Proteins have four levels of structure: primary, secondary, tertiary, and quaternary. The primary structure is the amino acid sequence. Secondary structures include alpha helices and beta sheets formed by hydrogen bonding. Tertiary structure involves folding of the polypeptide into a compact 3D structure. Quaternary structure involves the assembly of multiple polypeptide subunits. Proteins play important roles in gene expression, with mRNA carrying the code from DNA to the ribosome for protein synthesis via translation of codons to amino acids. Regulation of transcription and translation allows cells to control and adapt protein production.

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2. Proteins structure and their role in Gene Expression
Anwar Hussain (Ph. D. Scholar)
Roll No: MIC-2016-18
Second Semester, Session 2016
Subject Incharge: Prof. Dr. Pir Bux Ghumro
Subject: Genomics and proteomics
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SHAH ABDUL LATIF UNIVERSITY
DEPARTMENT OF MICROBIOLOGY

3. INTRODUCTION
• Proteins are an important class of
biological macromolecules which
are the polymers of amino acids.
• Biochemists have distinguished
several levels of structural
organization of proteins.
They are:
– Primary structure
– Secondary structure
– Tertiary structure
– Quaternary structure
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4. PRIMARY STRUCTURE
• Amino acid sequence of a protein’s
polypeptide chain or chains. Sometimes
referred to as the covalent structure.
• By convention, the 10 structure of a
protein starts from the amino-terminal
(N) end and ends in the carboxyl-
terminal (C) end.
• The bond that holds them together is
called a peptide bond
• They are formed by loss of water so is
called a condensation reaction.
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5. SECONDARY STRUCTURE
Alpha Helix
Beta
Sheets
Beta Bends/loops
Super
secondary
structure
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6. ALPHA HELIX
• Spiral structure
• Tightly packed, coiled polypeptide backbone
core.
• Side chain extend outwards
• Stabilized by H bonding b/w carbonyl
oxygen and amide hydrogen.
• Amino acids per turn – 3.6
• Alpha helical segments are found in many
globular proteins like myoglobins, troponin-
C etc.
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7. BETA SHEET
• Formed when 2 or more
polypeptides line up side by
side.
• Individual polypeptide - β
strand
• Each β strand is fully extended.
• They are stabilized by H bond
b/w N-H and carbonyl groups
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anti-parallel
parallel
‘twisted’

8. Beta Bends/loops
ribonuclease A
loop
(usually exposed on surface)
alpha-helix beta-sheet- there are various types of
turns, differing in the number of residues
and
H-bonding pattern
- loops are typically longer;
they are often called coils and do not have
a ‘regular’,
or repeating, structure
- Proline and Glycine are frequently found
in beta turns.
- Beta turns often promote the formation of
antiparallel beta sheets.
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9. SUPER SECONDARY
STRUCTURES (MOTIFS)
β-meander motif
beta-alpha-beta motif
Greek key motif
Certain groupings of secondary structural elements are
called motifs.
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Green
Fluorescent
Protein
(GFP)
Beta Barrel

10. TERTIARY STRUCTURE
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• Tertiary structure is the three-
dimensional conformation of a
polypeptide.
• The common features of protein
tertiary structure reveal much about
the biological functions of the proteins
and their evolutionary origins.
• The function of a protein depends on
its tertiary structure. If this is disrupted,
it loses its activity.

11. DOMAINS
• Polypeptide chains containing
more than ,200 residues usually
fold into two or more globular
clusters known as domains.
• Fundamental functional and 3
dimensional structure of
proteins.
• Domains often have a specific
function such as the binding of
a small molecule.
• Many domains are structurally
independent units that have the
characteristics of small globular
proteins
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Two-domain protein glyceraldehyde-
3-phosphate dehydrogenase.
NAD+

12. QUATERNARY STRUCTURE
• The biological function of so
me
molecules is determined by m
ultiple polypeptide chains –
multimeric proteins.
• Arrangement of polypeptide
sub unit is called quaternary
structure.
• Sub units are held together by
non covalent interactions.
• Eg: Hemoglobin has the
subunit composition a2b2
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Quaternary structure of hemoglobin.

13. Role in gene expression
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• RNA forms base pairs
with DNA
– C-G
– A-U
• Primary transcript- length
of RNA that results from
the process of
transcription

14. mRNA Processing
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• Primary transcript is not
mature mRNA
• DNA sequence has
coding regions (exons)
and non-coding regions
(introns)
• Introns must be
removed before primary
transcript is mRNA and
can leave nucleus

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Transcription is done…what now?
 Now we have mature mRNA transcribed
from the cell’s DNA. It is leaving the
nucleus through a nuclear pore.
 Once in the cytoplasm, it finds a ribosome
so that translation can begin.

16. Translation
• The language of
nucleic acids is
translated into the
language of
proteins
• Nucleic acids have
a 4 letter language
• Proteins have a 20
letter language
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17. Language conversion
Base to codon and A. Acids
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If 3 RNA bases code
for 1 amino acid, RNA
could code for 43 = 64
amino acids.
More than enough
coding capacity for 20
amino acids
Code is redundant for
most amino acids

18. Translation processing
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19. Amino Acids
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There are 20 amino
acids, each with a
basic structure
Amino acids are
held together by
peptide bonds

20. Conclusion
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Proteins are built as
chains of amino acids,
which then fold into
unique three
dimensional shapes.
Bonding within protein
molecules helps stabilize
their structure, and the
final folded forms of
proteins are well
adapted for their
functions.
To live, cells must be able to respond to
changes in their environment. Regulation
of the two main steps of protein
production — transcription and
translation — is critical to this
adaptability. Cells can control which
genes get transcribed and which
transcripts get translated; further, they
can biochemically process transcripts and
proteins in order to affect their activity.
Regulation of transcription and
translation occurs in both prokaryotes
and eukaryotes, but it is far more
complex in eukaryotes.

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