2012 Southeast Summer InstituteGroup 1: Biology-Chemistry Interface

University of Georgia• Wendy Dustman• Kimberly Hunt• Anne Summers

NC State University• Sarah Ash• Jane Lubischer• Lisa Parks

The interface between biology and chemistry

Context• First semester STEM majors• BIO 101: Intro to Scientific Thinking course

(NOT intro biology)• Sections of up to 60 students (group size 4)

Knowledge/experience assumed• Co-enrolled in intro chemistry and in intro biology• Experience with group activities and documented problem-

solving

Timing• Tidbit occurs mid-semester to end of semester (based on

chemistry course schedule)

Learning goalStudents should gain an appreciation of the importance of

chemistry in the study of life.

Learning Objectives/Outcomes1. Using the stomach as a model system:

• explain the roles of pH. • describe how pH can be changed. • predict the effects of changes in pH.

2. Analyze and interpret data sets and graphs.3. Illustrate how an understanding of chemistry can help to

explain a biological process (using correct terminology).

Unit 8: Can you stomach it?

Recognizing connections between chemistry and biology

*Make sure you have paper and pen/pencil ready.

concept map – identifying relationships

Rocky

HCl eggsprotein

biological process: digestion in the stomach

key chemical concept: pH effects on protein

self-check review opportunity (clickers; 30 sec)

Which of the following would you expect to measure if you added a neutralizing chemical to a beaker of hydrochloric acid?

A. change from pH 1.5 to pH 8.5B. change from pH 7.0 to pH 1.5C. change from pH 1.5 to pH 7.0D. change from pH 8.5 to pH 1.5

5 minute mini-lecture -- key concepts

• what is pH?• pH ranges in living organisms

• examples• place stomach in context (extremely acidic)• harsh environment: limits growth of most

microbes• protein structure (very basic)• effect of acid on protein structure

• unfolding (denaturation)

• effect of pepsin on protein structure• hydrolysis (digestion)

What is pH?• pH designates the negative logarithm of the molarity of the hydrogen ion, i.e. a

hydrogen atom without its electron or a proton: H+

• So, a solution that is 0.01 M H+ = 10-2 M has a pH of 2.• Since pH is inversely related molarity, the higher the pH, the lower the H+

concentration.• H+ occurs in the dissociation of water into a proton and a hydroxyl ion:

HOH <---> H+ + OH+. The association constant (pKa) for this reaction is 10-14 M-1 .

• When you add other compounds to water, they also contribute protons:– Compounds that readily donate protons are called acids– Compounds that readily accept protons are called bases

• When you mix an acid and a base the resulting pH will be set somewhere between their respective pKa’s, depending on the relative moles of each added

• Such mixtures, called buffers, are used in experimental biology and occur naturally in our bodily fluids.

Why do we care about pH?• Inorganic ions matter a lot in biology:

– Not just H+, but K+, Na+, Mg++, Ca++ and the essential metals • as electrolytes (i.e. charge carriers in bioelectric fields), • as cofactors in enzymatic catalysis• as counterions on the DNA and RNA phosphate backbones

But because we are “water-based” life,protons are special…

Life uses large pH ranges• Externally, microbes and larger organisms deal with:

– alkaline lakes (Mono Lake, CA, pH 10, set by carbonates)– Cu mine drainage (as low as pH -3.6, set by sulfates ; yes, that is

minus 3.6)– the ocean being acidified by rising CO2 (30% increase in acidity from

1751 to 1994)

• Internally, our bodies use different pH’s in different places: – Blood: 7.36 -7.44; set by CO2 and bicarbonates

– Urine: 6.5 -7.0 (a.m.) to 7.5-8.0 (p.m.); set by H+ and NH4+ ions

– Saliva: 6.2-7.4; set by carbonate-bicarbonate or phosphate– Armpit: 4.5-6.0; set by lactic and fatty acids in sweat– Vagina: 3.8-4.5; set by complex secretions and bacterial symbionts – Stomach: 1.5 - 3.5; set by H+ (as HCl) and bicarbonate

The Stomach: Our Model for this Unit• We use the stomach as an example because it has the most

extreme pH in the body

• The high concentration of hydrogen ions in the stomach unfolds (denatures) proteins by:– deamidating certain amino acid side chains– destabilizing hydrogen bonds necessary for the correct fold

• The result is that:– most proteins lose their normal functions– food proteins can readily be digested to free amino acids by

acid-resistant proteases such as pepsin– food-borne microbes ingested with foods

are inhibited or killed

self-check opportunity (clickers)

This beaker is half-full of an unbuffered solution (pH 3.0). If you fill the beaker with distilled water (pH 7.0), what will happen to the concentration of H+ (in the final solution compared to starting conditions)?

A. The [H+] will decrease.B. The [H+] will increase.C. The [H+] will remain the same.D. More information is needed.

Homework 1: Problem Set (handout on dropbox)

protein characteristic pH 5.0 pH 4.0 pH 3.5 pH 2.5

degree (%) of deamidation 6.2 18.2 32.6 59.9

degree (%) of hydrolysis 0.3 0.2 0.3 0.4

The problem set (to be completed individually as a homework assignment) will reinforce (and allow assessment of) key concepts on the effects of acid on protein structure. Part of the problem set will be a sample test question that asks them to analyze data presented in table format (below).

Gastric bypass = Acid bypass = So what?(A brief case study on bariatric surgery)

Homework 2: Case Studies (on dropbox)

Each student will receive one of two cases:• H. pylori and gastric ulcers• Acid indigestion prevention

Cases will build on class material and will again require analysis of data.

Students will work individually (before the next class), then groups will discuss both cases in class. In each group, two students will have had one case and the other two students will have had the other case.

Research Essay (end of Unit 8 assignment)

• Using your Intro Bio textbook, identify another biological process in which pH plays a role.

• In your own words (as always), write a summary of the role of pH in the biological process you chose – 200 words maximum.• Assume your audience is a high school science class.• See grading rubric guidelines and model essay (about

pH and the stomach).• Your paper is due on Monday by 9 am in our class

dropbox folder.

Overview of Assessments

Formative assessments• Concept map• Group discussions and report outs• Clicker questions• Documented problem solving

Summative assessments• Homework activities• Research essay• Exam questions

Addressing Diversity

• Variety of teaching and learning approaches– Group discussions– Individual activities– Concept mapping– Reading assessments – Written activities– Data analysis

Learning Objective

Assessments Active learning Low Order/High Order

content objectives

concept mapclicker questionshomework activitiescasesresearch essayexam questions

concept mapclicker questionscase discussions

both

analyzing data

homework activitiescasesdocumented problem

solvingexam questions

case discussions high

chem is important

concept mapcasesresearch essayexam questions

concept mapcase discussions

high

Diversity:

Diversity

Variety of teaching and learning approaches.