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Human Biology (BIOL 104). Talk two: The Chemistry of life C hapter Two Don’t Panic!. WHY?!!!!!!!!!!!!. In studying human biology, it’s useful to understand some basic chemistry Chemical reactions explain the effects – harmful or helpful – of substances we take into our bodies

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Human biology biol 104

Human Biology (BIOL 104)

Talk two:

The Chemistry of life

Chapter Two

Don’t Panic!


WHY?!!!!!!!!!!!!

  • In studying human biology, it’s useful to understand some basic chemistry

    • Chemical reactions explain the effects – harmful or helpful – of substances we take into our bodies

  • This will actually help you to identify structures, functions, and processes of many of the human body systems.

  • It will help you understand how everything in the human body works together for healthy life to exist.

    • In other words – it will help you connect up all the dots


Atoms and elements

Matter: Anything that takes up space.

Element: Substance composed of one type of atom.

Atom: Smallest unit of an element that retains the chemical and physical properties of that element

Neutron: atomic particle with one mass unit and no charge.

Proton: atomic particle with one mass unit and a positive charge.

Electron: atomic particle with a negative charge and “no” mass.

Atoms and Elements


Chemical bonding and molecules
Chemical Bonding and Molecules

  • Atoms want to fill their outer shells with electrons!

  • Chemical reactions enable atoms to giveup or acquire electrons in order to complete their outer shells

  • These interactions usually result in atoms staying close together

  • Interactions between outer shells of atoms = chemical bonds


1 ionic bonds
1) Ionic Bonds

  • When an atom loses or gains electrons, it becomes electrically charged

Sodium atom (Na)

Chlorine atom (Cl)

Complete

outer shells

  • Charged atoms are called ions

  • Ionic bonds are formed between oppositely charged ions (transfer of electrons)

Sodium ion (Na)

Chloride ion (Cl)

Sodium chloride (NaCl)


2 covalent bonds
2) Covalent Bonds

  • A covalent bond forms when two atoms share one or more pairs of outer-shell electrons


The number of covalent bonds an atom can

potentially form = number of additional electrons

needed to fill its outer shell.


Water
Water

  • Water - one of the most important molecules in life.

    • 70% of the bodies mass is water

    • 2/3 of total body water is intracellular (55-66% body weight of men and 10% less for women)

    • The rest is interstitial fluid of which 25% is in the blood plasma.

  • pH - The body tightly controls both the volume and pH of water.

    • The bicarbonate system is crucial for blood maintenance

    • changes of pH greater than 0.1 are dangerous and can lead to coma -diabetics


  • Life on Earth would not be possible without water Its chemical and physical properties actually defy some fundamental laws of physicsAlmost all biochemical reactions require water!


    How does water support life?

    • Water is cohesive

    • Water can moderate temperature of surroundingenvironment

    • Ice floats

    • Versatility of water as a solvent

    From the wikimedia free licensed media file repository


    Water is a polar molecule
    Water is a polar molecule

    • When electrons are not shared equally in a covalent bond, the molecule is described as polar.

    • Water molecules are polar. This means that while water molecules are neutral as a whole, one end of the water molecule tends to have a positive charge while the other has a negative charge.

    • The oxygen end has a slight negative charge while the hydrogen end has a slight positive charge.

    • Each end of a water molecule is attracted to the opposite charged end of another water molecule.

    • Water's polarity is responsible for the "stickiness" or cohesion between the molecules.

    From the wikimedia free licensed media file repository



    Water is a polar molecule1
    Water is a polar molecule

    • Water has a dipole moment

    • “like dissolves like”

    Oxygen is more electronegative than hydrogen so there is an uneven distribution of charge in this H-O bond

    Uneven distribution is called a dipole and the bond is said to be polar


    Water has hydrogen bonding potential
    Water has hydrogen bonding potential

    • H-bonds are non-covalent, weak interactions

    • H2O is both a Hydrogen donor and acceptor

    • One H2O can form up to four H-bonds


    Water2
    Water

    • (A) Hydrogen bonds between water molecules results in local aggregations of water molecules

    • (B) Theses are very short lived, break up rapidly to form more random configurations

    • Due to temperature variations in water


    Density
    Density

    • Another property of water is density during phase changes.

      • The density of most substances increases when a liquid becomes a solid. Solid water is actually less dense than liquid water.

    • It is for this reason that ice floats.

      • The fact that ice floats is essential for the survival of many aquatic ecosystems and ultimately life on Earth.

    Hydrogen bond

    Ice

    Liquid water

    Hydrogen bonds

    constantly break and re-form

    Stable hydrogen bonds


    Capillary action surface tension
    Capillary Action & Surface tension

    • Cohesion of water causes capillary attraction, which is the ability of water to move upward in small spaces.

    • Cohesion makes it possible for water to move up the fibers of a plant.

      • This is how plants get the water they need to survive.

      • In addition, it moves water upwards in soil.

      • Allows water to be taken into human cells attached to other molecules

    • Cohesion of water also causes surface tension, water's invisible skin which allows water striders to walk on water

    From the wikimedia free licensed media file repository


    Water is a solvent
    Water is a solvent

    • Water is the Universal Solvent.

      • Water “dissolves” polar molecules

      • Water allows chemical reactions to occur

    • Any dissolved substance is known as a solute.

    • When a substance dissolves, water molecules cluster around it forming spheres of hydration.

    • This is what happens to solutes in blood and other body fluids.

    • Almost all chemical reactions in the human body occur in water-based solutions.

    Used with permission from compchemmpi.wikispaces.com/


    Water is nucleophilic
    Water is nucleophilic

    • Water participates in many chemical reactions

      • it is electron rich

      • it is a weak nucleophile

      • it is present in high concentration

    Water weakly ionizes


    Ph and buffers
    pH and buffers

    • Measure of the acidity or basicity of an aqueous solution.

      • Solutions with a pH less than 7 are said to be acidic

      • Solutions with a pH greater than 7 are basic or alkaline.

      • Pure water has a pH very close to 7

    • Acid

      • A chemical compound that donates H+ ions to solutions.

    • Base

      • A compound that accepts H+ ions and removes them from solution.

      • Remember H3O+ and OH-?

      • The H3O+ donates H+ to a solution and the OH- removes H+ from a solution

      • If an equal number of these ions are present in a solution the pH will not change as it is said to be buffered.


    H 2 0 helps buffer our blood
    H20 helps buffer our blood

    • Water reacts with CO2 to form an important blood buffer

    • We breath in and out gaseous CO2

    • In the blood, CO2 reacts with water to form the buffering compound H2CO3 –carbonic acid

    • Disturbances in blood buffering system leads to acidosis (pH below 7.1) or alkalosis (pH above 7.6)

    • Bleeding in lungs – death!

    • “a few good men”


    The ph scale
    The pH scale

    • To describe the acidity of a solution, we use the pH scale.

    • Acids have a low pH, so they have a highconcentration of H+

    • Bases have a high pH, so they have a low concentration of H+

    Used with permission from purewaterproducts.com


    The biomolecules
    The Biomolecules

    • These are the molecules of life

      • Carbohydrates

      • Lipids

      • Proteins

        • Glycoproteins

      • Nucleotides and Nucleic acids

    • These molecules are involved in the chemical reactions that allow us to live.

    • Remember the levels of biological organization?

    • Understanding the molecules allows you to understand how the cell works

      • Which is the fundamental unit of life


    Carbohydrates
    Carbohydrates

    • Carbohydrates constitute more than 1/2 of organic molecules

    • Main role of carbohydrates in nature:

      • Storage of energy

      • Structural support

      • Lipid and protein modification:

        • membranes asymmetry, recognition by IgG/fertilization/virus recognition/cell cell communication

          Definition: Carbohydrates, Sugars and Saccharides- are all polyhydroxy

        • (at least 2 OH) Cn(H20) n = hydrate of carbon


    Basic facts
    Basic facts

    Monosaccharides - Simple sugars

    • Single polyhydroxyl

      • Can’t be hydrolyzed to simpler form

        Trioses - Smallest monosaccharides have three carbon atoms

        Tetroses(4C) Pentose (5C) Hexoses (6C) Heptoses(7C) etc…

        Disaccharide - two sugars linked together. Can be the same molecule or two different sugars. Attached together via a glycosidic linkage

        Oligosaccharide - 2 to 6 monosaccharides

        Polysaccharides - straight or branched long chain monosaccharides. Bonded together by glycosidic linkages


    Classification of monosaccharides
    Classification of monosaccharides

    • The a and b anomers of glucose.

    • Note the position of the hydroxyl group (red or green) on the anomeric carbon relative to the CH2OH group bound to carbon 5:

    • Either on the opposite sides (a)

    • Or the same side (b).

    From the wikimedia free licensed media file repository


    Important disaccharides
    Important disaccharides

    • Maltose

    • Malt sugar or corn sugar consists of two glucose molecules linked by an -1,4-glycosidic bond

    • It comes from partial hydrolysis of starch by the enzyme amylase, which is in saliva.

    • Maltose is an important intermediate in the digestion of starch. 

    • In humans, maltose is broken down by the enzyme maltase so that there are two glucose molecules from which the glucose metabolism obtains energy.


    Important disaccharides1
    Important disaccharides

    • Sucrose (table sugar)

    • Sugar beets, fruits and vegetables all contain sucrose.

    • When sucrose is consumed, it is broken down to glucose and fructose.

    • The body will use glucose as its main energy source

    • The excess energy from fructose, if not needed, will be poured into fat synthesis, which is stimulated by the insulin released in response to glucose

    From the wikimedia free licensed media file repository


    Sucrose table sugar
    Sucrose (table sugar)

    • Human health

    • Tooth decay has become a prominent health hazard associated with the consumption of sugars, especially sucrose.

      • Oral bacteria such as Streptococcus mutanslive in dental plaque and metabolize sucrose intolactic acid.

      • The resultant lactic acid lowers the pH of the tooth's surface, stripping it of minerals in the process known as tooth decay

    • Obesity

    • A United Nations report (2011) stated that obesity may correlate better with sugar consumption than with fat consumption, and that reducing fat consumption while increasing sugar consumption may increase the level of obesity.


    Important disaccharides2
    Important disaccharides

    • Lactose

    • Derived from galactose and glucose linked by an b-1,4-glycosidic bond and makes up around 2–8% of milk (by weight).

    • Lactose Intolerance is the inability or insufficient ability to digest lactose. Lactose intolerance is caused by reductions in the production of the enzyme lactase by the cells of the small intestine.

    • Lactase production is at its highest in infants at birth regardless of ethnicity. This allows infants to digest breast milk.

    • Primary lactase deficiency occurs when a person’s body decreases the formation of lactase.

    From the wikimedia free licensed media file repository


    Important disaccharides3
    Important disaccharides

    • Lactose

    • Symptoms of lactose intolerance can be mild to severe, depending on how much lactase your body makes. Symptoms usually begin 30 minutes to 2 hours after you eat or drink milk products.

    • If you have lactose intolerance, your symptoms may include

      • Bloating.

      • Pain or cramps.

      • Gurgling or rumbling sounds in your belly.

      • Gas.

      • Loose stools or diarrhea.

      • Throwing up.

    From the wikimedia free licensed media file repository


    Important disaccharides4
    Important disaccharides

    • Lactose

    • Primary lactose intolerance appears to have a genetic component with specific populations showing high levels of intolerance.

    • Lactose Intolerance: Information for Health Care Providers. U.S. Department of Health and Human Services. NIH Publication Number 05-5305B. 2006


    Important polysaccharides
    Important Polysaccharides:

    • Starch- energy reservoir in plants - made of two polysaccharides

    • Glycogen – same as starch – animals

    • Both starch and glycogen made up of:

    • Amylose -long unbranched glucose a (1,4) with open reducing end large tight helical forms.

    • Amylopectin is like amylose, but has extensive branching, with the branches using -1,6-glycosidic bonds.

    • A very highly coiled complex, allowing hundreds of thousands of glucose moieties to be stored in the smallest possible physical space.


    Important polysaccharides1
    Important Polysaccharides:

    - energyreservoir in plants - made of two polysaccharides

    • Amylose -long unbranched glucose a (1,4) with open reducing end large tight helical forms. Test by iodination.

    • Amylopectin- polymer of a(1,4) and a (1,6) branches. Not helical.


    Glycogen
    Glycogen

    • Mix both of these two types of polysaccharides together and you get glycogen.

    • In humans, glycogen is made and stored primarily in the cells of the liver and the muscles, and functions as the secondary long-term energy storage.

    • In the liver cells (hepatocytes), glycogen can compose up to 8% of its fresh weight (100–120 g in an adult) soon after a meal.

    • Only the glycogen stored in the liver can be made accessible to other organs.

    From the wikimedia free licensed media file repository


    Plant starch amylose and amylopectin
    Plant Starch (Amylose and Amylopectin)

    • Starch contains a mixture of amylose and amylopectin

    • Amylose is an unbranched polymer (forms -helix) of D-glucose molecules linked by -1,4-glycosidic bonds

    • Amylopectin is like amylose, but has extensive branching, with the branches using -1,6-glycosidic bonds


    Cellulose
    Cellulose

    • Linear glucan chains of unbranched (1-4)-b-linked-D-glucose in which every other glucose residue is rotated 180° with respect to its two neighbors and contrasts with other glucan polymers such as:

    • starch (1-4-a-glucan)

    • callose (1-3-b-glucan).


    Cellulose1
    Cellulose

    • This means that cellobiose, and not glucose, is the basic repeating unit of the cellulose molecule. Groups of 30 to 40 of these chains laterally hydrogen-bond to form crystalline or para-crystalline microfibrils.


    Lipids
    Lipids

    Lipids fats oils…. Greasy molecules, mmmmm donuts.

    Several levels of complexity:

    • Simple lipids - a lipid that cannot be broken down to smaller constituents by hydrolysis.

      • Fatty acids, waxes and cholesterol

    • Complex lipids - a lipid composed of different molecules held together mostly by ester linkages and susceptible to cleavage reactions.

      • acylglycerols - mono, di and triacylglycerols ( fatty acids and glycerol)

      • phospholipids - lipids which are made of fatty acids, glycerol, a phosphoryl group and an alcohol. Many also contain nitrogen


    General structure
    General Structure

    • glycerol (a type of alcohol with a hydroxyl group on each of its three carbons)

    • Three fatty acids joined by dehydration synthesis.

    • Since there are three fatty acids attached, these are known astriglycerides.

    • The longer the fatty acids the higher the melting point.

    From the wikimedia free licensed media file repository


    Saturated or not the power of h
    Saturated or not – the power of H

    • The terms saturated, mono-unsaturated, and poly-unsaturated refer to the number of hydrogens attached to the hydrocarbon tails of the fatty acids as compared to the number of double bonds between carbon atoms in the tail.

    • Oils, mostly from plant sources, have some double bonds between some of the carbons in the hydrocarbon tail, causing bends or “kinks” in the shape of the molecules.

    • Because some of the carbons share double bonds, they’re not bonded to as many hydrogens as they could if they weren’t double bonded to each other.

    From the wikimedia free licensed media file repository


    Trans and cis
    Trans and Cis

    • In unsaturated fatty acids, there are two ways the pieces of the hydrocarbon tail can be arranged around a C=C double bond.

    • TRANS

      • The two pieces of the molecule are on opposite sides of the double bond, that is, one “up” and one “down” across from each other.

    • CIS

      • the two pieces of the carbon chain on either side of the double bond are either both “up” or both “down,” such that both are on the same side of the molecule

    From the wikimedia free licensed media file repository


    Trans and cis1
    Trans and Cis

    • Naturally-occurring unsaturated vegetable oils have almost all cis bonds

      • but using oil for frying causes some of the cis bonds to convert to trans bonds.

    • If oil is used only once like when you fry an egg, only a few of the bonds do this so it’s not too bad.

    • However, if oil is constantly reused, like in fast food French fry machines, more and more of the cis bonds are changed to trans until significant numbers of fatty acids with trans bonds build up.

    • The reason this is of concern is that fatty acids with trans bonds are carcinogenic!

    From the wikimedia free licensed media file repository


    Phospholipids:

    • Two fatty acids covalently linked to a glycerol, which is linked to a phosphate.

    • All attached to a “head group”, such as choline, an amino acid.

    • Head group POLAR – so hydrophilic (loves water)

    • Tail is non-polar –hydrophobic

    • The tail varies in length from 14 to 28 carbons.


    Cholesterol
    Cholesterol

    • A lipid molecule known as a Sterol and is biosynthesized by all animal cells

    • Essential structural component of animal cell membranes that is required to maintain both membrane structural integrity and fluidity.

    • Has no fatty acid tail – instead have four fused together carbon rings.

    • Essential derivatives include:

    • Vitamin D – bones and teeth

    • Bile salts – fat digestion

    • The sex hormones - estrogen and testosterone

    • Mineralcorticoids – Na+ and K+ balance in the blood

    • Glucocorticoids - involved in reducing inflammation

    From the wikimedia free licensed media file repository


    Proteins peptides primary structure
    Proteins:Peptides & Primary Structure

    Protein Functions:

    • Enzymes -Catalyze a thermodynamically favorable reaction

    • Storage/transport - binding proteins fatty acids w/albumin

    • no catalytic activity but do form chemical bonds with ligands

    • Structure - Several levels

    • cytoskeleton, collagen, bone ...

    • Receptors

    • Growth factors

    • Antibodies


    Amino acids
    Amino acids

    • -20 common amino acids there are others found naturally but much less frequently

    • Common structure for amino acid

    • COOH, -NH2, H and R functional groups all attached to the alpha carbon


    Peptides

    When amino acids are linked together it is through the formation of a peptide bond

    The formation of a peptide bond occurs by the loss of a water or dehydration of water from the a carboxyl and of one amino acid and the a amino of another amino acid


    Proteins three dimensional structure
    Proteins: Three-dimensional structure

    • Background on protein composition:

    • Two general classes of proteins

      • Fibrous - long rod-shaped, insoluble proteins. These proteins are strong (high tensile strength).

      • Globular - compact spherical shaped proteins usually water-soluble. Most hydrophobic amino acids found in the interior away from the water. Nearly all enzymes are globular…

      • Proteins can be simple -no added groups or modifications, just amino acids

    • Or proteins can be conjugated.Additional groups covalently bound to the amino acids. The naked protein is called the apoprotein and the added group is the prosthetic group. Together the protein and prosthetic group is called the holoprotein. Ex. Hemoglobin


    Four levels of protein structure
    Four levels of protein structure

    • Primary structure: amino acid only. The actual amino acid sequence is specified by the DNA sequence. The primary structure is used to determine genetic relationships with other proteins - AKA homology. Amino acids that are not changed are consideredinvariant or conserved.

    Primary sequence is also used to determine important regions and functions of proteins - domains.


    Four levels of protein structure1
    Four levels of protein structure

    • Secondary structure:This level is only concerned with the local or close in structures on the protein - peptide backbone. The side chains are not considered here, even though they have an affect on the secondary structure.

    • Two common secondary structures - alpha helix and beta pleated sheet

    • Non- regular repeating structure is called a random coil.

      - no specific repeatable pattern


    Four levels of protein structure

    Tertiary structure- the overall three-dimensional shape that a protein assumes. This includes all of the secondary structures and the side groups as well as any prosthetic groups. This level is also where one looks for native vs. denatured state. The hydrophobic effect, salt bridges

    And other molecular forces are responsible for maintaining the tertiary structure


    Four levels of protein structure2
    Four levels of protein structure

    Quaternary structure: The overall interactions of more than one peptide chain. Called subunits.

    Each of the subunits can be different or identical subunits, hetero or homo – x mers

    (ex. Heterodimer is a protein composed of two different subunits).


    Glycoproteins
    Glycoproteins

    • Proteins that contain oligosaccharide chains covalently attached to polypeptide side-chains.

    • The carbohydrate is attached to the protein in a co-translational or posttranslational modification. This process is known as glycosylation.

      • In proteins that have segments extending extracellularly, the extracellular segments are often glycosylated.

    • Glycoproteins are often important integral membrane proteins, where they play a role in cell-cell interactions.

    • Glycoproteins also occur in the cytosol, but their functions and the pathways producing these modifications in this compartment are less well-understood


    Examples of glycoproteins found in the human body
    Examples of glycoproteins found in the human body

    • Mucins

    • secreted in the mucus of the respiratory and digestive tracts.

    • The sugars attached to mucins give them considerable water-holding capacity and also make them resistant to proteolysis by digestive enzymes.

    • In the immune system

    • white blood cell recognition molecules such as antibodies which interact directly with antigens

    • Molecules of the major histocompatibility complex (or MHC), which are expressed on the surface of cells and interact with T cells as part of the adaptive immune response.


    Examples of glycoproteins found in the human body1
    Examples of glycoproteins found in the human body

    • glycoprotein IIb/IIIa

      • an integrin found on platelets that is required for normal platelet aggregation and adherence to the endothelium.

    • The zonapellucida

      • which surrounds the oocyte, and is important for sperm-egg interaction.

    • connective tissue.

      • These help bind together the fibers, cells, and ground substance of connective tissue.

      • They may also help components of the tissue bind to inorganic substances, such as calcium in bone.

    From the wikimedia free licensed media file repository


    Examples of glycoproteins found in the human body2
    Examples of glycoproteins found in the human body

    • Hormones that are glycoproteins include:

    • Follicle-stimulating hormone

      • Stimulates the follicle to produce estrogen

    • Luteinizing hormone

      • Stimulates the corpus leuteum to produce progesterone.

    • Thyroid-stimulating hormone

    • Human chorionic gonadotropin

      • maintains the corpus luteum and allows the production of progesterone and estrogen until the placenta takes over this task.


    Nucleic acids
    Nucleic Acids

    • Composed of 4 nucleotide bases, 5 carbon sugar and phosphate.

    • Base pair = rungs of a ladder.

    • Edges = sugar-phosphate backbone.

    • Double Helix

    • Anti-Parallel


    The bases
    The bases

    Chargaff’s Rules

    A=T

    G=C

    led to suggestion of a double helix structure for DNA

    From the wikimedia free licensed media file repository


    The bases1
    The Bases

    Adenine (A) always base pairs with thymine (T)

    Guanine (G) always base pairs with Cytosine (C)

    From the wikimedia free licensed media file repository


    The bases2
    The Bases

    From the wikimedia free licensed media file repository

    The C#T pairing on the left suffers from carbonyl dipole repulsion, as well as steric crowding of the oxygens. The G#A pairing on the right is also destabilized by steric crowding (circled hydrogens).


    The structure of rna
    The structure of RNA

    • Formed from 4 nucleotides, 5 carbon sugar, phosphate.

    • Uracil is used in RNA.

      • It replaces Thymine

    • The 5 carbon sugar has an extra oxygen.

    • RNA is single stranded.


    Adenosine triphosphate atp
    Adenosine triphosphate (ATP)

    • Often called the "molecular unit of currency" of intracellular energy transfer.

    • Transports chemical energy within cells for metabolism.

    • Transfers a phosphate group to many molecules in the cell.

    • It is one of the end products of photophosphorylation, cellular respiration, and fermentation and used by enzymes and structural proteins in many cellular processes, including biosynthetic reactions, motility, and cell division

    From the wikimedia free licensed media file repository


    The end

    The End!

    Any Questions?


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