Biochemistry and Digestion

Unit 1

Topic 1The Nature of Matter

● 80% Water!● 20% Organic compounds

● Carbon● Hydrogen● Oxygen● Nitrogen● Phosphorus● Sulfur

● Trace Elements● Iron, iodine, fluoride, etc

What are your cells made of?

SPONCH

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Figure 2.2A

Goiter in a Burmese woman

Bohr Model and Structural Formulas

Chlorine – Bohr model

Alanine - structural formula

Glucose – structural formula

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Chemical Formula:C6H12O6

Key things for Exercise B and C● Bond types:

● Ionic● Polar Covalent● Nonpolar Covalent● Hydrogen (more like an attraction)

● O2 = Oxygen molecule CO2 ≠ Oxygen molecule

● Graphs:● Remember exothermic, endothermic??● The lines represent the starting and ending materials…

Topic 2Bonding and Properties of Water

● Ionic Bonds(don’t need to know for bio…)

● Covalent Bonds

● Electronegativity

Bonding

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Properties of Water● Why is water polar?

● Uneven distribution of electrons● Due to large differences in electronegativity between

the atoms● Greater chance of finding

electrons at one end of the molecule

● ENOxygen = 3.5● ENHydrogen = 2.1● Difference = 1.4

(strong polar covalent)

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Why do hydrogen bonds form?● Molecule acts like a magnet with positive and

negative poles● Allows them to form hydrogen bonds with each other,

giving special properties● Involved in as many as 4 H-bonds

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● Chart on the Board!

Properties of Water

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Objective 8: Explain the following properties of water (including how these are biologically relevant): high surface tension, high specific heat, solid water is less dense than liquid water, water as the “universal solvent,” and capillary action. Along the way, be sure to address cohesion and adhesion (2.11-2.14).

Objective 9: Define and relate the terms solution, solvent, and solute (2.14).

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● Atomic properties

● Intramolecular property

● Intermolecular properties● H-bonds – attraction between polar molecules● Cohesion – attraction of water to other water● Adhesion – attraction of water to other substances

Properties of water

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Cohesion● Attraction between molecules of the same substance● Cause molecules on surface to be drawn inward,

forming a bead

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Surface tension● Film on top of water● Water molecules “hold hands”● Allows insects and spiders to

walk on surface● Spread their weight over a large area

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Basilisk lizard!● Surface tension and rapid movement

● See video (also seen on The Animal Planet’s “Most Extreme: Speed”)

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Capillary Action● Causes water to rise in a narrow tube against force of

gravity● Adhesion on the sides of the tube; cohesion pulls

other molecules up● Try it out!

Water conducting cells

100 µmFigure 3.3

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Animation: Water TransportRight click on animation / Click play

High Specific Heat/Heat of Vaporization● Specific heat – heat to

change the temperature● Heat of vaporization –

heat to evaporate● Water absorbs a lot of

heat to change temperature or state

● Keeps coastal climates moderate

● Helps keep your body cool

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● Solution - mixture with one substance dissolving into the other

● Solute – substance being dissolved● Solvent – substance that does the dissolving● Ex. – sugar (solute) in water (solvent)

● Different regions of water interact with ionic compounds called solutes to dissolve them

● See NaCl video

“Universal Solvent”

“Universal Solvent”Negative

oxygen regions

of polar water molecules are

attracted to sodium cations (Na+).+

+

+

+Cl –

–

–

–

–

Na+

Positive hydrogen regions

of water molecules cling to chloride anions (Cl–).

+

+

+

+

–

–

–

–

–

–Na+

Cl–

“Universal Solvent”● Solvent = dissolving

agent● Solute = dissolved

substance● Solution = mixture of the

two

Ice!● Ice is less dense than liquid water● It floats!

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Why does ice float?● Hydrogen bonds in ice allow it to float● http://www.visionlearning.com/library/module_viewe

r.php?mid=57&l=&c3=

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Why does ice float?

Liquid waterHydrogen bonds

constantly break and re-form

IceHydrogen bonds are stable

Hydrogen bond

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● Chart on the Board!

Properties of Water

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Objective 8: Explain the following properties of water (including how these are biologically relevant): high surface tension, high specific heat, solid water is less dense than liquid water, water as the “universal solvent,” and capillary action. Along the way, be sure to address cohesion and adhesion (2.11-2.14).

Objective 9: Define and relate the terms solution, solvent, and solute (2.14).

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Topic 3Basic Chemistry

Acids and Bases – Activity D● Acids – contribute H+● Bases – contribue OH-● pH scale● Human blood = ??

● Biological fluids contain buffers to maintain this pH

7.4

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Figure 2.14_3

Acidicsolution

Neutralsolution

Basicsolution

Topic 4Organic Molecules

● Carbon-based● Functional groups

What is an organic molecule?

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● Macromolecule

● Polymer

● Monomer

● Dehydration synthesis

● Hydrolysis

Some basic definitions

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Four types of organic compounds● Carbohydrates (starch and sugar)

● Lipids (fats)

● Proteins

● Nucleic acids (DNA and RNA)

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What are carbohydrates?● Sugars and starches● Contain C, H, O● Always have 2 hydrogen

atoms for every 1 oxygen atom (2:1 ratio)

● Hydrophilic● Used for energy (short

and long term storage)● Monosaccharides,

disaccharides, and polysaccharides

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Types of carbohydrates● Monosaccharides –

glucose, fructose

● Disaccharides – sucrose, lactose, maltose

● Polysaccharides – starch, cellulose, glycogen

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Figure 3.7

Making polymers from monomers?

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Dehydration synthesis!

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Break down polymers into monomers?

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Degradation hydrolysis!

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© 2012 Pearson Education, Inc.

Animation: PolymersRight click on animation / Click play

● Glycogen and starch● Insulin lowers blood

glucose● Glucagon raises

blood glucose

● Homeostasis!!

How are carbohydrates stored?

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What are lipids?● Fats, oils, and waxes● Mainly hydrogen and

carbon atoms (some O)● Used for energy storage,

cushioning vital organs, insulating the body, and transmitting messages

● Hydrophobic ● Not true polymers…

(don’t have a monomer)

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Fatty Acid chains● Fatty Acids

● Unsaturated (one or more double bonds in hydrocarbon chain)

● Saturated (all single bonds in hydrocarbon chain)

Types of Lipids - Triglycerides● Energy storage● Made of:

● 1 Glycerol (glycerin)● 3 Fatty Acid chains

● Can be:● Unsaturated (one or

more double bonds in hydrocarbon chain)

● Saturated (all single bonds in hydrocarbon chain)

H

H

H

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© 2012 Pearson Education, Inc.

Animation: FatsRight click on animation / Click play

Lipids and Atherosclerosis

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Atherosclerosis

Types of Lipids - Steroids● All have rings of carbons● Examples:

● Cholesterol● Sex hormones

● How will you tell these apart from carbs?

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Types of Lipids - Phospholipids● Like a triglyceride:

● Glycerol ● Phosphate group● 2 Fatty acid chains

● Major components of cell membranes (barriers)

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What are proteins?● Contain C, H, O, N

(sometimes S)● Made of amino acids

(100s or 1000s of them)● Typically globular or

fibrous● Require a specific 3D

shape to function● Nearly all proteins

recognize and bind to another molecule

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Amino acids

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Figure 3.11B

Hydrophobic Hydrophilic

Aspartic acid (Asp)Serine (Ser)Leucine (Leu)

20 different amino acids

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● 2 amino acids = dipeptide● 3 - 50ish amino acids = polypeptide● 50ish – 100,000ish amino acids = protein

● The bond joining them is a peptide bond

Joining amino acids to make a dipeptide

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Joining amino acids to make a dipeptide

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● Hemoglobin● Cell structural proteins (cell surface, muscle fiber)● Body structural proteins (hair, fingernails, collagen) ● Contractile proteins (in muscle fibers)● Defensive proteins (antibodies)● Enzymes● Hormones (insulin, glucagon)● Growth factors (heals cuts, controls development)● Cell membrane component (transporters, receptors)● How can there be so many different proteins??

Types of proteins

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Protein folding

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Animation: Protein Structure IntroductionRight click on animation / Click play

© 2012 Pearson Education, Inc.

Animation: Primary Protein StructureRight click on animation / Click play

© 2012 Pearson Education, Inc.

Animation: Secondary Protein StructureRight click on animation / Click play

© 2012 Pearson Education, Inc.

Animation: Tertiary Protein StructureRight click on animation / Click play

© 2012 Pearson Education, Inc.

Animation: Quaternary Protein StructureRight click on animation / Click play

Nucleic Acids● DNA and RNA● Monomer - nucleotide

● Five-carbon sugar (deoxyribose or ribose)● Phosphate group● Nitrogenous base

● Adenine● Guanine● Cytosine● Thymine (DNA only) ● Uracil (RNA only)

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Topic 5Chemical reactions and enzymes

● Anabolism – building up● Catabolism – breaking down (CATastrophic…)

● Exergonic● Releases energy● Energy-rich reactants → Energy-poor products

● Endergonic● Absorbs/requires energy● Energy-poor reactants → Energy-rich products

Metabolism

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Enzyme shape

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Induced fit model of enzyme function

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© 2012 Pearson Education, Inc.

Animation: How Enzymes WorkRight click on animation / Click play

Endergonic vs. Exergonic reactions

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Reading an energy graph

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Topic 7The Methods of Science

1. Observe and state a problem2. Form a hypothesis

• Testable• Falsifiable• If (the independent variable affect the dependent variable),

then (this is my specific prediction).3. Test the hypothesis4. Record and analyze data

● Qualitative vs. Quantitative● Observation vs. Inference● “The grass on the front lawn is wet”● “Reaction B produced twice as many bubbles as Reaction

A”

Scientific Method

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1. Observe and state a problem2. Form a hypothesis

• Testable• Falsifiable• If (the independent variable affect the dependent

variable), then (this is my specific prediction).3. Test the hypothesis4. Record and analyze data5. Form a conclusion6. Repeat the experiment (or publish so others can)

Scientific Method

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Experiment Vocab● Experiment: test of hypothesis to see if two

variables have a cause and effect relationship● Independent variable: the changes an

experimenter purposefully makes (the believed “cause” in the experiment)

● Dependent variable: the response to the experimenter’s purposeful change (the “effect” in the experiment)

Experiment Vocab● Controlled variable: variable that is kept from

changing during the experiment (usually based off of possible confounding factors)

● Confounding factors: a hidden variable whose presence affects the variables being studied so the results you get do not reflect the actual relationship between the IV and DV

Experiment Vocab● Experimental Group:

● A setup that is testing the effects of your IV on your DV

● You may have a hypothesis, but the results are unknown

● Positive Control Group: ● A setup where you know there will be an effect● Used to prove the test’s ability to show the desired

effect

Experiment Vocab● Negative Control Group:

● A setup where you know there will be no effect● Makes sure no confounding variables are acting on

your experiment● If you get a positive result, there is some other

variable that you need to take into account for ALL treatments (or redesign the experiment)

Experiment Vocab● Treatment: the different measures of the

independent variable● Trial: Each test of a treatment● Sample Size: number of trials you do for each

treatment

Food Testing Lab: VariablesSuccessfully Controlled● Amount of food● Temperature of

environment● Plastic trays for every

group● Concentration of the

indicator

Needs to be controlled● Cleanliness of tray● How well we mixed the

sample with indicator● Amount of each sample

(take a mass of each)● How long we wait to read

results● How much (and if) we stir

samples

● Independent Variable – changed by scientist● Dependent Variable – observed/measured by scientist● Controlled Variables● Experimental Group● Control Group – used as a baseline to compare to

experimental group● Positive Control Group● Negative Control Group

● Confounding Variables – outside factors that may correlate with both independent and dependent variables (affects results)

Controlled Experiments

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1.9 Scientists form and test hypotheses and share their results

● Observations and generalizations:● poisonous animals are brightly colored and● imposters resemble poisonous species but are actually

harmless.● Prediction: Mimics benefit because predators confuse

them with the harmful species.● Hypothesis: If _______________ affects _____________,

then ___________________________________

© 2012 Pearson Education, Inc.

1.9 Scientists form and test hypotheses and share their results

● The scientists conducted a controlled experiment, comparing● an experimental group (artificial king snakes) and● a control group (artificial brown snakes).● The groups differed only by one factor, the coloration of

the artificial snakes.● The data fit the key prediction of the mimicry

hypothesis.

© 2012 Pearson Education, Inc.

Figure 1.9B

Figure 1.9C

Figure 1.9D

Figure 1.9E

Coral snakespresent

Artificialking snakes

Artificialbrown snakes

84%

0

20

40

60

80

100

Coral snakesabsent

17%

16%

Perc

ent o

f tot

al a

ttack

son

art

ifici

al s

nake

s

83%

Enzymes

What affects an enzyme's effectiveness?

pH Temp

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Protein denaturation

What about enzyme concentration?

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Substrate Concentration?

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Substrate surface area?

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● Are usually proteins● Speed up reactions● Work by lowering activation energy● Are not used up during the reaction● Are specific to one reaction● Have a precisely shaped active site

Enzymes…

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The End(Topics 1-6)

● Radioisotopes can be used for…● Research

● Diagnosis

Isotopes and RadioisotopesOBJ 11

● Have you seen any commercials making certain claims that you’d be interested in testing??

● Let’s design a controlled experiment to test them…

Designing a controlled experiment

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