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1/6/14 1 CAMPBELL BIOLOGY IN FOCUS © 2014 Pearson Education, Inc. Urry Cain Wasserman Minorsky Jackson Reece Questions prepared by Brad Stith, University of Colorado Denver Janet Lanza, University of Arkansas at Little Rock Louise Paquin, McDaniel College Instructor: Susan S Golden, PhD BILD 1 The Cell BILD 1 is a one-quarter introduction to molecular and cell biology A thorough understanding of basic chemistry is assumed. It is the student's responsibility to address deficiencies in prerequisites Discussion sections do not meet the first week. You will sign up for a section at: http://sections.ucsd.edu/ TA discussion sections and office hours are for questions and extra help to understand material. BILD 1 Materials Posted on TED Syllabus – read it, put exam dates on your calendar FAQ Lecture slides TA information (office hours, handouts) Announcements Q&A Grades Practice exams, exam keys, challenges You will need… Campbell: Biology in Focus Mastering Biology (online) – Masteringbiology.com i>clicker (original or i>clicker2) – Register it on TED To sign up for a section – Meet the TAs To check TED frequently for announcements

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CAMPBELL BIOLOGY IN FOCUS

© 2014 Pearson Education, Inc.

Urry • Cain • Wasserman • Minorsky • Jackson • Reece

Questions prepared by Brad Stith, University of Colorado Denver

Janet Lanza, University of Arkansas at Little Rock Louise Paquin, McDaniel College

Instructor: Susan S Golden, PhD BILD 1 The Cell

•  BILD 1 is a one-quarter introduction to molecular and cell biology

•  A thorough understanding of basic chemistry is

assumed. •  It is the student's responsibility to address

deficiencies in prerequisites

•  Discussion sections do not meet the first week. •  You will sign up for a section at:

•  http://sections.ucsd.edu/

•  TA discussion sections and office hours are for questions and extra help to understand material.

BILD 1 Materials Posted on TED •  Syllabus

–  read it, put exam dates on your calendar •  FAQ •  Lecture slides •  TA information (office hours, handouts) •  Announcements •  Q&A •  Grades •  Practice exams, exam keys, challenges

You will need…

•  Campbell: Biology in Focus •  Mastering Biology (online)

– Masteringbiology.com •  i>clicker (original or i>clicker2)

– Register it on TED •  To sign up for a section

– Meet the TAs •  To check TED frequently for

announcements

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How to Succeed in BILD 1 •  Keep up!

–  Come to class, read the textbook, use the MasteringBiology resources, attend section, and study every week

•  Read all textbook sections related to lecture material –  The textbook provides depth and examples that will help your

understanding •  Understand the material, don’t just memorize it

–  Apply your knowledge to different situations and contexts –  Integrate information and concepts between topics and chapters

•  “Know what you don’t know” –  Test yourself to identify areas of weakness to focus your study

Your Grade will come from… •  850 points from exams

–  2 midterm exams (40 questions, mc) –  A final (62 questions, mc)

•  150 points from assignments –  Mastering Biology (watch due dates)

•  Up to 3% "extra credit” from class participation –  i>clicker

•  Grade scale in syllabus –  Not curved

Please, Turn off or silence your mobile phones & Mute your computers If you are using a computer in class, please sit in the side sections to leave the center section free of screens and keyboards for others who find computers distracting. In general, have respect for your classmates (and instructor) and avoid distracting others. For example, please do not start packing up to leave before the lecture is over because it is distracting to others (and to me).

CAMPBELL BIOLOGY IN FOCUS

© 2014 Pearson Education, Inc.

Urry • Cain • Wasserman • Minorsky • Jackson • Reece

Lecture Presentations by Kathleen Fitzpatrick and Nicole Tunbridge

2 The Chemical Context of Life

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You are responsible for all of Chapter 2

•  Chem 6A is a prerequisite for BILD 1 –  And you should have 6B or be taking it now

•  There will be questions from this chapter on your exams –  Even if those slides are not covered in lecture

•  Chapter 2 homework in Mastering Biology –  To make sure you understand this material

•  Knowledge of basic chemistry is essential for understanding how biological molecules behave the way they do, and why biological processes exhibit their emergent properties

© 2011 Pearson Education, Inc.

Emergent Properties

•  Emergent properties result from the arrangement and interaction of parts within a system

•  Biological systems are much more than the sum of their parts

•  Emergent properties characterize non-biological entities as well

© 2011 Pearson Education, Inc.

Emergent Properties •  Emergent properties

– Examples from chemistry – Examples from mechanical objects

Sodium Chloride Sodium Chloride

+

Figure 2.2

Concept 2.3: The formation and function of molecules depend on chemical bonding between atoms

§ Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms

§  This usually results in atoms staying close together, held by attractions called chemical bonds

§ Reviewed in Mastering Biology assignment

© 2014 Pearson Education, Inc.

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§  In a nonpolar covalent bond, the atoms share the electron equally

§  In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally

§ Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule

© 2014 Pearson Education, Inc. Animation: Covalent Bonds

Weak Chemical Bonds

§ Most of the strongest bonds in organisms are covalent bonds that form a cell’s molecules

§ Weak chemical bonds, such as ionic bonds and hydrogen bonds, are also important

§ Many large biological molecules are held in their functional form by weak bonds §  Molecular shape determines how biological

molecules recognize and respond to one another

© 2014 Pearson Education, Inc.

Hydrogen Bonds

§ A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

§  In living cells, the electronegative partners are usually oxygen or nitrogen atoms

© 2014 Pearson Education, Inc. © 2014 Pearson Education, Inc.

Figure 2.12

Hydrogen bond

Ammonia (NH3)

Water (H2O)

δ− δ+

δ−

δ+

δ+

δ+

δ+

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Concept 2.5: Hydrogen bonding gives water properties that help make life possible on Earth

§ All organisms are made mostly of water and live in an environment dominated by water

§ Water molecules are polar, with the oxygen region having a partial negative charge (δ−) and the hydrogen region a slight positive charge (δ+)

§  Two water molecules are held together by a hydrogen bond

§  The abundance of water is the main reason the Earth is habitable

© 2014 Pearson Education, Inc.

Polar covalent bonds in water molecules result in hydrogen bonding •  The water molecule is a polar molecule: the

opposite ends have opposite charges •  Polarity allows water molecules to form hydrogen

bonds with each other

© 2011 Pearson Education, Inc.

Animation: Water Structure H2O H H

O

δ+

δ−

δ+

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Water is a Polar Molecule •  The polarity of water molecules

–  Allows them to form up to 4 hydrogen bonds with each other or other molecules

Hydrogen bonds

+

+

H H +

+

δ –

δ –

δ – δ –

Figure 2.16

§  Four emergent properties of water contribute to Earth’s suitability for life: §  Cohesive behavior

§  Ability to moderate temperature

§  Expansion upon freezing §  Versatility as a solvent

© 2014 Pearson Education, Inc.

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Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

(1) Cohesion •  Water molecules exhibit cohesion

–  the bonding of molecules to each other –  due to hydrogen bonding –  Helps pull water up through the microscopic vessels of

plants (along with adhesion) •  Adhesion, clinging of one ���

substance to another, ���causes water to adhere ���to the wall of vessels

Figure 3.3

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

•  Surface tension is a measure of how hard it is to break the surface of a liquid

•  Surface tension is related to cohesion

© 2011 Pearson Education, Inc.

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

(2) Moderation of Temperature by Water

•  Water absorbs heat from warmer air and releases stored heat to cooler air

•  Water can absorb or release a large amount of heat with only a slight change in its own temperature –  For temperature to increase, more heat must be

absorbed to break hydrogen bonds –  Heat is released when hydrogen bonds reform –  Allows water to moderate temperatures

© 2011 Pearson Education, Inc. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Heat and Temperature

•  Kinetic energy is the energy of motion •  Heat is a measure of the total amount of kinetic

energy due to molecular motion •  Temperature measures the intensity of heat due to

the average kinetic energy of molecules

© 2011 Pearson Education, Inc.

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Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

(3) Floating of Ice on Liquid Water

•  Ice floats in liquid water because hydrogen bonds in ice are more “ordered,” making ice less dense

•  Water reaches its greatest density at 4°C •  If ice sank, all bodies of water would eventually freeze

solid, making life impossible on Earth

© 2011 Pearson Education, Inc. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

(4) The Solvent of Life •  Water is a versatile solvent due to its polarity •  It can form aqueous solutions of a large variety of

charged and polar solutes (dissolved molecules) –  Salts –  Amino acids –  Sugars –  Etc.

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

•  Water is a versatile solvent due to its polarity, which allows it to form hydrogen bonds easily

•  When an ionic compound is dissolved in water, each ion is surrounded by a sphere of water molecules called a hydration shell

•  Even large nonionic polar molecules such as proteins can dissolve in water if they have ionic and polar regions

© 2011 Pearson Education, Inc. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Hydrophilic and Hydrophobic Substances •  A hydrophilic substance

–  Has an affinity for water •  charged molecules, ions •  polar molecules, which contain O-H or N-H polar

covalent bonds

•  A hydrophobic substance –  Does not have an affinity for water

•  Noncharged and nonpolar molecules such as fats and oils –  which do not form aqueous solutions

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Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Solute Concentration in Aqueous Solutions •  Life requires chemical reactions

•  Chemical reactions are affected by the concentrations of reactants and products

–  the relative numbers of molecules in solution

•  Since most biochemical reactions occur in water –  It is important to define the concentration of solutes in

an aqueous solution

•  Review your knowledge of –  Molecular weight –  Moles –  Molarity

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Effects of Changes in pH •  Water molecules can react

–  to form hydronium and hydroxide ions –  a hydrogen ion (H+) is transferred from one water molecule to

another •  By convention, H+ is used to represent the hydronium ion

–  these ions are reactive

•  The concentration of these ions affects: –  biological chemistry –  the weak bonds of proteins and cell structures resulting in

changes in their shape

H

Hydronium ion (H3O+)

H

Hydroxide ion (OH–)

H

HH

H

H

H

+ –

+ Figure on p. 34 of water dissociating

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Dissociation of Water •  A simpler view of this process

–  is that a water molecule dissociates into a hydrogen ion and a hydroxide ion:

–  H2O <=> H+ + OH-

•  Like almost all reactions, this is reversible •  At equilibrium, the concentrations of H+ and OH- in

pure water are both very low, 10-7M (at 25°C) –  Only one water molecule in 554 million is dissociated

•  Though statistically rare, the dissociation of water molecules has a great effect on organisms

•  Changes in concentrations of H+ and OH– can drastically affect the chemistry of a cell

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Acids and Bases •  An acid

–  Is any substance that increases the hydrogen ion concentration of a solution

–  For example, when hydrochloric acid is added to water, hydrogen ions dissociate from chloride ions: •  HCl -> H+ + Cl-

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Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Acids and Bases •  A base

–  Is any substance that decreases the hydrogen ion concentration of a solution

•  Some bases reduce [H+] directly by accepting hydrogen ions –  For example, ammonia, NH3 + H+ <=> NH4

+

•  Other bases reduce [H+] indirectly by producing OH- that then combines with an H+ to form water –  NaOH -> Na+ + OH- and then OH- + H+ -> H2O

•  which removes hydrogen ions

The pH Scale

§  In any aqueous solution at 25°C, the product of H+

and OH− is constant and can be written as

§ The pH of a solution is defined by the negative logarithm of H+ concentration, written as

§ For a neutral aqueous solution, [H+] is 10−7, so

[H+][OH−] = 10−14

pH = −log [H+]

−log [H+] = −(−7) = 7 © 2014 Pearson Education, Inc.

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

The pH Scale •  The H+ and OH- concentrations of aqueous solutions

can vary by a factor of 100 trillion or more. •  For convenience, the H+ concentrations can be

expressed via the logarithmic pH scale. •  pH = - log [H+]

–  for example, pH 7 = [H+] 10-7 M

•  Each pH unit represents a tenfold difference in H+ concentrations

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Figure 3.10 pH Scale

Battery acid

Gastric juice, lemon juice

Vinegar, wine, cola

Beer Tomato juice

Black coffee

Rainwater Urine

Saliva Pure water Human blood, tears Seawater Inside of small intestine

Milk of magnesia

Household ammonia

Household bleach

Oven cleaner

Basic solution

Neutral solution

Acidic solution

0

1

2

3

4

5

6

7

8

9

10

Neutral [H+] = [OH-]

Incr

easi

ngly

Bas

ic

[H+ ]

< [O

H- ]

Incr

easi

ngly

Aci

dic

[H+ ]

> [O

H- ] H+

H+

H+

H+ H+

H+ H+ H+

OH- OH-

H+

OH-

H+ OH-

OH- OH- OH-

H+ H+ H+

H+ OH-

OH-

OH-

OH- OH- OH-

OH- H+

11

12

13

14

•  The pH scale •  Values for [OH-]

can be easily calculated because –  [H+] [OH-] = 10-14

–  Example: at pH 8, [H+] = 10-8 and [OH-] = 10-6

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Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Buffers •  Most biological fluids have pH values in the range of 6

to 8 –  cells and organisms need to control their internal pH

•  Buffers –  Are substances that minimize changes in the

concentrations of hydrogen and hydroxide ions in a solution

–  We don't have time for the details of the chemistry, but buffers •  can accept H+ ions from solution if an acid is added •  and donate H+ to solution if a base is added

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

•  The burning of fossil fuels is a major source of sulfur oxides and nitrogen oxides

•  These compounds react with water in the air to form strong acids that fall in rain or snow

•  Acid precipitation is rain, fog, or snow with a pH lower than 5.2

•  Acid precipitation damages life in lakes and streams and changes soil chemistry on land

© 2011 Pearson Education, Inc.

Acidification: A Threat to Our Oceans

§ Burning fossil fuels threaten water quality

§ CO2 is the main product of fossil fuel combustion

§ About 25% of human-generated CO2 is absorbed by the oceans §  CO2 dissolved in seawater forms carbonic acid §  As seawater acidifies, H+ ions combine with carbonate

ions to produce bicarbonate §  Carbonate is required for calcification (production of

calcium carbonate) by many marine organisms, including reef-building corals

© 2014 Pearson Education, Inc.