mrs c’s chem lecture. h bonds: weak attraction between polar covalent molecules van der waals:...
TRANSCRIPT
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