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Proteins and Nucleic Acids

a confused dna
Proteins (Polypeptides)
• Contain carbon, hydrogen, oxygen, nitrogen, and
sulfur
• Basic building block is the amino acid
• There are 20 different kinds of amino acids
• Amino acids are bonded together by peptide bonds
(polypeptides).

Amino Acids (aa)

aa1 aa2 aa3 aa4 aa5 aa6

Peptide Bonds

2
Proteins (Polypeptides)
 Proteins play a central role in the structure and
metabolism of all living organisms.

 Protein molecules have a huge variety of shapes
and sizes. This versatility of form and function is the
key to the role of proteins in the cell.
Biological function of Protein

 Protein acts as storage material of food and
energy.
 Many proteins are enzymes that catalyze
biochemical reactions, and are vital to metabolism.
 Proteins are molecular instrument through which
genetic information is expressed.
 They act as antibodies to prevent disease.
 The milk proteins help the growth of infant
mammals.
Biological function of Protein

 Protein acts as regulatory molecules (Hormones)
 Protein acts as Transport molecules (hemoglobin)
which transport oxygen in our body
 Proteins help in movement (muscles)
 Proteins provide structures (hair, nails,
membranes)
The composition of Proteins
 Proteins contain the elements carbon, hydrogen and oxygen, in addition, they
always contain nitrogen and sometimes sulphur.
 The building blocks of proteins are called amino acids.

Fig: Basic structure of amino acids

All amino acids contain an amino group (-NH2) and a carboxylic acid group (-COOH).
Both of these groups are attached to a central carbon atom, known as the α-carbon.
The backbone of an amino acid contain three atoms C-C-N.
The R group varies between different amino acids. The following chart
shows the different R-groups in the 20 amino acids that make up all of
the proteins in living organisms.

Table: The 20
amino acids
found in all living
things.
Amino acids in solution

Amino acids are soluble in water.

 The carboxyl group (like all acids) loses a hydrogen ion (H+) to become COO-.
The amino group (like all bases) gains a hydrogen ion to become NH3+. In
solution, therefore, an amino acid carries both positive and negative charges. For
this reason, it is known as a zwitter ion, meaning double ion.

 An amino acid can behave as an acid or a base. Any molecule that does this is
described as amphoteric. Amino acids can resist a change in pH and therefore, it
can act as a buffer.
How amino acids form Protein

 Proteins form long chains of amino acids that are joined together by peptide
bonds.

A reaction occurs between the
amino group of one amino acid and
the carboxyl group of another: a
molecule of water is removed and
the two amino acids become joined
by a peptide bond to form a
dipeptide.

Fig: Peptide Bond
Structure of proteins

All proteins are complex molecules and biochemists look at their structure at four
different levels:

1. Primary Structure
2. Secondary structure
3. Tertiary structure
4. Quaternary structure
Structure of proteins

Fig: Structure of proteins
Fibrous and globular proteins

The final 3D structure of proteins results in two main classes of protein:
1. Fibrous Protein
2. Globular protein

1. Fibrous Protein:
 They are physically tough and insoluble in
water.
 Collagen and keratin are two such fibrous
proteins.

2. Globular Protein:
 Spherical or globular in shape.
Most are soluble in water and they tend to
be functional proteins.
 Example: enzymes-are roughly spherical
and soluble.
How stable are proteins?
 Proteins are very sensitive to increases in temperature and undergoes
change. Because, the final shape of globular proteins is maintained by
relatively weak molecular interactions such as hydrogen bonds that are easy
to break.
 As the temperature rises above 400C, the molecular variation increases to
the point where bonds holding together the tertiary or quaternary structure
break and the shape of the molecule changes. This is known as
Denaturation.
 Different proteins are denatured at different temperatures but the lethal
temperature for organisms is reached when the first vital proteins become
denatured, usually at 450C.
 Proteins can also be denatured by adverse chemical conditions. Any
chemical that affect the weak bonds tend to alter the overall structure and
even a slight change in protein shape can mean loss of function. Some
proteins are particularly sensitive to changes in pH.
Nucleic acid
 Nucleic Acids contain carbon, hydrogen, oxygen, nitrogen and phosphorus.
 There are two types of nucleic acid:
a) Deoxyribonucleic acid (DNA)
b) Ribonucleic Acid (RNA)

a) Deoxyribonucleic acid (DNA)
 DNA are the macromolecule that carries the genetic code, the information for
making cells protein.
 Most of the DNA in a eukaryotic cell is in the nucleus, much smaller amounts
are present in the mitochondria and chloroplasts.
 DNA molecules consist of billions of nucleotides per strand.
 DNA molecules are the permanent store for genetic information and last for
many years.
b) Ribonucleic Acid (RNA)
 RNA molecules are much smaller than DNA molecules.
 RNA molecules consist of a few hundred nucleotides.
 RNA is less stable, they are ‘workhorses’. They have a short-term function
and are easily replaced.
 There are three different forms of ribonucleic acid (RNA) in the cell:
1. Messenger RNA
2. Ribosomal RNA
3. Transfer RNA
1. Messenger RNA
 can be thought as a mobile copy of a gene.
 Small lengths of mRNA are assembled in the nucleus using a single gene
within the DNA as a template. When a complete copy of the gene has been
produced, the mRNA moves out of the nucleus to the ribosome, where the
protein is synthesized according to the code taken from the DNA.
2. Ribosomal RNA:
 makes up part of the ribosome, a small organelle that bring together all the
chemicals associated with protein synthesis.

3. Transfer RNA:
 is found in the cytoplasm and is a carrier molecule, bringing amino acids to
the ribosomes for assembly into a new amino acid chain, according to the
order specified on the mRNA code.

Fig: A transfer RNA
The structure of Nucleic Acids:
Nucleotides are the building blocks of nucleic acids. A nucleotide consists of
three units:
 A sugar (Ribose or deoxyribose)
 A phosphate group
 A nitrogen containing base.
As the name imply, deoxyribonucleic acid
has nucleotides in which the sugar is
deoxyribose while ribonucleic acid contains
Fig: A Nucleotide
ribose.

The nucleotides in DNA can contain any
one of four nitrogenous bases: adenine,
guanine, cytosine or thymine.

The nucleotides in RNA contain the bases
Adenine, guanine, cytosine and uracil-
instead of thymine.

When DNA replicates, (Copies itself),
new strands are made by adding
nucleotides. These are available as free
molecules in the cytoplasm.
How the bases pair?
Thymine and Cytosine belong to a group of chemicals called
pyrimidines and Adenine and guanine are purines.
 Because of the shape of the two types of molecule, each purine
always bond with only one pyrimidine. So, in DNA , Adenine always
bonds with thymine and cytosine with guanine.
In RNA, cytosine bonds with guanine and adenine bonds with
uracil.
 The base pair are held together by hydrogen bonds; there are two H-
bonds between A and T (or U) and three between C and G.

DNA: RNA:

A T A U

C G C G
sugar phosphate sugar phosphate sugar phosphate sugar ...

T A C G

¦ ¦ ¦ ¦

A T G C
sugar phosphate sugar phosphate sugar phosphate sugar ...

Fig: How the base pairs with DNA fit together to
form a double-stranded helix. The side chains
are formed by alternating sugar –phosphate
units, while the base pairs form cross-bridges,
like the rungs of a ladder. Each base pairing
causes a twist in the helix and there is a
complete 3600 turn every 10 base pairs.
Double helix of DNA
How DNA stores the information

 The DNA that makes up an individual gene
contains the information needed to build a
particular protein. This information is, known as
the genetic code, is held in the sequences of
bases.
 In DNA and mRNA each group of three bases
is a triplet code or codon, which codes for a
particular amino acid.
 Research has shown that in front of each
gene, there is a promoter sequence, which
effectively says ‘start transcribing here’.

Why a triplet code
There are only four different bases but 20
amino acids. Obviously one base can’t code for
an amino acid. Neither can two, since there are Fig: A series of codons in part of a
only 16 possible combinations (4x4). Three mRNA molecule. Each codon
consists of three nucleotides,
bases however, gives plenty of different
usually representing a single
combinations (4x4x4 = 64). There are often
amino acid.
different triplet codes for one amino acid.
Do you know??
• A complete 3 billion base genome would take 3 gigabytes
of storage space.
• If you unwrap all the DNA you have in all your cells, you
could reach the moon 6000 times!
• If all the DNA in your body was put end to end, it would
reach to the sun and back over 600 times (100 trillion
times six feet divided by 92 million miles).
• We eat DNA every day.
The Central Dogma of Molecular Biology

Flow of genetic information
Cell

Transcription DNA

mRNA
Translation
Ribosome

Polypeptide
(protein)
The Central Dogma
The Dogma is: DNA -> RNA ->
Protein
The Central Dogma is:
 DNA is transcribed to RNA
which is translated to protein.

 Protein is never back-
translated to RNA or DNA;
and

 except for retroviruses, DNA
is never created from RNA.

Furthermore, DNA is never
directly translated to protein.
DNA to RNA to protein.
Transcription
Transcription is the process by which the information
contained in a section of DNA is transferred to a newly
assembled piece of messenger RNA (mRNA). It is
facilitated by RNA polymerase and transcription factors.

Transcription occurs in the nucleus.

Translation
Translation is the process where ribosomes synthesize
proteins using the mature mRNA transcript produced
during transcription.

Translation occurs in the cytoplasm.
Chromosome

Gene Expression
GENE

DNA

From gene
to
protein mRNA in nucleus

mRNA in cytoplasm

Polypeptide

ACTIVE
PROTEIN