Structure and function of proteins, lipids and carbohydrates

Question 1

Describe the secondary structures of protein

Answer 1

Protein can form two different structures in its secondary form. Alpha helix twist or/and beta pleated sheets. Both are held together with intramolecular hydrogen bonds that are formed between the C=O and N-H on two amino acids. The type of amino acid affects the alpha-helixes formation. Pro and Gly helix breakers (they have large bulky R Groups), Ala and Leu are helix formers. Beta sheets form anti-parallel sheets with many hydrogen bonds or extended parallel sheets where the hydrogen bonds are at more of an angle.

Question 2

Describe the primary structure of proteins

Answer 2

The primary structure of a protein is made up of a sequence of amino acids held together by peptide bonds that are formed by a condensation reaction. One carbonyl group from one amino acid comes into contact with an amino group from another amino acid.

Question 3

How many different types of amino acids are there?

Answer 3

There are 20 different amino acids, but more are formed via post transnational modifications

Question 4

Describe the tertiary structure of protein

Answer 4

The tertiary structure of a protein is the result of the folding of the already twisted polypeptide chains. There are 4 different types on bonding that cause the distinct folding in each protein. Depending on which amino acids are close to each other and their side groups depends on which different bonding can form. Hydrogen, Van der Waals (between non-polar amino acids), electrostatic (an attraction between a positive and negative ion), sulphide bond (covalent) (between two cysteine amino acids).

Question 5

Describe the difference between fibrous and globular proteins

Answer 5

With fibrous proteins there is little or no tertiary structure.

Question 6

Describe the difference between fibrous and globular proteins

Answer 6

With fibrous proteins there is little or no tertiary structure. There are long parallel polypeptide chains with cross linkages at intervals between the parallel chains, forming fibres and sheets. Most likely these will be insoluble, due to the non-polar groups on the outside of the structures. Most fibrous proteins have structural role. eg. collagen, keratin, silk, bones.

Globular proteins have folding of the polypeptide chain, with the polar groups being on the outside of the structure and the non-polar groups on the inside of the structure. The structure is circular/globular in shape. They are mainly soluble. Some also have a quaternary structure and mainly have a metabolic function. EG. Haemoglobin which is responsible for carrying oxygen tin the blood. Enzymes, hormones, antibodies.

Question 7

What are lipids?

Answer 7

Any of a class of organic compounds that are fatty acids or their derivatives and are insoluble in water but soluble in organic (non-polar) solvents. They include many natural oils, waxes, steroids (cholesterol (sterol containing), fat-soluble vitamins (such as vitamins A, D, E, and K), monoglycerides, diglycerides, triglycerides, phospholipids, and others.

Question 8

What is the structure of a triglyceride?

Answer 8

Three fatty acid chains attached to a glycerol molecule which forms the glycerol backbone. Lipids are often referred to as fats, however fats are triglycerides a subunit of lipids.

Question 9

What are the main biological functions of lipids?

Answer 9

Storing energy, signalling, and acting as structural components of cell membranes.

Question 10

Explain and describe the different organisations of phospholipids.

Answer 10

Phospholipids can form several different shapes/structures including bilayer, liposomes and micelle.

Question 11

Explain the process of fatty acid synthesis.

Answer 11

Fatty acid

Question 12

Is the cis or trans configuration of carbons in the fatty acid tails most common?

Answer 12

The cis formation is the most common in naturally formed fatty acids. Although there are some trans formations in natural formed fatty acids and partially hydrogenated fatty acids.

Question 13

Why does the type of carbon bonding (cis or trans) effect its properties?

Answer 13

Cis bonding causes bends in the fatty acid carbon chain. The more cis bonds the higher the degree of bonding. Resulting in a lower melting point.

Question 14

Typically how long is the carbon chain in a fatty acid molecule?

Answer 14

Usually a fatty acid chain consists of 4 to 24 carbon molecules.

Question 15

What is the basic structure of an amino acid? and draw the structure.

Answer 15

All amino acids have the same basic structure, only differing in the R (side group). There is a carboxyl group on one side of the carbon that is negatively charged and a amino group on the other side of the carbon that is positively charged. COOH and NH2. COO- & NH3 + when a hydrogen is removed and added respectively.

Chiral carbon is surrounded by an amino group, a carboxyl group, a hydrogen and a variable R group (side chain). It is the R group that determines the amino acid properties. Only L-isomers are found in humans.

Question 16

Explain the process in the formation of a peptide bond and draw a peptide bond.

Answer 16

The formation of a peptide bond occurs in a condensation reaction in which a H2O molecule is lost.
C=O-N-H

Question 17

What are amphipathic molecules?

Answer 17

A chemical compound possessing both hydrophilic (water-loving, polar) and lipophilic (fat-loving) properties

Question 18

Describe the structure of carbohydrates

Answer 18

Carbohydrates are made from carbon, hydrogen and oxygen molecules normally in the flowing ratio (CH2O)n. They varry in size. Those that are of biological importance include monosaccharides, disaccharides ad poloysaccharides.

Question 19

What is a protein domain?

Answer 19

A protein domain is one continuous stretch of polypeptide, which can fold into a self-contained ‘unit’ independent of any other part of the polypeptide chain. A fully-functional protein may comprise several distinct domains linked together by unstructured polypeptide.

Question 20

What amino acids are good/bad at forming alpha-helixs?

Answer 20

While some amino acids (including leucine) are very good at forming alpha helices, proline is known as a helix disrupter because of its inhibitory effect on helix formation.

Question 21

What are the key nutrients needed for the body?

Answer 21

Carbohydrates, proteins, lipids, vitamins, electrolytes and water.

Large organic molecules must be broken down before they are able to be absorbed into the circulatory system. Water, electrolytes and vitamins can be absorbed without preliminary processing, but special transport mechanisms may be involved.

Question 22

Discuss carbohydrate digestion and absorption

Answer 22

Involves salivary amylase and pancreatic alpha-amylase.

Question 23

What are the key nutrients needed for the body?

Answer 23

Carbohydrates, proteins, lipids, vitamins, electrolytes and water.

Large organic molecules must be broken down before they are able to be absorbed into the circulatory system. Water, electrolytes and vitamins can be absorbed without preliminary processing, but special transport mechanisms may be involved.

Once the large organic often insoulbe molecules have been broken down and the molecules absorbed into the blood, they will be used as an energy sources for the synthesis of ATP or used to synthesise carbohydrates, proteins or lipids.

Most ingested organic materials are made up of smaller simpler molecules. They are broken down into these molecules by digestive enzymes that break the bonds inbetween the molecules in a process called hydrolysis. Different enzymes have different target molecules e.g Carboydrase, lipases, protease. These enzymes are secreted by the salivary glands, tongune, stomach and pancrease and are mixed with the ingested material as it passes along the digestive tract. The final enzymatic step involves brush border enzymes which are attached to the exposed surface of microvilli.

Question 24

Discus protein digestion and absorption

Answer 24

Proteins are complex 3D structures that require intial mechanical digestion in the mouth. Then chemical digestion in the stomach under very low pH (due to the hydrochloric acid), which breaks down cell walls, connective tissue and kills pathogen. Pepsin is a proteolytic enzyme that is secreted from the chief cells in the stomach. It works in low pH conditions and breaks the peptide bonds between the amino acids.

In the small intestines the (duenum) there are several other enzymes that break the peptide bonds between amino acids. They each target peptide bonds between specific amino acids. These enzymes involve : trypsin, chymotrysin, pancreatic protease. This results in varrying lengths of polypeptide chains. Carboxypeptidases however has no specificity for specfic amino acids and act by cleaving peptide bonds at the end of amino acid chains resulting in free amino acids. Dipeptidases breaks dipeptides into free amino acids. They can then be absorbed by facilitated diffusion and cotransport into the interstitual fluid and then into the intestinal capillaries for transport to the liver.

Question 25

Discus lipid digestion

Answer 25

Involves pancreatic lipase and lingual lipase from the glands of the tongue. The most common lipids to digest are triglyerides which consist of three fatty acids attached to a glycerol backbone.

Question 26

Discuss different types of enzymes and their function

Answer 26

Enzymes accelerate chemical reactions. The molecules upon which enzymes may act are called substrates and the enzyme converts the substrates into different molecules known as products. Almost all metabolic processes in the cell need enzymes in order to occur at rates fast enough to sustain life. Most enzymes are proteins, although a few are catalytic RNA molecules. The latter are called ribozymes. Enzymes’ specificity comes from their unique three-dimensional structures.
Like all catalysts, enzymes increase the reaction rate by lowering its activation energy. Enzymes do not alter the equilibrium of the reaction. An enzyme’s activity decreases markedly outside its optimal temperature and pH.

Enzymes are generally globular proteins, acting alone or in larger complexes. The sequence of the amino acids specifies the structure which in turn determines the catalytic activity of the enzyme. Only a small portion of their structure (around 2–4 amino acids) is directly involved in catalysis: the catalytic site.[27] This catalytic site is located next to one or more binding sites where residues orient the substrates. The catalytic site and binding site together comprise the enzyme’s active site. The remaining majority of the enzyme structure serves to maintain the precise orientation and dynamics of the active site.

Types of inhibition: competitive (binds to the active site), non-competitve (can not be over come by substrate concentration). Uncompetitive binds to the substrate-enzyme complex.

Some enzymes do not need additional components to show full activity. Others require non-protein molecules called cofactors to be bound for activity. Cofactors can be either inorganic (e.g., metal ions and iron-sulfur clusters) or organic compounds (e.g., flavin and heme). These cofactors serve many purposes; for instance, metal ions can help in stabilizing nucleophilic species within the active site.[