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SBI4U-Metabolic Processes

The Chemical Basis of Life – A Biology Prerequisite

Chapter 1, “The Molecules of Life”, is a review of chemical concepts from the grade 11 biology and chemistry courses. Coverage of material for this section will be primarily of an independent nature, with only some topics covered by the biology teacher. The most effective method to complete this diagnostic assessment is to complete what you know first, and then refer to your textbook/course notes for details or understanding gaps.

1. Distinguish between:a) atom b) element

c) molecule d) compound

2. Give five examples of elements and five examples compounds that are found in the human body.

3. Draw a representative (chemistry appropriate) diagram of a carbon atom showing the placement of protons, neutrons, and electrons.

4. Show your elemental atom in standard atomic notation. Use labels to show what each item represents.

5. a) Carbon-14 is considered to be an isotope of carbon. What does this mean? Draw a Bohr diagram to represent it.

b) How is carbon-14 different than some other isotopes? What happens to it over time?

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c) Define half-life.

d) What are three biological uses of isotopes?

6. Distinguish between an energy level and an orbital? What is an orbital’s maximum capacity?

7. What are valence electrons? Why are they particularly of interest to scientists?

8. Show a biological element with a Lewis dot diagram.

9. a) What is meant by an atom being neutral?

b) What is an ion? Describe its electron arrangement.

c) Differentiate between a cation and anion.

d) Give 5 examples of ions found in the human body.

10. a) What is a chemical bond?

b) Why is this an important term for biologists to understand?

11. a) Differentiate between:

i) ionic bond ii) pure covalent bond iii) polar covalent bond

b) What types of atoms form these types of bonds?


c) What does the term electronegativity refer to? What is the importance of such a measure?

12. Draw Lewis dot/electron dot diagrams or structural diagrams for the compounds below. State the type of bonding that is taking place (pure covalent, polar covalent, ionic)

a) O2 b) H2O

c) NaCl d) CH4

13. What happens to orbitals of different atoms during bonding? Why is this significant with respect to the molecule?

14. What does it mean if a molecule is polar?

15. How can a molecule have polar covalent bonds but be classified as non-polar?

16. Why would polarity be an important idea for biologists to understand?

17. Differentiate between an intermolecular and intramolecular force. Give an example of each.

18. Give three examples of biological reactions? (See 2 – 35).


19. a) Differentiate between an acid and base.

b) What does pH mean?

c) Draw and label the pH scale demonstrating where the acids would be found, and where the bases would be found.

d) What is the approximate pH of your stomach? blood? small intestine?

e) What is a hydronium ion? Why is it technically incorrect to call a hydronium ion a hydrogen ion?

f) What is it called when an acid is added to a base in equal proportions? Provide a sample equation. Identify the products.

g) What is the difference between a strong acid and a weak acid?


Review of Atomic Structure

All elements and compounds are composed of tiny particles called _______________.

The majority of the atom is made up of empty space. At the centre, of the atom is the tiny, dense nucleus, where the majority of the mass lies. The components of the atom are found in the chart:

Part of the Atom Charge Symbol Location in Atom

Relative Mass(1 amu = 1.67 x 10-24 g)

PROTON

ELECTRONNEUTRON

________________ define the identity of an element. This is represented by the atomic number. If the number changes, so does the element. Compare carbon (6) vs nitrogen (7).

Practice: Compare the number of protons in magnesium and phosphorous

Mg – _____ protons P – _____ protons

________________ can vary for atoms of the __________element (called ________________). Isotopes can be recognized by their differing atomic masses.

On earth, one will find a different percentage of each isotope (this is why the atomic mass on periodic tables are not whole numbers)

EXAMPLE: Carbon three different isotopes, ______, _______, and _______

Carbon-12 (12C) ____ protons and ____ neutronsCarbon-13 (13C) ____ protons and ____ neutronsCarbon-14 (14C) ____ protons and ____neutrons

indicates radioactive form (radioisotope); this means that the nucleus is unstable and will release radiation over time

Question: What are some applications of these radioisotopes for biologists?

ELECTRONS


e

Orbitals can be different shapes:Spherical shape (s)Dumb-belled shape (p)“Too Complex for Biology” shape (d)

- only 2 electrons can occupy an orbital (that’s why we draw electrons in pairs on Bohr diagrams)

- there is a special stability associated with complete orbitals (that’s why we often say that atoms are stable when they have a complete outer electron shell noble gas configuration)

Energy Level Maximum # of e- in Orbitals Max # of e- per Energy Level1 1s2

2 2s2p6

3 3s2p6d10

- Because the d orbitals are not bonding orbitals in biological elements, we will ignore these electrons from now on. So, effectively, aside from the first shell, the maximum number of electrons we will talk about in an outer shell is 8 (consistent with what you’ve learned in younger grades) SORRY CHEMISTS!!!

For Biologists in this Class Energy Level Max # of e- per Energy Level

1

2

3

4

- electrons occupy specific distances away from the nucleus corresponding to energy levels (n = 1,2,3….. further away)

- it is impossible to know the exact position of an electron, but there are volumes of space where the electrons are MOST likely to be found

- volumes of space called _________________

P+ N0

Increasingenergy


______________ electrons refer to those electrons in the outermost energy level (s and p orbitals*)

- are important because these are the electrons most likely involved in chemical reactions- Lewis structures can be used to illustrate the valence electrons, predict the number of bonds formed and/or to determine the ionic charge they will have:

Chlorine 2, 8, 7*

Why?If the electron orbitals are not complete, atoms will want to react with other “willing” elements in such a way to fill these orbitals

- when atoms lose or gain electrons to become stable, they become ____________

- when most biological elements lose or gain electrons to become stable, they will end up with 0 or 8 e- in their outermost shell; this is called a ____________________

ION charged atom, resulting from a loss or gain of electrons

Consider 11Na It has an electron arrangement of ___, ___, ___; it will want to ______ electron to have a stable octet (2, 8 )

Results - one extra proton (+11) vs electrons (-10); it will be positively charged. We write this as _______.

Consider 16S It has an electron arrangement of ___, ___, ___; it will want to ______ electrons to have a stable octet (2, 8, 8 )

Result - two extra electrons (-18) vs protons (+16); it will be negatively charged. We write this as ________.

You try: What is the electron arrangement of 7N? How many electrons would it lose or gain? What is the ionic charge?

Most metallic and non-metallic elements existing in your body will be in the form of ions. This means that they are already in stable form.

KEEP IN MIND…

When atoms lose or gain electrons, there must be a “willing” element to exchange with. This leads us into the topic of CHEMICAL BONDING.

Recall from yesterday:


- Elements identified by atomic # (# of protons)- isotopes of an element have different # of neutrons- nucleus of atom hold protons and neutrons- electrons found in orbitals around nucleus of atom; can have

different shapes: spherical (s) , dumb-bell (p)- valence electrons are in outermost orbital and are involved in

reactions; Lewis structures show valence electrons around the element symbol

- atoms react to create a stable octet in the valence shell (either gain or lose electrons to become stable)

o cations are positive ions (lost electrons)o anions are negative ions (gained electrons)

_______________________________ (En)– the measure of an atom’s ability to attract electrons (see table pg 14);

_______________________________ - attractive forces existing between atoms that allow molecules to form

2 Types: 1. _____________________________bond: the bonds that form molecules or compoundsA) _______________– form between a __________and ______________. – electrons are transferred, forming a cation and an anion; the attraction forms the bond; ionic compounds form crystalline structures that dissolve in water (dissociate into ions in water)

ΔEn > 1.7

Example: NaCl

B) ________________– form between ____ ________________.- electrons are _______________between atoms to achieve a stable octet: orbitals overlap and change shape (hybridize)

i) __________covalent – ____________ sharing of electrons ΔEn = 0

SINGLE DOUBLE TRIPLE


– share one pair -share 2 pairs – share 3 pairs (CH4) (O2, CO2, unsaturated fat) (N2, HCN)ii) __________________covalent – ______________ sharing of electrons, creates a slight charge separation due electronegativity differences: 0 < ΔEn < 1.7

- the atom with higher En will pull the shared pair closer becoming δ- (dipole) while the other atom with the lower En becomes δ+ (dipole)

e.g. H2O ICl

Polarity of Moleculesp. 11-12- we often need to look at the 3-D shape to determine if a molecule is polar (it may have polar bonds and yet still be a non-polar molecule if it has a symmetrical shape)

POLAR NON-POLAR

H2O CH4

NH3 CO2

- polarity of molecules allows interactions to occur between molecules; this explains _______________________ of covalent compounds (the ability of a substance to dissolve in a solvent)

Like dissolves like “Polar dissolves Polar”“Non-polar dissolves Non-polar”

_____________ – liquids that will dissolve in each other

_________________– liquids that will form separate layers instead of dissolving when

mixed

Hydrophilic “water loving” Hydrophobic “water fearing”


- polar molecules dissolve in water - non-polar molecules DO NOT dissolve in water

2. __________________________________ forces *weaker than ionic and covalent– collectively called the van der Waals forces

i) _____________________________ –weakest; found between all molecules (nucleus and electron orbitals); the only force holding nonpolar molecules to one another

ii) _________________________________________– hold polar molecules to one another; attraction between δ- and δ+ ends of polar molecules; stronger than London forces

iii) _____________________________ – found between H of one polar molecule and N, O, F or S of another polar molecule

water molecules held together by H bonds gives it unique properties

Unique Properties of Water1. has the ability to “_________________”; surface tension is created by:

- ___________________ (H bonding between water molecules) - ___________________ (H-bonding with other polar molecules)

2. absorbs a lot of ___________– high specific heat capacity and specific heat of vaporizations (H bonding cause large amounts of heat to be absorbed before changing temp or vaporizing) allowing for temp moderation, evaporation and cooling

3. solid water is __________ _____________ than liquid water – below 00 a crystal lattice forms (freeze) and H bonds between molecules spread further apart, thus reducing density

*Ionic compounds will dissociate in water; a hydration shell forms around ions (charge separation) – see diagram in text

Homework: Text p. 17 Do #1-6, 8-9, 11-13.Additional Questions:

1. What is the reason for water’s ability to dissolve a variety of substances?2. Give examples of substances that dissolve easily in water.3. Give examples of substances that do not dissolve easily in water.4. Why do small, non-polar substances like O2 not dissolve in water?5. How are substances like O2 transported?6. Give an example of hydrophobic and hydrophilic substances.


Unique Properties of Water

Water is the _____________________________. More substances dissolve in water than in any other liquid solvent, mostly due to it’s polarity and H-bonding:

Water has the ability to “cling” due to _______________ ( H-bonding between water molecules – creates high surface tension) and _____________________ (H-bonding with other polar molecules – allows for capillary action and solubility of polar molecules); water molecules create a _________________; H-bonds constantly break and reform giving water it’s fluid properties.

Solid water is __________ ____________ than liquid water – below 00, crystal lattice forms and H-bonds between molecules spread further apart, thus reducing density ice floats on water.

Water is able to ___________________________________– it has a high specific heat capacity and specific heat of vaporization energy is used to break H-bonds, thus large amounts of heat are absorbed before changing temperature, evaporating or cooling.

Aqueous solutionsWater molecules will readily surround polar, charged molecules and ions of other substances, forming a _________________________________ which reduces attraction between molecules and promotes separation.This allows substances to form __________________________________ in which the water is the solvent and the substance is the solute.

__________________________ – polar or charged molecules that are strongly attracted to water (‘water-loving’) ______________________

__________________________– non-polar molecules that are not strongly attracted to water (‘water fearing’) ______________________________

**Water dissolves thousands of solutes necessary for life these solutes are able to float around and collide, allowing chemical reactions to occur.


Instructions: The following are scenarios that can all be explained by water’s unique personality (eg. physical properties). Use the handout from Biology 12 to help you complete the following table.

Scenario Property ExplanationA toddler takes some salt, puts some on his tongue, and watches in amazement as it disappears.

Polarity

That same toddler makes some Kool-aid and watches as the sugar he adds disappears. Is it the same magical trick?

Polarity

When the stems of red carnations are placed in black dye, the carnations eventually turn black.

Lakes are always slower to warm up in the spring (versus the air) and slower to cool down in the fall. So why does this happen?

Oh to be a water strider! If they see water, they walk on it. When we see water, we take a bridge.

Oceans and lakes don’t freeze solid; instead the ice floats on the water, and acts to help preserve the aquatic life below with an insulating effect. So, why does solid


water float?

Ionization

Pure water will ______________________ into _____________________(H3O+) and ________________________(OH-) ions in equal proportions. Other substances will alter the balance between these ions, creating acidic and basic solutions.

ACIDS, BASES, pH, BUFFERS

When _________ is greater than _________, the solution has properties of an ____________ ______________taste, conduct electricity, turn ______ litmus ___

___________ are substances that increase [_______] in solution (donate protons).

*________________ acids tend to dissociate completely, whereas _________ acids have little dissociation.

e.g.

When __________ is greater than __________, the solution has properties of a _____________ ______________ taste, _______________ feel, conduct electricity, turn ____________ litmus _________

____________ are substances that increase [_______] in solution (accept protons)*Strong bases tend to dissociate completely, whereas other bases combine directly with H+ ions.

e.g.

pH – “Power of Hydrogen” - a measure of the ___________________ of a solution; describes the [H3O+]; can be calculated using the formula: pH = – log [H+]

Note: [H+] represents the concentration of H+ or H3O+


pH scale – also see pg. 32 in text.

Note: Each whole number on the pH scale represents a 10X difference; pure water at room temp.

has a [H3O+] = 1.0 x 10-7 pH 7

Components of living cells are sensitive to pH levels - most* cellular processes operate best within a range of pH ________ __________; very small changes in pH can have huge impacts on biological reactions and molecule functioning.

Various factors can alter/change pH:o cellular processes (produce acids or bases)o foods we consumeo health; vomiting pH, diarrhea pH

When strong acid and bases dissolve, they dissociate completely;HCl donate all H+ to water - [_________] goes up – pH ____________NaOH donate all OH- to water - [_______] goes up – pH _____________

Weak acids and bases only partially ionize in water - this is a _____________________ reaction (ions can reassociate once in solution)

In order to keep pH levels constant, living organisms have ______________________, consisting of _______________________and _____________, that minimize changes in pH (they do this by absorbing or releasing H+ ions)

One of the most important buffers in human extracellular fluid and blood is ___________ ____________________________________:


When reactions increase H+ in the blood, ________ ions react with extra protons (H+) to produce __________.

When reactions increase OH- levels in the blood, OH- ions react with ______ forming ________, then H2CO3 dissociates to replace the H+

Result: [H+/H3O+] is maintained within narrow limits, keeping the pH constant


The Chemicals of Life

_________________ atoms make up the base of every organic compound, including the 4 major classes of biologically important molecules: _____________________, ____________, _____________, ____________________

Why Carbon?

it is the ______ _____________ ___________– has _____ unpaired valence electrons and can form 4 bonds with other atoms

covalent bonds of carbon are _____________ and ______________ joins with other carbons in various ways: straight chains, branched chains, rings of various size/complexity

form covalent bonds with Hydrogen; molecules called _______________________:

Methane (CH4) Propane (C3H8) Benzene (C6H6)

*These structures are ________________________ due to symmetry, even

though individual C-H bonds are ______________.

Molecules of living organisms contain other elements in addition to C and H;

__________ ______________________ contain _________________groups of

atoms, called __________________ _________________, which give the molecule

distinct characteristics (usually ionic or strongly polar).


Biological Functional Groups are often the site of chemical reactions between molecules:

Try these……circle and name the functional groups:

H H O O H O HH–C–H O H2N–C–C–OH HO–P–O–C–C –C–OH

H2N–C–C=C–C–H H–C–C–SH O H HO H H O


Biologically Important Molecules

Macromolecules are large organic molecules composed of ____________________ simple/single molecular units

______________________– consist of many identical or similar monomers linked by bonds; include carbohydrates, proteins, nucleic acids

__________________________________ – consist of different monomers; include lipids

There is unity in life, as there are only ~40-50 common monomers used to construct macromolecules.

Special reactions that require catalysts or enzymes are needed to build and break macromolecules:

_________________________________: require energy to build macromolecules

(usually ____________________________________ reactions water is

__________________ at the union site)

______________________________________: releases energy when bonds of

macromolecules are broken (______________________– a water molecule is

____________________ where the bond is broken)


a) MonosaccharidesCarbohydrates b) Disaccharides/Oligosaccharides

c) Polysaccharides

contain ____:_____:_____in the ratio ____:_____:_____ empirical formula (___________) where n = # of C atoms the ______________ source of __________ due to the high number of C-H bonds also found as structural compounds and energy reserves almost exclusively from _________________ sources contain ____________________________ groups; ____________________

a. Monosaccharides- simplest, _____________ sugars; most common with 3, 5 or 6 C- 5 carbons __________; 4 alcohol groups, 1 aldehyde or ketone; C5H10O5

- 6 carbons __________; 5 alcohol groups, 1 aldehyde or ketone; C6H12O6

Examples: Glucose, Galactose, Fructose; all have the same molecular formula (C6H12O6),but different structural formulae called ______________.

- in _________________, monosaccharides react intramolecularly to form ___________ (making it easier to move around):


b. Disaccharides/Oligosaccharides _________________________ covalently bonded together (________________); the covalent bond is called a _________________________________.

Disaccharide Monomers Sources

Dehydration Synthesis: pg. 34 -35

c. Polysaccharides- ________________ of glucose (100’s – 1000’s); ___________, but _____________ in water due to large size- formed by dehydration linking C1 with C4 or C6 of another monomer

Key functions:

1. ENERGY STORAGE: i. *___________________ long, ______________ chain of several hundred

glucose; α-1,4 linkage

ii. *___________________ highly ______________ (every 30th glucose has short side chain attached to C6); α-1,4 and α-1,6 linkages

* both forms of _____________________ from ____________

iii. ____________________ similar structure

+ H2O

+ H2O


to amylopectin, but with ____________ branches and ___________ side chains; storage in _______________ (liver and muscle)

2. STRUCTURAL INTEGRITY

iv. _____________________long, ________________ chains, with _____________________ glucose molecules – β-1,4 linkages; allow ___________________ to form between parallel chains; creates a _________, ______________ fibre; (______________________ walls)

a. ________________ modified form of cellulose (contains ______); abundant in nature (_____________,__________________________)

Lipids


- ________________, _____________________,________________* in water

- Smaller than carbohydrates; have H, C and fewer O

There are 5 main categories of lipids: Fatty acids, fats, phospholipids, steroids, waxes.

1. Fatty Acids a _______________________chain with a _________________

functional group (gives it acidic properties) have 4 or more C in the carbon chain (most common are

even numbered chains) as chain length increases, solubility

__________________________ if C are all __________________ bonded and contain the max.

# of hydrogen, it is a __________________________ chain if there are __________________ bonds between carbons, it is

an __________________________ chain (only 1: mono-, more than 1: poly-)

2. Fats Energy __________________________(long periods of time) contain many more C – H bonds and fewer polar –OH

Structure:- ______________________are a composite molecule made up of:

- __________________________o a 3 carbon alcohol with each carbon

bearing a hydroxyl group (-OH)


- ___________________________ side chains (see above) *can be the same or different fatty acids

Triglycerides are formed through ____________________________ reactions; an _______________________ bond or linkage holds the fatty acid to the glycerol backbone.

The properties of the fatty acid side chain determine the type of fat: i) _____________________ - only __________ bonds (C-C) in the carbon chain; mainly from _____________________ sources; ____________ at room temperature due to close fit of the side chains (many van der Waals forces at work) ex: ______________,_______________

ii) _____________________(a.k.a. oils)– one or more _________________ bonds (C=C) in the carbon chain; mainly from ______________ sources; ___________ at room temperature due to the bends in the chain @ double bond sites (fewer van der Waals forces)The more double bonds the side chains contain, the more fluid the fat. ________________________ fatty acids contain many double bonds (C=C)

ex: ___________ oil, __________oil, _________oil


_________________________ is the process of adding H’s to an unsaturated fat (splitting double bonds); the fatty acids becomes more saturated, thus the fat becomes more solid (e.g. margarine)

3. Phospholipids Primary component of __________________________________ create a phospholipid bilayer: _______________outside, _________________ inside composed of a glycerol backbone attached to 2 non-polar fatty acid chains and a highly polar phosphate ___________________________ molecule: the phosphate “head” is hydrophilic and the fatty acid “tails” are hydrophobic

4. Steroids mostly _______________________*, very __________________ contain 4 ____________ hydrocarbon ______________ with several functional groups


sterols have an –OH group (hydrophilic) _______________________ is an important steroid in cell membranes; cells convert cholesterol into vitamin D and bile salts other steroids include ________ hormones – testosterone, estrogen, progesterone (different side-chains)

5. Waxes large, contain long-chain fatty acids linked to alcohols or carbon rings extremely _____________________, _____________________, __________ with a firm, pliable consistency form ____________________________ coatings on plant and animal partseg. stems, leaves, fruit – (cutin); bird feathers; beeswax

Proteins- most diverse molecules in living organisms; consist of C, H, O, _____ & ______- proteins are _______________ ____________ polymers, folded into _______ structures- proteins accomplish more tasks than any other group of biological molecules:

1) ___________________ – catalyze chemical reactions in the body

2) ___________________ – hair, nails, skin, tendon3) ___________________ – fight infection, form antibodies, form

blood clots4) ___________________ – Hormone messenger5) ___________________ - Transport i.e. hemoglobin (CO2/O2)6) ___________________ /___________________ - Cell

markers/protein channels7) ___________________ – form muscle fibres (actin/myosin)


General Structural of an Amino Acid:

- in solution, _____________ group releases H+ and _______ accepts H+

- each amino acid has it’s own _____________ _______________ (R- group), which gives it unique properties; there are _______ different R groups ( 20 different amino acids)

- side groups can be polar, non-polar, charged, acidic or basic; they may contain __________ , _________, __________, or __________ which can interact with other molecules both in and outside of the same protein.

- 8 amino acids are ____________________ (we cannot make them – must come from our food)

- amino acids are linked together in _______________________ reactions between the __________ group of one a.a. and the _________________group of another a.a.; the link is called a ____________________________ ; thus _______________ _____________ are formed*Note: in cells, a.a. are added only to the carboxyl end (1 direction)


- amino acid polymers are called _______________________ (have >50

aa)

- a protein is one or more polypepetides folded into precise 3-D shapes.- the _____________________________ (shape) of the protein is determined by the sequence of amino acids; 3D structure is directly related to the protein’s function

Protein Structure and Function


Proteins have 4 levels of structure:

a) ______________________ structure – the _________________ ____________________ of amino acids that make up the polypeptide chain (DNA codes specifically for this order)


Example: Cys – gly – ala Each sequence is different Gly – ala – cys each would form a differentAla – cys – gly protein

b) ______________________ structure – the _________ or ______________ that develop in a polypeptide chain due to _____________________ between amino and carboxyl groups of neighbouring a.a.

There are 2 types of secondary structures:i) ________________(every 4th a.a.)ii) ________________(side-by-side)

c) ____________________ structure – the overall 3D shape of the protein; depends on secondary structure

if secondary is β-pleats, the 3D shape will be ________________, and the protein function will be ______________________ e.g. hair, nails, silk if secondary is α-helices, the 3D shape will be ________________, and the protein function will be ______________________ e.g. enzymes

* 3D shape folding occurs due to ____________________________________:

- hydrophobic interactions these a.a. congregate at the core/centre of protein (away from water)

- van der Waals forces these strengthen/reinforce hydrophobic interactions

- H-bonding occurs between polar side chains

- Ionic bonding – occurs between negatively and positively charged side chains (R groups)

- Disulfid bridge (covalent) – occur when 2 cysteine amino acids are close together

Weak interactions;Have a cumulative effect

Strong interactions;

Increase stability


d) _______________________ structure – a.k.a functional protein; result from the interaction of ____________________ polypeptide chains (each is called a subunit)

E.g. hemoglobin (4 chains)

*These contain prosthetic groups (non-protein) that help the protein function

Factors that affect protein shape:- in primary structure, altering the __________________ of a.a. will alter the shape of the protein, since each side chain has different chemical properties- cell conditions: pH, temperature, [salt] can cause ____________________-the protein loses its shape (bonding interactions disrupted); protein can become inactive. **This is reversible or permanent depending on nature of external stimulus.

Dangers and uses of denaturation:- gastrin works best at pH 2, is denatured in small intestine at pH 10- fever above 39C could denature critical brain enzymes


- curing meat with salts denatures bacterial enzymes (prevent spoil)

- heat denatures hair proteins; temporarily straighten/curl

Nucleic AcidsNucleic Acids

- are informational polymers; serve as assembly instructions for ______________ production

- two main types exist: o ______________________________________ (DNA) – stores hereditary

info for all organisms (prokaryote, eukaryote, most viruses)o ______________________________________ (RNA) – hereditary

molecule of some viruses; also involved in protein synthesis

- the __________________________ is the monomer of nucleic acids; each nucleotide consists of 3 subunits:

o ________________ group(s)

o a 5-C _____________ (pentose)

o a ___________________ base

- the sugars in DNA and RNA differ:

- There are 2 different groups of Nitrogenous bases:_______________________ – have a ________________ ring; _________________ (C), ________________ (T)-DNA only, ________________ (U)-RNA only

Glycosyl bond


________________ – larger, have _____________ rings(in both DNA and RNA); ___________________(A) and __________________ (G)

- nucleotides form a polymer or ______________________ strand through _______________________ reactions between the phosphate group of 1 nucleotide and the –OH group on the 3-C (sugar) of another nucleotide; this is called a _______________________________ bond (polar covalent, hydrophilic)

*the alternating phosphates and sugars form the ___________________ of a nucleic acid chain

- DNA coils into a ___________________________________ (twisted staircase); the 2 strands are held together by _________________between N-bases

DNA base pairs will always match a purine with a pyrimidine

_______________________Note: this central region with N-bases is

hydrophobic

- to form the H-bonds properly between N-bases, the 2 strands must run in opposite directions, called __________________ (one DNA strand is upside down compared to the other)

- DNA strands are very long (coiled around histones to fit into a nucleus),

are soluble in water and insoluble in alcohol

- RNA remain single stranded as short chains that can be straight or folded (clover or hairpin)


The nucleotides *_________* (adenosine triphosphate) and __________ (guanosine triphosphate) are the primary energy-transferring molecule in living organisms which drive almost all reactions in a cell (they regulate and adjust cellular activity).

Enzymes spontaneous chemical reactions may occur very slowly; energy must be absorbed

by reactants in order to rearrange bonds, called ____________________________ ______________ - ______ (reactants must collide with enough force and proper geometry to break bonds, reach transition state and form products)

heat can speed up the rate of a chemical reaction, but high temperatures can kill cells

enzymes are ________________ ___________________ they ______________ the rate of chemical reaction without being ______________ or _______________ and keep ________________________ in acceptable ranges

enzymes have specific shapes and will bind and orient reactant molecules, called_________________________, to _________________ the activation energy and speed up reactions

HOW? A substrate binds to the __________________________ of an enzyme (pocket or groove that matches the shape of the substrate). The enzyme _______________ its shape to ____________________ the connection to the substrate, called an ___________________ _________; this alteration stresses the substrate bond,


lowering the activation energy, driving the reaction.

Enzyme-substrate specificity

- Each enzyme has a unique 3D shape, this makes it specific to the substrate(s) it works on:

e.g. amylose + ________

maltose + ________Cofactors and Coenzymes

_____________________ – _______________________ group that binds to an enzyme and is essential for catalytic activity; often _________________ (e.g. ____, ______, ______, ______)

_____________________ – ________________ molecules that act as cofactors; many derived from ___________________; many will ____________________ molecules from one enzyme to another e.g. NAD+ from Vit.B3 (niacin) electron carrier in c.r.

Conditions and Factors Affecting Enzyme Activity

1. Concentration of Enzyme and/or Substrate

_________________________: Excess substrate is proportional to enzyme concentration: if [enzyme] is _________________, then more substrate = ________________________________ up to the saturation level

______________________: There are a ________________ number of enzyme molecules in a cell at one time; each reaction takes time to complete; when all enzymes are ____________________ working, the rate of reaction is much faster; the more enzymes present/working, the __________________ the reaction

2. _______________________

Reactions increase in _______________ as temperature ______________________ BUT beyond a ___________


temperature (for most enzymes <55C), an enzyme will __________________________ first, slowing enzyme activity then stopping it completely3. _________

Each enzyme works at an optimal pH (depends on properties of the enzyme); altering the pH can cause _________________________ changes and ____________ the enzyme’s ability to catalyze a reaction (e.g. pepsin – pH ______, trypsin – pH ______)

4. _______________________________

Chemicals bind to an enzyme, decreasing its activity (lower rate of reaction).

a) _____________________ inhibition – a ___________________ molecule that resembles the normal substrate binds to the ________________ site, blocking the substrate and ________________ the reaction.

b) _______________________ inhibition – molecules that bind to the enzyme at _________ locations (NOT the active site) causing a change in ______________; the active site is not longer ____________________ (substrate cannot bind)

Weak inhibitors can be _______________________; Strong inhibitors are not released _______________________ (e.g. Toxins cyanide, antibiotics). The cell must produce more enzyme to overcome irreversible inhibition.

c) _______________________________________(reversible non-competitive)

________________________ molecules bind to an enzyme on its ______________ site, causing a ___________________________ to the active site. This can either ____________________ or ___________________ enzyme


activity, referred to as allosteric ____________________and allosteric __________________ respectively.

Feedback inhibitionA method used to control or regulate ________________________ pathways one of the __________________ of this pathway acts as an _________________ to earlier enzymes, thus ________________ or _________________ the process. If the [inhibitor] is __________ , it will ___________________ from the enzyme, allowing it to function, thus turning ______ the pathway. **See handout


Cells: The Basic Units of Life: PowerPoint Notes

Types of Cells Prokaryotic Cells

Earliest Cells Do not have a nucleus Have very few organelles Examples: bacteria and archaea

Eukaryotic Cells Evolved from prokaryotic cells Do have a nucleus Have many organelles Examples: plants, animals, fungi and protistsOrganelles*(Eukaryotes) An organelle is a small structure inside the cell that is specialized to perform a particular job. Animal cells and plant cells have many organelles in common, but also have some

differences. The following are important organelles:

Cell or Plasma Membrane All cells have a cell or plasma membrane; it is the outer most portion of a cell, or it lies just

inside the cell wall (plant, fungi, bacteria). It forms a dynamic barrier around the cytosol to maintain the internal environment of the

cell. It is semi-permeable, and controls the movement of material in and out of the cell

**more on this later** Cytosol The jelly-like fluid inside the cell; suspends the organelles. **Cytoplasm is a term that refers to all of the internal components of the cell, excluding the

nucleus


Nucleus The control center of the cell. It is keep separate from the rest of the cell by the nuclear membrane (double membrane;

outer part of E.R.). The nuclear membrane has holes in it called nuclear pores which allow items in and out. Inside the nucleus there is DNA and usually a nucleolus. DNA when uncoiled is called chromatin.

Nucleolus Dense, irregular shape It makes the subunits of ribosomes out of proteins and RNA

Ribosomes Can be free-floating or attached to an endoplasmic reticulum. The site of protein synthesis.

**more on structure and function in Molecular Genetics unit**

Endoplasmic Reticulum (ER) A series of canals that connect the nucleus to the cell membrane; flattened & folded tubes. It is like a subway system in which molecules made by the cell can travel all over. Rough ER have ribosomes on them; make proteins. Smooth ER do not have ribosomes ; make lipids and break down carbs, fatty acids, drugs

and poisons. Molecules made in the ER are packaged into vesicles.

Vesicles Membrane bound, saclike organelles Transports, stores or digests substances within a cell Several types include: peroxiosomes, vacuoles and lysosomes. Peroxisomes Mainly found in liver and kidney cells. Contain enzymes; they are used to break down toxins like hydrogen peroxide, alcohol and

heavy metals. Similar in appearance to lysosomes.Vacuoles Large, fluid-filled, storage organelles that isolates water, metabolic wastes, and can store

nutrients. Usually very large in plant cells – its fluid pressure keeps the plant cell firm (turgid).Lysosomes Small, membrane-bound sacs that contain digestive enzymes. They fuse with vacuoles and the enzymes breakdown broken cell parts or are used to digest

nutrients.


Found in animal cells.

Golgi Bodies Stacked, folded membranes It processes the lipids and proteins made in the ER and then ships them to the cell membrane

or to lysosomes. Vesicles are the bubbles of protein/lipid that it receives from the ER and ships out towards

the cell membrane.

Mitochondria (pl.) Cellular respiration occurs in the mitochondrion, making energy (ATP)for the cell. (# vary

depending on cell type) It has two membranes: an outer membrane and the inner called the cristae; the space

between the membranes is the intermembrane space (IMS); the mitochondrial matrix lies inside the cristae.

Plastids Found only in plants and algae. Used for photosynthesis or storage.Chromoplasts – make and store pigments other than chlorophyllAmyloplasts – store starch Chloroplasts Site of photosynthesis (make sugars); green due to chlorophyll pigment (reflects green

light). Oval or disc shape with two outer membranes. Has an inner membrane that surrounds a compartment called a thylakoid. The thylakoids stack up on one another to make grana. The fluid inside the chloroplast is the stroma.

Cytoskeleton Made up of microfilaments (with actin protein) and microtubules ( hollow tubes) which

strengthen the cell, help maintain the shape, and move organelles and other structures through the cytoplasm.

Centrosome Located near the nucleus, this organelle organizes the cytoskeleton and contains centrioles

which help separate chromosomes during mitosis.

Flagella (sing. Flagellum) Whip-like tails found in some animal cells, bacteria and protists. Usually quite long compared to the cell. Used for propulsionCilia Tiny hair like projections found in some animal and protist cells. Move water and mucus in eukaryotes; used for movement/propulsion of prokaryotes


Pseudopods Extensions (lobes) that stretch out from the cell to engulf a target, or to move the cell

Cell Wall The outer most portion of a plant, fungal or protist cell. It protects, supports and keeps the cell’s shape. It is not as selective as the cell membrane; porous. Plant cell walls are made of cellulose, a sugar filled with lots of energy, however humans

cannot digest it. *Primary wall – cellulose *Secondary wall – thicker coating; internal

Extra-cellular matrix Found in multi-cellular organisms; non-living mixture of proteins and polysaccharides

secreted by cells; varies depending on cell type. Functions: support and anchors cells, separates tissues, function in cell signaling Examples: Plant cell wall (cellulose), Fungi cell wall (chitin), animals bone, insect

exoskeleton, shells. Cell junctions are structures that allow cells to interact with each other and the surrounding

environment

The Structure of the Cell Membrane: PowerPoint Notes

Cell membranes are very intricate. They are made up of fat molecules called phospholipids, cholesterol and some proteins and carbohydrates.

All of these make sure the membrane stays fluid so it can do its job.

The plasma membrane is a thin outer layer that surrounds all cells. This membrane has four main functions:

1. allow the transport of raw materials into the cell

2. allow the transport of manufactured products and wastes out of the cell

3. prevent the entry of unwanted material into the cell

4. prevent the leakage of essential matter out of the cell

Cellular functions depend on a watery environment like the one that is found on the inside of the cell. In order to maintain their integrity, cells need to be surrounded by an environment through which water cannot flow. A membrane composed of fatty molecules serves this purpose.

History of the Cell MembraneIn 1924, using an electron microscope, two Dutch physicians, E. Gorter and F. Grendel found that the cell membrane was composed primarily of phospholipids (shown on the right).


Phospholipids are made up of a glycerol backbone with a hydrophilic head region containing a phosphate group and a hydrophobic tail region containing a saturated fatty acid and an unsaturated fatty acid.

The fact that it has both types of fatty acids ensures the cell membrane is fluid.

They deduced, based on the properties of phospholipids, that the cell membrane was in fact a bilayer.

By the 1930s experimental evidence showed that proteins were also part of the cell membrane.

In 1935, James Danielli and Hugh Davson proposed the sandwich model: a phospholipid bilayer between two layers of protein with pores for molecules to travel through.

Stronger electron microscopes would show that the cell membrane was not covered in protein, but rather had protein embedded in it.In 1972, S. J. Singer and Garth Nicholson presented the fluid mosaic model of the cell membrane, which displayed the cell membrane as an integration of proteins and other molecules into the phospholipid bilayer.

Structures in the Fluid Mosaic Model of the Cell Membrane

Cholesterol is interspersed throughout the cell membrane to add rigidity to it. It also allows the cell membrane to stay fluid over a wider range of temperatures. Various proteins are associated with the cell membrane with 4 main functions: transport, enzymatic activity, triggering signals, and attachment/recognition.

Integral Proteins (a.k.a. trans-membrane proteins) span the width of the cell membrane: these create channels through which charged molecules or large molecules can pass through

Peripheral Proteins are found on the surface of the cell membrane and are primarily used in cell to cell signaling with surface carbohydrate chains or linking with the cytoskeleton for support.The cytoskeleton is attached to the cell membrane for added stability, since membrane proteins and phospholipids can shift places in the membrane.

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