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Calling names
Cycloalkanes with Side Groups
CH3
• ALKANES
methylcyclopentane
• ALKENES
CH3
CH3
1,2-dimethylcyclopentane
• ALKYNES
CH3
• CYCLO-
CH3
1,2,4-trimethylcyclohexane
• ALKYLCH3
Figure 22.12: Some selected substituted benzenes and
their names
Bonding in ethane
CH3-CH3
Bonding in ethylene
Bonding in acytylene
CH2=CH2
CH=CH
1
isomers
Cis and Trans Isomers
Double bond is fixed
Cis/trans Isomers are possible
• Structural – chain
butane
methyl propane
• Structural - position
2methylhexane
3methylhexane
• Structural – function
CH3
CH3
CH3
• Stereo - geometrical
CH = CH
CH = CH
cis
trans
CH3
cis
trans
• Stereo - optical
Amino Acids and Proteins
alkan-OL
Types of Proteins
Amino Acids
The Peptide Bond
alkan-AL
alkan-ONE
Amino Acids
•
•
•
•
Building blocks of proteins
Carboxylic acid group
Amino group
Side group R gives unique characteristics
R side chain
I
H2N—C —COOH
I
H
Amino Acids as Acids and Bases
• Ionization of the –NH2 and the –COOH
group
• Zwitterion has both a + and – charge
• Zwitterion is neutral overall
NH2–CH2–COOH
glycine
+
H3N–CH2–COO–
zwitterion of glycine
2
Most Amino Acids Have
pH and ionization
Non-Superimposable Mirror Images
What is the exception?
H+
+
OH+
H3N–CH2–COOH
H3N–CH2–COO–
H2N–CH2–COO–
Positive ion
zwitterion
Negative ion
Low pH
neutral pH
High pH
Examples of Amino Acids
H
I
H2N—C —COOH
I
H
glycine
CH3
I
D vs L Alanine
H2N—C —COOH
I
H
alanine
Classification of Amino Acids by Polarity
Types of Amino Acids
NONPOLAR
Nonpolar R = H, CH3, alkyl groups, aromatic
O
Polar
ll
R = –CH2OH, –CH2SH, –CH2C–NH2,
(polar groups with –O-, -SH, -N-)
Polar/Acidic
R = –CH2COOH, or -COOH
Polar/ Basic
R = –CH2CH2NH2
POLAR
Acidic
Neutral
Basic
Asp
Asn Ser
Arg
Cys
Tyr
His
Gln Thr
Lys
Glu
Gly
Ala Ile
Phe Trp
Met
Val Leu
Pro
Polar or non-polar, it is the bases of the amino acid properties.
Juang RH (2003) Biochemistry
3
Nonpolar R groups
Polar R groups.
ISOPROPYL
Polar R groups
20 “standard” amino acids used by
cells in protein biosynthesis
Alanine
(Ala / A)
Glutamic acid
(Glu / E)
Leucine
(Leu / L)
Serine
(Ser / S)
Arginine
(Arg / R)
Glutamine
(Gln / Q)
Aspartic acid
(Asp / D)
Glycine
(Gly / G)
Lysine
Methionine
(Lys / K)
(Met / M)
Threonine
(Thr / T)
Asparagine
(Asn / N)
Histidine
Cysteine
(Cys / C)
(His / H)
Isoleucine
(Ile / I)
Phenylalanine
(Phe / F)
(Pro / P)
Proline
Tryptophan
Tyrosine
Valine
(Trp / W)
(Tyr / Y)
(Val / V)
This
information
will be
available on
information
sheets
provided
with the
final exam,
If needed
Essential Amino Acids
ala
arg
gln
leu
ser
glu
lys
thr
asn
asp
cys
gly
his
ile
met
phe
pro
trp
tyr
val
• 10 amino acids not synthesized by the
body
• arg, his, ile, leu, lys, met, phe, thr, trp,
val
• Must obtain from the diet
• All in dairy products
• 1 or more missing in grains
and vegetables
20 “Standard” Amino Acids
4
Formation of Peptide Bonds by Dehydration
Amino acids are connected head to tail
NH2
1
COOH
NH2
2
COOH
Dehydration
O
1
C N
2
CH3 O
I
||
HN—C —COH
I
I
H H
ala
Peptide Linkage
-H2O
NH2
H O
I
||
H2N—C —COH
I
H
gly
COOH
H
CH3 O
H O
I
||
I
||
H2N—C —C —N—C —COH
I
I I
H
H H
glyala
Dipeptide
Juang RH (2004) BCbasics
Peptides
• Amino acids linked by amide (peptide)
bonds
Gly
Lys
Phe
H2N- end
Arg
Ser
-COOH end
Peptide bonds
(N-terminus)
name:
Symbol:
Or:
What are the possible tripeptides
formed from one each of leucine,
glycine, and alanine?
(C-terminus)
Glycyllysylphenylalanylarginylserine
GlyLysPheArgSer
GKFRS
5
Tripeptide containing glycine, cysteine,
and alanine
Tripeptides possible from one each of
leucine, glycine, and alanine
Leu-Gly-Ala
Leu-Ala-Gly
Ala-Leu-Gly
Ala-Gly-Leu
Gly-Ala-Leu
Gly-Leu-Ala
Source: Photo Researchers, Inc.
Proteins
Write the three-letter abbreviations for the following
tetrapeptide:
CH
CH3
SH
CH2
CH
O
CH2 O
CH2 O
Focus
Attention on
the Side
Group
CH
C
CH
O
CH3
CH3
CH3 O
H 3N
CH
C
N
S
H
Alanine
(Ala / A)
N
CH
C
H
Leucine
(Leu / L)
N
C
-
H
Cysteine
(Cys / C)
Type
Structural
Contractile
Transport
Storage
Hormonal
Enzyme
Protection
– Amino acid: carbon atom (C), amino group
(NH3),carboxyl group (COOH), variable sidechain (20
different types)
– Amino acids are linked with the peptide bond
• Protein structure:
Methionine
(Met / M)
Types of Proteins
•
•
•
•
•
•
•
• Proteins are sequences of amino acid residues
Examples
tendons, cartilage, hair, nails
muscles
hemoglobin
milk
insulin, growth hormone
catalyzes reactions in cells
immune response
–
–
–
–
Primary – sequence of amino acids
Secondary – local 3D arrangement of amino acids
Tertiary – 3D structure of a complete protein
Quaternary – 3D structure of functional protein
(complex)
Proteins Vary Tremendously in
Size
• Insulin - A-chain of 21 residues, B-chain of 30
residues -total mol. wt. of 5,733
• Glutamine synthetase - 12 subunits of 468
residues each - total mol. wt. of 600,000
• Connectin proteins - alpha - MW 2.8 million!
•
beta connectin - MW of 2.1 million, with a
length of 1000 nm -it can stretch to 3000 nm!
6
HIERARCHY OF PROTEIN STRUCTURE
Four Levels of Protein Structure
1.
2.
• Primary, 1o
– the amino acid sequence
• Secondary, 2o
– Local conformation of main-chain atoms (Φ
and Ψ angles)
• Tertiary, 3o
3.
4.
Tertiary
– 3-D arrangement of all the atoms in space
(main-chain and side-chain)
• Quaternary, 4o
– 3-D arrangement of subunit chains
Helices (1)
Secondary Structure
• The two most common regular
(repetitive) 2˚ structures are:
Cter
ƒα-helix
ƒβ-sheet
• Both use hydrogen bonding between
N-H & C=O of peptide group as
primary stabilizing force.
Nter
Hydrogen bonds: O (i) <-> N (i+4)
The β-strand
N-H---O-C
Hydrogen
bonds
Extended chain is flat
“Real β-strand is twisted”
7
Pleated sheet
Tertiary Structure
• Specific overall shape of a protein
• Cross links between R groups of amino acids in
chain
Ionic
H-bond
Disulfide Hydrophobic H-bond
Figure 22.26: Permanent waving of hair
Building the Hemoglobin Protein
Urey/Miller Experiment
Figure 2 – 09
Urey/Miller Experiment
Figure 2 – 09
8
DNA Double Helix-Held Together with
Central Dogma
H-Bonds
DNA is the genetic material
within the nucleus.
Replication
The process of replication
creates new copies of DNA.
DNA
Transcription
The process of transcription
creates an RNA using
DNA information.
RNA
Nucleus
Translation
The process of translation
creates a protein using
RNA information.
Protein
Cytoplasm
Base Pairs Double Helix
Three Components of DNA Structure
Pyrimidines used in Base Pairs,
DNA
base: thymine
(pyrimidine)
monophosphate
α
sugar: 2’-deoxyribose
5’
4’
3’
(5’ to 3’)
1’
2’
3’ linkage
base:adenine
(purine)
5’ linkage
no 2’-hydroxyl
6-membered rings only
9
Purines used in Base Pairs, DNA
DNA Base Pairing
A-T pairing
2 H-Bonds
Fused 5 and 6 member rings
G-C pairing
3 H-bonds
A-T and G-C Base Pairs Hold the
DNA helices together
A-T and G-C Base Pairs Hold the
DNA helices together
A-T and G-C Base Pairs Hold the
DNA helices together
A-T and G-C Base Pairs Hold the
DNA helices together
10
A-T and G-C Base Pairs Hold the
DNA helices together
A-T and G-C Base Pairs Hold the
DNA helices together
Transcription
Hydrogen-Bonding’s Role in DNA Structure
• The new RNA molecule is formed by incorporating
• nucleotides that are complementary to the
template strand.
DNA coding strand
5’
DNA
G T C A T T C G G
3’
3’
G U C A U U C G G
3’
C A G T A A G C C
5’
DNA template strand
5’
RNA
# of strands
kind of sugar
bases used
11
RNA Polymerase is the Enzyme that Catalyzes
Transcription of DNA Information to RNA
DNA (Blue)
Newly Synthesized
RNA (Red)
Bridge Helix Moves
DNA through
Polymerase during
RNA Synthesis
(Green)
Active Site Metal
(Pink)
Genetic information written in codons is
translated into amino acid sequences
• The “words” of the DNA “language” are
triplets of bases called codons
– 3 bases or nucleotides make one
codon
– Each codon specifies an amino acid
– The codons in a gene specify the amino
acid sequence of a polypeptide
The genetic code is the Rosetta stone of life
• Virtually all
organisms
share the same
genetic code
• All organisms
use the same
20 aa
• Each codon
specifies a
particular aa
Figure 10.8A
Translation
• The process of reading the RNA sequence of an
mRNA and creating the amino acid sequence of a
protein is called translation.
• Tryptophan and
Methionine have
only 1 codon each
• All the rest have
more than one
• AUG has a dual
function
• 3 stop codons that
code for termination
of protein synthesis
• Redundancy in the
code but no
ambiguity
DNA
Transcription
T
T
C
A
G
T
C
A
G
A
A
G
U
C
A
G
U
C
DNA
template
strand
Messenger
RNA
mRNA
Codon
Codon
Codon
Lysine
Serine
Valine
Translation
Figure 10.8A
Protein
Polypeptide
(amino acid
sequence)
12
Structure of the Heme Group
Heme Group Found Bonded to Proteins
Porphyrin Ligand
Hemoglobin
• Multi-subunit protein (tetramer)
– 2 α and 2 β subunits
• Heme
– One per subunit
– Has an iron atom
– Carries O2
• In red blood cells
Sickle Cell Hemoglobin
Sickle Cell Anemia
Genetic Disease
z Heterozygous individuals – carriers
z Homozygous individuals – diseased
Hemoglobin
z Found in red blood cells
z Carries oxygen to tissues
SCA Results from Defective Hemoglobin
z Hemoglobins stick together
z Red blood cells damaged
Complications from low oxygen supply to tissues
z Pain, organ damage, strokes, increased infections, etc.
Incidence highest among Africans and Indians
z Heterozygotes protected from Malaria
Structures of Amino Acids
Normal mRNA
GUG CAC CUG ACU CCU GAG GAG AAG
val his leu thr pro glu glu lys
1
2
3
4
5
6
7
8
Normal protein
Mutation
(in DNA)
Mutant mRNA
GUG CAC CUG ACU CCU GUG GAG AAG
val his leu thr pro val glu lys
1
2
3
4
5
6
7
8
Glutamic Acid
Valine
Polar, Acidic
Non-polar, Neutral
Mutant protein
Glutamate (glu), a negatively charged amino acid,
is replaced by valine (val), which has no charge.
13
Glu 6
→
Val
A single amino acid substitution in
a protein causes sickle-cell disease
14