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Biochemistry. Life is all about bags of biochemical reactions Atoms, Molecules and Chemical Bonds The Chemistry of Water The Chemistry of Carbon Carbohydrates Lipids Nucleic Acids Protein. The Chemistry of Life.

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biochemistry
Biochemistry

Life is all about bags of biochemical reactions

  • Atoms, Molecules and Chemical Bonds
  • The Chemistry of Water
  • The Chemistry of Carbon
  • Carbohydrates
  • Lipids
  • Nucleic Acids
  • Protein
the chemistry of life
The Chemistry of Life
  • All living things are made of cells, and all cells are made of a set of molecules known as biochemicals.
  • There are two very different types of biochemicals
      • small inorganic molecules such as water and salt ions,
      • large organic molecules such as sugars, fats, proteins, and DNA
  • By definition, organic molecules contain atoms of the element carbon.
  • Organic molecules are composed primarily of carbon, hydrogen, oxygen, and nitrogen.
atoms
Atoms
  • All of the matter in the universe is made from atoms.
  • Atoms are composed of protons, neutrons, and electrons.
      • Protons have a positive charge and a mass of 1 atomic unit
      • Neutrons have no charge, but also have a mass of 1
      • Electrons carry a negative charge but have very little mass
the atom
The Atom
  • The protons and neutrons form the nucleus of the atom, which contains most of the mass and the positive charges.
  • The electrons orbit very rapidly around the nucleus carrying negative charges.
  • Protons and electrons have equal and opposite charges.
  • In its neutral state, an atom has the same number of protons and electrons
elements
Elements
  • All of the atoms in the universe fall into a set of distinct categories called elements based on the number of protons in the nucleus.
  • All of the atoms of an element have the same number of protons (atomic number) and they share the same chemical properties.
  • The Periodic Table of Elements groups elements according to their atomic number and shared chemical properties.
chemical bonds
Chemical Bonds
  • Atoms interact with each other by either sharing or exchanging electrons.
  • This interaction can take place between atoms of the same element, or atoms of different elements.
  • Sharing a pair of electrons creates a covalent bond that holds atoms tightly together in a structure known as a molecule.
  • Some pairs of atoms may share more than one pair of electron, forming double or even triple covalent bonds, which are proportionately stronger.
  • Atoms often form covalent bonds with several other atoms, creating larger molecules.
ionic bonds
Ionic Bonds
  • Exchanging electrons creates charged atoms (ions), which form weak ionic bonds.
  • An atom that picks up an extra electron gets a negative charge, an atom that gives up an electron gains a positive charge.
  • An entire molecule may also exchange an electron with another molecule or with a single atom to form an ion, so a group of covalently linked atoms can be both a molecule and an ion.
chemistry of water
Chemistry of Water
  • All life, and all biochemistry, occurs in water.
  • Water has a number of special properties that make it both an essential matrix and an essential ingredient for biochemistry
  • The water molecule is composed of one oxygen atom covalently bound to two hydrogen atoms:
      • H-O-H = H20
water is polar
Water is Polar
  • In water, the two hydrogen atoms are not located on opposite sides of the oxygen atom, but instead are both on one side, forming an H-O-H angle of 104.45°.
water is polar cont
Water is Polar (cont.)
  • The oxygen has a stronger attraction for the shared electrons,
  • so the oxygen end of the molecule has a slightly negative charge and the hydrogen end has a net positive charge.
  • This makes water a polar molecule.
  • In liquid water, groups of H2O molecules stack up in loose head-to-tail formations where the positive end of one water molecule is attracted to the negative end of one or more other water molecules.
water ions ph
Water ions = pH
  • Water also has a tendency to form ions.
  • One hydrogen splits off, leaving behind its electron, so a positive H+ ion and a negative OH- ion are formed.
  • These ions are constantly available to participate in any biochemical reaction that might take place in a water solution.
  • An excess of H+ gives an acid pH, excess OH- give basic pH.
carbon chemistry
Carbon Chemistry
  • The carbon atom has 6 protons and 6 electrons
  • 4 of these electrons are held in an outer position where they can easily interact with other atoms: generally forming covalent bonds.
  • The 4 outer electrons tend to mutually repel each other, making a tetrahedron shape
carbon bonds
Carbon Bonds
  • The tendency of carbon to interact with four other atoms at once allows it to form the central linkage point of complex molecules that are assembled like tinkertoys.
carbon bonds20
Carbon Bonds
  • The simplest carbon molecules are hydrocarbons – combinations of carbon and hydrogen.
  • The simplest hydrocarbon molecule is methane: one carbon bound to 4 hydrogen atoms.
  • This is a non-polar molecule with very little attraction between molecules, and as a result, it is a gas at room temperature.
carbon bonds cont
Carbon Bonds (cont.)
  • Hydrocarbon molecules can grow larger by adding carbon-carbon bonds
  • either in a straight line, such as ethane (2 carbons) or hexane (6 carbons)
  • in a branching structure such as isohexane
  • or in a ring such as cyclohexane.
double bonds
Double Bonds
  • Each carbon atom has 4 bonds - either to hydrogen, or to another carbon.
  • Carbon atoms can also form double and triple bonds, providing a great deal of flexibility in the linkage possibilities.
  • Double and triple bonds hold more energy than single bonds.
oh groups
-OH groups
  • Any of the hydrogen atoms can be substituted for other atoms or larger groups.
  • In a simple hydrocarbon like ethane, if one hydrogen is replaced by a hydroxyl group (–OH), it forms the alcohol ethanol.
  • This is a polar molecule that is liquid at room temperatures and is much more biologically active than ethane.
other carbon bonds
Other Carbon Bonds
  • Organic molecules can also contain carbon-oxygen double bonds, and carbon-nitrogen bonds.
classes of biochemicals
Classes of Biochemicals
  • Biochemistry is primarily concerned with a few types of complex organic molecules
  • The most common types of bio-molecules are
      • sugars
      • fats
      • proteins
      • nucleic acids
  • Other complex organic molecules such as alkaloids do play important roles in biology,but only in certain specific organisms.
sugars
Sugars
  • Sugars are relatively simple molecules composed of just carbon, hydrogen, and oxygen (carbohydrates).
  • Glyceraldehyde is a simple 3-carbon sugar
      • each carbon has one of its hydrogens replaced with an –OH group
      • the last carbon has a double bond to its oxygen
glucose
Glucose
  • Glucose, a 6-carbon sugar, is the most common sugar molecule in living tissue.
  • The –CH=O group at the end is somewhat unstable, so the molecule tends to form a ring where the oxygen in the CH=O group reacts with the #2 carbon, replacing one of its hydrogens to form a C–O–C bond
ribose
Ribose
  • There are also a number of common 5-carbon sugars, which also tend to form rings. The most important of these is ribose, which is a component of all nucleic acids.
starch
Starch
  • It is very easy to link up sugar molecules into simple chains.
  • The reaction, called glycosylation, takes two C-OH groups and combines them into a single C–O–C, releasing H2O. .
  • This reaction costs little energy and is easily reversible.
polymers
Polymers
  • Large molecules that are built by linking up many smaller units are called polymers.
  • Biochemistry is full of polymers.
      • Starch is a polymer of sugar units
      • Fats are hydrocarbon polymers
      • Proteins are amino acid polymers
      • DNA and RNA are polymers of nucleotides
  • Plastics are synthetic polymers made from hydrocarbons.
fats lipids
Fats & Lipids
  • Lipids are long chain hydrocarbons with a carbonyl group (COH=O) at one end
      • lipids are hydrophobic (insoluble in water) and energy rich.
      • Lipids are the primary component of cell walls.
  • Individual lipid molecules can be joined up with glycerol to form fats,
      • It takes cells substantially longer to synthesize and break down fats compared to starch, so they are used for long-term energy storage.
nucleic acids
Nucleic Acids
  • DNA and RNA are two types of nucleic acids.
      • These are one of the primary subjects of bioinformatics
  • They are both large polymer molecules that are formed from subunits called nucleotides.
  • Nucleotides play many essential roles in biochemistry, so they are worth quite a bit of attention.
nucleotides
Nucleotides
  • Nucleotides are complex molecules that are composed of three parts:
    • a ribose sugar (5 carbons)
    • a phosphate (PO4) group substituted for the OH on the #5 carbon of the ribose
    • a cyclic nitrogen base substituted for the OH on the #1 carbon.
slide37
There are 4 different types of nitrogen bases:
  • the 2 purine bases (adenine and guanine) that have a double nitrogen ring and
  • the 2 pyrimidine bases (cytosine and thymidine) that have a single nitrogen ring.

pyrimidine

purine

slide38
ATP
  • The phosphate group on a nucleotide is able to form additional chemical bonds.
  • It can bond to one or two more phosphates, creating nucleotide di-phosphate and tri-phosphates.
      • These phosphate-phosphate bonds contain a large amount of energy.
  • Adenosine tri-phosphate (ATP) is the primary form of short-term energy storage for almost all biochemical reactions.
      • Energy is produced when one or two phosphates are removed, energy is stored by putting them back on.
nucleotide chains
Nucleotide Chains
  • The phosphate group on a nucleotide can form a bond with the #3 carbon of the ribose sugar in another nucleotide
      • (phosphodiester bonds: 5C–O–P–O–3C)
      • links up the nucleotides in a chain.
  • This nucleotide polymer is a nucleic acid.
  • The nucleotides in a DNA chain are generally abbreviated as A, C, G, and T
    • but remember that these letters stand for large, complex molecular sub-units.
poly nucleotides are polar
Poly-nucleotides are Polar
  • Note that the ends of the nucleotide polymer are not symmetrical.
      • the 5’ end has a free phosphate group on the #5 carbon
      • the 3’ end has a free –OH on the #3 carbon.
  • Also, note that the nitrogen bases do not participate in the phosphodiester bonds between nucleotides in the chain.
      • The chain is formed by links between the phosphate group and the ribose carbon rings
      • The nitrogen bases are free to form other chemical bonds.
dna has two chians
DNA has Two Chians
  • In the DNA chain, each nucleotide base can form hydrogen bonds with one other nucleotide in another DNA chain.
  • The geometry of this linkage is very precise and specific:
    • Adenine can only pair with thymine and guanine only pairs with cytosine.
  • Note that the G–C linkage involves 3 hydrogen bonds while the A–T linkage involves only 2.
    • Thus A–T base pairs form a weaker bond than do G–C pairs.
the double helix
The Double Helix
  • The two chains of a DNA molecule run in opposite directions:
    • one strand goes 5’ to 3’ and the opposite strand runs 3’ to 5’.
  • Also, the two chains do not lie flat, but rather twist around each other to form a double helix.
slide46
RNA
  • RNA molecules are very similar to DNA, except that the ribose sugar has an extra -OH group on the #2 sugar.
  • Instead of tyhmine, RNA uses the base uracil
  • Interestingly, single stranded RNA molecules do not form a double helix with other RNA strands, but only with complementary strands of DNA.
  • RNA molecules are much less chemically stable than DNA.
proteins

Proteins

Proteins are the most structurally and functionally diverse group of biomolecules. They also make up the majority of the dry weight of all living cells.

Proteins are used as motors, structural elements, enzymes, receptors, channels through membranes, intra-cellular transporters, regulatory switches, and much more.

amino acid polymers
Amino Acid Polymers
  • Proteins are a polymer of amino acids.
      • There are 20 different types of amino acids, but they all have the same basic structure.
  • A central carbon atom is linked to an amino group (NH2), a carboxyl group (COOH), and a variable side chain – shown as “R” below.
amino acids
Amino Acids
  • The 20 kinds of amino acids each have a different group as the side chain,
  • The amino acids can be divided into sub-groups based on the chemical properties of their side chains.
      • The non-polar amino acids have simple hydrocarbon side chains, which tend to make them insoluble in water (hydrophobic)

alanine, valine, leucine, isoleucine, proline, methionine, phenylalanine, tryptophan

      • Another group is polar, but has a neutral charge/pH

glycine, serine, threonine, cysteine, asparagines, glutamine, tyrosine

      • Aspartic acid and glutamic acid are negatively charged in water.
      • Lysine, arginine, and histidine are positively charged in water.
peptide bonds
Peptide Bonds
  • Amino acids are joined together by peptide bonds to form poly-peptide chains.
  • The peptide bond forms between the amino group of one amino acid and the carboxyl group of another
    • an –OH is lost from the carboxyl and an –H from the amino to form a C–N bond plus a free water molecule.
  • The resulting poly-peptide chain has a free amino group at one end and a free carboxyl group at the other end (the N-terminal and C-terminal ends)
protein sequence
Protein Sequence
  • Since a protein can have any amino acid at each position in the polypeptide chain, and proteins may be many hundreds of amino acids long, the potential number of different proteins is huge (3x10020 for a 300 amino acid protein)
  • The chemical diversity of the 20 amino acids means that different proteins can have vastly different biochemical properties.
  • Proteins are generally described as a string of letters – GCVFRTLLSAGR that represent abbreviations for the 20 amino acids
    • (asparagines=A, glycine=G, etc),
    • but remember that each of these amino acids is actually a complex molecular sub-unit with its own unique chemical properties.
protein modifications
Protein Modifications
  • Protein molecules are always linear polypeptide chains, never branched. However, some of the side chains do become linked to other molecules.
  • A variety of sugar molecules can be attached to serine, threonine, and asparagine side chains (glycosylation)
  • A phosphate group can be added to tyrosine (phosphorylation).
  • Cysteine amino acids can bond with other cysteines to form di-sulfide (S–S) bonds,
      • can link one part of a polypeptide to another part of the same molecule – creating a permanent fold,
      • or form a bond between two different polypeptides to create a multi-subunit protein.
protein structure function
Protein Structure & Function
  • Although proteins are synthesized as linear chains of amino acids, they do not remain flat and stretched out.
  • Under biological conditions, proteins fold up into complex 3-dimensional shapes.
  • These 3-dimensional shapes play a major role in determining the interactions of proteins with other molecules.
    • Lock and key model of enzyme function
protein folding
Protein Folding
  • Protein folding can start to be understood by looking at small sections of a protein,
  • There are just a few types of “secondary structures”
      • a-helices,
      • ß-pleated sheets
      • turns
  • These shapes are the product of local interactions between each amino acid and its immediate neighbors.
      • each type of amino acid has an innate “helix forming” or “sheet-forming” tendency on its own and in association with particular types of neighboring amino acids.
      • a group of about 6 amino acids can be predicted to form a helix or sheet with good accuracy.
slide62

alpha

helix

beta sheet

slide63

The segments of helix, sheets, and turns then interact to form the overall structure of the molecule (tertiary structure).

slide64

Multiple polypeptide chains can come together to form complex multi-subunit molecular machines (quaternary structure).

enzymes
Enzymes
  • One of the most important functions of proteins are as enzymes.
  • Enzymes provide a catalytic function – enabling specific chemical reactions to occur at physiological temperatures and concentrations, and allowing the cell to control the reaction rate.
  • each enzyme has a specific shape that fits its substrates (an active site)
      • “lock and key” model
  • through interaction with amino acid side chains and/or additional co-factors (such as metal atoms), the desired reaction is facilitated
metabolic pathways
Metabolic Pathways
  • Enzymes are involved in essentially all chemical reactions that take place inside a cell
      • synthesis and degradation of all biochemical molecules
  • Complex biochemical processes, such as the digestion of glucose or the synthesis of an amino acid, generally take place in a series of steps.
  • Each step is a separate chemical reaction, which is catalyzed by a different enzyme.
  • Taken together, the steps comprise a metabolic pathway.
regulation
Regulation
  • Regulation of metabolic pathways is a fundamental characteristic of living things.
  • Enzymes provide a very flexible system for the regulation of biochemical pathways.
  • The absolute amount of enzyme present can control the pathway, or the enzyme can be activated and inactivated by interaction with some other molecule.
  • Feedback inhibition is a very common regulatory system – the final product of a pathway inhibits an enzyme at the beginning of the pathway.
      • When lots of product is available, the pathway is shut down, when the product is in short supply, it is activated.
interconnection
Interconnection
  • Biochemical pathways do not operate in isolation.
  • The various inputs and outputs of each pathway are involved in other reactions,
  • and many pathways have branch points where a particular molecule may be an intermediate in the synthesis of several different products.
  • Each of these branch points represents another opportunity for regulation.