lecture biology

Saba malikbs-3

statistics chemical basis

University of gujrat

Lecture 2Chemical Basis of Life

Why study chemistry in an Anatomy and Physiology class?

- body functions depend on cellular functions

- cellular functions result from chemical changes

- biochemistry helps to explain physiological processes, and develop new drugs and methods for treating diseases

2-2

Fig. 2.1

AIM: What’s the matter?Chapter 2 - The Chemical Basis of Life

Structure of Matter

Matter – anything that takes up space and has weight; composed of elements

Elements – composed of chemically identical atoms• bulk elements – required by the body in large amounts• trace elements – required by the body in small amounts

Atoms – smallest particle of an element

2-3

Table 2.1


Fig 2.3b



A lack of iodine in one’s diet can cause swelling of the thyroid gland resulting in a GOITER. The condition is reversible if iodine is taken. (Don’t worry, we iodize salt)

Iodine is used by thyroid cells to make hormones (chemicals released by one cell into the blood and bind to a receptor on another cell, which is one way cells talk to each other).

Fig 2.3b

AIM: What’s the matter?

ElementCompound

vs

(Emergent Properties)

Chapter 2 - The Chemical Basis of Life


Elements – composed of the same types of atoms

Compounds – composed of two or more types of atoms


Element

CompoundEx) a bar of pure gold, nitrogen gas (N2), oxygen gas (O2)

- Any substance composed of two or more elements


- Any substance composed of only ONE element

Ex) Na+Cl- (table salt), H2O, CO2


EMERGENT PROPERTIES (EP’s)


+ =

Pure sodium (element)Chlorine (Cl2) gas (element)Na+Cl- Table Salt (Compound)

Fig 2.2


What are atoms made of and how are they organized?


(The Bohr Model)

Niels BohrDanish Physicist1885-1962


Nucleus Organization:

Atomic Structure

Atoms - composed of subatomic particles:

• protons – carry a positive charge• neutrons – carry no electrical charge• electrons – carry a negative charge

Nucleus• central part of atom• composed of protons and neutrons• electrons move around the nucleus 2-4


protonneutronelectron

chargemass+10-1

1 amu (dalton)

1 amu (dalton)

1/1836th an amu (dalton)

amu = atomic mass unit1 amu or 1 dalton = 1.67 x 10-27 kg

Subatomic particles(sub = below, below the atom level)


How are the electrons “held” to the nucleus? Why do they not just shoot away?

Electrons are held to the nucleus by the electromagnetic (EM) force since electrons are negative and the nucleus is positive – opposite charges attract / like charges repel.


How are the protons “held” together in the nucleus? Why do they not break apart due to the EM force?The strong force holds the nucleus together. The strong force is only “felt” at extremely small distances, which is why the electrons do not feel it. You would need to be on the nucleus to feel it. For example, if gravity were like this, you would only feel it on Earth, but if you jumped up a few feet, you would no longer be pulled down by it...


Electron Organization:Electrons are present in shells and move around the nucleus at a speed of ~2200 km/s. They can only be in these shells and nowhere else!!The first shell (n=1) can hold up to 2 electrons. That means it can have 0, 1 or 2 electrons in it at any time.The second shell (n=2) can hold up to 8 electrons.

There are many more shells, but you only need to know the first three for AP Bio.

n=1n=2

The third shell (not shown, n=3) can also hold up to 8 electrons.


Electron Organization:Which shell contains higher energy electrons, shell 1 (n=1) or shell 2 (n=2)? Explain.Shell 2. The further from the nucleus the electron, the further it can fall toward the nucleus and therefore it has more energy (a greater ability to accelerate matter) than shell 1 electrons.

n=1n=2


Electron Organization:Electrons can jump between shells (called a quantum leap)

In order to get an electron to “leap” from n=1 to n=2, what is required?

n=1n=2


Electron Organization:Electrons can jump between shells (called s quantum leap)

n=1n=2

n=3

The nucleus is charged and therefore is pulling on the electron. It will take energy to pull the electron away from the nucleus and move it further away to shell 2. This is analogous to picking up a bowling ball. Earth is pulling on the bowling ball like the nucleus is pulling on the electron. It takes energy to pick up a bowling ball.

Fig 2.7

Atomic Number and Atomic Weight

Atomic Number • number of protons in the nucleus of one atom • each element has a unique atomic number• equals the number of electrons in the atom

Atomic Weight• the number of protons plus the number of neutrons in one atom • electrons do not contribute to the weight of the atom 2-5


The atomic mass (A)Why do we not add the electrons mass?

Electrons are soooo small relative to protons and neutrons (1/2000th the size) that we ignore them.

= protons + neutrons


The atomic chargeCompare number of protons to the number of electrons.

Ex. If there are 10 protons (+10) and 7 electrons (-7) the overall charge is +3


What happens if wechange the number of protons?


You change the identity of the atom (becomes a different element) as well as the mass.


What happens if wechange the number of neutrons?


You change the mass and perhaps the stability....

Isotopes

Isotopes• atoms with the same atomic numbers but with different atomic weights• atoms with the same number of protons and electrons but a different number of neutrons• oxygen often forms isotopes (O16, O17, O18)• unstable isotopes are radioactive; they emit subatomic particles

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Isotopes are atoms that have the same elemental identity (same number of protons/same properties), but different number of neutrons.


Certain ratios of protons to neutrons are unstable resulting in breakdown of the nucleus (nuclear radiation). Ex. 6 protons and 6 neutrons in a nucleus

(Carbon-12) is stable, but 6 protons and 8 neutrons (carbon-14) is unstable and will undergo radioactive decay to become stable. C-14 is called a radioactive isotope.

stable stable unstable


Radioactive decay


Carbon-14 (radioactive) will decay to Nitrogen-14 (stable). Seven protons and 7 neutrons in a nucleus is stable. An electron is shot out during the decay making it dangerous and useful.

Radioactive decay

Clinical ApplicationsRadioactive Isotopes Reveal Physiology

• can be detected in the body using a scintillation counter

• injected into the body• different types taken up by different organs

• can be used to destroy specific tissues• commonly used

• iodine-131 for thyroid function• thallium-201 for heart function• gallium-67 and cobalt-60 for cancer• others used to assess kidney functions, measure hormone levels and bone density changes 2-31


What if we alter thenumber of electrons?


If you alter the electrons, you simply change the charge of the atom


Review:

4. How many protons, neutrons and electrons does the above element contain?



Review:

5. Which of the following models is correct according to the Bohr model of the atom?


Molecules and Compounds

Molecules – particle formed when two or more atoms chemically combine

Compound – particle formed when two or more atoms of different elements chemically combine

Molecular formulas – depict the elements present and the number of each atom present in the molecule

H2 C6H12O6 H2O

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Electrons

• found in regions of space called electron shells (energy shells)• each shell can hold a limited number of electrons• for atoms with atomic numbers of 18 or less, the following rules apply:

• the first shell can hold up to 2 electrons• the second shell can hold up to 8 electrons• the third shell can hold up to 8 electrons

• lower shells are filled first• if the outermost shell is full, the atom is stable

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Ions

Ion• an atom that has gained or lost an electron(s)• an electrically charged atom• atoms form ions to become stable Cation• a positively charged ion• formed when an atom loses an electron(s)

Anion• a negatively charged ion• formed when an atom gains an electron(s) 2-9

AIM: How do atoms interact with each other?


When are atomsmost happy ?

When their valence shell is full.

Chapter 2 - The Chemical Basis of Life AIM: How do atoms interact with each other?

To be “happy” (stable) the sodium atom will need to either get 7 electrons or lose 1. Which is easier?The sodium will give away its outer shell electron.


Chlorine needs one electron for its outer shell to be full.

Ionic Bond

• an attraction between a cation and an anionIonic Bond

• formed when electrons are transferred from one atom to another atom

2-10


Chlorine has a higher AFFINITY for the electron and therefore the electron will “fall” from sodium to chlorine.


When the piece of elemental sodium (countless numbers of sodium molecules) is placed in the chlorine gas in the video, all those ridiculous number of electrons jump to the countless chlorines. This causes all the molecules to move around violently (heat up) and electrons to jump between shells (give off light).


ionsCation vs Anion

Ionic bond


When sodium loses an electron it becomes positively charged (a cation). When chlorine picks it up it becomes negatively charged (a anion). Cations and Anions are collectively called ions = fully charged atoms/molecules.


ionsCation vs Anion

Ionic bond


The sodium and chloride ions are now attracted to each other and form an ionic bond.ionic bond = bond between two oppositely charged ions


Salt crystals


Na+Cl- crystals are repeating arrays of Na+ and Cl- held together by the electromagnetic force.


SaltAIM: How do atoms interact with each other?

-general name given to ANY ionic compound (not just sodium chloride (Na+Cl-) held together in a lattice structure.

Na+Cl-K+Cl-Mg2+Cl2-

Mn2+Cl2-

Ca2+CO32-

Covalent Bond

Formed when atoms share electrons

•Hydrogen atoms form single bonds•Oxygen atoms form two bonds•Nitrogen atoms form three bonds•Carbon atoms form four bonds

H ― HO = ON ≡ NO = C = O

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http://www.visionlearning.com/library/flash_viewer.php?oid=1348&mid=55

AIM: How do atoms interact with each other?How else can atoms fill their outer shells?





Single Covalent Bond

In this case, to be stable and fill their outer shells, unlike in an ionic bond, the atoms will SHARE their electrons to form a covalent bond.

H-H or H2



F-F or F2


Double Covalent Bonds (double bond)

O=C=O or CO2


Draw :CH4 or H2O


Structural Formula

Structural formulas show how atoms bond and are arranged in various molecules

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Polar Molecules

Polar Molecule• molecule with a slightly negative end and a slightly positive end• results when electrons are not shared equally in covalent bonds• water is an important polar molecule

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Hydrogen Bonds

Hydrogen Bond• a weak attraction between the positive end of one polar molecule and the negative end of another polar molecule• formed between water molecules• important for protein and nucleic acid structure

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Chemical Reactions

Chemical reactions occur when chemical bonds form or break among atoms, ions, or molecules

Reactants are substances being changed by the chemical reaction

Products are substances formed at the end of the chemical reaction

NaCl ’ Na+ + Cl-

Reactant Products2-15

Types of Chemical Reactions

Synthesis Reaction – chemical bonds are formed A + B ’ AB

Decomposition Reaction – chemical bonds are brokenAB ’ A + B

Exchange Reaction – chemical bonds are broken and formed AB + CD ’ AD + CB (NaCl+ AgNO3→ NaNO3+ AgCl)

Reversible Reaction – the products can change back to the reactants

A + B AB2-16

ALL CHEMICAL REACTIONS INVOLVE ENERGY

• WHEN BONDS FORM,ENERGY IS STORED

• WHEN BONDSBREAK, ENERGY IS RELEASED

ATP = energy carrier of a cell

Metabolism

• All the chemical reactions that take place in the organism

• These reactions need to be balanced to keep the organism alive– The balance is called homeostasis

Acids, Bases, and SaltsElectrolytes – substances that release ions in water

Acids – electrolytes that release hydrogen ions in waterHCl H+ + Cl-

Bases – substances that release ions that can combine with hydrogen ions

NaOH Na+ + OH-

Salts – electrolytes formed by the reaction between an acid and a base

NaCl Na+ + Cl-

HCl + NaOH H2O + NaCl 2-17

Acid and Base Concentrations

pH scale - indicates the concentration of hydrogen ions insolution

Neutral – pH 7; indicates equal concentrations of H+ and OH-

Acidic – pH less than 7; indicates a greater concentration of H+

Basic or alkaline – pH greater than 7;indicates a greater concentration of OH- 2-18

pH scale

• Most chemical reactions in humans take place between 6+8– However, stomach acid is 2-3– Enzymes are pH specific

2.2 Introduction to Chemistry

Blood - 7.5 (lethal if more acidic than 7 and more basic than 7.8)

Stomach acid - 2 -3 A change in pH --in your body results

in halting some enzyme functions


Acid rain --contains sulfuric acid and nitric acid

Acid rain pH < 5.6 Acid rain washes away vital

minerals from soil, kills aquatic organisms & strip nutrients from plants

Organic Versus InorganicOrganic molecules

• contain C and H• usually larger than inorganic molecules• dissolve in water and organic liquids• carbohydrates, proteins, lipids, and nucleic acidsInorganic molecules • generally do not contain C• usually smaller than organic molecules• usually dissolve in water or react with water to release ions• water, oxygen, carbon dioxide, and inorganic salts 2-19

Inorganic Substances

Water • most abundant compound in living material• two-thirds of the weight of an adult human• major component of all body fluids• medium for most metabolic reactions• important role in transporting chemicals in the body• can absorb and transport heat

Oxygen (O2) • used by organelles to release energy from nutrients• necessary for survival 2-20


• Solutions --Water is known as the universal solvent

• Chemical properties of water are important b/c they allow it to form solutions (Uniform mixtures)


• Solute --That which is being dissolved (sugar)

• Solvent --That which does the dissolving (water)


Ionic Compounds --dissolve readily in water b/c

water is polar Polar covalent compounds --

dissolve in water

Inorganic Substances

Carbon dioxide (CO2)• waste product released during metabolic reactions• must be removed from the body

Inorganic salts• abundant in body fluids• sources of necessary ions (Na+, Cl-, K+, Ca2+, etc.)• play important roles in metabolic processes

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ORGANIC COMPOUNDS

• COMPOUNDS THAT CONTAIN CARBON, HYDROGEN AND OXYGEN IN DEFINITE PROPORTIONS.

• USUALLY ASSOCIATED WITH LIVING THINGS

Organic SubstancesCarbohydrates

• provide energy to cells• supply materials to build cell structures• water-soluble• contain C, H, and O• ratio of H to O close to 2:1 (C6H12O6)• monosaccharides – glucose, fructose• disaccharides – sucrose, lactose• polysaccharides – glycogen, cellulose

2-22

CARBOHYDRATES• BUILDING BLOCKS = SIMPLE SUGARS

(MONOSACCHARIDES).• MONOSACCHARIDES INCLUDE

– GLUCOSE– FRUCTOSE ISOMERS– GALACTOSEALL THREE HAVE THE SAME MOLECULAR

FORMULA, BUT DIFFERENT STRUCTURE:C6H1206

THESE MOLECULES ARE THE MOST COMMON SOURCE OF ENERGY FOR LIVING THINGS.

Organic SubstancesCarbohydrates

2-23

Isomers – C6H12O6glucose

CARBON

• Carbon is important biological element because it can form four bonds with other elements and long chains or rings

• Polymer – large molecule made up of many smaller units like starch

• Monomer – unit that makes up polymer; glucose is the monomer for starch

GLUCOSE• Monomer of starch, glycogen, and cellulose

MORE COMPLEX CARBS

• DISACCHARIDES– MADE UP OF TWO MONOSACCHARIDES

CHEMICALLY COMBINED. – GLUCOSE + GLUCOSE = MALTOSE– GLUCOSE + GALACTOSE = LACTOSE

• THIS IS MILK SUGAR– GLUCOSE + FRUCTOSE = SUCROSE

• THIS IS TABLE SUGAR

• These molecules store energy for later use

2. 3 The Compounds of Life

• Glycogen - animals stored energy made from sugars (same

saccharides)• Cellulose - simple sugars that make

structural carbos in plants

THE MOST COMPLEX CARBS• STARCH – MADE UP OF MANY GLUCOSE UNITS

COMBINED.– PLANT LONG-TERM FOOD STORAGE

• GLYCOGEN – MADE OF MANY GLUCOSE UNITS COMBINED– ANIMAL STORAGE IN LIVER AND MUSCLES

• CELLULOSE – MADE OF MANY GLUCOSE UNITS COMBINED.– PLANT CELL WALLS; FIBER

• CHITIN – PROTECTIVE COVERINGS IN INSECTS AND OTHER ARTHROPODS; ALSO IN FUNGUS CELL WALLS

DEHYDRATION SYNTHESIS

• In order for two molecules to join together, each molecule must break off atoms to provide a bonding place.

• Most organic molecules do this by losing a hydrogen atom from one molecule and a hydroxyl group from the other.

• These two join to form water, and allow the molecules to make a bond.

Dehydration Synthesis

disaccharideC6H12O6 + C6H12O6 C12H22O11 + H2O

Hydrolysis

• In order to break down a large molecule to make smaller molecules, a molecule of water has to be added.

• This fills in the spots where the bond broke – one molecule gets a hydrogen atom, the other gets the hydroxyl group.

Hydrolysis

ADD WATER

POLYSACCHARIDE

MONOSACCHARIDES

TO A

AND FORM MANY

Dehydration Synthesis and Hydrolysis store and release energy

• Dehydration synthesis stores energy by forming bonds.– As in the formation of polysaccharides from

monosacharides• Hydrolysis releases energy by breaking

bonds.

Organic SubstancesLipids

• soluble in organic solvents• fats (triglycerides)

• used primarily for energy• contain C, H, and O but less O than carbohydrates (C57H110O6)• building blocks are 1 glycerol and 3 fatty acids per molecule• saturated and unsaturated

2-24

Lipids: fats, oils, waxes, phospholipids,

steroids • Used for longer-term storage of energy• Fats – in animals• Oils – in plants• Waxes – water repellent (In your ears, beeswax, coat

plant leaves), waterproof bird feathers. • Steroids – in animal cell membranes and some

hormones.• Phospholipids – make up parts of cell membranes

A common fat = Triglyceride

• Composed of one glycerol and three fatty acids, joined together by dehydration synthesis:

GLYCEROL

3FATTYACIDS

Saturated and unsaturated fats:

• Saturated fats have no C=C bonds within the fatty acids– These are considered unhealthy – they clog up the

coronary (heart) arteries.– These are solid at room temperature.– From animals.

• Unsaturated fats have at least one C=C bond in one of its fatty acids– These are considered healthier.– Plant oils are usually unsaturated.– Liquid at room temperature.

Organic SubstancesLipids

• phospholipids • building blocks are 1 glycerol, 2 fatty acids, and 1 phosphate per molecule

• hydrophilic and hydrophobic

• major component of cell membranes

2-25

Organic Substances Lipids

• steroids• connected rings of carbon• component of cell membrane• used to synthesize hormones• cholesterol

2-26

Organic SubstancesProteins

• structural material• energy source• hormones• receptors• enzymes• antibodies• building blocks are amino acids

• amino acids held together with peptide bonds

2-27

2. 3 The Compounds of Life• Proteins - make enzymes that

help control chemical reactions (ex. Speed up

digestion, releasing energy during cellular respiration, building

up proteins


• Proteins - large, complex molecules composed of many smaller molecules called amino acids (only

20 amino acids make different combinations & proteins)– Amino acids are held together by

peptide bonds to form proteins

PROTEINS

• Important for movement, structure, regulation, transport, nutrition, and defense.

• Composed of building blocks called amino acids• Humans cannot make these from scratch – we

must eat foods with proteins, then use the amino acids to make our own proteins.

Amino Acids• There are 20 different aa’s • They are combined in various numbers and orders to

produce a great number of different proteins. • Each aa has an amino group, an acid group (carboxyl), and

a variable group (there are 20 different variable groups).• Amino acids attach to each other by dehydration synthesis

forming a peptide bond between the amino group of one aa and the acid group of the other aa.

• Change the number or arrangement of the aa’s and the protein is changed.

Amino acidsAcid group

Amino group

Dipeptide – two aa’s joined by a peptide bond.

Polypeptide

Organic Substances Proteins

Four Levels of Structure

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Nucleic Acids• Molecules of heredity.• DNA – deoxyribonucleic acid

– makes up chromosomes (GENES)– Contains the genetic code

• Determines the organism’s traits• Contains the code for making proteins

Which control the cell’s activities • RNA – ribonucleic acid

– Helps DNA make proteins


• Nucleic Acids - large, complex molecules that contain

hereditary or genetic info – two types

• monomer – nucleotide (made up of nitrogen base, phosphate, and sugar)


DNA - carries instruction that control activities of cell (blueprint)

Organic SubstancesNucleic Acids

2-30

Enzymes – Special Proteins

• Change the rate of chemical reactions without being used up themselves (biological catalyst).

• Can be used over and over.• Action is very specific –

each enzyme will only work on one particular substance (the substrate).

HOW DOES AN ENZYME WORK?

• LOCK AND KEY MODEL

• INDUCED FIT MODEL

2.4 Chemical Reactions and Enzymes

*Type of protein

*Act as a catalyst, speeding up chemical reactions

1. Substrate- substance being changed by enzyme

2. Active site- region on enzyme where substrate attaches (this is the enzyme substrate complex)

2.4 Chemical Reactions and Enzymes3. Substrate is altered (bond

weakened) so that bond is broken

4. Products released and enzyme is unchanged (only the substrate changes)

5. Enzyme is free to bond with another substrate

*Enzyme affected by high temperature

2.4 Chemical Reactions and Enzymes

Chemical Reaction – creation of new substances by

breaking or forming chem. bondsCarbs broken for energyAll chemical reactions involve energy (absorbed or released)


Chemical Reactions and Chemical EquilibriumBiological Example:

Glycolysis is shown to the right. The circled numbers are enzymes.

Which reactions are reversible?Which reactions are irreversible?

Those catalyzed by enzymes 3, 4, 6, 7, 8, 9, 10, and 11

Those catalyzed by enzymes 1, 2, 5 and 12

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