Chapter 6 Proteins and Amino Acids. General Amino Acid Structure.
Chapter 1: Molecules of life [ 5 major classes molecules ... chapter 1... · Chapter 1: Molecules...
Transcript of Chapter 1: Molecules of life [ 5 major classes molecules ... chapter 1... · Chapter 1: Molecules...
Chapter 1: Molecules of life [ 5 major classes molecules which make up the bodies of living organism]
Learning outcome
Water Carbohydrate Lipid Protein Nucleic acid
Explain the structure of
water molecule
Describe the properties
of water and its
importance: universal
solvent, low viscosity,
high specific heat
capacity, high latent
heat of vaporization,
high surface tension,
maximum density at 4
ºC.
Describe various forms
and classes of
carbohydrates such as
monosaccharide,
disaccharides and
polysaccharides
Describe the formation
and breakdown of
maltose
Describe the structures
and function of starch,
glycogen and cellulose
State the types of lipid:
fat, oil, phospholipids
and steroids
Describe the structure
of fatty acid and
glycerol
Describe the formation
and breakdown of
triglycerides.
Describe the basic
structure and classes of
amino acids
Explain how amino
acids are grouped.
Describe the formation
and breakdown of
dipeptide.
Explain primary (1º),
secondary (2º), tertiary
(3º) and quartenary (4º)
levels of proteins and
the types of bonds
involved)
Describe the structure
of nucleotide as the
basic composition of
nucleic acid (DNA and
RNA)
Describe the structure
of DNA based on
Watson and Crick
Model
State the types and
function of RNA
State the differences of
DNA and RNA
1.1: Water
Structure of Water molecule
Water molecule is consists of one ……………………… atom and two …………………………………. Atoms.
The 2 hydrogen atoms are combined with the oxygen atom by ………………….. of electron
which form the ………………………… bond.
The water molecule is a …………………………. Molecule.
The bond angle of water is …………………………………….
Water molecule is a …………………………….. molecule, due to the ……………………………. Distribution of shared electrons.
The uneven distribution of electrons is course by the different ………………………………………. Between oxygen and hydrogen.
Oxygen are ………………………. Electronegative than hydrogen,
Shared electrons are more …………………….. to oxygen than to hydrogen.
Therefore, ……………………………. Is partial negative (…………….) and hydrogen is partial …………………………. (∂+).
Hydrogen bond
Polarity of water causes water molecules to
be ………………………….to each other.
A partial positive ………………… of one
molecule attracted to the partial
negative …………………… from another water
molecule forming a ……………………….. bond.
Hydrogen bond is a type of weak attraction
that able to holds water molecules together.
Table of properties n importance
Water properties Description Importance
Low viscosity Viscosity: a measure of liquid resistance to flow. Samller the size of molecules, .................................... the viscosity. Water is a ............................... polar molecule, which have ......................... viscosity.
Suitable medium for transportation in living organism.
Example: blood flow easily through vessels; flow of water in xylem and phloem vessels to transport nutrient around their bodies.
Less energy used by aquatic organism when swimming in water.
High latent heat of vaporization
Most liquid contract on cooling, reaching its …………….. density at freezing point, but water reach it maximum density at……………………………………….., not at freezing point.
Explanation: 1. 2.
High specific heat capacity
Water have a high specific heat capacity due to the present of ……………………………. Bond. …………………………………. Energy needed to break the ………………………….. bonding between the water molecules. Hence, temperature of water always remain constant.
– Make water as good heat absorber because large amount of heat need to raise water temperature
– Enable water temperature remain constant against sudden temperature change
– Allow aquatic environments maintain constant temperature
– give strong support for hydrogen-bonded network of liquid water.
High surface tension
Maximum density at 40C
Universal solvent • …………………..of water makes it a universal solvent for ionic substances *example:………………………+and many covalent compound.*example:……………………………….+
• Ionic compound dissolve in water: - Ionic compound consists of ..............................(cation)
and .............................. (anion) - The partial positive hydrogen atoms in the water molecule attract
negatively charged ions, while - The partially negative oxygen atom in the water molecules attracts
positively charged ions.
• Organic compound dissolve in water: - Only ........................ organic molecule dissolve in water. - Example: - Becauce water molecule able to form ....................... bond between
water molecules and ................................... groups in these organic molecule.
• Most cell component (including some protein, and polysaccharides) dissolve in water
• Metabolic reactions normally takes place in solution
• Able to dissolve salts, acids, sugar, as well as nutrients and gases which make it able to transport within and between the cell.
Carbohydrate
Describe various forms and classes of carbohydrate
Describe the formation and breakdown of maltose
Describe the structures and functions of starch, glycogen and cellulose
Monosaccharide:
Ring form
form
Disaccharide:
Characteristic of disaccharide :
1.
2.
3.
Formation of maltose: involve the ……………………………………… reaction.
Breakdown of ………………………………… bond in maltose
Polysaccharide
Polysaccharide Monomer Types of glycosidic bond function Structure + diagram
Starch Amylose Energy storage in ……………………
Amylopectin
Glycogen Energy storage in …………………….. Usually found in …………………… and ………………………. tissues
Cellulose
Building component of cell ……………………………
Long, parallel , ………………….. chain hold together by ………………………………. Bond.
Lipid:
Characteristic:
- Insoluble in water [……………………….]
- Soluble in ……………………….. solvent, example:……………………………………………….
- Non polymer
Type of lipid: *base on the……………………………………………..+
Lipid Triglyceride
Phospholipids Steroid Fat Oil [Unsaturated fat]
• One type of lipid molecule made of 3 molecules of fatty acids join to 1 molecule of glycerol by an ester linkage/bond
• One type of lipid molecule made of 3 molecules of fatty acids join to 1 molecule of glycerol by an ester linkage/bond
• At least ………………… unsaturated fatty acid must present.
A type of lipids in which one glycerol join to two fatty acids and one of fatty acid groups is replaced by phosphorus & nitrogen.
A type of lipid containing carbon skeleton consisting of 4 fused rings.
Triglyceride
3 Fatty Acid
An alcohol containing 3 carbon atom
A molecule containing a long chain of hydrogen and carbon atom ( hydrocarbon chain), with a ………………group (-COOH) at one end.
Glycerol
Fatty Acid: A molecule containing a long chain of hydrogen and carbon atom (………………………………………chain), with a ……………………………… group (-COOH) at one end.
Unsaturated fatty acid Saturated fatty acid
Contain one or more …………………………..bond between carbon atoms in the hydrocarbon chain
A ………………………………………..fatty acid contain two or more double bond.
…………………………..double bond in the hydrocarbon chain.
[diagram]
Comparison of saturated fat and unsaturated fat
Aspect Saturated Fat Unsaturated Fat
State of matter ……………….in room
temperature
………………………….in room
temperature
Fatty acid …………………double bond Contain one or more double bond
Source Most ………………… fat Most ………………. fat (oil)
Example Butter Olive oil, all vegetative oil
Protein : Large, complex molecule composed of …………………….which linked together by …………………. bond.
Structure of amino acid
All amino acids have an ……………………………… group, -
NH2, and a ……………………………….. group, -COOH
R: also called ………………………….. chain / side group
Different amino acid have different …………………………….
group, it is used in the grouping of amino acid.
Classification of amino acid
On the basis of polarity of R group, 20 amino acids can be classified into 4 groups:
i. Non polar amino acid
ii. Polar amino acid (no charge in R group)
iii. Acidic amino acid (negative charge in R group)
iv. Basic amino acid (positive charge in R group)
Non polar
amino acid
Consist amino acids with non polar side group Hydrophobic molecules (except proline) have no electrical charge It’s hard to create ions from side groups
- electrical charge of R is symmetrically distributed
Polar amino acid
Consist amino acids with polar side group Hydrophilic molecules Produce partially charge but do not
receive/donate electron Electrical charge in the polar groups is
asymmetrical
Acidic amino acid
Side chain : negative in charge Due to presence of additional carboxyl group in
side chains often exist in anionic (COO–) form Hydrophilic molecules
Basic amino acid
Side chain: positive in charge Hydrophilic molecules addition of hydrogen ion can be neutralised by
amino groups of the side chains - which then become cations (NH3
+)
Exlain the Formation and breakdown of peptide bond ,
state the reaction take place
Level of the protein
Level of Protein
Description Example Types of bond
involve Diagram Importance Explanation
Primary Protein
……………………….. bonds
1. determines the protein overall …………… & ………………….
2. The sequence of amino acids is determined by …………………in the cell nucleus.
3. The change in the sequence of amino acids will influence the biological function of particular protein.
1. describes the linear sequence of amino acids in the protein chain
2. Each amino acids joints together by the peptide bond in specific sequence.
Secondary protein
………………….……… bonds at regular interval along the polypeptide backbone.
A repeating coiled or folded pattern that contribute to the protein’s overall conformation. (3D structure of polypeptide backbone)
α-helix A delicate coil held together by hydrogen bonding between every fourth amino acids. β pleated sheet 2 or more regions of the polypeptide chain lie parallel to each other. Hydrogen bonds between the parts of the backbone in the parallel regions hold the structure together.
These interaction (bonds) include:
Hydrogen bond Ionic bond Disulphide bridge Van der Waals forces and hydrophobic interaction
The three-dimensional structure of a polypeptide Group the protein into the globular protein and fibrous protein.
The shape is held firmly in position by the interaction between side chains of the various amino acids.
Quaternary protein
proteins consists more than one polypeptide chain
Classification of protein: *base on the ………………………………… of protein+
Type of protein
Conjugated protein Fibrous protein Globular Protein
Description Polypeptide chains which associated with ………………………………………..(non protein)
• Remains as long chain • Often with several polypeptide
chains cross-linked together for additional strength
• Insoluble protein • Important structural molecule
• Polypeptide chains folded into a compact spherical shape
• Soluble in water: due to hydrophobic side chain projected from outside of the molecules
• Important in metabolic reactions
Example Glycoprotein- protein +
Lipoprotein
Haemoglobin
• Keratin (in hair and skin), collagen (in skin, tendon, bones, cartilage and blood vessel walls)
All enzyme, antibodiees, haemoglobin, myoglobin
Fibrous Protein Globular Protein
Repetitive …………………………. sequences of amino acids …………………………………. amino acid sequence
Actual sequences may vary slightly between two examples of the same
protein
Sequence ……………………………..specific and never varies between two
examples of the same protein
Polypeptide chains form long ……………………………strands Polypeptide chains folded into ……………………………………shape
Length of chain may vary in two examples of the same protein Length always identical in two examples of the same protein (specific
conformation)
Relatively ………………………… structure (able to denature by heat and pH)
Soluble- forms …………………………… suspension
……………………… and structural function
Example: collagen, keratin Example: all enzymes, some hormone and haemoglobin
Factors affecting protein.
i. pH
Extreme pH condition can caused protein to lose its conformation.
It will breaks the bonds that cause the 3D shape to be changed.
In many cases the globular proteins go back (revert) to a more fibrous
form.
Any sudden change in pH could adversely affect in performance of
enzymes.
ii. Temperature
High temperatures cause protein to lose its conformation.
This process breaks all non-covalent bonds (especially hydrogen
bonds) in the molecule, but leaves the linear sequence unaltered.
So the primary structure is saved while the secondary and higher
structures are disrupted.
This transformation is called denaturation.
Denaturation under physiological conditions can be reversed – this is
called renaturation.
However, non-physiological conditions usually cause an irreversible
change of conformation.
Nucleic Acid: A polymer (………………………………………) consisting of many …………………………………monomer
Structure of Nucleotide
Pentose sugar:
- 2 types of pentose sugar ……………………………………..*for DNA+
and ……………………………….. *for RNA+
Nitrogenous bases: 2 types ……………………………..*2 ring+,
and …………………………………………………. *1 ring+
Formation of phosphodiester bond.
• - Phosphodiester bond – covalent bond that join OH group on carbon 3
of 1 nucleotide & phosphate group on carbon 5 carbon another
nucleotide
Deoxyribonucleic acid
Double stranded polymer of nucleotides (polynucleotide)
Pentose sugar: Deoxyribose
Contains 4 types of bases (not include uracil (U) ):
i. Adenine (A) iii. Thymine (T)
ii. Guanine (G) iv. Cytosine (C)
Very long & thin molecule
Amount A = T and G = C because: A pair with T
G pair with C.
Helix shape is maintained by hydrogen bonds
A only pairs with T and G only pairs to C. This is called complementary
base pairing. The purine always pair to the pyrimedine.
Antiparellel: 2 strands of the DNA double helix are found to be orientated
in opposite directions.
Ribonucleic acid
Single stranded polymer of nucleotides
Pentose sugar : ribose
Nitrogenous bases :
Guanine Adenine
Cytosine Uracil (replacing thymine)
3 types of RNA :
Types of RNA Function
Ribosomal RNA Combines with proteins to form ribosomes.
Messenger RNA Provides the instructions for assembling amino acids into a polypeptide.
Transfer RNA Delivers amino acids to a ribosome for their addition into a growing polypeptide chain
Comparison between DNA and RNA
DNA RNA
Double stranded & helix Single stranded & linear
Larger molecular mass Smaller molecular mass
Pentose sugar : deoxyribose Pentose sugar : ribose
Organic bases: A,T,C,G Organic bases: A,U,C,G
Manufactured in nucleus Manufactured in nucleus but found throughout the cell
Chemically very stable Chemically unstable
Permanent Temporary existing
Only one basic form 3 basic forms : mRNA, tRNA & rRNA
A:T & G:C = 1 : 1 A&U : G&C = varies