Molecular Biology and Biochemistry

 

6.1 Molecular Biology and Biochemistry

a. Demonstrate that a small subset of elements (C, H, N, P, S, H) makes up most of the chemical compounds in living organisms by combining in many ways
b. Recognize and differentiate the structure and function of molecules in living organisms, including carbohydrates, lipids, proteins, and nucleic acids
c. Describe the process of protein synthesis, including transcription and translation
d. Compare anaerobic and aerobic respiration
e. Describe the process of photosynthesis in terms of light-induced reactions and the Calvin Cycle

 

 

1. Demonstrate that a small subset of elements (C, H, N, P, S, H) makes up most of the chemical compounds in living organisms by combining in many ways

 

The drawing of the periodic table above shows all the stable atoms discovered to the present. It is interesting to note that of all the atoms in this table only six are those atoms that make up all living things. They are in red above... Hydrogen (H), Carbon (C), Nitrogen (N), Oxygen (O), Phosphorous (P) and Sulfur (S). They make up the biotic world in which we live. The rest are part of the abiotic world. Many of the abiotic elements work in conjunction with living things to help them do their job better. An example is that of enzymes and proteins that require copper(some serum proteins) or iron (hemoglobin) to help these proteins function appropriately.

We cannot see an individual atom with our eyes. If there were billions and billions and billions of atoms of the same kind together in one small area, then we would be able to see it. A copper wire is an element THAT IS COMPOSED MILLIONS OF INDIVIDUAL COPPER ATOMS. We can see and hold elements in our hand.

Elements are substances that are made up of billions of atoms of the same kind. An atom is the smallest part of matter. There are more than 109 elements known today. Copper (Cu) above is an example of one of the elements.


Compounds are substances made of more than one kind of atom or element. There are 2 kinds of compounds: 1) ionic compounds (like table salt, NaCl) which are part of the abiotic world and 2) molecular compound or the molecules of life and food (like sugar, C6H12O6).

 

Ionic compounds are made of two charged elements or atoms:

1. Positively (+) charged elements or atoms. Sodium (Na) ions are positively charged. The atoms in sugar cannot be separated into a positively charged ion as sodium chloride can. Positively charged ions are called CATIONS.

2. Negatively (-) charged elements or atoms. Chloride (Cl)) ions are negatively charged. Sugar cannot be separated into a positively charged ion sodium chloride can. Negatively charged ions are called ANIONS.

-ionic compounds are called salts.

-in solid form, salts are held together because opposite charges attract each other.

 

 

 

If one could look at a highly magnified crystal of table salt it would look like the drawing to the left. One tiny grain of salt contains millions of cubic units like those seen to the left. Scroll down to see details of ONE cubic unit.

 

 

 

 

 

 

 

This is a single cubic unit of solid sodium chloride salt. It contains 14 chloride ions (anions) and 13 sodium ions cations). The sodium (NA) and chloride (CL) ions are held together because they have an opposite charge. There are millions of these cubic units in each small sodium chloride crystal. The larger green spheres represent chloride ion and the smaller blue spheres represent the positive sodium ion.

 

 

 

 

 

Molecular Compounds

Text of drawing to the left: MOLECULAR COMPOUNDS (EXAMPLES) H2O = water, carbon containing compounds of blood, skin, food, animals, plants, fish, some toxic chemicals, products of plants C6H12O6 = sugar (glucose), gases in our atmosphere.

 

-Molecular compounds are made up of from 2 to thousands of elements or atoms that ARE NOT charged (NO cations or anions)

-Elements or atoms in molecular compounds are carbon and hydrogen (most often) and many times oxygen. Other elements such as sulfur, phosphorous and others are common in some kinds of molecular compounds. These compounds are held together by covalent bonds (sharing of electrons) rather than by the opposite charges of the ions in the salt.

-Examples of some molecular compounds are shown in the drawing above. These are sugar (glucose), gases in our atmosphere, toxic chemicals, the components of foods and all living things on the earth, including most of the components of blood and water.

 

 

 

The formulas to the left represent gases with covalent bonds. Those are nitrogen (N2), oxygen (O2) and bromine (Br2). Covalent bonds occur when electrons between their atoms are shared. In this manner, atoms can be linked one to another in chains and branches.

 

 

 

 

 

 

 

Now you see the electron "dot" formulas of the same three gasses. The red and blue dots represent electrons. The 'red' electrons come from the 'red' atoms and the 'blue' electrons come from the 'blue' atoms.

Notice how an electron from each of the atoms of each pair (represented by red and blue dots) are in between the atoms. This is what a covalent bond is; the sharing of one or more electrons from one atom with one or more electrons from another atom right next to it.

When there is only a single pair of electrons shared (such as Br2) the bond is called a single covalent bond. When there are two pairs of electrons shared (such as O2), the bond is called a double covalent bond. When there are three pairs of electrons shared (N2), the bond is called a triple covalent bond.

 

 

 

Another way of showing covalent bonds when writing chemical formulas is to use lines (drawing to the left). A single covalent bond (one pair of shared electrons) is shown by a single line (Br2) (bottom molecule). The triple covalent bond (three pairs of shared electrons) is also seen to the left for N2 (top molecule). The double covalent bond (two pairs of shared electrons) is seen for O2 (middle molecule). Although most of the covalent bonds formed come from electrons from different atoms, a few take the shared pair from one atom only. You will learn about this kind of covalent bond when you study about acids.

 

 

 

The molecule to the left is made of five carbon atoms linked together by single covalent bonds. Its formula is C5H10O.

The first carbon atom to the left also has three hydrogen atoms attached to it by single covalent bonds. The next three carbon atoms each have two hydrogens linked by a single covalent bond. The last carbon (above) has one hydrogen (single covalent bond) and one oxygen atom (double covalent bond) attached to it, in addition to a carbon atom.

Notice how the sharing of electrons takes place by following the color-coding of the electrons and atoms. All of the atoms above and on previous pages have no electric charge like ions do. They are basically neutral. The line representation of this molecule is seen below.

The six elements can combine in many ways to form molecules with different functions and purposes. Several of these are described below.

For those studying Standard 12.1 "Structure and Properties of Matter" Click here to return to your study about atoms

THOSE STUDYING MOLECULAR BIOLOGY AND BIOCHEMISTRY, CONTINUE BELOW.

 

2. Recognize and differentiate the structure and function of molecules in living organisms, including carbohydrates, lipids, proteins, and nucleic acids...

 

DNA and RNA are present in small quantities in any living thing, but their importance is great.

-- Nucleic acids are polymers (chains) of individual nucleotides.

-- Each nucleotide is made of three things

a) a sugar,

RNA Sugar, Ribose (left)

DNA Sugar, Deoxyribose (right)...........................

Sugar molecules are an important part of the DNA and RNA molecule and serve as part of the structure to hold the strands of DNA or RNA together.

One of the differences between RNA and DNA is the absence of an oxygen molecule (O) in the DNA sugar (see red arrow and compare to the same position on the RNA ribose molecule to the left.)

Deoxy means without oxygen. Deoxyribose is the name of the DNA sugar.

The single blue lines (thick and thin) between atoms of the sugars represent the covalent bonds that hold the sugars together. The pictures above represent a three dimensional view of the sugars. The O in the back of the molecule is smaller than the O's at the front of the molecule. That is why the covalent bonds (blue lines) at the back O looks thinner than those that are closer to the front of the drawing.

The HOCH2 molecules also have covalent bonds between them but it would be too crowded to put them into the picture.

 

b) a nitrogen base

 

NITROGEN BASES

 

 

 

Adenine and guanine are nitrogen bases in both DNA and RNA. They are called "purines"

-These chemicals are bases because of the high content of nitrogen (N) atoms.

 

 

 

 

 

1) Cytosine (C) is a nitrogen base in DNA and RNA.

2) Thymine (T) is a nitrogen base in DNA only.

3) Uracil (U) replaces thymine in RNA. It only is found in RNA.

These are called pyrimidines.

 

and

 

 

 

 

c) a phosphate group.

PO4 - This is the formula for phosphate. In DNA and RNA the oxygen's have hydrogen attached to some of them. (See drawing to the left) The red line next to two of the oxygen atoms represent the negative charge from one electron being available for covalent bonding with other molecules.

The phosphate molecule and the sugar molecule form the sides of the ladder called DNA. Just like the sides of the ladder hold the steps together, the sugar and phosphate complex hold the DNA "steps together". The steps are made of nucleotides. The word nucleotide will be described shortly.

-- When the sugar, nitrogen base and phosphate are put together, they are called a nucleotide. When put together. The nucleotides, make up the DNA (deoxyribonucleic acid) or RNA (ribonucleic acid). DNA contains all of the genetic material of a species and serves as a template to make different kinds of RNA that are used to help build the body.

 

2. Cell membrane (Above)- Specialized structures surrounding cells and cell organelles. These membranes are made of lipids and proteins and are selectively permeable. This means that they allow some chemicals to enter or leave the cell but not other chemicals.

  • Under a regular microscope the cell membranes appear like a "single line". Greatly magnified by an electron microscope, they show two layers separated by a space (see above).
  • Scientists first said that the membrane was like a sandwich. The protein was the "bread" surrounding the inside of the sandwich of lipids. This did not explain the selective permeability of membranes.
  • The model was changed (see drawing, upper right). Scientists kept the lipids in the center (orange color) and the round blue spheres covering the internal lipids. They put the specialized proteins (proteins to be explained later in this section) perpendicular (at 90 degrees angle) to the membrane in between the lipid molecules. These proteins go through the entire membrane. These membrane proteins may be lipoproteins (proteins that have lipids chemically attached to them).

See below to learn more about lipids and how they can cause selective permeability in cell membranes.

 

 

Lipids, Cell Membranes and Selective Permeability

 

Selective Permeability

I.. Diffusion

II. Semi-permeable Membranes:

If animal or vegetable tissues are dissolved by ethanol, ether, gasoline, benzene, chloroform, petroleum ether, etc. a portion of the tissue "dissolves" or becomes soluble. The solvents described above cannot dissolve water.

THE CHEMICALS THAT DISSOLVE IN THE SOLVENTS ABOVE ARE KNOWN AS LIPIDS.

MEMBRANE LIPIDS ARE DIVIDED INTO THE FOLLOWING CATEGORIES

I. Fatty acids

FATTY ACIDS

  • Fatty acids are part of phospholipids (see phospholipids).
  • Fatty acids are long chains of carbon atoms (C) to which hydrogen atoms (H) are attached.
  • All attachments occur by covalent bonds (sharing of electrons between atoms). These bonds hold the carbon atoms together as well as the hydrogen and the carbon atoms together.
  • Fatty acids end in the chemical group COOH (O= oxygen)
  • The single lines represent a single pair of electrons that are shared between the atoms and hold the atoms together. This is a single covalent bond. Two single lines represent the two pairs of electrons shared between the atoms that hold them together. This is a double covalent bond. You will learn more about these bonds later.

    The carbon chains get longer by adding a single carbon atom and two hydrogen atoms (CH2) in between the CH3 and the COOH. The two hydrogen atoms are above and below the C in the detailed drawing.

     

    II. Lipids containing glycerol

     

     

    PHOSPHOLIPIDS

     

    Neutral fats are made of fatty acids linked to glycerol through covalent bonding of the carbon atom of the glycerol and the oxygen atom of the fatty acid. These are not present in cell membranes.

     

    The actual structure of lecithin is much more complicated. Each molecule of lecithin bears a positive electric charge around the nitrogen (N) atom and a negative electric charge around the lower oxygen atom of the phosphate molecule. Cephalin does not contain the triple covalent bond or the three (CH3) groups. Instead, the positively charged nitrogen group is present as NH3 only.

     

    III. Lipids not containing glycerol

     

     

    STEROIDS

    Cholesterol has both chains and rings of carbon atoms linked together by covalent bonds. The hydrogen atoms attached to each of the carbon atoms in the ring structures are not shown because of lack of space.

     

    IV. Lipids combined with other classes of compounds

    LIPOPOLYSACCARIDES

     

     

    Glycolipids (and glycoproteins) with different carbohydrate chains tell doctors whether we have the A, B, O blood groups on the surfaces of our red blood cells. This is important when we need blood transfusions.

    The glycoproteins also may participate in the transport of chemicals across the membrane. The exact role is not known. The carbohydrate chains usually point to the outside surface of the cell membrane.

     

     

     

    SELECTIVE PERMEABILITY

    Cell Membrane Model below modified and adapted from Scott, Forseman Biology, Copyright 1980

    Text for above picture: Cell membranes are a lipid bilayer- The hydrophobic (water repelling) end of the lipid molecules is directed towards the interior of the membrane. The hydrophilic (water loving) end of the lipid molecules is directed towards the inside or outside of the cell. Hydrophobic area is red arrow. Hydrophilic area are blue arrows.

     

    The glycolipids (the molecules that determine the surface properties of the cell) point toward the outside surface of the cell membrane.

    Text for drawing above: The round spheres on both sides of the phospholipids and cholesterol represent the polar portion of the lipid molecules. Cholesterol is represented by the black lines in between the phospholipids. The phospholipids cephalin and lecithin are represented in orange.

    The word polar means that a molecule (not an ion/electrically charged atom) has areas of positivity and areas of negativity. Water is an example of a polar molecule.

    The lipid bilayer is fluid-like, permitting movement of the imbedded lipids and proteins sideways within the membrane.

     

     

    Text for above drawing: A classic experiment showed that imbedded protein molecules could move from place to place on the cell membrane. Membrane fluidity is affected by a) the placement and number of double bonds in the fatty acid molecules of lecithin and cephalin and by b) the amount of cholesterol filling those spaces between the phospholipid molecules. Cholesterol stabilizes the membrane structure.

    Membrane fluidity is affected by temperature. The mammalian cell membrane is stable at body temperature but is not too rigid. Fish adjust the proportion of different lipids in their cell membranes as they migrate from waters of one temperature to another.

    Lipid bilayers do NOT allow larger ions and polar molecules to be transported across the membrane unaided. (Most materials needing to get into cells are in these categories)

    Movement of these substances across the membrane involves imbedded membrane proteins. These proteins may connect to the energy producing organelles of the cell to cause active, aided transport.

     

     

     

     


     

    Proteins are substances in all living things that are made up of individual pieces called amino acids. A drawing of one kind of protein is shown to the left.

     

     

     

     

    The individual amino acids in a protein are like the letters of the alphabet. Letters of the alphabet can be put together in different orders and lengths and spell different words. Amino acids can be put together in different orders and lengths and make different proteins that do different things.

     

     

     

     

     

    A word processor with your help puts letters together to make words. Amino acids with the help of the ribosome factories are put together to make different proteins.

     

     

     

    The amino acids in proteins are held together by special bonds called peptide bonds.

     

     

     

     

    Amino acids are made up of carbon (C), hydrogen (H), oxygen (O) and nitrogen (N). Some amino acids have sulfur (S) in addition to C, H, O and N. Of the 20 amino acids, two have S.

     

    One of the differences between words and proteins is that proteins almost always fold together in three dimensional space. Words do not.

     

     

     

     

    Why do proteins fold?

    This is the drawing of a small protein of about 200 amino acids that has not yet folded. It is not functional in this form.

    The eight red marks on the unfolded protein represent the position of the cysteine amino acids. This is one kind of amino acid that contains sulfur.

     

     

    When the protein above folds the eight cysteine amino acids form four disulfide bonds (see left). This is what gives the protein its three-dimensional folding pattern and holds it in this shape. This protein is now able to perform its function. You will learn about the amino acid cysteine soon.

     

     

    Most proteins are not able to do their job without being folded in a specific way. Enzymes that are unfolded do not work. Folding is a requirement for activity of the protein.

     

    The kind of folding that occurs is determined by the number of cysteine amino acids and where they are located in the protein. It folds automatically after it is made without the help of any other protein or enzyme because of the disulfide bonds that form.

     

    Structure of Amino Acids

    The structure above is the general "formula" for all amino acids. The red portion of the molecule is present in ALL amino acids. The letter "G" (and sometimes "R") is used to indicate the space where additional atoms are placed. The atoms placed where the letter "G" is, makes each amino acid different.

     

    The "G" atoms that specify the types of amino acids (or letters in the protein alphabet) are shown below.

     

    The atoms that stand for G for the different amino acids are shown where each attaches to the basic amino acid structure below the letter "G". There are several types of amino acid groups.

    1. Dicarboxilic amino acids: Di means two COOH groups

    These are amino acids where the "G" atoms contain the atoms COOH or CONH2. See drawing to the left: from left to right are: Glutamic acid (Glu), Asparagine (Asn), Glutamine (Gln), and Aspartic acid (Asp

     

     

     

     

     

     

     

    2. Amino acids having basic functions:

    These are amino acids with NH2 in the "G" atoms as a separate group (not with CO). See drawing to the left: from left to right are Histidine (His), Arginine (Arg) and Lysine (Lys).

     

     

     

     

     

     

     

     

    3. Aromatic amino acids:

    These are amino acids with carbon atoms (C) that are connected in circles or rings (rather than in chains). They have no nitrogen (N) in the ring itself as does Histidine in group 2. See drawing above: from left to right are Tyrosine (Tyr), Tryptophan (Try) and Phenylalanine (Phe).

     

     

     

     

     

     

    4. Sulfur-containing amino acids:

    These are amino acids that have the atom sulfur (S) in them. See drawing to the left: from left to right are Cysteine (Cys) and Cystine (Cys----Cys). You notice that in Cystine, there is a disulfide bond holding one Cysteine together with another Cysteine within the same protein and in between two proteins in a large protein with two or more peptide chains. This is what causes a single protein to fold and a multi-peptide protein to remain together as one.

    Multi-peptide chain proteins are called polypeptides or polypeptide chains.

     

     

     

    Text for drawings to the left:

    5. Aliphatic amino acids: These amino acids have chains of C and/or H in the "G" atoms...no other atoms. From left to right: Alanine, Leucine, Isoleucine, Glycine, and Valine.

     

    6. Hydroxy amino acids: These amino acids have OH without CO (no COOH) in the "G" atoms. From left to right: Threonine and Serine.

     

    Proteins are made from individual amino acids. Details of protein synthesis is part of another instructional unit.

     

    CARBOHYDRATES: Substances in cells that contain carbon (C), hydrogen (H) and oxygen (O).

    The fructose 1,6-diphosphate is a high energy sugar that is produced during the "Dark Reaction" of photosynthesis. Enzymes easily convert this sugar to fructose 6-phosphate and ultimately to glucose. Fructose and glucose are high-energy sugars. The energy from the bonds in glucose comes from the sun during photosynthesis (as part of the oxygen/carbon cycle).

    Glucose and fructose combine enzymatically to form sucrose...common table sugar.

    The high-energy storage molecules ATP, ADP, NADP and NADPH2 all have the 5-carbon sugar ribose however their energy is not stored in the bonds of the sugar. It is the phosphate or hydrogen bonds with phosphate that contain the stored energy..This energy is used for all cell operations.

     

    Almost all carbohydrates are sugars or chains of sugars.

    -- In animals carbohydrates are stored as glycogen. In plants carbohydrates are stored as starch. Both glycogen and starch are long chains of the simple sugar glucose.

    -- Living things get their energy by breaking down carbohydrates to carbon dioxide and water. The energy comes from the forces that hold the glucose molecule together (called covalent bonds).

     

     

     

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