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1
MCB 3020, Spring 20051-10-2004
Chapter 3:The Building Blocks of Life I
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2Chapter 3
I. The chemistry of life II. Macromolecules of the cell
A. polysaccharidesB. lipidsC. nucleic acidsD. proteins
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3
CH2-CH2 CH2- O-P=OO O ORC=O C=O CH2 CH2 CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH3 CH3
O-
membrane lipids
All cells are made of organic molecules.
The Chemistry of Life
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4I. The Chemistry of Life: a review
A. the 6 major bioelementsB. charge distribution in moleculesC. attractive forcesD. important functional groups
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5A. The 6 Major Bioelements
C Carbon H Hydrogen O Oxygen N Nitrogen P Phosphorus S Sulfur
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1. electronegativity2. hydrophilic (polar) 3. hydrophobic (nonpolar)4. amphipathic
B. Charge distribution in molecules
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71. Electronegativity
A measure of the degree of attractionof valence electrons
Among the major bioelementsoxygen and nitrogen have the highest electronegativity
TB
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82. Polar (hydrophilic)
+ -
asymmetric charge distribution in a molecule
TBH - O - CH2 CH3
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9Polar molecules
H - O - H
Polar molecules result from the bonding ofatoms with very different electronegativities
TB
H - C - O-
O
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103. Nonpolar (hydrophobic)
little charge asymmetry
TB
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11Nonpolar molecules
hydrocarbon chain
aromatic rings
Nonpolar molecules result from the bonding ofatoms with similar electronegativities. TB
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124. Amphipathic
partly polar, partly nonpolar
-negativelycharged
head
nonpolarhydrocarbon
tail
phospholipid molecule
TB
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13
1. ionic bonds 2. covalent bonds3. hydrogen bonds4. van der Waals forces5. hydrophobic interactions6. comparison of bond strengths
C. Attractive forces
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141. Ionic bonds
Na+ Cl-• • • •NaCl attraction between charged particles
2. Covalent bondselectron sharing between atoms
C H
HHH
• •
• •• •• • H– C – H
H
H
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153. Hydrogen bonds (H-bonds)noncovalent bonds formed between the following:
1. A highly electronegative atom (usually O or N)
2. A hydrogen atom bonded toa highly electronegative atom(usually O or N) TB
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16Hydrogen bonding of water molecules
H-bonding of hydroxyl groupsHOR
H
O R
H
O H
H
O H
H
O HH
O H
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17
Keto groups
OR H O RH-bonds will form with various combinationsof hydroxyl, amino and keto groups thatmeet the H-bonding criteria. TB
H-bonding of amino groups
HN
R
N
R
R
R
R —
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18Hydrogen bonding between amino
acids in a protein | H-C-R1 | C=O | N-H | H-C-R2 | C=O | N-H | H-C-R3 |
| R4-C-H | H –N | O=C | R5-C-H | H –N | O=C | Rc- C-H |
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19Hydrogen bonding between bases in DNA
Three H-bonds between G and C
N
NNH
NN-H
H
H
Oguanine cytosine
NN
H-N-H
O H
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204. van der Waals forces
+ -- +
nucleus
electronsinduced dipoles (polar)
van der Waals attractions result from attractions between induced dipoles
Attraction between molecules that are very close together
TB
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215. Hydrophobic forces (interactions)Attraction between hydrophobic molecules or hydrophobic portions of molecules
TB
• driven by an increase in entropy (disorder) due to water exclusion
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22Water is the biological solvent of life as we know it.• cells are 70 to 90% water • water is polar• many polar biological molecules dissolve in water• nonpolar (hydrophobic) molecules tend to aggregate together in water
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236. Comparison of bond strength
1. Covalent bonds2. ionic bonds3. hydrogen bonds4. van der waals forces5. hydrophobic forces
-50 to -100-80 or -1-3 to -6-0.5 to -1-0.5 to -3
type of bond strength (kcal/mol)
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24D. Important functional groups
carboxylicacid
organic acids,amino and fatty acids
Biological importance
aldehyde reducing sugars,like glucose
alcohol lipids andcarbohydrates
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25Important functional groups (contd.)
ketopyruvate,citric acid cyleintermediates
lipids of Bacteriaand Eukarya
DNA, RNA,ATP
phosphoester
ester
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26Important functional groups (contd.)
ether lipids(archaea)
-NH2amino amino acids,
nucleotides
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27What functional groups are present
in the amino acid serine?
OH C O
H2N – C – H CH2OH
O-
C O +H3N – C – H
CH2OHserine at pH 7
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28II. Macromolecules of the cell
A. polysaccharidesB. lipidsC. nucleic acidsD. proteins
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29
covalent bond
polymer (eg. protein)
macromolecules are polymers of covalently linked monomers
Monomers and polymers
monomer(eg. amino acid)
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30 Macromolecules are large molecules made of repeating units (monomers).
DNAa nucleic acid: a chain
(polymer) of nucleotides
a proteina polymer of amino acids
ss s
s
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31Macromolecules make up 96% of the dry weight of cells.
nucleic acids
proteinspolysaccharides
lipids
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32The 4 major cellular macromolecules*:chains (polymers) of repeating units
*Important recurring theme
polysaccharide sugars cell wall glycosidic
lipid fatty acids or membranes ester or ether isoprenoids
nucleic acid nucleotides DNA, RNA phosphodiester
protein amino acids enzymes peptide
polymer monomer example covalent bond(see notes for other examples)
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33B. Polysaccharidespolymers of sugars linked by glycosidic bonds
1. common sugar monomers2. glycosidic bonds3. cellular polysaccharides
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34
O
OHHO
OH
OH
CH2OH
a. glucose (ring form)
b. fructose (ring form) OH
O CH2OH
HO
HO
HOH2C
TB
1. common sugar monomers
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OH
O
HOHO
HOH2C
OH
O
HO
HOH2C
c. ribose
d. deoxyribose
TB
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O OH
HO
NH2
OH
CH2OH
e. glucosamine
f. muramic acidO OH
HO
NH2-OOCCHCH3
CH2OH
TB
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372. Glycosidic bonds: a. -1,4-glycosidic bond
O
O
HO
OH
OH
CH2OHO OH
OH
OH
CH2OH
H H
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38
O
O
HO
OH
OH
CH2OH
O OH
OH
OH
CH2OH
HH
b. -1,4-glycosidic bond
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39
a. starch
glucose storage molecule of plants
-1,4 glycosidic bonds
mostly -1,4 glycosidic bondslarge polymer of glucose
TB
3. cellular polysaccharides
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40b. glycogen
glucose storage molecule of animals and some microorganisms
-1,6-1,6
large branched polymer of glucosemostly -1,4 glycosidic bonds
TB
-1,6 glycosidic bonds produce branching
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41c. cellulose
major structural polysaccharide of plants
mostly -1,4 glycosidic bondsonly microbes can break the -1,4 bond
large glucose polymer
TB
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42d. peptidoglycanlarge polymer of N-acetyl glucosamine and N-acetyl muramic acidthe main structural component of most Bacterial cell walls-1,4-glycosidic bonds
*Penicillin inhibits Bacterial cell wall synthesis by inhibiting the formation of peptidoglycan. TB
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431. Memorize the 6 major bioelements.2. Understand the terms electronegativity, hydrophilic, hydrophobic, polar, nonpolar, amphipathic. Know how these properties are important in chemical bonds and interactions.3. Very important recurring theme: Understand the attractive forces (ionic, covalent, hydrogen bonds, van der Waals forces, and hydrophobic interactions), the examples presented in class, where they might occur. Which are strong bonds? Which are weaker? 4. Understand the role of water as the solvent of life.5. Know the functional groups. Be able to recognize their structures. Know their biological importance and where they occur in cellular molecules. 6. Recurring theme: Know the four important cellular macromolecules (polymers), the monomers that comprise them, the bonds that connect the monomers, and the specific example presented in class. These macromolecules are the building blocks of cells.7. In what parts of cells are the four macromolecules found?
Study objectives
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44Study objectives 8. Describe the structure and functions of the four cellular macromolecules, the monomers, connecting bonds. Memorize the specific examples of monomers, polymers, and bonds presented in class. 9. Be able to recognize the structures of glucose, ribose, and deoxyribose.10. Know the difference between -1,4 glycosidic bonds and -1,4-glycosidic bonds and where they can be found. Know the features of the cellular polysaccharides presented. How does penicillin inhibit microbial growth? 8.
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45
MCB 3020, Spring 20041-14-2004
Chapter 2The Building Blocks of Life II:
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46Chapter 2 (contd.)
II. Macromolecules of the cellA. polysaccharidesB. lipidsC. nucleic acidsD. proteins
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47B. Lipids1. fatty acids (glycerol) 2. membrane lipids a. bacterial and eukaryal b. archaeal
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48B. Lipids glycerol bonded to fatty acids (or isoprenoid units) and other groups by ester or ether linkages
CH2OH
CHOH
CH2OH
glycerol
OHO - C
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49
palmitic (C16)COO-
COO-stearic (C18)
oleic (C18)COO-
a monounsaturated fatty acid
a. common fatty acids
TB
1. Fatty acids
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50
saturated: no double bondsb. saturated and unsaturated fatty acids
COO-
monounsaturated: 1 double bond
polyunsaturated: > 1 double bondCOO-
COO-
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51Unsaturated fatty acids can make the membrane more fluid.
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522. Membrane lipids:
Membrane lipids are amphipathic.
hydrophobic tailpolar head
glycerol phosphate bonded to fatty acids and other groups by ester or ether bonds
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53In aqueous solution lipids associatespontaneously to form bilayers that are the basis of biological membranes
The polar heads are in contact with water the nonpolar tails group with one another.
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54a. bacterial and eukaryal membrane lipids
phosphatidic acidphosphatidyl ethanolaminephosphatidyl serine
fatty acids connected to glycerolphosphate through ester bonds
TB
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55
fatty acid
-o-o
o-oP
o-o
-o-o
phosphatidic acid
ester bond
TB
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56
o-oP
o-o
fatty acid
-o-o
-o-o
phosphatidyl ethanolamine
CH2CH2NH3+
serine
o-CH2CH2CHCOO-
NH3+
ethanolamine
TB
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57b. archaeal lipidsisoprenoid units connected to glycerolphosphate through ether bonds
-O-
-O-
OH
ether bond -C-O-C-
polar nonpolar TB
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58C. Nucleic acids (DNA, RNA)polymer of nucleotides covalentlylinked by phosphodiester bonds
RNADNA
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591. Nucleotides = Base + sugar + phosphate(s)
(up to 3)
thymine (T) (DNA only)
cytosine (C)uracil (U) (RNA only)
OCH2
pyrimidines
adenine (A)guanine (G)
purines: O-
— P=O O-
ribose (RNA)deoxyribose
(DNA)
HOCH2
a.
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60
O O - P – O -
O -O -P - O-
O O - P – O -
Detailed picture of a nucleotide (ATP)5' phosphate end
O-CH2
OH OH3' hydroxyl
ON
NH2
N
N
N
adenosine triphosphate
(ATP)
5'
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61
5'
3'
b. phosphodiester bonds5'
O H
O baseOCH2 P P P
3'
5' phosphate
O-CH2
OH H
O base
3'
O = P - O-
sugars of the nucleotides are covalently linked by phosphodiester bonds
3' hydroxyl
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62c. Nitrogen bases
purinesadenineguanine
pyrimidinescytosinethymineuracil
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63
N
N NH
N NH2H
O
guanine
N
N N
N
NH2
H
adenine
Purines
TB
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64
cytosine
N
N
NH2
OH
NH
N
O
O
thymine
NH
N
O
O
uracil
Pyrimidines
H HTBin RNA
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652. DNA structurea. double-stranded helixb. sugar-phosphate backbone *sugar = deoxyribosec. nucleotide bases pair through hydrogen bonds between the helical strandsd. the sequence of the bases is the "primary structure"
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66c. nucleotide base pairingThe most stable complementary DNA base pairing pattern is called "Watson-Crick base pairing" where A=T and GC
Two H-bonds between T and A
H-NN
O
ON
NN
N
N
H
HH
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67c. nucleotide base pairing
Three H-bonds between G and C
N
NNH
N N-HH
H
O
guanine cytosine
NN
H-N-H
O H
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68
DNA carries genetic information in the sequence of the bases.
DNA mRNA protein
d. DNA sequence (primary structure)
transcription
translation
AAA… UUU…
(an amino acid)
phenylalanine
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693. RNA structure• RNA is usually single stranded (ssRNA)• ribose instead of deoxyribose• uracil instead of thymine
ssRNAintramolecular base pairing RNA stem-loop
• primary structure = the base sequence • secondary structure = complementary base pairing in a single RNA molecule• G C A = U
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70RNA secondary structureA-G-A-C-A-A-A-C-C-G-U-C-A
RNA stem loopA - -A
C G A UG C
A
A ACC
e.g. tRNA stem loops
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71Functions of the major RNAs
1. messenger RNAs (mRNA) contain genetic information to encode a protein
3. ribosomal RNAs (rRNA) are structural and catalytic component of ribosomes, the protein-synthesizing machinery of cells
2. transfer RNAs (tRNA) act as adapters between the mRNA nucleotide code and amino acids during protein synthesis
phe
DNA
mRNA
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72D. Proteins1. general structure2. the 21 amino acids3. peptide bonds4. levels of protein structure5. stereoisomers
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73D. Proteinslinear chains of L-amino acids linked by peptide bonds
met leu his val glu asn asp cys
peptide bond
e.g. enzymes, transport proteins, antibodies insulin, structural proteins, regulatory proteins, hair, flagella, viral protein coat
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741. General structure of L-amino acids
O C – OH
H2N – C – H R O
C – O-
H3N – C – H R
at pH 7
+
carboxylic acidaminogroup
R-group orside chain
-carbon
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752. The 21 amino acids encoded by DNA
ACIDICaspartateglutamate
BASIC lysine
arginine histidine
POLAR, NEUTRALserinethreoninetyrosine
asparagine glutaminecysteineselenocysteine
NONPOLAR (HYDROPHOBIC)glycinealaninevaline
phenylalaninetryptophanproline
leucineisoleucinemethionine
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76Hydrophobic amino acids tend to be associated with hydrophobic environments • membranes • inside of proteins
Hydrophilic amino acids are often in contact with water Lysozyme
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77
aspartate (asp) glutamate (glu)
O C - O-
H3N - C - H CH2
COO-
O C - O-
H3N - C - H CH2
CH2
COO-
+ +
a. Acidic amino acids net negative charge at pH 7
TB
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78
lysine (lys) arginine (arg) histidine (his)
b. Basic amino acids:
CH2
CH2
CH2
CH2
NH3+ NH2H2N
CH2
CH2
CH2
C
NH
+
CH2
NNH+
H
net positive charge at pH 7
TB
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79c. Polar but neutral
CH2
OHCH- CH3
OH
CH2
OH
CH2
SH
Ser (S) Thr (T) Tyr (Y) Cys (C)
TB
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80
CNH2
O
CH2
CNH2
O
CH2
SeH
Asn (N) Gln (Q) Sec (U)
CH2
CH2
c. Polar but neutral (contd.)
TB
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81d. Nonpolar (hydrophobic)
CH3
CHCH3H3C
CH2
CHCH3H3C
H
Gly(G) Ala (A) Val (V) Leu (L) Ile (I)
CH
CH2
CH3
CH3
TB
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82
CHC
OOH
HN
CH2
CH2
CH2
CH2
NHCH2
CH2
CH2
CH3
S
Pro (P) Trp (W) Phe (F) Met (M)
d. Nonpolar (hydrophobic)
TB
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83
O C - O-
H3N - C - H CH2
S
O C - O-
H3N - C - H CH2
S
disulfide bridges antibody
Disulfide bridge covalent bond between two sulfhydryl groups (eg. of cysteines)
+ +
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84
O C - O-
H3N - C - H CH2
SeH
selenocysteine: the 21st amino acid
• found in some microbial enzymes like hydrogenase
+
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853. Peptide bonds join L-amino acids in proteins
O C - OH
H2N - C - H R1
O C
H2N - C - H R1
O H C - OH N - C - H
R2
O C - OH
H -N - C - H R2
H
H2 O
peptide bond
dehydration
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864. Levels of protein structure
a. Primary (1°) structure amino acid sequence
met leu his val glu asn asp cys
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87b. Secondary (2°) structurePatterns of folding due to hydrogen bonds between groups of the peptide backbone
-helix -sheet
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881. alpha helix (coil)
H
NCHC
O
RH
NCHC
O
RH
NCHC
O
R
H
NCHC
O
RH
NCHC
O
RH
NCHC
O
R
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892. beta sheetN
CC
C
O
N
R
R
H
O C
N
CC
C
O
N
R
R
H
O C
H
N
CC
C
O
N
R
R
H
O C
N
CC
C
O
N
R
R
H
O C
H
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90c. Tertiary (3°) structureNative 3-D structure of a protein
Stabilized by H-bonds, hydrophobic interactions, van der Waals forces,covalent disulfide bridges, and some ionic bonds
ribonucleasehexokinase
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91d. Quaternary (4°) structureassociation of two or more polypeptides
hemoglobin
-chains
-chains
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925. StereoisomersMirror-image compounds with the same molecular formula
COOHH2N - C - H
CH3
L-alanine
COOHH - C - NH2
CH3
D-alanine
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93Why is this important?
In biology, D-sugars predominate L-amino acids are found in proteins D-amino acids are less common, but are found in bacterial cell walls and antibiotics
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94The 4 major cellular macromolecules*:chains (polymers) of repeating units
*Important recurring theme
polysaccharide sugars cell wall glycosidic
lipid fatty acids or membranes ester or ether isoprenoids
nucleic acid nucleotides DNA, RNA phosphodiester
protein amino acids enzymes peptide
polymer monomer example covalent bond(see notes for other examples)
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95Study objectives1. Contrast saturated and unsaturated fatty acids. Understand how and why they influence membrane fluidity. Know the general structure of membrane lipids. Know the names of the fatty acids and lipids presented in class. You do NOT need to memorize the structure of the individual fatty acids, ethanolamine, or serine. 2. Compare and contrast bacterial,eukaryal, and archaeal lipids, especially the molecular components and the bonds. More details later.3. What are nucleic acids? Understand that nucleotides are composed of a nitrogenous base (purine or pyrimidine), a sugar (ribose or deoxyribose), and one to three phosphates. Know the structure of the phosphodiester bond. What parts of the nucleotides are connected by the phosphate of the phosphodiester bond? What is meant by the 5' and 3' ends of DNA and RNA?4. Memorize the structure of the nucleotide ATP. This is a very important molecule and we will discuss it in great detail throughout the semester. 5. Know the purines and pyrimidines. Know the number of rings in each. What is the structural difference between thymine (T) and uracil (U)?