NUCLEIC ACIDS

PROTEIN SYNTHESIS

1
 Nucleic acid Outline
 Nucleic acids:
 Structure & functions of DNA & RNA:
 H-bonding, base pairing, similarities and
differences
 DNA replication

 Protein Synthesis

2
Objectives: At the end of this lecture you
should be able to:

1. Describe the structure of nucleotides

2. Describe the structure of the nucleic acid DNA
3. Describe how DNA replicates
4. Differentiate between DNA and RNA
5. State the functions of the different types of RNA
6. Describe how proteins are synthesized in a cell.

3
 Introduction
• One of the factors that distinguish living things is
their ability to produce offspring that have
characteristics similar to the parent(s).
• In order to preserve these specific individual
characteristics, the cell must have a machinery
and mechanism to accurately house and transfer
information from one generation to another.
• Nucleic acids carry out this important
function.

4
 Nucleic Acids

 Like carbohydrates, proteins and lipids,

nucleic acid molecules are complex polymers
formed from linked monomers.

 What is/are the monomers of nucleic acid?

nucleotide

5
 Nucleic Acids
 2 kinds of nucleic acids:
 Deoxyribonucleic acid (DNA), which is
the genetic material containing instructions
for the order of amino acids in
polypeptides

 Ribonucleic acid (RNA) which

participates in polypeptide synthesis.

6
Nucleic Acids Constituents

 Nucleic acid monomers are called

nucleotides.

 Each nucleotide, in turn is composed of a

nucleoside and a phosphate group.

 Nucleosides are composed of a ring-

shaped organic nitrogenous base and a
pentose (5 c) sugar (ribose/ deoxyribose).
7
NUCLEIC ACID: General structure

Phosphate

Pentose
sugar

Nucleoside = Nitrogen base + 5 Carbon sugar

Nucleotide = Nitrogen base + 5 Carbon sugar + Phosphate

8
Nucleotide Constituents - Pentose sugar

9
Nucleotide Constituents - Base

 5 different types of nitrogenous bases; each

denoted by a single letter:
 Adenine (A), Cytosine (C), Guanine (G),
Thymine (T), and Uracil (U).
 DNA contains A, C, G and T.
 RNA contains A, C, G and U.

 The base is attached to the first carbon

atom
10
Nucleotide Constituents - Base
 The bases are derivatives of either:
 a pyrimidine (single six-sided ring)
 E.g. Cytosine, Thymine, and Uracil
OR
 a purine (double-ringed base; one six-
sided and one five-sided);
 E.g. Adenine and Guanine.

11
Nucleotide Constituents - Base
single ring structures

double ring structures

12
 Nucleotide Constituents - Phosphate

• The phosphate group is linked to

the 5th carbon atom of the sugar

• Cells contain nucleotides in the form

of nucleosides linked to one, two, or
three phosphate groups
(monophosphates, diphosphates, and
triphosphates).

13
Nucleotide Constituents

Hydrolysis of
the phosphate
group of a
nucleotide
yields the
nucleoside
(sugar &
nitrogenous
base)

14
Nucleic Acid Constituents Summary

Nucleic acids are polymers

of nucleotide monomers N ring base
by Phosphodiester bonds.
P group

Nucleotide consist of:

1. A pentose (5C) sugar
2. A base; N-containing ring
Pentose
3. Phosphate group(s): 1, 2 or 3 sugar
groups, attached to C #5 of
the pentose sugar. Adenosine monophosphate (AMP)

: 15
RNA Structure

• RNA is a single-stranded polymer of

nucleotides.

• Sugar is ribose
• Bases may be Adenine, Guanine, Cytosine,
Uracil. (depending on the DNA based on which
the RNA is produced)

16
RNA structure

17
 DNA Structure
 DNA has two polynucleotide strands (like a
twisted ladder) linked by hydrogen bonds.
 Sugar = deoxyribose; bases = A, T, C, G
 The 2 vertical strands consist of chains of
alternating sugar and phosphate groups.
 The 2 horizontal strands are held together by
bases linking inwards; they link up by a specific
relationship: A with T and C with G.
 The two chains run in opposite directions
(antiparallel).
18
DNA Structure
hydrogen bonds
base: adenine base: thymine

P
P
deoxyribose
deoxyribose

base: guanine base: cytosine

deoxyribose P

deoxyribose

19
DNA

20
http://library.thinkquest.org/C0123260/basic%20knowledge/images/basic%20knowledge/DNA/DNA%20model%202.jpg
DNA structure

• configuration - double helix

• chromosomes – DNA + protein

21
DNA

 The sequence of bases on one side of the

DNA strand is a code that determines the
sequence on the other side (the other
strand).
 e.g., CGGATACAG determines
GCCTATGTC (since A matches T and C matches G)

 It also determines what the sequence of

amino acids will be (in the polypeptide).
22
 DNA REPLICATION

23
 DNA Replication

 All cells in body except mature red blood cells

carry a full complement of hereditary material.
 As organisms grow and new cells are formed,
exact copies of the DNA must be
generated for each cell.

 The DNA must be replicated before cell

division (mitosis or meiosis) so the cells to be
formed will contain the genetic material of the
organism.
24
 DNA Replication

 During replication, the sequence of

nitrogenous bases and their pairing scheme
(A-T, C-G) on the DNA must be kept exact
and specific so the correct information will
be transmitted from one generation to the
next.

 Three summary steps.

1. Uncoiling of the double helix
2. Complementary base pairing on both
strands
3.
25
Polymerization and coiling
DNA Replication
1. Uncoiling
First the double
helix is separated
into the individual
DNA strands by
successively
breaking of
hydrogen bonds
between the base
pairs.
26
DNA Replication
 Uncoiling
Helicase is the enzyme
responsible for
unwinding the double
helix.
Single Strand Binding
Protein
Interacts and stabilizes
the single strands of
DNA
27
DNA Replication
2. Complimentary Base pairing
As a segment of "unwound" DNA
is exposed, free nucleotides from
the surroundings encounter it,
align with the complementary
bases on the exposed DNA strands
and form the proper base pairs, A
with T and C with G.They bind
with hydrogen bonds.
28
DNA Replication

1. Unwinding

2. Complimentary
base pairing

29
DNA Replication

3. Polymerization.

The individual nucleotides are joined

to each other by the formation of
phosphodiester bonds between a
phosphate of one nucleotide and the
3' OH group (C 3) of the next
nucleotide.
DNA ligase
Coiling
31
to form the double helix
DNA Replication
3. Polymerization

deoxyadenosine
monophosphate

deoxythymidine
monophosphate
32
DNA Replication

33
DNA Replication

34
DNA Replication

 Eachstep in this process is assisted

and controlled by enzymes

 There is also a "proofreading" function

involved so that mismatched base pairs
(such as an A-G pair) are excised and
repaired.
 Nucleases
35
 RNA FUNCTIONS

36
RNA Functions

• There are 3 types of RNA in cells, all of

which are involved in protein synthesis.
– Ribosomal RNA (rRNA)
– Transfer RNA (tRNA)
– Messenger RNA (mRNA)

37
Ribosomal RNA (rRNA)
 Manufactured in the nucleus from DNA
 Found in the cytoplasm of the cell
 A major component of
ribosomes which are the sites of
protein synthesis.

 Ribosomes have rRNA + structural proteins + enzyme

to catalyze formation of peptide bond.

38
 Messenger RNA (mRNA)

 Made in the nucleus from DNA.

 Is
complimentary to part of one strand of the
DNA helix

 Acts as a template for protein synthesis.

39
RNA functions - Genetic Code
 The genetic code is a triplet code
(3 bases = codon) on mRNA
(determined by DNA) that
determines one amino acid.

 E.g., the
code for tryptophan is UGG.
(uracil, guanine, guanine)
 There are 64 codes in all.
40
Transfer RNA (tRNA)

 Made by nuclear DNA.

 At least 20 types, each for a different
amino acid.
 Has anticodon to mRNA code &
 Has site for attachment of an amino
acid
 Carries amino acids one by one to
the polypeptide chain growing at
41the ribosome.
 Genetic Code
PROTEIN SYNTHESIS

42
The genetic code

 The genetic code consist of triplicates

called codons.
 The genetic code consists of 64 triplets
 Codes (on the mRNA) for an amino acid has a
sequence of 3 bases
 Remember nucleotides are named by their
nitrogenous bases A, U, C, G.

 (4 bases; 3 bases per code = 64 codes); 43=64

43
 The genetic code (on mRNA)
 With 3 exceptions, each codon codes for one of
the 20 amino acids used in protein synthesis.
 Most amino acids are encoded by > one codon.

 Eg. Methionine (Met) = AUG

 Eg. Aspartic acid (Asp) = GAU or GAC
 Eg. Valine (Val) = GGU or GUC or GCA or GCG

 NB. Abbreviations for amino acids are written Initials Capital while
the abbreviation for nucleotide bases are ALL CAPITAL.
44
 Codons

To determine the
code for a particular
amino acid, use base
at left,
then top,
then right
45
 The genetic code

 The codon, AUG is referred to as a

start codon.

 START codon - signals the start of

translation (RNA to protein)

 The 3 STOP codons (UAG, UGA and UAA)

do not code for amino acids.

46
Protein synthesis
2 main stages in the synthesis of a protein
in a organism.
 Transcription
 Translation

Transcription Translation
DNA mRNA PROTEIN

Both processes requires the use of enzymes.

47
Protein synthesis (summary)
1. Transcription (mRNA formation)
• Parts of DNA unwind and function as a
template for assembling mRNA.
• Different RNAs assemble from different genes.

2. Translation (polypeptide formation)

• mRNA, tRNA and rRNA interact to build
polypeptide chains.

48
Protein Synthesis - Transcription
NB.
 The DNA gene is not used directly to make polypeptides
in the nucleus.
 Instead RNA copies of the gene are made; these leave the
nucleus.

Process of Transcription.
 One strand of the DNA with a particular
gene is used to make many copies of
messenger RNA, which have a
complimentary code.
 (A particular base coding is the initiator –
states the start of a gene)

49
 Protein Synthesis - Transcription

 The
base sequence of the mRNA made is
complementary to the coding strand of
DNA. Remember Uracil replaces Thymine.
 Eg. DNA code TAC gives mRNA code AUG

 RNA polymerase joins the mRNA

nucleotides to each other (phosphodiester bonds).
 RNA Nucleotide = Nitrogen Ring Base (A, G, C, U) +
Phosphate group + Ribose
50
Protein synthesis - Translation
 Translation follows the genetic code.
 Codons (triplet codes on mRNA) combine
with complimentary anticodons on tRNA
which in turn specifies a particular amino acid.
 The combination of codons on mRNA
therefore determines the final sequence of a
polypeptide chain.
 Ribosomes (rRNA) provide the location
where these interactions occur.
51
Protein synthesis -
Translation

 The mRNA (produced from DNA in the nucleus)

passes out of the nucleus and attaches to
ribosomes on the rough endoplasmic
reticulum in the cytoplasm.
52
 Protein synthesis - Translation

 The rough ER has a

supply of tRNA
molecules that bind
to specific amino
acids.

tRNA
53
Transcription
 The tRNA molecules pick up their specific
amino acids (enzyme aminoacyl tRNA synthetase)
from the cytoplasm and bring them to the
mRNA on the ribosome.
 The tRNA molecules have anticodons that
bind to the corresponding mRNA codon
(which is attached to the ribosome).
 Eg. mRNA codon UGC activates tRNA with anticodon
ACG which therefore takes the aa Cystine to the
ribosome. [The mRNA codon UGC, determines the aa]
54
55
 Translation
 Only 2 tRNA fit into a ribosome at a time.
 The 2 amino acids are brought side by side
(catalyzed by the enzyme protein on the ribosome - ribozyme) and

peptide bonds form between them.

Amino acid
(Glycine)

tRNA

mRNA code
determines the
amino acid

56
Translation -Process
 The ribosome moves along the mRNA,
exposing the next codon.
 A third tRNA brings a third amino acid,
which joins the second one.
 The first tRNA leaves.
 The polypeptide chain grows until a ‘STOP’
codon is reached.This process is
translation.
57
Protein synthesis (summary)
1. Transcription (mRNA formation)
• Parts of DNA unwind and function as a
template for assembling mRNA.
• Different RNAs assemble from different genes.

http://medlab.lzu.edu.cn/image/flash/8.swf

http://sce.uhcl.edu/boetticher/ML_DataMining/ge
ne2.swf
58
Protein synthesis (summary)
2. Translation (polypeptide
formation)
• mRNA, tRNA and rRNA interact to build
polypeptide chains.

• http://medlab.lzu.edu.cn/image/flash/15.swf

 http://highered.mcgraw-
hill.com/olcweb/cgi/pluginpop.cgi?it=swf::525::530::/sites/dl
/free/0072464631/291136/translation.swf::translation.swf
59
Proteins
 The polypeptides formed can then be
used to make a specific protein,
which may be, for example, an
enzyme, a membrane protein or a
structural protein.

60
If a DNA sequence read: TACGATCTCACCATC
The complimentary DNA: ATGCTAGAGTGGTAG
________________________________________

If a DNA sequence read: TACGATCTCACCATC

The mRNA code: AUG CUA GAG UGG UAG
The tRNA anticodon: UAC GAU CUC ACC
The polypeptide sequence: Met (Start) Leu Glu Trp Stop

61