Mrs C’s Chem Lecture

Fig. 2-16 +

+

+

+

+

Water (H2O)

Ammonia (NH3)

Hydrogen bond

H bonds: weak attraction between polar covalent molecules

Van der Waals: very weak attraction between nonpolar covalent molecules (even molecules themselves)

Fig. 2-18

(a) Structures of endorphin and morphine

(b) Binding to endorphin receptors

Naturalendorphin

Endorphinreceptors

Morphine

Brain cell

Morphine

Natural endorphin

CarbonHydrogen

NitrogenSulfur

Oxygen

STRUCTURE = FUNCTIONMolecular Shape

-crucial in biology

Determines:

- Recognition

- Specific responses

Morphine and heroin (opiates)

- Mimic brain’s endorphins

- Affect pain perception and emotional state

Fig. 4-2

Water vapor

H 2NH

3

“Atmosphere”

Electrode

Condenser

Coldwater

Cooled watercontainingorganicmolecules

Sample forchemical analysis

H2O“sea”

EXPERIMENT

CH4

Fig. 4-8

Drug

Ibuprofen

Albuterol

Condition

Pain;inflammation

Asthma

EffectiveEnantiomer

S-Ibuprofen

R-Albuterol

R-Ibuprofen

S-Albuterol

IneffectiveEnantiomer

Fig. 4-7

Pentane

(a) Structural isomers

(b) Geometric isomers

2-methyl butane

cis isomer: The two Xs areon the same side.

trans isomer: The two Xs areon opposite sides.

(c) Enantiomers

L isomer D isomer

Fig. 4-10c

STRUCTURE

EXAMPLE

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

Carboxyl

Acetic acid, which gives vinegar its sour taste

Carboxylic acids, or organic acids

Has acidic propertiesbecause the covalent bond between oxygen and hydrogen is so polar; for example,

Found in cells in the ionized form with a charge of 1– and called a carboxylate ion (here, specifically, the acetate ion).

Acetic acid Acetate ion

Fig. 4-10d

STRUCTURE

EXAMPLE

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

Amino

Because it also has a carboxyl group, glycine is both an amine anda carboxylic acid; compounds with both groups are called amino acids.

Amines

Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms).

Ionized, with a charge of 1+, under cellular conditions.

(ionized)(nonionized)

Glycine

Fig. 4-10e

STRUCTURE

EXAMPLE

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

Sulfhydryl

(may be written HS—)

Cysteine

Cysteine is an important sulfur-containing amino acid.

Thiols

Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure.

Cross-linking ofcysteines in hairproteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers, then breakingand re-forming thecross-linking bonds.

Fig. 4-10f

STRUCTURE

EXAMPLE

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

Phosphate

In addition to taking part in many important chemical reactions in cells, glycerol phosphate provides the backbone for phospholipids, the most prevalent molecules in cell membranes.

Glycerol phosphate

Organic phosphates

Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule; 1– when located internally in a chain of phosphates).

Has the potential to react with water, releasing energy.

Fig. 4-10g

STRUCTURE

EXAMPLE

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

Methyl

5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group.

5-Methyl cytidine

Methylated compounds

Addition of a methyl group to DNA, or to molecules bound to DNA, affects expression of genes.

Arrangement of methyl groups in male and female sex hormones affectstheir shape and function.

Fig. 5-5

(b) Dehydration reaction in the synthesis of sucrose

Glucose Fructose Sucrose

MaltoseGlucoseGlucose

(a) Dehydration reaction in the synthesis of maltose

1–4glycosidic

linkage

1–2glycosidic

linkage

Fig. 5-6

(b) Glycogen: an animal polysaccharide

Starch

GlycogenAmylose

Chloroplast

(a) Starch: a plant polysaccharide

Amylopectin

Mitochondria Glycogen granules

0.5 µm

1 µm

Liver:

Glucagon causes breakdown of glycogen into glucose

Glucose ATP

triglyceride glycogen

liver muscles

Fig. 5-7

(a) and glucose ring structures

Glucose Glucose

(b) Starch: 1–4 linkage of glucose monomers (b) Cellulose: 1–4 linkage of glucose monomers

Fig. 5-11

Fatty acid(palmitic acid)

Glycerol

(a) Dehydration reaction in the synthesis of a fat

Ester linkage

(b) Fat molecule (triacylglycerol)

Fig. 5-12

Structuralformula of asaturated fatmolecule

Stearic acid, asaturated fattyacid

(a) Saturated fat

Structural formulaof an unsaturatedfat molecule

Oleic acid, anunsaturatedfatty acid

(b) Unsaturated fat

cis doublebond causesbending

Fig. 5-13

(b) Space-filling model(a) (c)Structural formula Phospholipid symbol

Fatty acids

Hydrophilichead

Hydrophobictails

Choline

Phosphate

Glycerol

Hyd

rop

ho

bic

tai

lsH

ydro

ph

ilic

hea

d

Fig. 5-14

Hydrophilichead

Hydrophobictail WATER

WATER

Table 5-1

Fig. 5-16

Enzyme(sucrase)

Substrate(sucrose)

Fructose

Glucose

OH

HO

H2O

Fig. 5-UN1

Aminogroup

Carboxylgroup

carbon

Fig. 5-17Nonpolar

Glycine(Gly or G)

Alanine(Ala or A)

Valine(Val or V)

Leucine(Leu or L)

Isoleucine(Ile or I)

Methionine(Met or M)

Phenylalanine(Phe or F)

Trypotphan(Trp or W)

Proline(Pro or P)

Polar

Serine(Ser or S)

Threonine(Thr or T)

Cysteine(Cys or C)

Tyrosine(Tyr or Y)

Asparagine(Asn or N)

Glutamine(Gln or Q)

Electricallycharged

Acidic Basic

Aspartic acid(Asp or D)

Glutamic acid(Glu or E)

Lysine(Lys or K)

Arginine(Arg or R)

Histidine(His or H)

Peptidebond

Fig. 5-18

Amino end(N-terminus)

Peptidebond

Side chains

Backbone

Carboxyl end(C-terminus)

(a)

(b)

Fig. 5-21

PrimaryStructure

SecondaryStructure

TertiaryStructure

pleated sheet

Examples ofamino acidsubunits

+H3N Amino end

helix

QuaternaryStructure

Fig. 5-21f

Polypeptidebackbone

Hydrophobicinteractions andvan der Waalsinteractions

Disulfide bridge

Ionic bond

Hydrogenbond

Fig. 5-21g

Polypeptidechain

Chains

HemeIron

Chains

CollagenHemoglobin

Fig. 5-22

Primarystructure

Secondaryand tertiarystructures

Quaternarystructure

Normalhemoglobin(top view)

Primarystructure

Secondaryand tertiarystructures

Quaternarystructure

Function Function

subunit

Molecules donot associatewith oneanother; eachcarries oxygen.

Red bloodcell shape

Normal red bloodcells are full ofindividualhemoglobinmoledules, eachcarrying oxygen.

10 µm

Normal hemoglobin

1 2 3 4 5 6 7

Val His Leu Thr Pro Glu Glu

Red bloodcell shape

subunit

Exposedhydrophobicregion

Sickle-cellhemoglobin

Moleculesinteract withone another andcrystallize intoa fiber; capacityto carry oxygenis greatly reduced.

Fibers of abnormalhemoglobin deformred blood cell intosickle shape.

10 µm

Sickle-cell hemoglobin

GluProThrLeuHisVal Val

1 2 3 4 5 6 7

Fig. 5-22c

Normal red bloodcells are full ofindividualhemoglobinmolecules, each carrying oxygen.

Fibers of abnormalhemoglobin deformred blood cell intosickle shape.

10 µm 10 µm

Fig. 5-24

Hollowcylinder

Cap

Chaperonin(fully assembled)

Polypeptide

Steps of ChaperoninAction:

An unfolded poly-peptide enters thecylinder from one end.

1

2 3The cap attaches, causing thecylinder to change shape insuch a way that it creates ahydrophilic environment forthe folding of the polypeptide.

The cap comesoff, and the properlyfolded protein isreleased.

Correctlyfoldedprotein

Effect of time on Amylase Reaction Rate

y = -0.0034x2 + 0.7533x - 0.1324

-5

0

5

10

15

20

25

30

35

40

45

0 20 40 60 80 100

Time (sec)

Nu

mb

er

of t

oo

thp

icks

hyd

roly

sed

Series1

Poly. (Series1)

V max: slope of the steepest part of the line

When comparing different rates use the steepest line = constant rate of change

Q10: a measurement of a rate of a chemical reaction and its relationship to temp.

http://www.csupomona.edu/~seskandari/physiology/physiological_calculators/Q10.html

Temp mL

4 C 2

14 C 4

Q10= 2 R : rate of reaction = slope of the line

Q10 calculator

What are the costs and benefits of being an Ectotherm (poikilotherm) or endotherm (homeotherm

Q10 Effect = Rates for most enzyme mediated reactions increase by a factor of 2-3 for 10 degree temp increases

Fig. 5-UN3

% o

f g

lyco

sid

iclin

kag

es b

roke

n

100

50

0Time

~ constant rate : not enough products to collide with active site

- Assume substrate is in excess

Rxn rate = slope of linear portion of the curve

Enzyme lab prelab

• What is catalase?

• Where is it found?– Organs, aerobes, anaerobes, animals,

plants…

• What does it do? Why do we have it?

• Research function of the liver and kidney, potatoes and green plants in relation to catalase.

Enzymatic Activity cont

• Draw a diagram(s) and label the following terms with brief explanations: – Active site– Allosteric site– Feedback inhibition (find a loop)

Draw idealized graphs for enzymatic activity for pH, temp, concentration and ion concentration

Procedure

• Scenarios

• Temp, catalase sources

• Diagrams

• Steps (why do you need each step?)

• Data tables

• Graphs