BIOCHEMICAL MOLECULES 2

Proteins Proteins are made up of the elements C,H,O, and N (but in no set ratio). Proteins are chains of Amino Acids (usually 75 or more) that bond together via dehydration synthesis. 40% of the average human body is made up of protein.

Proteins The building blocks of Proteins are amino acids. There are three parts to an amino acids: Amino Group (NH2 or NH3+) acts as a base (accepts H+) Carboxyl Group (COOH or COO-) acts as an acid (donates H+) R Group: there are 20 different possible R groups

20 Different Amino Acids

Proteins Amino acids bond together via dehydration synthesis. The amino acids bind together with a peptide bond. The PEPTIDE bond is formed between C and N and one water is lost (dehydration synthesis).

Proteins When the original two amino acids form the beginning of the chain (with one peptide bond) it is called a DIPEPTIDE.

Proteins Then the chain grows to become a TRIPEPTIDE.

Proteins Ultimately you end up with a POLYPEPTIDE (which can have anywhere between 30 and 30,000 amino acids). Another name for a polypeptide is protein.

Proteins Every protein is different because the ORDER of amino acids is different. The chains come together differently due to the order of the different R groups and how they bond together. This structural difference also makes the polypeptides (proteins) functionally different.

Levels of Protein Structure primary structure: 1 This is the first level of how proteins are formed. It is simply the order of amino acids joined together with peptide bonds. It is the amino acid sequence that determines the nature and chemistry of the protein. If you change the order of amino acids, the protein may not be able to do its job.

Levels of Protein Structure secondary structure: 2 This is the second step in the formation of a protein. When a peptide bond is formed, a double bonded oxygen is left over, which is partially negative (the carboxyl group: COO-). It is attracted to the positive NH3+ amino group from other amino acids in the chain. This attraction forms a HYDROGEN BOND. This causes the chain to twist into either a spiral called an alpha helix or a beta pleated sheet.

Levels of Protein Structure tertiary structure: 3 The next interactions take place between the R groups. Some R groups are reactive and will interact with other reactive R groups in the chain. These are the amino acids that are either charged or that have a sulphur atom. The interactions ( + and – attractions and S-S bridges) will fold the molecule over into a highly specific 3-dimensional shape. It is the 3-D shape that will determine the protein’s job or role in the body.

Charged amino acids

Amino Acids with Sulphur groups

Neutral Amino Acids

Levels of Protein Structure quaternary structure: 4 The last level in protein formation is not seen in all proteins. However, some proteins are actually 2 or more molecules joined to form a functional protein. They are held together with an ionic bond. Two examples: Insulin has 2 subunits Hemoglobin has 4 subunits.

hemoglobin insulin

The Whole Process Peptide Bonds Hydrogen Bonds Interactions between R groups Ionic Bonds

Denaturation The final shape of a protein (its tertiary or quaternary structure) is very specific and enables it to do its job/function. Any change in a proteins’ shape will affect its function. Denaturation is when a protein's tertiary structure is lost. This happens when the bonds between the R groups are broken. When a protein is denatured, the protein can’t do its job and becomes useless.

Denaturation Temperature: How can this happen? There are three common ways: Temperature: High temperatures affect the weak Hydrogen bonds and can distort or break them, thus changing the structural shape. A slight increase in temperature an cause a reversible change (ie: fever). A high temperature increase can cause an irreversible change (ie: cooking an egg).

Denaturation 2. Chemicals: How can this happen? There are three common ways: 2. Chemicals: Heavy metals such as lead and mercury are large atoms that are attracted the R groups of amino acids. They bond to the R group and distort the protein’s shape. This is usually irreversible (they usually don’t want to ‘let go’).

Denaturation pH: How can this happen? There are three common ways: As some of the R groups are acids and some are bases, every protein (enzyme) has a preferred pH. Any change in pH causes a change in the acid-base R group interactions and this will change the shape of the protein.

Functions of Proteins 1. Structural: proteins help make up all structures in living things Actin & Myosin: muscle proteins Collagen: bones, teeth, cartilage, tendon, ligament, blood vessels, skin matrix Keratin: nails, hair, horns, feathers

Functions of Proteins 2. Functional: other proteins help us to keep our bodies functioning properly and to digest our food. Enzymes: are proteins that are catalysts which speed up reactions and control all cell activities. Hemoglobin

Functions of Proteins Food Source: once we have used up all of our carbohydrates and fats, proteins will be used for energy. Proteins are worth the least amount of energy per gram. Anorexia and Bolimia

Nucleic Acids Nucleic acids are acidic molecules that are found in the nucleus of cells. There are two types, both of which are very LARGE. DNA: Deoxyribonucleic Acid RNA: Ribonucleic Acid

Nucleic Acids All nucleic acids are composed of units called NUCLEOTIDES, which are composed of three sub-molecules: 1. Pentose Sugar (ribose or deoxyribose) 2. Phosphate 3. Nitrogen Base (purine or pyrimidine)

Nucleic Acids They are formed by joining their subunits together via dehydration synthesis (nucleotide + nucleotide … = nucleic acid). This is quite a complex process to which we will devote an entire unit to.

nitrogen base: purines Nucleic Acids nitrogen base: purines Adenine and Guanine Have two rings Found in both DNA and RNA Memory Trick: It’s Got 2 Be GAP

nitrogen base: pyrimidines Nucleic Acids nitrogen base: pyrimidines Cytosine, Thymine, and Uracil Have only one ring Cytosine is in both DNA and RNA Thymine is in DNA only Uracil is in RNA only Uracil Memory Trick: CUT the Pyramid

Deoxyribonucleic Acid Structure of DNA: DNA is composed of two complimentary strands of nucleotides. The two strands are joined by hydrogen bonds which form between complimentary nitrogen bases: Adenine with Thymine (A-T or T-A) They join with 2 hydrogen bonds Cytosine with Guanine (C-G or G-C) They join with 3 hydrogen bonds

Deoxyribonucleic Acid

Deoxyribonucleic Acid When DNA is first made, it is just two linear strands of nucleotides joined together. Due to internal bonding, the DNA molecule then forms into a double helix (twisted ladder).

Functions of DNA Directs and controls all cell activities by making all of the proteins and enzymes b) Contains all of the genetic information necessary to make one complete organism of very exact specifications

Ribonucleic Acid RNA is made by DNA. It is not confined to the nucleus, it moves out of the nucleus into the cytoplasm of the cell. It has Ribose sugar instead of Deoxyribose. It has no thymines, and uses URACIL’s instead. It is single stranded and therefore, no helix is formed. There are 3 types of RNA. The function of RNA is to assist DNA in making proteins.

A Comparison

Found in the nucleus only Found in the nucleus and the cytoplasm DNA RNA Nitrogen bases: A,T,G,C Nitrogen bases: A, U, G, C Sugar: deoxyribose Sugar: ribose Double stranded Single stranded 1 type 3 types: a) mRNA – messenger b) tRNA – transfer c) rRNA – ribosomal Found in the nucleus only Found in the nucleus and the cytoplasm Forms a double helix No helix DNA makes DNA DNA makes RNA Very big molecule Much smaller molecule

Adenosine Triphosphate ATP is also thought of as a nucleic acid as it has the same structure as a nucleotide. The only difference is that it has THREE phosphate groups instead of one. This is the energy source for the body.

Adenosine Triphosphate Celllular Respiration Our mitochondria turn the energy of glucose into ATP. Why is it a good molecule to store energy? It takes a lot of energy to put two phosphate molecules together (both –’ve). So when you break that bond, a lot of energy is released. C6H12O6 + 6O2 -----> 6CO2 + 6H20 + energy (heat and ATP)