond, so a polymer of amino acids is called a polypeptide bond.

Question 11

Protein

Answer 11

A protein is a biologically functional molecule made up of one or more polypeptides folded and coiled into specific 3D structures. Proteins are all constructed from the same set of 20 amino acids, linked in unbranched polymers.

Question 12

Amino acid

Answer 12

All amino acids share a common structure. It is an organic molecule with both an amino group and a carboxyl group. The amino end is called the N-terminal and the carboxyl end is called the C-terminal. Connecting these two groups, is a carbon dubbed the alfa-carbon, with a hydrogen on the 3rd bond. Which group sits on the 4th bond of the alfa-carbon determines which amino acid it is. That group is called the R group.

Question 13

Peptide bond

Answer 13

When two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other, they can become joined in a dehydration reaction, with the removal of a water molecule. The resulting covalent bond is called a peptide bond.

Question 14

Antibody binding

Answer 14

When using X-ray crystallography, you can see the exact match of shape between an antibody (protein in the body) and the particular foreign substance on a flu virus that the antibody binds to and marks for destruction. This is also true for receptors, which have unique shapes that only a certain molecule in the body or a drug matches to trigger it.

Question 15

Primary structure

Answer 15

The primary structure of a protein is its sequence of amino acids, (the polypeptide chain).

Question 16

Secondary structure

Answer 16

Most proteins have segments of their polypeptide chain repeatedly coiled or folded in patterns that contribute to the proteins overall shape. These coils and folds, is collectively referred to as the secondary structure. The coiled bits are alfa helix and the folded bits are beta pleated sheets.

Question 17

Alfa helix

Answer 17

A delicate coil held together by hydrogen bonding between every 4th amino acid. While some only has one stretch of alfa helix, proteins like hemoglobin have multiple stretches.

Question 18

Beta pleated sheet

Answer 18

The other main type of secondary structure is beta pleated sheets, where it is shown as an arrow pointing towards the C-terminal. Entire segments lie side by side and are connected by hydrogen bonds between parts of the two parallel segments of the polypeptide backbone. Beta pleated sheets make up the core of many globular proteins.

Question 19

Tertiary structure

Answer 19

While secondary structures involves interactions between backbone constituents, tertiary structure is the overall shape of a polypeptide resulting from interactions between the side chains (R groups) of the various amino acids. One type of interaction that contributes to tertiary structure is called (misleadingly), hydrophobic interaction.

Question 20

Hydrophobic interaction

Answer 20

One type of interaction that contributes to tertiary structure is called (misleadingly), hydrophobic interaction. As a polypeptide folds into its functional shape, amino acids with hydrophobic (nonpolar) side chains usually end up in clusters at the core of the protein, out of contact with water. The hydrophobic interaction is therefore caused by the exclusion of nonpolar substances by water molecules.

Question 21

Disulfide bridges

Answer 21

Covalent bonds called disulfide bridges may further reinforce the shape of the protein. Disulfide bridges form where 2 cysteine monomers, which have sulfhydryl groups (-SH) on their side chains, are brought together by the folding of the protein. The sulfur on one cysteine bonds with the sulfur on the other cysteine which contributes to the tertiary structure.

Question 22

Quaternary structure

Answer 22

This is the overall protein structure that results from the aggregation of these polypeptide subunits. For example, you can have 2 or more polypeptides in their tertiary structure that fit together to create a protein.

Question 23

Collagen

Answer 23

An example of a quaternary structure is collagen, which is a fibrous protein that has 3 identical helical polypeptides intertwined into a larger triple helix, giving the long fibers great strength. This suits collagen fibers to their function as the girders of connective tissue in skin, bone, tendons, ligaments and other body parts. Collagen accounts for about 40% of the protein in the body.

Question 24

Hemoglobin

Answer 24

The oxygen binding protein of red blood cells, is another example of a globular protein with quaternary structure. It consists of 4 polypeptide subunits, two of on kind (alfa) and two of another kind (beta). Both alfa and beta subunits consist primarily of alfa-helical secondary structure. Each has a nonpolypeptide component, called heme, with an iron atom that binds oxygen.

Question 25

Sickle-cell disease

Answer 25

For an example of change in primary structure, sickle cell disease is an example. It is an inherited blood disorder, caused by the substitution of valine for glutamic acid. Because it is valine instead, the fibers deform the red blood cell into a sickle shape, which greatly reduces the capacity to carry oxygen.

Question 26

Denaturation

Answer 26

Denaturation is when physical or chemical conditions affect the proteins environment, which causes it to lose its structure and thereby its function. In theory, if the proper conditions are restored, it could reassemble. Most proteins become denaturated if they are transferred from an aqueous environment to a nonpolar solvent, since the protein refolds to have its hydrophobic side outward, where it was inward before.

Question 27

X-ray crystallography

Answer 27

The method most commonly used to determine the 3D shape of a protein is X-ray crystallography, which depends on the diffraction of an X-ray beam of a crystallized molecule. Using this method, scientists can build exact models of proteins.

Question 28

Gene

Answer 28

The amino acid sequence of a polypeptide is programmed by a discrete unit of inheritance known as a gene. Genes consist of DNA which belongs to the class of compounds called nucleic acids.

Question 29

Nucleic acids

Answer 29

Nucleic acids are polymers made of monomers called nucleotides.

Question 30

Deoxyribonucleic acid (DNA)

Answer 30

There are 2 types of nucleic acids, DNA and RNA, they enable living organisms to reproduce their complex components from one generation to the next. Unique among molecules, DNA provides directions for its own replication, DNA also directs the RNA synthesis and through RNA, controls protein synthesis; this entire process is called gene expression.

Question 31

Ribonucleic acid (RNA)

Answer 31

There are 2 types of nucleic acids, DNA and RNA, they enable living organisms to reproduce their complex components from one generation to the next. Unique among molecules, DNA provides directions for its own replication, DNA also directs the RNA synthesis and through RNA, controls protein synthesis; this entire process is called gene expression.

Question 32

Gene expression

Answer 32

There are 2 types of nucleic acids, DNA and RNA, they enable living organisms to reproduce their complex components from one generation to the next. Unique among molecules, DNA provides directions for its own replication, DNA also directs the RNA synthesis and through RNA, controls protein synthesis; this entire process is called gene expression.

Question 33

Polynucleotides

Answer 33

Nucleic acids are macromolecules that exists as polymers called polynucleotides. As indicated by the name, each polynucleotide consists of monomers called nucleotides.

Question 34

Nucleotides

Answer 34

A nucleotide, in general, is composed of 3 parts, a nitrogen-containing (nitrogenous) base, a five-carbon sugar (pentose), and 1-3 phosphate groups. The portion of a nucleotide without the phosphate groups is called the nucleoside. 2 of the 3 phosphate groups on a nucleotide is lost during polymerization.

Question 35

Pyrimidine

Answer 35

Each nitrogenous base has one or two rings that include nitrogen atoms. They are called nitrogenous bases because the nitrogen atoms tend to take up H+ from solution, thus acting as bases. There are two families of nitrogenous bases, pyrimidines and purines. Pyrimidine has one 6-membered ring of carbon and nitrogen atoms. The members of the pyrimidine family are cytosine C, thymine T, and Uracil U.

Question 36

Purine

Answer 36

Each nitrogenous base has one or two rings that include nitrogen atoms. They are called nitrogenous bases because the nitrogen atoms tend to take up H+ from solution, thus acting as bases. There are two families of nitrogenous bases, pyrimidines and purines. Purines are larger, with a 6-membered ring fused to a 5-membered ring. The purines are adenine A and guanine G.

Question 37

Deoxyribose

Answer 37

In DNA the sugar is deoxyribose. The difference between the 2 sugars found in DNA and RNA is that deoxyribose lacks an oxygen atoms on the second carbon in the ring, hence the name, “deoxy” ribose.

Question 38

Ribose

Answer 38

In RNA the sugar is ribose. The difference between the 2 sugars found in DNA and RNA is that deoxyribose lacks an oxygen atoms on the second carbon in the ring, hence the name, “deoxy” ribose.

Question 39

Double helix

Answer 39

DNA have two polynucleotides or strands that wind around an imaginary axis, forming a double helix. The sugar phosphate backbones are on the outside of the helix and the nitrogenous bases are paired on the inside. A with T or U, G with C.

Question 40

Antiparallel

Answer 40

The two sugar phosphate backbones run in the opposite 5’->3’ directions from each other. This is referred to as antiparallel, somewhat like a divided highway.

Question 41

Genomics

Answer 41

Biologists often look at problems by analyzing large sets of genes or even comparing whole genomes of different species, an approach called genomics.

Question 42

Proteonomics

Answer 42

Biologists often look at problems by analyzing large sets of genes or even comparing whole genomes of different species, an approach called genomics. A similar analysis of large sets of proteins, including their sequence is called proteonomics.