1

2

Proteins structure and their role in Gene Expression

Anwar Hussain (Ph. D. Scholar)Roll No: MIC-2016-18

Second Semester, Session 2016Subject Incharge: Prof. Dr. Pir Bux Ghumro

Subject: Genomics and proteomics

SHAH ABDUL LATIF UNIVERSITYDEPARTMENT 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

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.

5

SECONDARY STRUCTURE

Alpha Helix

Beta Sheets

Beta Bends/loops

Super second

ary structur

e

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.

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

anti-parallel

parallel‘twisted’

8

Beta Bends/loops

ribonuclease A

loop(usually exposed on surface)

alpha-helix beta-sheet- there are various types ofturns, differing in the number of residues andH-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.

9

SUPER SECONDARY STRUCTURES (MOTIFS)

β-meander motif

beta-alpha-beta motifGreek key motif

Certain groupings of secondary structural elements are called motifs.

GreenFluorescent

Protein(GFP)

Beta Barrel

10

TERTIARY STRUCTURE• 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

Two-domain protein glyceraldehyde-3-phosphate dehydrogenase.

NAD+

12

QUATERNARY STRUCTURE

• The biological function of some

molecules is determined by multiple 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

Quaternary structure of hemoglobin.

13

Role in gene expression

• 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

• 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

15

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

17

Language conversionBase to codon and A. Acids

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 acidsCode is redundant for most amino acids

18

Translation processing

19

Amino Acids

There are 20 amino acids, each with a basic structure

Amino acids are held together by peptide bonds

20

Conclusion

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.

21