Biological Molecules, To Branch or Not to Branch? Chapter 3/AP Bio

Biological Molecules , To Biological Molecules , To Branch or Not to Branch or Not to

Branch?Branch?Chapter 3/AP Bio.Chapter 3/AP Bio.

Biochemistry

Cells have molecules with low molecular weight, less than 300 and over 10,000 (high) molecular weight , but few intermediate. Large molecules are called macro, made of small molecules linked together. All are made of chains of C atoms.

C and H containing compounds are organic; organic chemistry is the study of them and biochemistry is the study of chemical reactions in living organisms. There are 4 classes of molecules that form living structures.

Sugars, amino acids, nucleotides and lipids are the main biochemicals. Sugars form long-chained polysaccharides (starch). Amino Acids form proteins, or nucleic acids like DNA (genes). Lipids (fats) don’t form long chains.

Lipids form sheets like cell membranes. Evidence that all life on earth has a common ancestor is supported by most organisms using sugar as an energy source and a million+ species use the same 20 amino acids.

Structures can be made of long chains of C atoms. C bonds to the next C by a single or double covalent bond; H atoms link to the sides. These are called hydrocarbon chains . Ex. Octane. 8 C’s and 18 H’s.

Hydrocarbon chains form rings. C can form covalent bonds at certain angles. C rings usually have 5 or 6 C atoms. If atoms of the rings are formed by alternating single and double bonds the ring is flat. If they use single bonds they bend into a chair or boat shape.

The structure of a molecule determines its function. “Functional groups” predict properties of molecules. (Functional groups are life attachments on a swiss army knife.) Combinations of functional groups determine the way a molecule acts.

Ethane has 2 C’s , 3 H’s attach to each. It is 9% of natural gas.

Ethanol is like ethane with a hydroxyl group (-OH). The extra O makes ethanol different from ethane. It is a solvent.

Ethanol is hydrophilic, dissolves readily with water because of the slight + charge of the H in the –OH group. In acetic acid the C is attached to the carboxyl group, -COOH, resulting in acetic acid like vinegar, with a sour smell and bite.

The structure of a molecule determines its function. “Functional groups” predict properties of molecules. (Functional groups are

life attachments on a swiss army knife.) If we substitute an amino group, NH2, the molecule tends to be basic , it attracts H ions forming NH3+.

H

C-C-N

H

2 other functional groups are –SH (sulfhydryl) and phosphate (PO4).

Again the properties are different. It has an ammonia smell. Most amines are bad-smelling. Cadavarine gives a rotting smell to corpses. Functional groups are shown attached to an R in the amino acids that make up proteins. (Table 3-1)

Building organic molecules requires starting with a C skeleton. Whether the molecule is hydrophobic, hydrophilic, or both, (amphipathic) depends on polarity of molecular bonds, determining how it reacts with water.

The 4 kinds of building blocks are:

1.Lipids – fatty, non-polar, do not dissolve in water.

2.Sugars-2 H’s and 1 O for every C atom.

3.Amino acids- contain both amino and carboxyl groups.

4.Nucleotides- consist of a nitrogen ring, a sugar, and a phosphoric acid.

3 of these form long chains.

1. Sugars can form polysaccharides.

2. Nucleotides can form nucleic acids.

3.Amino acids can form proteins.

Lipids do not form long chains.

Proteins and nucleic acids form unbranched chains but can be complex as they coil and fold into 3-D shapes. These shapes determine their function.

Polysaccharide chains can have many branches. Bonds that hold macromolecules together have to be strong enough to not fall apart but can break easily when catalyzed.

Enzymes make or break chemical bonds. Removing 2 H’s and 1 O from between 2 molecules joins them in a reaction called a dehydration condensation reaction (1 molecule of H2O is removed). They can be broken by adding one molecule of H2O, hydrolysis.

Glycosidic bonds join sugars. Peptide bonds join amino acids. Triglycerides are formed by hydrolysis. See p.50 for a description of hydrophilic and hydrophobic ends of the phospholipid cell membrane. Hydrophobic tails of phospholipids form an oily interior and hydrophilic ends turn outward. Outer and inner membranes have this structure.

Steroids- hydrocarbon chains with 4 rings form hormones. The starting one is cholesterol. With 4 rings, different functional groups can attach causing variations in their effects. Cells can make testosterone from progesterone. Estrogen is made from testosterone.

Some sugars form short chains (oligosaccharides). The longest are polysaccharides – including thousands of simple sugars, starch in bread, cellulose in wood.

Ribose and deoxyribose are 5 C sugars in DNA and RNA. All sugars and polysaccharides are carbohydrates, 1 molecule of water for every C. H atoms are on one side and hydroxyl (-OH-) groups on the other side. Most dissolve well in water.

Cholesterol

is not bad for you! You can’t live without it. It is on the outer membranes of cells. It comes from the liver and diet. 180mg./deciliter is average for young people but you get more as you age. It travels in lipoprotein complexes.

Low density lipoproteins (LDL’s) deliver cholesterol to cells. HDL’s remove cholesterol to the liver where it forms bile. HDL’s are good because they get rid of LDL’s.

Excess LDL’s can build up in arteries forming deposits called plaques. Plaques cause hardening of the arteries by atherosclerosis which increases blood pressure and risk of heart attack. Smoking reduces HDL’s. Many other variables are related to heart attack risk.

Sugar is a basic energy source for all organisms. Simple ones are monosaccharides, (3 to 9 C’s). Glucose and fructose have 6 C’s. Cells link these by dehydration condensation formed by glycosidic bonds. 2 sugars form a disaccharide (sucrose is table sugar).

Monosaccharides and disaccharides store energy for a few hours. Polysaccharides (starches) can store energy for weeks or years. Glucose is blood sugar. Most biochemical reactions are related to glucose. Making glucose stores energy. Linking chains of glucose stores energy as glycogen.

Glycogen has short branches so enzymes can easily release glucose as needed. Plants store starch as amylopectin or as amylase. Other polysaccharides are chitin (makes up the exoskeleton of arthropods). Wood, paper, and cotton are cellulose.

Properties of polysaccharides depend on the kind of sugar and how they are joined. The most important to us are: starch, cellulose, and glycogen. Glycogen is released as glucose as we need it, starch is broken into glucose by digestion, but cellulose is indigestible to us and forms fiber.

Cellulose has straight chains of glucose which supports plants. Animals that digest cellulose use microorganisms that secrete enzymes that break it down. So grazing animals get lots of nutrients from grass but we do not.

Cellulose that is good for our digestion are oligosaccharides, short chains. They can attach to proteins forming glycoproteins found on cell membranes and help cells to remember one another. Inside cells glycoproteins help tell a cell where to send new proteins.

Nucleotides are building blocks of DNA and RNA. They have 3 parts: sugar (ribose or deoxyribose), one or more phosphate groups and a nitrogen base. Most cells use 5 bases; 2 – ring purines (adenine and guanine), and 1- ring pyrimidines (thymine, cytosine, and uracil).

Thymine has a methyl group,CH3, not found in uracil. Nucleotides with 1, 2, or 3 phosphates as in ATP (adenosine triphosphate) play a central role in production of energy.

ATP is the immediate source of energy for all biological processes. Energy from breakdown of glucose is stored in ATP and can be released by hydrolysis of a phosphate bond.

Nucleotides of nucleic acids are linked together by phosphodiester bonds into long unbranched chains such as in DNA or RNA. DNA contains genes. RNA is an interpreter.

Polypeptides are made of amino acids joined by peptide bonds that form proteins. Proteins perform thousands of functions: support bones, transport molecules, regulate passage of ions.

Humans have about 80,000 kinds. Collagen is the most common. It strengthens connective tissue in tendons, bones, muscle, and skin.

Elastin makes the skin stretchy. Keratin toughens hair and nails. Hemoglobin binds to oxygen. Proteins act as hormones, antibodies, and poisons. Glycoproteins on cell surfaces help other molecules to recognize them, important in the immune response.

Proteins like neurotransmitters make nerve cells communicate. Enzymes speed up chemical reactions. Each protein is made of chains of amino acids. The chain is a polypeptide. A protein can be a simple chain or can be 3,500 or more amino acids long.

Each amino acid has a carboxyl group, -COOH and an amino group, NH2. They are attached to the same C called the alpha-carbon which also attaches to the R group. In most amino acids the alpha - carbon, carboxyl group, and amino groups are the same. (not proline).

The R groups are different, varying in functional groups and length. R groups’ side chains determine the properties of the amino acid and then the polypeptide.

Each amino acid in a chain is oriented the same way as the others , amino, carboxl, amino, carboxyl… forming a backbone. The R groups hang off the side not involved in peptide bonds but may interact with each other.

All proteins have different shapes related to function. They are classified as globular like hemoglobin. Fibrous proteins form keratin (hair), and collagen (skin).

Proteins may have up to 4 levels of structure.

1.The primary structure is the amino acid sequence of the peptide chain. 2.The secondary structure is its shape.

Ex. of secondary. The alpha - Helix is twisted like a phone cord. Another is beta - pleated sheets with the pleats held together by sticky H bonds. A collagen helix consists of 3 polypeptide chains wound around each other.

3.The tertiary structure (conformation) is the 3 dimensional folding of the entire polypeptide chain into another shape.

4.The quaternary structure is the fitting together of 2 or more folded chains.

Even changing one amino acid can destroy a protein’s biological activity. In hemoglobin substituting valine for glutamic acid produces defective hemoglobin that causes sickle cell anemia.

Polypeptides are linear, not branched like polysaccharides. But they can coil into helices, sheets, or balls and act like a single huge molecule. The alpha helix, beta sheet and alpha collagen allow them to function in an organism as building materials.

The alpha-helix and beta-structure are made of repeating sequences so globular proteins are more flexible as they fold. They have more diverse roles than fibrous proteins. Globular proteins can be hormones, antibodies, or enzymes.

Tertiary folding is caused by interaction of side chains. Side chains may be polar, non polar, proton donors or acceptors. They cause the 3 –D structure that is stable in certain chemical environments. Changes in a chemical environment can change the shape and activity of a protein.

Seconds after it forms a polypeptide takes shape determined by the sequence of the amino acids.

A biochemist, Anfinsen, studied the enzyme ribonuclease that breaks bonds in RNA. First he chemically interferred with hydrogen bonds and hydrophobic interactions changing the enzyme’s shape and ability to function. (denatured)

After removing ribonuclease from the altered environment it again became active. So the right amino acid sequence and right chemical environment are all that is needed to determine the enzyme’s 3-D shape.

Anfinsen showed that there are obstacles to protein- folding. In a cell, concentration of protein and other molecules is high. Peptide chains form bonds with other peptides (promiscuous interactions). To prevent this some enzymes and special proteins called chaperones bind to new polypeptides and help them fold to the correct shape.