Biology

·         one of the most obvious characteristics of lipids is that they are hydrophobic

·         like carbohydrates, they are made of the atoms carbon, hydrogen, and oxygen, however, they contain less polar O-H bonds and significantly more hydrocarbon bonds

·         this is what makes them insoluble in water

·         lipids can be used to store energy (fatty tissue), building membranes and other cell parts, and as chemical signaling molecules

·         there are four groups of lipids:

        1.  Fats      - long term energy storage molecules

                         - excess sugar in animals is converted into fat and is stored in adipose cells (fatty tissue)

 - the most common form of fats are triacylglycerols (triglycerides) – three fatty acids +   one glycerol

   molecule (see Figure 16, p. 35)

- the three-carbon alcohol glycerol attaches itself to three fatty acid molecules via the hydroxyl groups of the

  glycerol

- the attachment takes place via dehydration synthesis 

- the bonds that result between the glycerol and fatty acid chains are called ester linkages

- the fatty acid molecules are approximately 16 to 18 carbons long

- fatty acid molecules can be saturated or unsaturated

- saturated means that only single bonds exist between the carbon atoms in the chain – this means that each

  carbon contains a maximum number of hydrogen atoms bonded to it – the molecule is “saturated” with

  hydrogens

- unsaturated means that at least one bond in the chain is a double bond

- fatty acids that have many double bonds in them are called polyunsaturated fatty acids

- notice that the unsaturated fatty acid is a liquid at room temperature, whereas the saturated fatty acid is solid

- the chain that contains the double bonds has a bend or “kink” in it

- when the chains are saturated, they are straight in shape

- straight chains can stack one on top of each other, closer together

- the closer they are together, the more London forces can establish, resulting in a solid consistency at room

  temperature (i.e. butter, animal lard, etc.)

- the rigid kinks in the unsaturated fatty acid tails result in chains that are further apart, resulting in fewer London

  forces between each chain – this causes the chains to stay further apart and creates a more fluid type

  substance at room temperature 

- a process called hydrogenation (adding hydrogen) can turn polyunsaturated fatty acids corn oil or canola oil

  into semisolid material like margarine or shortening

                2.  Phospholipids

                        - composed of a glycerol molecule attached to two fatty acids and a highly polar phosphate group 

                       - the phosphate group is referred to as the polar hydrophilic “head” of the molecule, while the two fatty acid

                         chains are the non-polar hydrophobic “tails” of the molecule

                        - when added to water, phospholipids form micelles 

                        - the phospholipid is an ideal building block for cell membranes because it can separate the E.C.F. and

                          cytoplasm of cells, effectively creating a barrier, while at the same time, contain many of the necessary

                          non-polar, hydrophobic proteins and special molecules within the membrane, that are crucial to healthy

                          membrane function 

                3.  Steroids

                                - compact hydrophobic molecules consisting of 4 fused hydrocarbon rings, and several different

                                  functional groups

                                -  4 important steroid molecules, cholesterol, testosterone, estradiol, and progesterone

                                - most people associate cholesterol with heart disease

                                - high concentrations of cholesterol and saturated fats in the blood lead to the development of artery

                                  hardening (atherosclerosis) and heart disease

                                - however, cholesterol is an essential molecule in the membranes of cells – it helps to maintain the fluidity

                                  of the inner membrane of the phospholipids bilayer, which is very important to its healthy function

                                - also, cells convert cholesterol into vitamin D -- needed for healthy bones and teeth, and bile – needed

                                  for the digestion of fats in the small intestine

                                - testosterone, estradiol, and progesterone are sex hormones that are vital in the development of sex

                                  traits

                4.  Waxes

                                - lipids containing long-chain fatty acids linked to alcohols or carbon rings

                                - these are hydrocarbon molecules that have a firm, yet pliable consistency

                                - this gives them a waterproof coating property – ideal for the prevention of water loss in plants (cutin -- the protection against moisture (secreted by birds to keep their feathers dry), and the

                                  construction of various structures (honeycombs built from beeswax)

 

PROTEINS

 

·         the most versatile of the 4 kinds of biological molecules

·         found in gelatin desserts, hair, antibodies, spider webs, blood clots, egg whites, fingernails!

·         the importance of proteins to the survival of living systems is emphasized by the fact that DNA’s sole function is to code for their production

·         aside from water, proteins make up approx. 50% of the mass of most cells, which further emphasizes the fact that they are extremely vital to the healthy operation of living cells

·         proteins are major players in all of the cell’s processes

·         each cell may contain thousands of different protein molecules, each performing their own specific task within the cell

·         they can:

                1.  be used as part of the cell’s structure

                                - hair and fingernails

                                - blood clots

                                - bones, skin, ligaments, and tendons

                2.  be used as catalysts (enzymes) to help biological reactions proceed properly, effectively, and efficiently

                3.  be used as cell markers on the membranes of cells for incoming messenger molecules in cell-to-cell

                    communication

                4.  be the special messenger (trigger) molecules themselves (i.e. hormones) that “turn on” a biological process

                5.  be used as antibodies to fight off foreign substances (i.e. viruses and bacteria)

                                - some proteins called immunoglobulins protect animals against foreign microbes and cancer cells

                6.  be used within the membrane of cells, within the cell itself, or anywhere outside the cell, to help transport material

                    throughout the bodies of plants and animals

                                - hemoglobin is a protein that shuttles oxygen to cells, and carbon dioxide away from cells

                                - protein carriers help to move sucrose through phloem tissue in plants, away from the leaves and to

                                  various parts of the plant

·         the most important property of a protein is its 3-dimensional shape

·         a proteins shape gives it its character and determines its specific function

·         any modification to the shape of a protein may render the protein completely useless and inactive

·         however, it is important to note that not all protein shape modifications result in the inactivity of the molecule – sometimes slight changes result in large-scale effects in function, and large changes have no effect at all in the function of the protein – each case is specific and different

·         proteins are polymers made of amino acid monomers

·         the basic structure of an amino acid is seen in 

·         all amino acids share this basic structure:

                1.  a central carbon that has the following attached to it….

                2.  an amino group

                3.  a carboxyl group

                4.  a hydgrogen atom

                5.  a variable group of atoms called a side chain, usually symbolized by R

·         there are 20 different R groups commonly found in living organisms, therefore, 20 different amino acids 

·         the simplest is glycine (gly)

·         it is important to note that amino and carboxyl groups of the amino acids are charged

·         amino acids have both acidic (carboxyl) and basic (amino) ends to them – referred to as amphiprotic

·         when dissolved in water, the carboxyl group will donate a proton (hydrogen) to the amino group, which results in one end of the molecule being negatively charged and the other positively charged

·         amino acids are organized into three different categories:  polar, non-polar, or  charged (acidic or basic)

·         the nature of the side chain in the amino acid dictates the category that the amino acid falls into

·         praline (pro) it the only amino acid that forms covalent bonds with its own amino group

·         amino acids that have carboxyl groups in their side chains are acidic

·         amino acids that have amino groups in their side chains are basic

·         in the construction of a protein, after the amino acid links are all condensed together, the chain undergoes a series of changes that result in a specific 3-D shape

·         the final shape, or conformation of a protein is determined by the specific sequence of amino acids that make up the chain

·         an amino acid polymer is called a polypeptide

·         polypeptides are made in the cytoplasm of cells through a complex process called protein synthesis

·         cells possess many copies of each of the 20 amino acids 

·         think of them as “leggo” blocks where each amino acid is a different colour and shape

·         the cells make them from simpler compounds or from compounds obtained in food

·         of the 20, 8 are essential amino acids – they cannot be made from the body, therefore must come directly from the diet

·         these are tryptophan, methionine, valine, threonine, phenylalanine, leucine, isoleucine, and lysine

·         the basic procedure in protein synthesis is the following:

                - the genetic code in the DNA of cells (and sometimes in the RNA) directs ribosomes, RNA, and special enzymes to

                  join specific aacids to one another in a particular sequence – they govern the order in which individual amino acids

                  are linked to form the polypeptide chains that fold into functional protein molecules

                - depending on which amino acids are linked together (via dehydration synthesis), various physical interactions (i.e.

                  H-bonding, dipole-dipole bonds or London forces) take place between side chains of the same polypeptide

                 sequence

                - these interactions basically cause the chain to physically bend, fold and twist into a unique 3-D shape

                - the particular 3-D shape that results at the end of the synthesis process, dictates the specific function or role that the

                  protein molecule has

 

shows how amino acids are linked together

·         the water that is removed comes from the “head” end of one amino acid (called the carboxyl terminus) and the tail end of the adjacent amino acid (called the amino terminus)

·         the bond that is formed between both amino acids is called a peptide bond

·         polypeptides range in length from a few amino acids long to over a thousand amino acids long

·         many of the proteins that have a structural function are linear in shape and are in a strand or sheet arrangement

·         most of the enzymes or other functional proteins have a 3-D character to them – called globular proteins

·         globular proteins are described in terms of 4 levels of structure:

 

1.        Primary

2.        Secondary

3.        Tertiary

4.        Quaternary

 

·        note that the first three structures apply to the individual polypeptide chains of the protein, while the fourth, quaternary structure, describes the interactions that occur between polypeptide strands in proteins composed of two or more polypeptides at the tertiary level

·         it is extremely vital that the sequencing of the amino acid is correct, since the physical interactions that occur within the same polypeptide are dictated by which amino acids exist in the chain

·         and since the physical interactions (i.e. H-bonding, etc.) dictate the over all shape of the protein, and the protein shape determines the function, a mistake in the sequencing can result in a useless protein molecule

·         it’s kind of like getting the first part to a 4 part question wrong, where each of the previous question’s answers carry over to the next question

·         an example of such a “mistake” in sequencing, resulting in a dysfunctional protein is in the making of the hemoglobin molecule

·         here, a single substitution in the sequencing of the polypeptide chain of hemoglobin, results in an abnormal hemoglobin molecule, with a modified shape

·         the deformed hemoglobin causes red blood cells to have a sickle shape, which clog in blood vessels and impede blood flow

·         the result is less oxygen distributed to cells – the condition is called sickle-cell anemia

·         after the primary structure is made, H-bonds occur between the electronegative oxygen of the carboxyl group of one peptide bond and the hydrogen of an amino group several peptide bonds away, further down the chain

·         the result is an a helix coiled structure 

·         an example of such a functional protein is a-keratin, the protein in hair

·         some globular, quaternary structure proteins, like lysozyme – a natural disinfectant in saliva, sweat, and tears, have both regions of a helix and nonhelical regions of b-pleated sheets

·         another fibrous protein that contains large amounts of b-plated sheets is the protein secreted by spiders to make their webs

·         spiders secrete it in liquid form – as it dries in air, H-bonds form in the regions of the b-pleated sheets and make the silk thread stronger than steel!

·         the tertiary structure is dictated by more H-bonds forming along the chain, as well as the hydrophobic and hydrophilic character of each to the R groups of the chain

·         the hydrophobic regions will fold into themselves, and the hydrophilic regions will be exposed to water as the protein’s structure establishes itself

·         the tertiary structure is ultimately governed by the following R group interactions:

 

1.        H-bonds between polar R groups

2.        ionic bonds between oppositely charged R groups

3.        van der Waals forces between non-polar R groups

 

·         one kind of very strong force that holds the structure of a tertiary protein is a disulfide bridge – a bond that occurs between two cysteine amino acid side chains within the same polypeptide sequence

·         the sulfur of one cysteine R group bonds with the sulfur of another cysteine R group to form the disulfide bridge, a very strong stabilizer of tertiary structure

 illustrates a tertiary structure and the interactions that may occur to help maintain its shape

·         when two or more tertiary chains come together to form a functional protein, it is called a quaternary structure 

·         some examples are:

 

1.        collagen – tough fibrous protein found in skin, bones, tendons and ligaments

2.        keratin – fibrous protein in hair and fingernails 

3.        hemoglobin – the globular protein that transports oxygen to cells and carbon dioxide away from cells 

·         hemoglobin consists of 4 tertiary polypeptide subunits “tangled” up together – two identical a-chains and two identical b-chains

·         each subunit contains its own nonproteinaceous porphyrin ring system (or heme group) containing an iron atom at the centre, which binds to the oxygen and CO2

·         however, it is important to note that the sequencing does not affect the shape alone – chemical and physical environmental factors also help to determine the final shape of the protein molecule

·         a protein is constructed in the cytoplasm, which is mostly water

·         the cytoplasm pH is mostly neutral, and its temperature is maintained between a range of tolerance

·         a protein made in unfavorable conditions, such as changes in temperature, pH, ionic concentration, may unravel or become modified

·         this change in shape due to environmental factors is called denaturation

·         heat, pH, or various chemicals break up H-bonds, ionic bonds, disulfide bridges, and hydrophobic interactions that help maintain the shape of a tertiary structure, resulting in a denatured protein that cannot carry out its biological functions

·         once the unfavorable condition is removed, the protein returns to its normal, stable, proper functioning shape

·         but, if the unfavorable condition breaks up the peptide bonds, the protein is permanently damaged

·         each protein has its own specific set of environmental conditions that it works best in

·         for example, gastrin, a digestive enzyme in the stomach, works best at pH 2 – if it moves down into the small intestine, it will become denatured since the pH there is 10

·         when a person has a prolonged fever of 39˚C or higher, critical enzymes are denatured, which could result in seizures or possibly death

·         the reason why curing meat or pickling vegetables in vinegar helps to preserve them, is because these environmental conditions denature the enzymes in the bacteria that work to spoil food

·         styling hair with excessive heat (i.e. blow drying) denatures the proteins in the hair, allowing people to straighten or curl their hair

·         the re-establishment of the tertiary structure is most likely to be successful with small protein molecules

·         however, large globular proteins fail to refold and reshape themselves spontaneously since the folds and bends in the polypeptide are too intricate and detailed

·         special proteins called chaperone proteins, are the ones responsible in helping the primary polypeptide chains to fold and develop into tertiary structures

·         research indicates that individuals who have cystic fibrosis (a genetic disorder characterized by the inability of certain proteins to move across cell membranes) lack the chaperone proteins necessary to aid in the proper formation of tertiary proteins

·         the sequence of a polypeptide can be achieved by a process called protein sequencing

·         a substance called phenylisothicyanate (PITC) was found to bind to the amino acid terminus and weaken the first peptide bond

·         then trifluoracetic acid is added and the modified amino-terminal amino acid breaks off, leaving the rest of the chain intact

·         the piece that breaks off, now called a phenylthiohydantoin (PTH) derivative, is separated from the rest of the chain, purified, and identified

·         this procedure is repeated until the rest of the polypeptide chain is completely sequenced; now done with automated sequencing equipment, and is called Edman degradation process

·         PROTEIN SYNTHESIS ACTIVITY WITH MOLECULAR MODEL KITS

NUCLEIC ACIDS

·         these macromolecules have an informational function

·         they are made of units that represent a universal code which carries genetic information that determines the structure and functional characteristics of organisms

·         all living systems use the exact same code

·         they are basically the instructions that govern the creation of an organism

·         they code for the proper construction of proteins that play a large part in the survival of an organism

·         there are two types of nucleic acids:  DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)

·         these are both nucleotide polymers

·         a nucleotide unit contains the following parts: 

1.        nitrogenous base

2.        five-carbon (pentose) sugar

3.        phosphate group

·         the difference between the DNA and RNA sugar i

·         DNA contains the sugar deoxyribose, whereas RNA contains the sugar ribose – basically, DNA lacks an oxygen on carbon 2 of the pentose sugar

·         there are five types of nitrogenous bases in nucleic acids, each falling under a specific category:

Double-Ringed Purines:

1.        adenine (A)

2.        guanine (G)

        Single-Ringed Pyrimidines:

3.        cytosine (C)

4.        thymine (T)

5.        uracil (U)

 

·         another difference between the DNA and RNA molecules, is that the DNA possesses the bases A, G, C, and T, whereas the RNA molecule has A, G, C, and U, instead of T

·         there is a slight difference between the structure of U and T

·         finally, a third difference between RNA and DNA is that the DNA molecule is most stable as a double helix structure, whereas the RNA molecule is stable in a one chain, or strand arrangement

·         a nucleic acid strand is formed by linking up nucleotides together, with the help of special enzymes

·         a dehydration synthesis occurs between the phosphate group of one nucleotide and the hydroxyl group attached to carbon 3 of the sugar of the adjacent nucleotide

·         the bond that results is called a phosphodiester bond

·         RNA coils into a helix structure, but remains single stranded

·         the two strands are held together by H-bonds between the nitrogenous bases of each DNA single strand

·         the base pairs that result because of the H-bonds holding them together, are always A with T, and G with C

·         A forms 2 H-bonds with T, and G forms 3 H-bonds with C

·         the H-bonds form in such a way that the two adjacent strands are running in opposite direction – one is right side up, and the other is up side down – thus the strands are running antiparallel to each other

·         the base pairings are always a purine with a pyrimadine

·         other very important nucleotides are those that function as important intermediates in a cell’s energy transformation

·         these are:

 

1.        ATP (adenosine triphosphate) – drives all the energy-requiring reactions in a cell

2.        GTP (guanosine triphosphate) – temporary energy carrier that transfers its energy to ATP in respiration

3.        NAD+ (nicotinamide adenine dinucleotide) – temporary energy carriers that help produce ATP

4.        FAD (flavin adenine dinucleotide) – same function as NAD+

5.        NADP+ (nicotinamide adenine dinucleotide phosphate) – intermediate energy carrier used as a coenzyme in photosynthesis

6.        cAMP (cyclic adenosine monophosphate) – used as a “second messenger” in various hormone interactions