Biochemistry

1
Biochemistry

• Proteins
• Polysaccharides
• Nucleic Acids
• Lipids
• Adenosine Triphosphate

2
Biochemistry

• The branch of chemistry that is concerned with
  substances and reactions in living systems.
• Living systems rely on many large molecules and
  biopolymers.
• Proteins
• Polysaccharides
• Nucleic acids

3
Proteins

• These are biopolymers that are constructed from a
  limited set of amino acids.
• They are the most plentiful organic substances in
  the cell.
• About half of the dry mass of a cell is composed
  of proteins.
• They serve a wide range of functions.

4
Protein function

• Enzymes biological catalysts.
• Immuno- antibodies of immune system.
• globulins
• Transport move materials around -
• hemoglobin for O2.
• Regulatory hormones, control of metabolism.
• Structural coverings and support -
• skin, tendons, hair, bone.
• Movement muscle, cilia, flagella.

5
Amino acids

• All proteins are composed of amino acids.
• Twenty common amino acids.
• All are ?-amino acids.
• Except for proline, primary amino- group is
  attached to the ? carbon - the carbon just after
  the acid group.

? carbon
H R-C-COOH
NH2
General Structure
6
Amino acids

• Because both acid and base groups are present, an
  amino acid can form a /- ion.
• H H
• R-C-COOH R-C-COO-
• NH2 NH3
• The position of the equilibrium is based on pH
  and the type of amino acid. Called a zwitterion.

7
Some amino acid examples
H3C H \ HC-C-COO-
/ H3C NH3
H CH3-C-COO-
NH3
valine
alanine
H
CH3
-S-CH2-CH2-C-COO-
NH3
methionine
tryptophan
8
Some amino acid examples
H
HO-CH2-C-COO-
NH3
H H-C-COO-
NH3
serine
glycine
O H
H2N-C-CH2-C-COO-
NH3
O H
-O-C-CH2-CH2-C-COO-

NH3
asparagine
glutamic acid
9
Primary protein structure

• Proteins are polymers made up of amino acids.
• Peptide bond - how the amino acids are
• linked together to make
• a protein.

H H2NCCOOH
R
H H2NCCOOH
R
H O H2N -
C - C - R
H N - C - COOH H
R

H2O
10
Four levels of protein structure

• Primary structure
• The sequence of amino acids in a protein.
• Secondary structure
• Way that chains of amino acids are coiled or
  folded - (?-helix, ?-sheet, random coil).
• Tertiary structure
• Way ?-helix, ?-sheet, random coils fold and
  coil.
• Quaternary structure
• Way that two or more peptide chains pack
  together.

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Primary structure

• All proteins have the same covalent backbone.
• Part of a protein.

12
Secondary structure

• Long chains of amino acids commonly fold or curl
  into a regular repeating structure.
• Structure is a result of hydrogen bonding between
  amino acids within the protein.
• Common secondary structures are
• ? - helix
• ? - pleated sheet
• Secondary structure adds new properties to a
  protein like strength, flexibility, ...

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?-helix
One common type of secondary structure. Propertie
s of an ?-helix include strength and
low solubility in water. Originally proposed
by Pauling and Corey in 1951.
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a-helix
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?-helix
Every amide hydrogen and carbonyl oxygen is
involved in a hydrogen bond.
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Collagen

• Family of related proteins.
• About one third of all protein in humans.
• Structural protein
• Provides strength to bones, tendon, skin, blood
  vessels.
• Forms triple helix - tropocollagen.

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Tropocollagen
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?-Pleated sheets

• Another secondary structure for protein.
• Held together by hydrogen bonding between
  adjacent sheets of protein.

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?-Pleated sheets

• Silk fibroin - main protein of silk is an example
• of a ? pleated sheet structure.

Composed primarily of glycine and alanine. Stack
like corrugated cardboard for extra strength.
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Beta sheet
21
Tertiary structure of proteins

• Fibrous proteins
• insoluble in water
• form used by connective tissues
• silk, collagen, ?-keratins
• Globular proteins
• soluble in water
• form used by cell proteins
• 3-D structure - tertiary

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Tertiary structure of proteins

• Results from interaction of side chains.
• The protein folds into a tertiary structure.
• Possible side chain interactions
• Similar solubilities
• Ionic attractions
• Electrostatic attraction between ? and ?-
  sidechains
• Covalent bonding

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Tertiary structureof proteins
Sulfide crosslink
Hydrophobic interaction
- S - S -
-COO- H3N-
Hydrogen bonding
Salt bridge
24
Quaternary structureof proteins

• Many proteins are not single peptide strands.
• They are combinations of several proteins
• - aggregate of smaller globular proteins.
• Conjugated protein - incorporate another type of
  group that performs a specific function.
• prosthetic group

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Quaternary structureof proteins
Aggregate structure This example shows
four different proteins and two
prosthetic groups.
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Example - cytochrome C 550
Heme structure Contains Fe2 Used
in metabolism.
Aggregate of proteins and other structures.
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Hemoglobin and myoglobin

• Hemoglobin
• oxygen transport protein of red blood cells.
• Myoglobin
• oxygen storage protein of skeletal muscles.
• As with the cytochrome example, both proteins
  use heme groups. It acts as the binding site
  for molecular oxygen.

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Heme

• myoglobin
• 1 heme group
• hemoglobin
• 4 heme groups

29
Myoglobin
Heme
30
Hemoglobin
2 ? chains
4 heme
2 ? chains
31
Sickle cell anemia

• Defective gene results in production of mutant
  hemoglobin.
• Still transports oxygen but results in deformed
  blood cells - elongated, sickle shaped.
• Difficult to pass through capillaries. Causes
  organ damage, reduced circulation.
• Affects 0.4 of African-American.

32
Comparison of normal andsickle cell hemoglobin
Normal
Sickle
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Summary of protein structure
primary
secondary
tertiary
quaternary
34
Polysaccharides

• These are biopolymers composed of hundreds to
  thousands of simple sugar units
  (monosaccharides).
• The most common monosaccharide used
  in polysaccharides
• is glucose.

35
Intramolecular cyclization

• Simple sugars tend to exist primarily in cyclic
  form. It is the most stable arrangement.

CH2OH
CH2OH
H
C
OH
C
O
O
C
C
C
C
OH
C
C
C
C
36
Intramolecular cyclization

• The -OH group that forms can be above or below
  the ring resulting in two forms - anomers
• ? and ? are used to identify the two forms.
• ? - OH group is down compared to CH2OH (trans).
• ? - OH group is up compared to CH2OH (cis).

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Cyclization of D-glucose
? -D - glucose
? - D - glucose
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Polysaccharides

• Uses for polysaccharides
• Storage polysaccharides
• Energy storage - starch and glycogen
• Structural polysaccharides
• Used to provide protective walls or
  lubricative coating to cells - cellulose and
  mucopolysaccharides.
• Structural peptidoglycans
• Bacterial cell walls

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Starch

• Energy storage used by plants
• Long repeating chain of ?-D-glucose
• Chains up to 4000 units
• Amylose straight chain
• Amylopectin branched structure
• Starch is a mixture of about 75 amylopectin and
  25 amylose.

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Amylose starch

• Straight chain that forms coils ? (1 4)
  linkage.

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Amylose starch
Example showing coiled structure - 12 glucose
units - hydrogens and side chains are omitted.
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Amylopectin starch

• Amylopectin differs from amylose only in that it
  has side chains. These are formed from
• a (1 6) links
• Side chains occur every 24-30 units.
• Starch is stored as starch grains. They cannot
  diffuse from the cell and have little effect on
  the osmotic pressure of the cell.

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Glycogen

• Energy storage of animals.
• Stored in liver and muscles as granules.
• Similar to amylopectin but more highly branched.

44
Cellulose

• Most abundant polysaccharide.
• ? (1 4) glycosidic linkages.
• Result in long fibers - for plant structure.

45
Mucopolysaccharides

• These materials provide a thin, viscous,
  jelly-like coating to cells.
• The most abundant form is hyaluronic acid.
• Alternating units of
• N-acetylglucosamine and
• D-glucuronic acid.

46
Structural peptidoglycans

• Bacterial cell walls are composed primarily of an
  unbranched polymer of alternating units of
  N-acetylglucosamine and N-acetylmuramic acid.

R
crosslink for Staphylococcus aureus
47
The nucleic acids

• Nucleic acids are complex structures used to
  store genetic information.
• DNA deoxyribonucleic acid
• Serves as the Master Copy for most
  information in the cell.
• RNA ribonucleic acid
• Several types. Overall, it acts to transfer
  information from DNA to the rest of the cell.

48
DNA and RNA composition

• Primary structure of both materials is very
  similar.
• Each consists of a sugar/phosphate backbone with
  nitrogenous bases attached.

sugar
phosphate
base
Major difference is in the type of sugar and
bases used.
49
Sugars used
ribose used in RNA
deoxyribose used in DNA
Not a very big difference!
50
Nucleoside

• A sugar - base combination.

Base
?-N-glycosidic linkage
Sugar In this case deoxyribose
51
The nitrogenous bases

• Five bases are used that fall in two classes
• Purines
• A double ring (6 and 5 membered) structure
• Includes adenine and guanine
• Used by both DNA and RNA
• Pyrimidines
• A six membered ring structure
• Cytosine is used in both DNA and RNA
• Thymine is used in DNA, Uracil used in RNA

52
The nitrogenous bases
adenine
guanine
cytosine
thymine
uracil
53
Nucleotides

• Produced if the -OH on the sugar of a nucleoside
  is converted into a phosphate ester.

deoxyadenosine monophosphate (dAMP)
Each is named based on sugar and base name and
then the number of phosphates is indicated.
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Primary structure

• Phosphate bonds link DNA or RNA nucleotides
  together in a linear sequence.
• 3,5-phosphodiester

55
DNA
Number of Length Organism Base
Pairs (?m) Conformation Viruses
SV40 5 100
1.7 circular Adenovirus 36 000
12 linear ? phage 48 600
17 circular Bacteria E. coli
4 700 000 1 400 circular Eukaryotes Yeast
13 500 000 4 600 linear Fruit fly
165 000 000 56 000 linear Human 3 000 000
000 1-2 x 106 linear
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DNA structural elements

• Sugar-phosphate backbone
• Causes DNA chain to coil around the outside of
  the attached bases like a spiral staircase.
• Base Pairing
• Hydrogen bonding occurs between purines and
  pyrimidines. This causes two DNA strands to bond
  together.
• adenine - thymine guanine - cytosine
• Always pair together!
• Results in a double helix structure.

57
Base pairing and hydrogen bonding
58
Hydrogen bonding
Each base wants to form either two or three
hydrogen bonds. Thats why only certain bases
will form pairs.
59
The double helix
One complete turn is 3.4 nm
The combination of the stairstep sugar-phosphate
backbone and the bonding between pairs
results in a double helix.
2 nm between strands
60
RNA

• Approximately 5-10 of the total weight of a cell
  is RNA. DNA is only about 1
• RNA exists in three major forms.
• Ribosomal RNA - rRNA. Combined with protein to
  form ribosomes, the site of protein synthesis.
• Messenger RNA - mRNA. Carries instructions from
  a single gene from DNA to the ribosome.
• Transfer RNA - tRNA. Forms esters with specific
  amino acids for use in protein synthesis.

61
tRNA structure
The smallest type of RNA. It consists of 74-93
nucleotides. These molecules are the carriers
of the 20 amino acids with at least one tRNA for
each. They often contain several unusual purines
or pyrimidine bases -modifications of the basic
four.
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tRNA structure
3

• All tRNA have a common 2o and 3o structure.

5
anticodon
63
rRNA

• These molecules have 2o and 3o structure similar
  to tRNA. However, they are much larger.

16S rRNA E. Coli
64
rRNA

• Ribosome.
• A complex of ribosomal RNA and proteins. It is
  used as the platform for protein synthesis.
• Made of two subunits
• Large - three rRNA and about 49 proteins.
• Small - one rRNA and about 33 proteins.
• Together they provide a platform for
  synthesis.
• You can think of a ribosome like a tape player,
  where the tape is mRNA.

65
Ribosomes

• Two ribosomal subunits join to form a polysome.

small subunit
large subunit
synthesis platform
66
Genetic code, mRNAand protein amino acids

• The genetic code
• Triplet
• A set of three nucleotide bases on mRNA for one
  amino acid.
• Nonoverlapping
• A set of three adjacent bases are treated as a
  complete group - codon.
• No punctuation
• There are no intervening bases between
  triplets.

67
Genetic code, mRNAand protein amino acids

• The genetic code
• Degenerate
• A single amino acid may have more than one
  triplet code. There is usually a sequential
  relationship between these codes.
• Universal
• The same genetic code is used by all organisms
  except mitochondria and some algae.

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Amino acid codons
alanine GCA, GCC, GCG GCU arginine AGA, AGG,
CGA CGC, CGG, CGU asparagine AAC,
AAU aspartate GAC, GAU cysteine UGC,
UGU glutamate GAA, GAG glutamine CAA,
CAG glycine GGA, GGC, GGG GGU histidine CAC,
CAU isoleucine AUA, AUC, AUU leucine CUA, CUC,
CUG CUU, UUA, UUG
lysine AAA, AAG methionine
AUG phenylalanine UUC, UUU proline CCA,
CCC CCG, CCU serine UCA, UCC UCG,
UCU AGC, AGU threonine ACA, ACC
ACG, ACU tryptophan UGG tyrosine UCA,
UCU valine GUA, GUC GUG, GUU
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Steps in protein synthesis

• Step One - Initiation
• A special protein is required to bring the
  ribosome parts and mRNA together.
• It recognizes the initiation (START) codon
  (AUG).
• Once formed, the ribosome complex will
• - hold the mRNA in place.
• - provide binding sites for the growing
  protein and incoming amino acids.

70
Steps in protein synthesis

• Step Two - Chain elongation
• Amino acid is added sequentially to the peptide
  chain.
• An enzyme, peptidyl transferase, is used to move
  the ribosome down the mRNA strand -
  translocation.

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Steps in protein synthesis

• Step Three - Termination
• When one of three codons (UAA, UAG or UGA) is
  encountered, there is no tRNA that matches.
• Protein synthesis stops.
• A releasing factor is attracted to the site.
• This results in the growing protein being
  released from the ribosome.
• The ribosome complex then falls apart into the
  original subcomplexes.

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Protein synthesis
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Types of lipids
Fatty Acids Saturated Unsaturated
Acylglycerols Neutral Phosphoglycerols
Nonacylglycerols Sphingolipids Steroids
Waxes
Complex Lipids Lipoproteins Glycolipids
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Lipid functions

• Cell membrane structure
• Creates a barrier for the cell.
• Controls flow of materials.
• Energy storage
• Fats stored in adipose tissue.
• Hormones and Vitamins
• Hormones - communication between cells.
• Vitamins - assist in the regulation of biological
  processes.

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Fatty acids

• Long chain monocarboxylic acids
• CH3(CH2)nCOOH
• Size Range C12 - C24
• Always an even number of carbon.
• Saturated - no double bonds.
• Unsaturated - one or more double bonds.

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Fatty acid structure
Saturated fatty acid
Unsaturated fatty acid
77
Unsaturated fatty acids
trans-
cis, cis-
cis-
78
Some common fatty acids

• Common IUPAC Name mp Formula
• Lauric n-dodecanoic 44 C11H23COOH
• Palmitic n-hexadecanoic 63 C15H31COOH
• Stearic n-octadecanoic 70 C17H35COOH
• Palmitoleic cis-9-hexadecenoic
  0 C15H29COOH
• Oleic cis-9-octadecenoic 4 C17H33COOH
• Linoleic cis,cis-9,12- -12 C17H31COOH
• octadecadienoic
• Presence of double bonds reduces melting point.
• Melting points are in oC.

79
Neutral acylglycerols

• Ester of glycerol and a fatty acid.
• Principal function is energy storage - fat

glycerol
H
O
H
80
Steroids

• Broad class of compounds that all have the same
  base structure.

Steroid nucleus
81
Steroids

• Cholesterol
• Principal membrane lipid for fluidity.

82
Cholesterol

• Associated with hardening of the arteries.
• Appears to coat the arteries - plaque formation.
• Results in
• Increased blood pressure from
• Narrowing of arteries
• Reduced ability to stretch
• Clot formation leading to
• Myocardial Infarction
• Stroke

83
Steroids
CH
3

• Some reproductive hormones.

C
O
CH
3
progesterone
CH
3
O
testosterone
84
Complex lipids
cholesterol
protein
phospholipid
cholesterol ester

• Lipids bound to other molecules.

85
Biomembranes

• Cell and organelle membranes are composed of two
  layers - lipid bilayers.

86
Adenosine triphosphate (ATP)

• The principal energy carrier in living systems.

Removal of a phosphate will result in the
release of 31kJ/mol. This energy is used to
drive many of the chemical reactions in the
body.
87
ATP

• ATP adenosine triphosphate
• a nucleotide composed of three basic units.

adenine
phosphate chain
O
O
O
N
N
O
P
O
P
O
P
N
N
O
OH
OH
ribose
88
ATP and ADP
It takes energy to put on the third
phosphate. Energy is released when it is
removed. ADP - ATP conversions act as a major
method of transferring energy.