Calling names

1
Calling names

• ALKANES
• ALKENES
• ALKYNES
• CYCLO-
• ALKYL-

2
Cycloalkanes with Side Groups
3
Figure 22.12 Some selected substituted benzenes
and their names
4
Bonding in ethane
CH3-CH3
5
Bonding in ethylene
CH2CH2
6
Bonding in acytylene
CHCH
7
Cis and Trans Isomers

• Double bond is fixed
• Cis/trans Isomers are possible
• CH3 CH3 CH3
• CH CH CH CH
• cis trans CH3

8
isomers
butane methyl propane

• Structural chain
• Structural - position
• Structural function
• Stereo - geometrical
• Stereo - optical

2methylhexane 3methylhexane
cis trans
9
alkan-OL
alkan-AL
alkan-ONE
10
Amino Acids and Proteins

• Types of Proteins
• Amino Acids
• The Peptide Bond

11
Amino Acids

• Building blocks of proteins
• Carboxylic acid group
• Amino group
• Side group R gives unique characteristics
• R side chain
• I
• H2NC COOH
• I
• H

12
Amino Acids as Acids and Bases

• Ionization of the NH2 and the COOH group
• Zwitterion has both a and charge
• Zwitterion is neutral overall
• NH2CH2COOH H3NCH2COO

glycine zwitterion of glycine
13
pH and ionization

• H OH-
• H3NCH2COOH H3NCH2COO H2NCH2COO
• Positive ion zwitterion Negative ion
• Low pH neutral pH High pH

14
Most Amino Acids Have Non-Superimposable Mirror
Images
What is the exception?
15
D vs L Alanine
16
Examples of Amino Acids

• H
• I
• H2NC COOH
• I
• H glycine
• CH3
• I
• H2NC COOH
• I
• H alanine

17
Types of Amino Acids

• Nonpolar R H, CH3, alkyl groups, aromatic
• O
• Polar ll
• R CH2OH, CH2SH, CH2CNH2,
• (polar groups with O-, -SH, -N-)
• Polar/Acidic
• R CH2COOH, or -COOH
• Polar/ Basic
• R CH2CH2NH2

18
Classification of Amino Acids by Polarity
Acidic
Neutral
Basic
Asp
Asn
Arg
Ser
POLAR
Tyr
His
Cys
Gln
Thr
Lys
Glu
Gly
Ala
Ile
Phe
NON- POLAR
Trp
Met
Val
Leu
Pro
Polar or non-polar, it is the bases of the amino
acid properties.
Juang RH (2003) Biochemistry
19
Nonpolar R groups
ISOPROPYL
20
Polar R groups.
21
Polar R groups
22
20 standard amino acids used by cells in
protein biosynthesis
This information will be available on information
sheets provided with the final exam, If needed
23
ala arg
asn asp cys
gln glu
gly his ile
leu lys
met phe pro
ser thr
trp tyr val 20
Standard Amino Acids
24
Essential Amino Acids

• 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

25
(No Transcript)
26
(No Transcript)
27
Formation of Peptide Bonds by Dehydration
Amino acids are connected head to tail
Dehydration -H2O
Juang RH (2004) BCbasics
28
H O I ?? H2NC
COH I H gly
CH3 O I ?? HNC COH I
I H H ala

Peptide Linkage
H O I ?? H2NC C
I H glyala
CH3 O I ?? NC COH I
I H H Dipeptide
29
Peptides

• Amino acids linked by amide (peptide) bonds
• Gly Lys Phe Arg
  Ser

H2N- end -COOH end Peptide bonds
(N-terminus)
(C-terminus)
name Glycyllysylphenylalanylarginylserine Symb
ol GlyLysPheArgSer Or GKFRS
30

What are the possible tripeptides formed from
one each of leucine, glycine, and alanine?
31

• 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

32
Tripeptide containing glycine, cysteine, and
alanine
Source Photo Researchers, Inc.
33

• Write the three-letter abbreviations for the
  following tetrapeptide

Focus Attention on the Side Group
Alanine(Ala / A)
Leucine(Leu / L)
Cysteine(Cys / C)
Methionine(Met / M)
34
Proteins

• Proteins are sequences of amino acid residues
• 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
• 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)

35
Types of Proteins

• Type Examples
• Structural tendons, cartilage, hair, nails
• Contractile muscles
• Transport hemoglobin
• Storage milk
• Hormonal insulin, growth hormone
• Enzyme catalyzes reactions in cells
• Protection immune response

36
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!

37
Four Levels of Protein Structure

• Primary, 1o
• the amino acid sequence
• Secondary, 2o
• Local conformation of main-chain atoms (F and Y
  angles)
• Tertiary, 3o
• 3-D arrangement of all the atoms in space
  (main-chain and side-chain)
• Quaternary, 4o
• 3-D arrangement of subunit chains

38
HIERARCHY OF PROTEIN STRUCTURE
1.
2.
3.
4.
Tertiary
39
Secondary Structure

• The two most common regular (repetitive) 2
  structures are
• a-helix
• b-sheet
• Both use hydrogen bonding between N-H CO of
  peptide group as primary stabilizing force.

40
Helices (1)
Cter
Nter
Hydrogen bonds O (i) lt-gt N (i4)
41
(No Transcript)
42
The b-strand
N-H---O-C Hydrogen bonds
Real b-strand is twisted
Extended chain is flat
43
Pleated sheet
44
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
45
Figure 22.26 Permanent waving of hair
46
Building the Hemoglobin Protein
47
Urey/Miller Experiment
Figure 2 09
48
Urey/Miller Experiment
Figure 2 09
49
Central Dogma
50
DNA Double Helix-Held Together with H-Bonds
51
(No Transcript)
52
Base Pairs Double Helix
53
Three Components of DNA Structure
base thymine (pyrimidine)
monophosphate
sugar 2-deoxyribose
?
5
1
4
3
2
(5 to 3)
3 linkage
baseadenine (purine)
5 linkage
no 2-hydroxyl
54
Pyrimidines used in Base Pairs, DNA
6-membered rings only
55
Purines used in Base Pairs, DNA
Fused 5 and 6 member rings
56
DNA Base Pairing
A-T pairing 2 H-Bonds
G-C pairing 3 H-bonds
57
A-T and G-C Base Pairs Hold the DNA helices
together
58
A-T and G-C Base Pairs Hold the DNA helices
together
59
A-T and G-C Base Pairs Hold the DNA helices
together
60
A-T and G-C Base Pairs Hold the DNA helices
together
61
A-T and G-C Base Pairs Hold the DNA helices
together
62
Hydrogen-Bondings Role in DNA Structure
63
Transcription

• The new RNA molecule is formed by incorporating
• nucleotides that are complementary to the
  template strand.

DNA
DNA coding strand
5
G
T
C
A
T
T
C
G
G
3
3
C
A
G
T
A
A
G
C
C
5
DNA template strand
64
of strands
kind of sugar
bases used
65
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)
66
Transcription

• The new RNA molecule is formed by incorporating
• nucleotides that are complementary to the
  template strand.

DNA
DNA coding strand
5
G
T
C
A
T
T
C
G
G
3
3
C
A
G
T
A
A
G
C
C
5
DNA template strand
67
Translation

• The process of reading the RNA sequence of an
  mRNA and creating the amino acid sequence of a
  protein is called translation.

68
(No Transcript)
69
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

70
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
71

• 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

Figure 10.8A
72
(No Transcript)
73
Structure of the Heme Group
Porphyrin Ligand
74
Heme Group Found Bonded to Proteins
75
Hemoglobin

• Multi-subunit protein (tetramer)
• 2 ? and 2 ? subunits
• Heme
• One per subunit
• Has an iron atom
• Carries O2
• In red blood cells

76
Sickle Cell Anemia

• Genetic Disease
• Heterozygous individuals carriers
• Homozygous individuals diseased
• Hemoglobin
• Found in red blood cells
• Carries oxygen to tissues
• SCA Results from Defective Hemoglobin
• Hemoglobins stick together
• Red blood cells damaged
• Complications from low oxygen supply to tissues
• Pain, organ damage, strokes, increased
  infections, etc.
• Incidence highest among Africans and Indians
• Heterozygotes protected from Malaria

77
Sickle Cell Hemoglobin
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
Mutant protein
Glutamate (glu), a negatively charged amino acid,
is replaced by valine (val), which has no charge.
78
Structures of Amino Acids
Glutamic Acid Polar, Acidic
Valine Non-polar, Neutral
79
(No Transcript)
80
Glu 6 ? Val
81
A single amino acid substitution in a protein
causes sickle-cell disease
82
(No Transcript)