calling names
DESCRIPTION
Calling names. ALK ANE S ALK ENE S ALK YNE S CYCLO - ALK YL -. Cycloalkanes with Side Groups. Bonding in ethane. CH 3 -CH 3. Bonding in ethylene. CH 2 =CH 2. Bonding in acytylene. CH=CH. Cis and Trans Isomers. Double bond is fixed Cis/trans Isomers are possible - PowerPoint PPT PresentationTRANSCRIPT
Calling names
• ALKANES
• ALKENES
• ALKYNES
• CYCLO-
• ALKYL-
Cycloalkanes with Side GroupsCH3
CH3
CH3
CH3
CH3
CH3
methylcyclopentane
1,2-dimethylcyclopentane
1,2,4-trimethylcyclohexane
Bonding in ethane
CH3-CH3
Bonding in ethylene
CH2=CH2
Bonding in acytylene
CH=CH
Cis and Trans Isomers
Double bond is fixed Cis/trans Isomers are possible
CH3 CH3 CH3
CH = CH CH = CH
cis trans CH3
isomers
• Structural – chain
• Structural - position
• Structural – function
• Stereo - geometrical
• Stereo - optical
butanemethyl propane
2methylhexane3methylhexane
cistrans
alkan-OL
alkan-AL
alkan-ONE
Amino Acids and Proteins
Types of Proteins
Amino Acids
The Peptide Bond
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 H3N–CH2–COO– glycine zwitterion of glycine
+
pH and ionization
H+ OH-
H3N–CH2–COOH H3N–CH2–COO– H2N–CH2–
COO–
Positive ion zwitterion Negative ion
Low pH neutral pH High pH
+ +
Most Amino Acids Have
Non-Superimposable Mirror Images
What is the exception?
D vs L Alanine
Examples of Amino Acids
H I
H2N—C —COOH I
H glycine
CH3 I
H2N—C —COOH I
H alanine
Types of Amino Acids
Nonpolar R = H, CH3, alkyl groups, aromatic
OPolar ll
R = –CH2OH, –CH2SH, –CH2C–NH2,
(polar groups with –O-, -SH, -N-)
Polar/Acidic
R = –CH2COOH, or -COOH
Polar/ Basic
R = –CH2CH2NH2
PO
LAR
NO
N-
PO
LAR
Tyr His
Gly
Acidic Neutral Basic
Asp
Glu GlnCys
Asn Ser
Thr Lys
Arg
Ala
ValIle
Leu MetPhe Trp
Pro
Classification of Amino Acids by Polarity
Polar or non-polar, it is the bases of the amino acid properties.
Juang RH (2003) Biochemistry
Nonpolar R groups
ISOPROPYL
Polar R groups.
Polar R groups
20 “standard” amino acids used by cells in protein biosynthesis
Alanine(Ala / A)
Arginine(Arg / R)
Asparagine(Asn / N)
Aspartic acid
(Asp / D) Cysteine(Cys / C)
Glutamic acid(Glu / E)
Glutamine(Gln / Q)
Glycine(Gly / G)
Histidine
(His / H) Isoleucine(Ile / I)
Leucine(Leu / L)
Lysine
(Lys / K) Methionine
(Met / M) Phenylalanine(Phe / F)
Proline
(Pro / P)
Serine(Ser / S)
Threonine(Thr / T)
Tryptophan
(Trp / W) Tyrosine
(Tyr / Y) Valine
(Val / V)
This information will be available on information sheets provided with the final exam,
If needed
ala arg asn asp cys
gln glu gly his ile
leu lys met phe pro
ser thr trp tyr val20 “Standard” Amino Acids
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
NH2 COOH1 NH2 COOH2
NH2 C N COOH
O
H21
Amino acids are connected head to tail
Formation of Peptide Bonds by Dehydration
Dehydration-H2O
Juang RH (2004) BCbasics
H O I H2N—C —COH I H gly
CH3 OI
HN—C —COH I I H H ala
H O I H2N—C —C — I
H glyala
CH3 O I N—C —COH I IH H Dipeptide
Peptide Linkage
Peptides• Amino acids linked by amide (peptide)
bonds
Gly Lys Phe Arg Ser
name: Glycyllysylphenylalanylarginylserine
Symbol: GlyLysPheArgSer
Or: GKFRS
H2N- end -COOH end
Peptide bonds (N-terminus) (C-terminus)
What are the possible tripeptides formed from one each of leucine, glycine, 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
Tripeptide containing glycine, cysteine, and alanine
Source: Photo Researchers, Inc.
Write the three-letter abbreviations for the following tetrapeptide:
H3N CH
CH3
C
O
N
H
CH C
O
N
H
CH C
O
N
H
CH C O-
OCH
CH CH3
CH3
CH2
SH
CH2
CH2
S
CH3
Alanine(Ala / A)
Leucine(Leu / L)
Cysteine(Cys / C)
Methionine(Met / M)
Focus Attention on the Side Group
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)
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
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!
Four Levels of Protein Structure
• Primary, 1o
– the amino acid sequence• Secondary, 2o
– Local conformation of main-chain atoms ( and 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
HIERARCHY OF PROTEIN STRUCTURE
Tertiary
1. 2.
3. 4.
Secondary Structure
• The two most common regular (repetitive) 2˚ structures are:
-helix-sheet
• Both use hydrogen bonding between N-H & C=O of peptide group as primary stabilizing force.
Nter
Cter
Helices (1)
Hydrogen bonds: O (i) <-> N (i+4)
The -strand
Extended chain is flat “Real -strand is twisted”
N-H---O-CHydrogen bonds
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
Figure 2 – 09
Urey/Miller Experiment
Figure 2 – 09
Urey/Miller Experiment
Cytoplasm
Nucleus
DNA
DNA is the genetic material within the nucleus.
Central Dogma
RNA
Protein
Replication
The process of replication creates new copies of DNA.
TranscriptionThe process of transcription
creates an RNA using
DNA information.
TranslationThe process of translation
creates a protein using
RNA information.
DNA Double Helix-Held Together with
H-Bonds
Base Pairs Double Helix
base: thymine(pyrimidine)
sugar: 2’-deoxyribose
monophosphate
no 2’-hydroxyl
(5’ to 3’)
5’
3’
base:adenine(purine)
1’2’
4’
3’ linkage
5’ linkage
Three Components of DNA Structure
Pyrimidines used in Base Pairs, DNA
6-membered rings only
Purines used in Base Pairs, DNA
Fused 5 and 6 member rings
DNA Base Pairing
A-T pairing
2 H-Bonds
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
A-T and G-C Base Pairs Hold the DNA helices together
Transcription• The new RNA molecule is formed by incorporating • nucleotides that are complementary to the
template strand.
DNA coding strand
DNA template strand
DNA
5’
3’
5’
3’
G T C A T T C G G
C A G T A A G C C
G
RNA
5’
GG U C A U U C
3’
# of strands
kind of sugar
bases used
RNA Polymerase is the Enzyme that Catalyzes Transcription of DNA Information to RNA
DNA (Blue)
Newly Synthesized RNA (Red)
Active Site Metal (Pink)
Bridge Helix Moves DNA through Polymerase during RNA Synthesis (Green)
Transcription• The new RNA molecule is formed by incorporating • nucleotides that are complementary to the
template strand.
DNA coding strand
DNA template strand
DNA
5’
3’
5’
3’
G T C A T T C G G
C A G T A A G C C
G
RNA
5’
GG U C A U U C
3’
Translation• The process of reading the RNA sequence of an
mRNA and creating the amino acid sequence of a protein is called translation.
Transcription
Codon Codon Codon
Translation
DNA
T T C A G T C A G
DNAtemplatestrand
mRNA
A A G U C A G U C MessengerRNA
Protein Lysine Serine ValinePolypeptide(amino acidsequence)
• 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
Genetic information written in codons is translated into amino acid sequences
• Virtually all organisms share the same genetic code
• All organisms use the same 20 aa
• Each codon specifies a particular aa
The genetic code is the Rosetta stone of life
Figure 10.8A
• 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
Structure of the Heme GroupPorphyrin Ligand
Heme Group Found Bonded to Proteins
Hemoglobin• Multi-subunit protein (tetramer)
– 2 and 2 subunits
• Heme– One per subunit– Has an iron atom
– Carries O2
• In red blood cells
Sickle Cell AnemiaGenetic 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
Sickle Cell Hemoglobin
GUG CAC CUG ACU CCU GAG GAG AAGval his leu thr pro glu glu lys 1 2 3 4 5 6 7 8
GUG CAC CUG ACU CCU GUG GAG AAGval his leu thr pro val glu lys 1 2 3 4 5 6 7 8
Mutation (in DNA)
Normal mRNA
Normal protein
Mutant mRNA
Mutant protein
Glutamate (glu), a negatively charged amino acid, is replaced by valine (val), which has no charge.
Structures of Amino Acids
Glutamic Acid
Polar, Acidic
Valine
Non-polar, Neutral
Glu 6 Val
A single amino acid substitution in a protein causes sickle-cell disease