DNA and proteins

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2 Οκτ 2013 (πριν από 3 χρόνια και 8 μήνες)

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DNA and Amino Acids

Molecular Structure

Lecture 3

Chromosome to DNA molecule


A chromosome is essentially a long strand of DNA wound around proteins;
e.g.
histones
, to form condensed structure called chromatin.



However it order for the DNA to carry out its function is must be
unwound from the proteins: chromatin to a long strand of DNA



This DNA is shaped in the form of, the now famous, “double Helix”



DNA is an
abbrevation

for
Deoxyribose

Nucleic acid [see
next slide]



It consists of a long strand of DNA nucleotides which are joined together.



The DNA “double Helix” is two such strands which are coiled and
connected together via what are referred to as: nucleotide bases or bases

The Crick and Watson double Helix

Adapted from [1] p.194 [
the original article by C and W p 195
]

RNA: Ribose nucleic acid


A molecule closely associate with DNA and
which a part of the “gene expression” process
is referred to as RNA


The RNA [nucleotide] is very similar to DNA
[nucleotide] except:


Its nucleic acid has a ribose sugar as opposed to a
deoxyribose

sugar.


The
Neuleotide

base thymine is replace with an
equivalent base called
Uracil

[
klug

p.191]


The RNA strand unlike the DNA double helix
strand is single stranded

DNA version of genetic code table


Later we will see how gene expression and
protein production [the basis of life] works.


The process involves the use of a genetic code
where sets of 3, triplets, of
nucletides

bases
[
Codon
] is converted into an amino acid [
described shortly]


The following tables show the code form the
prespective

of the DNA
codon

or RNA
codon


The genetic code

RNA conversion table

DNA conversion table

Adapted from Ref [1] p. 247

Note: the only difference is T being replaced with U

Amino acids


The genetic code table shows DNA/RNA being
converted into “amino acids”


An amino is a molecule that has two main
elements: a constant part [shown in pink in the
next slide] and a variable part. This variable part
has specific chemical properties which are
essential to its function.


In proteins [chains of amino acids] the constant
regions are referred to as the “backbone” and the
variable region as the side chains.

AMINO Acids (AA) and their properties

Alanine

-
> name of
Amino acid

Ala
-
> the common
abbreviation

A
-
> code used in
protein sequences
(this letter is not
always the first letter
of the AA; e.g.
tryptophan is W)

MW: molecular
weight or weight of
the amino acid


“the amino acids are grouped according to their polarity and charge. They are divided
into four categories, those with polar uncharged R groups [
hydrophilic
], those with
(
nonpolar
) R groups [
hydrophobic
], acidic and basic groups.” Ref [2]. Also
Cystine

is
the only amino acid with a
sulphur

atom.

An amino chain or Polypeptide


When two AA are joined together
it is by, what are called, “peptide”
bonds of the constant element of
each amino acid


A third is the joined to the second
using the same type of
connection or “bond”


When a number of
AAs

are joined
together they start to form the
main chain


Subsequent addition results in a
polypeptide chain

or (primary
protein structure). the peptide
has two elements: the main chain
connected via peptide bonds;
and side chains ( generally
associated with functionality).




Polypeptide Bond


When two amino acids bond together a H20
water molecule is formed along with the
peptide bond



Polypetide

chain
-
> Secondary structure

The primary chain
(polypeptide chain) then
begins to change its shape
depending on the side
chain properties of the
amino acid to firstly form:

the secondary structure
:
e.g.
α

helixes and
β

sheets
both

These structures are found
in all proteins and form the
next level in the formation
of the 3D structure

The pink “backbone”
corresponds to main chain
the other elements show
side chains and their
bonding



Secondary to Tertiary structure

Secondary structures interact to form
the tertiary or 3
-
D structure of the
protein : essentially the polypeptide
chain after it has been twisted and
turned to form the most
thermodynamically stable structure:


Since most proteins are in water A
number of factors affect the
formation:


1.
Polar (Hydrophilic) AA try to stay
on the outside of the structure

2.
Non polar (hydrophobic) stay on
the inside

3.

disulphide bonds between
cistine

AA


However in some cases the proteins
are in hydrophobic solution [Lipids in
the cell membrane] and in this case
the structure would alter: non polar
outside, polar inside.


Myoglobin
: Adapted from [1] p 279

Exam question


Discuss how a DNA sequence forms the final
3
-
D configuration of proteins.



Discuss why a DNA is crucial in the formation
of a 3
-
D
protein structure.

References


[1] Klug 7
th

ed


[2]
Http://biotech.matcmadison.edu/resources/proteins
/labManual/chapter_2.htm
; accessed on the
21/9/2011