Download Replication of the DNA

Chapter 7. Proteins: the buck
stops here
Prepared by Woojoo Choi
Introduction to proteins
1) Protein
– biological polymers that carry out most of the cell’s functions.
– made from a linear chain of monomers, known as amino acids
– folded into a variety of complex 3-D shapes
– a chain of amino acids is called a polypeptide chain
2) What’s the difference between a polypeptide chain and a protein?
– some protein consists of more than one polypeptide chain
Introduction to proteins
Role of proteins in the cell
1) Structural proteins
– A protein that forms part of a cellular structure
Role of proteins in the cell
2) Enzymes
– A protein that carries out
a chemical reaction
– First binds its substrate, and
then performs some chemical
operations with it
– Active site: special site or pocket
on a protein where the chemical
reaction occurs
Role of proteins in the cell
2) Enzymes
Role of proteins in the cell
– Analog: molecules resembling natural substances well enough to fool
the enzyme that use them
– Some analogs inhibit the enzyme
• Competitive inhibitor: chemical substance which inhibits the
action of an enzyme by mimicking the true substrate well enough
to be mistaken for it.
– Other analogs do react
• ONPG: an artificial substrate which releases a yellow color when
split by the enzyme β-galactosidase
• X-gal: split by β-galactosidase into a blue dye and
galactose(Ch16)
Role of proteins in the cell
3) Regulatory proteins
– A protein that controls the expression of a gene or the activity of
another protein
4) Transport proteins
– A protein that carries other molecules across membranes or around
the body
How are proteins Constructed?
1) Amino acid
– The monomer or subunit from which proteins are built
– There are 20 different amino acids.
– They all have a central carbon atom, the alpha carbon, surrounded by
the four features.
– R group: chemical group forming side chain of amino acid
Formation of polypeptide chains
1) Amino acids are joined together by peptide bonds to give a polypeptide
chain
– Amino- or N-terminus: the end of a polypeptide chain that is made
first and has a free amino group
– Carboxyl- or C-terminus: the end of a polypeptide chain that is made
last and has a free carboxy group
Three-dimensional structures
1) Primary structure
– The linear order in which subunits of a polymer are arranged
2) Secondary structure
– Initial folding of a polymer due to hydrogen bonding
Three-dimensional structures
– There are two alternative secondary structures alpha-helix and betasheet
Three-dimensional structures
3) Tertiary structure
– Final 3-D folding of a polymer chain
– The polypeptide chain, with its performed regions of a-helix and bsheet, to give the final 3-D structure.
– The level of folding depends on the side chains of 20 different amino
acids
– 3-D folding is the result of two factors, hydrophilic and hydrophobic.
– Some side chains are hydrophilic and others are hydrophobic.
Three-dimensional structures
Three-dimensional structures
Quaternary structure of proteins
4) Quaternary structure
– Aggregation of more than one polymer chain in final structure
– Not all proteins have more than one polypeptide chain
– The hydrophilic and hydrophobic forces are responsible
Twenty different amino acids
1) 20 different amino acids allow for a great variety of 3-D structure and of
chemical reactivity
Amino Acid
3-Letter Code
1-Letter Code
Alanine
Ala
A
Arginine
Arg
R
Asparagine
Asn
N
Aspartic acid
Asp
D
Cysteine
Cys
C
Gultamic acid
Glu
E
Glutamine
Gln
Q
Glycine
Gly
G
Histidine
His
H
Isoleucine
Ile
I
Twenty different amino acids
Amino Acid
3-Letter Code
1-Letter Code
Leucine
Leu
L
Lysine
Lys
K
Methionine
Met
M
Phenylalanine
Phe
F
Proline
Pro
P
Serine
Ser
S
Threonine
Thr
T
Tryptophan
Trp
W
Tyrosine
Tyr
Y
Valine
Val
V
How are proteins made?
1) Translation
– Making a protein using the information provided by mRNA
– Central dogma: basic plan of genetic information flow in living cells
that relates genes(DNA), RNA, and proteins
Decoding the genetic code
1) Codon
– Group of three RNA and DNA bases which encodes a single amino
acid
– Some amino acids are encoded by more than one codon
Ribosome – The cell’s decoding machine
1) Ribosome
– The cell’s machinery for making proteins
– Bind mRNA and translate it, so synthesizing a polypeptide chain.
– Consist of two subunits, 50s and 30s
How may tRNA
1) To
–
–
–
read the codons, transfer RNA(tRNA) is needed
tRNA: RNA molecule that carry amino acids to ribosome
tRNA has an anticodon
Anticodon: group of three complementary bases that recognize and
bind to a codon on the mRNA
How does the tRNA get its amino acid?
1) Amino-acyl tRNA synthetase: enzyme that attaches an amino acid to
tRNA
2) Uncharged tRNA: tRNA without an amino acid attached
3) Charged tRNA: tRNA with an amino acid attached
Structure of transfer RNA
1)
2)
3)
4)
5)
6)
Typical tRNA: 4 short base-paired stems, 3 loops
At acceptor stem: amino acid
In the anticodon loop: anticodon
TψC-loop: contains pseudouracil
D-loop: contains dihydrouracil
In real life, the tRNA cloverleaf is folded up further
Reading Frames
1) Start codon
– the special AUG codon that signals that start of a protein
Reading Frames
GAAAUGUAUGCAUGCCAAAGGAGGCAUCUAAGGA
111 222 333 444 555 666 777 888
111 222 333 444 555 666 777 888
111 222 333 444 555 666 777 888
2) Reading frame
– One of three possible ways to read off the bases of mRNA in groups
of three so as to give codons
3) Open reading frame
– Sequence of mRNA that can be translated to give a protein
– Any mRNA will have several possble ORFs and we have to find
correct one
Getting protein synthesis started
1) fMet or formyl methionine
– Chemically tagged version of methionine used to start the
polypeptide chain in prokaryotic cells
2) Ribosome binding site
– Sequence on mRNA at the front of the message which is recognized
by the ribosome (Shine Delgarno sequence)
3) Anti-Shine-Dalgarno sequence
– Sequence on 16S rRNA that is complementary to the Shine Delgarno
sequence
Getting protein synthesis started
– A (acceptor) site: binding site on the ribosome for the tRNA which
brings in the next amino acid
– P (peptide) site: binding site on the ribosome for the tRNA that is
holding the growing polypeptide chain
Elongation of a growing protein
The elongation factors
1) Elongation factors: Proteins that oversee the elongation of a growing
polypeptide chain
2) EF-T (EF-Tu and EF-Ts): The tRNA is delivered to the ribosome and
instaled into the A-site
3) EF-G: moving everybody sideways
Termination of protein synthesis
1) Stop codon
– Codon that signals the end of a protein
– UGA, UAG, and UAA
2) Releas factors
– Proteins that supervise the release of a finished polypeptide chain
from the ribosome
One mRNA can code for several proteins
1) In bacteria several protein may be encoded by the same messenger RNA
2) Cistron
– Segment of DNA that encodes a single polypeptide chain
3) Polycistronic mRNA
– mRNA carrying multiple cistron and which may be translated to give
several different protein molecule.
Several ribosomes can read the same message at once
1) Polysome (polyribosome)
– Group of ribosomes that bind to and translate the same mRNA
Coupled translation and transcription in bacteria
1) Coupled transcription-translation
– When ribosomes of bacteria start translating an mRNA which is still
being transcribed from the genes
(In eukaryotic cells, this is verboten, because the DNA is inside the
nucleus and the ribosomes are outside.)
Some proteins come to a bad end
1) When ribosomes receive a defective mRNA, they have problems
2) If there is no stop codon, a ribosome will just sit there forever and
trapped
Some proteins come to a bad end
tmRNA
– a special RNA used to terminate protein synthesis when it find a
ribosome stalled by a bad mRNA
– It acts partly like tRNA and mRNA
– Leave the short strech of amino acids added to the end of the
defective protein
– The short stretch act as a signal which is recognized by tail specific
protease.
– Tail specific protease: enzyme that destroys mismade proteins by
eating them tail first