2. Building blocks of proteins are called Amino Acids.
All proteins contain the elements Carbon, Hydrogen,
Oxygen and Nitrogen.
 Amino Acids contain the -NH2 group which is called the amino
group
 And the COOH group or the Carboxyl group.
 Amino Acids are defined by the side group or R-Group.

3.  The bond that holds
amino acids together is
called a peptide bond.
 When two more amino
acids are put together
they become a
polypeptide.
 The order in which amino acids are placed in the chain
determines the structure of the protein.
 The structure of the protein determines
the function of the protein.

4. From amino acids to protein:
N-terminus
terminates
by an amino group
Peptide bond
Amino acid
C-terminus
terminates by a
carboxyl group
A peptide: Phe-Ser-Glu-Lys (F-S-E-K)

5. The Shape of proteins:
Occurs
Spontaneously
Native conformation
determined by different
Levels of structure

6. Non covalent
interactions involved
in the shape of
proteins

7. Four Levels of Structure Determine the
Shape of Proteins
Primary structure
The linear arrangement (sequence) of amino acids and the location of covalent (mostly
disulfide) bonds within a polypeptide chain. Determined by the genetic code.
Secondary structure
local folding of a polypeptide chain into regular structures including the helix,
sheet, and U-shaped turns and loops.
Tertiary structure
overall three-dimensional form of a polypeptide chain, which is stabilized by multiple
non-covalent interactions between side chains.
Quaternary structure:
The number and relative positions of the polypeptide chains in multisubunit
proteins. Not all protein have a quaternary structure.

8. Primary Structure Pro-insulin is
produced in the
C-peptide Pancreatic islet cells
Pro-insulin protein
65/66 30/31
Human: Thr-Ser-Ile
Cow: Ala-Ser-Val
Pig: Thr-Ser-Ile
Chiken: His-Asn-Thr
Insuline
C-peptide
+ C peptide

9. Protein conformation: most of the proteins fold
into only one stable conformation or native
conformation
More than 50 amino acids becomes a protein

10. Protein conformation: most of the proteins fold
into only one stable conformation or native
conformation
More than 50 amino acids becomes a protein

11. SECONDARY STRUCTURE
 Stabilized by hydrogen bonds
 H- bonds are between –CO and –NH groups of
peptide backbone
 H-bonds are either intra- or inter- molecular
 3 types : a-helix, b-sheet and triple-helix
Helix:
helix conformation was discovered 50 years ago in keratine
abundant in hair nails, and horns
Sheet:
discovered within a year of the discovery of helix. Found in
protein fibroin the major constituant of silk

12. The helix:
result from hydrogen bonding, does not involve the side chain of the amino
acid

13. sheet:
result from hydrogen bonding, does not involve the side chain of the amino acid

14. Two type of
Sheet structures
An anti paralellel
sheet
A paralellel
sheet

15. TRIPLE HELIX
 Limited to tropocollagen molecule
 Sequence motif of –(Gly-X-Pro/Hypro)n-
 3 left-handed helices wound together to give a
right-handed superhelix
 Stable superhelix : glycines located on the
central axis (small R group) of triple helix
 One interchain H-bond for each triplet of aas
– between NH of Gly and CO of X (or Proline)
in the adjacent chain
Triple helix of Collagen

16. NONREPETITIVE STRUCTURES
 Helices/ -sheets: ~50% of regular
2ostructures of globular proteins
 Remaining : coil or loop conformation
 Also quite regular, but difficult to describe
 Examples : reverse turns, -bends
(connect successive strands of antiparallel
-sheets)

17. The Beta Turn
(aka beta bend, tight turn)
 allows the peptide chain to reverse direction
 carbonyl O of one residue is H-bonded to the amide proton of a residue
three residues away
 proline and glycine are prevalent in beta turns (?)

18. -bulge
 A strand of polypeptide in a -sheet may contain an “extra” residue
 This extra residue is not hydrogen bonded to a neighbouring strand
 This is known as a -bulge.

19. Tertiary structure: the overall shape of a protein
The secondary structure of a telephone
cord
A telephone cord, specifically the coil of a
telephone cord, can be used as an analogy
to the alpha helix secondary structure of a
protein.
The tertiary structure of a telephone cord
The tertiary structure of a protein refers to the
way the secondary structure folds back upon
itself or twists around to form a three-
dimensional structure. The secondary coil
structure is still there, but the tertiary tangle has
been superimposed on it.

20. Tertiary structure: the overall shape of a protein
Full three dimensional organization of a protein
 R-group interactions result in 3D
structures of globular proteins
 Types of interactions : H-, ionic-
(salt linkage), hydrophobic- and
disulphide- bond
 Hydrophilic R groups on surface
while hydrophobic R groups
buried inside of molecule
 Wide variety of 3o structures:
since large variation in protein
sizes and amino acid sequences
The three-dimensional structure of a protein kinase

21. The role of side chain in the shape of proteins
Hydrophili
c
Hydrophobic

23. A coiled-coil:
Structure occurs when the 2 a
helix have most of their nonpolar
(hydrophobic) side chains on one
side, so that they can twist around
each other with these side chain
facing inwards

24. Quaternery
structure:
If protein is formed as a
complex of more than one
protein chain, the complete
structure is designed as
quaternery structure:
• Generally formed by non-
covalent interactions
between subunits
• Either as homo- or
hetero-multimers

25. QUATERNARY STRUCTURE:
ADVANTAGES
 Oligomers (multimers) are more stable than
dissociated subunits
 They prolong life of protein in vivo
 Active sites can be formed by residues from adjacent
subunits/chains
 A subunit may not constitute a complete active site
 Error of synthesis is greater for longer polypeptide
chains
 Subunit interactions : cooperativity/ allosteric effects

26. Primary structure
Secondary structure
Tertiary structure
Quaternary structure

27. Protein domains:
•Any part of a protein that can fold
independently into a compact, stable
structure. A domain usually contains between
40 and 350 amino acids.
• A domain is the modular unit from which
many larger proteins are constructed.
• The different domain of protein are often
associated with different functions.

28. Protein domains
The NAD-binding
Cytochrome b562 domain of
A single domain protein the enzyme lactic
dehydrogenase The variable domain
involved in electron transport
of an immunoglobulin
in mitochondria

29. Protein Folding
is the physical process by which a polypeptide folds into its characteristic and
functional three-dimensional structure from random coil.[1] Each protein exists as
an unfolded polypeptide or random coil when translated from a sequence
ofmRNA to a linear chain of amino acids.
This polypeptide lacks any developed three-dimensional structure.
Amino acids interact with each other to produce a well-defined three dimensional
structure, the folded protein, known as the native state. The resulting three-
dimensional structure is determined by the amino acid sequence.
For many proteins the correct three dimensional structure is essential to
function. Failure to fold into the intended shape usually produces inactive
proteins with different properties including toxic prions.
Several neurodegenerative and other diseases are believed to result from the
accumulation of misfolded (incorrectly folded) proteins.
Many allergies are caused by the folding of the proteins, for the immune system
does not produce antibodies for certain protein structures.

30. Function of proteins
• Enzymatic catalysis
• Transport and storage (the protein hemoglobin, albumins)
• Coordinated motion (actin and myosin).
• Mechanical support (collagen).
• Immune protection (antibodies)
• Generation and transmission of nerve impulses - some
amino acids act as neurotransmitters, receptors for
neurotransmitters, drugs, etc. are protein in nature. (the
acetylcholine receptor),
• Control of growth and differentiation - transcription factors
Hormones growth factors ( insulin or thyroid stimulating
hormone)

31. Enzymes
 Enzymes are proteins that catalyze (i.e. speed up)
chemical reactions. Enzymes are catalysts.
 Enzymes work on things called Substrates
 Each enzyme is specific for its substrate
 Almost all processes in a cell need enzymes in order to
occur at significant rates.
 Enzymes are not used up by the reaction.
 After they have done their work they release the products
and are not changed
 Each enzyme can work on many molecules of the substrate

32. Lock and Key Model
 The method in which enzymes work is called the lock
and key model

33. Transport and storage - small molecules are often carried by proteins
in the physiological setting (for example, the protein hemoglobin is responsible
for the transport of oxygen to tissues). Many drug molecules are partially bound
to serum albumins in the plasma.
The binding of oxygen is affected by molecules such as
carbon monoxide (CO) (for example from tobacco
smoking, cars and furnaces).
CO competes with oxygen at the heme binding site.
Hemoglobin binding affinity for CO is 200 times greater
than its affinity for oxygen, meaning that small amounts
of CO dramatically reduces hemoglobin's ability to
transport oxygen. When hemoglobin combines with
CO, it forms a very bright red compound called
carboxyhemoglobin.
When inspired air contains CO levels as low as 0.02%,
headache and nausea occur; if the CO concentration is
3-dimensional structure of hemoglobin. increased to 0.1%, unconsciousness will follow. In
The four subunits are shown in red and heavy smokers, up to 20% of the oxygen-active sites
yellow, and the heme groups in green. can be blocked by CO.

34. Coordinated motion - muscle is mostly protein, and muscle contraction is
mediated by the sliding motion of two protein filaments, actin and myosin.
Platelet activation is a controlled
sequence of actin filament:
Severing
Uncapping
Elongating
Cross linking
That creates a dramatic shape
change in the platelet
Activated platelet
Platelet before activation Activated platelet
at a later stage than C)

35. Mechanical support –
skin and bone are strengthened by the protein collagen.
Abnormal collagen synthesis
or structure causes
dysfunction of
• cardiovascular organs,
• bone,
• skin,
• joints
• eyes
Refer to Devlin
Clinical correlation 3.4 p121

36. Immune protection - antibodies are protein structures that are
responsible for reacting with specific foreign substances in the body.

37. Generation and transmission of nerve impulses
Some amino acids act as neurotransmitters, which transmit electrical
signals from one nerve cell to another. In addition, receptors for
neurotransmitters, drugs, etc. are protein in nature.
An example of this is the acetylcholine receptor, which is a protein
structure that is embedded in postsynaptic neurons.
GABA:
gamma Amino butyric acid
Synthesised from glutamate
GABA acts at inhibitory synapses in the
brain. GABA acts by binding to specific
receptors in the plasma membrane of both
pre- and postsynaptic neurons.
Neurotransmetter

38. Control of growth and differentiation -
proteins can be critical to the control of growth, cell differentiation and expression of
DNA.
For example, repressor proteins may bind to specific segments of DNA,
preventing expression and thus the formation of the product of that DNA
segment.
Also, many hormones and growth factors that regulate cell function, such as
insulin or thyroid stimulating hormone are proteins.

39.  DNA is found packed in the nucleus of
eukaryotic organisms; it is found in the
cytoplasm of prokaryotic organisms
 DNA is packed together and wrapped
around special proteins called HISTONES
 DNA bound protein is called
CHROMATIN
 When chromatin condenses (gets thicker)
it forms CHROMOSOMES

40. Nucleosome
Chromosome
DNA
double
helix
Coils
Supercoils
Histones

41. DNA Structure
 Double Helix - twisted ladder
 Made up of monomers
called nucleotides
 Nucleotides are composed of:
 Deoxyribose sugar
 Phosphate group
 Nitrogenous base

42. Nitrogenous Bases
 Two types:
 Purines (two rings)
 Pyrimidines (one ring)
 Purines
 Adenine and Guanine
 Pyrimidines
 Thymine and Cytosine

43. Purines Pyrimidines
Adenine Guanine Cytosine Thymine
Phosphate Deoxyribose
group

44. Bonding
TEMPLATE STRAND
A C G G T A
T G C C A T
Weak HYDROGEN bonds form
between the Nitrogen Base Pairs.

45. Chargaff’s rules:
 Base pairing rule is A-T and G-C
 Thymine is replaced by Uracil in RNA
 Bases are bonded to each other by Hydrogen bonds
 Discovered because of the relative percent of each
base; (notice that A-T is similar and C-G are similar)

46. DNA Structure
Backbone alternates with phosphate & sugr/deoxyriboes
with the nucleotides forming the rungs or steps of the ladder

47. The backbone of it all…
TEMPLATE STRAND
A C G G T A
T G C C A T
The backbone is made of alternating
sugars and phosphates.
- Remember: Sugar ALWAYS
attaches to the Nitrogen base

52. Decoding the Information in DNA
 How does DNA (a twisted latter of atoms) control
everything in a cell and ultimately an organism?
 DNA controls the manufacture of all cellular
proteins including enzymes
 A gene is a region of DNA that contains the
instructions for the manufacture of on
particular polypeptide chain (chain of amino
acids)
DNA is a set of blueprints
or code from making proteins

53. Genetic Code
 Genetic code – the language of mRNA
instructions (blueprints)
 Read in three letters at a time
 Each letter represents one of the nitrogenous
bases: A, U, C, G
 Codon found on mRNA; consists of three bases
(one right after the other)
 64 codons for 20 amino acids

54. Codon (cont’d)
 For example, consider the following RNA
sequence:
UCGCACGGU
The sequence would be read three base pairs at a
time:
UCG – CAC – GGU
The codons represent the amino acids:
 Serine – Histidine – Glycine
 AUG – start codon or Methionine
 UAA, UAG, UGA – stop codons; code for nothing;
like the period at the end of a sentence

55. The gene-enzyme relationship has been
revised to the one-gene, one-polypeptide
relationship.
Example: In hemoglobin, each polypeptide
chain is specified by a separate gene.
Other genes code for RNA that is not
translated to polypeptides; some genes are
involved in controlling other genes.

57. DNA & RNA
 Before mitosis (during S phase of interphase) , a
complete copy of a cell’s DNA is made through a process
called replication.
 When a cell divides, each daughter cell gets one
complete copy of the DNA.
 Similar to photocopying a document – the end
result is two identical documents that contain the
same information.
 Now that we know something about DNA’s structure,
lets look at how it replicates.

58. Steps of DNA Replication
1) DNA must unwind and break the hydrogen bonds
2) Each strand is used as a template (blueprint)
3) Two new strands of DNA are formed from the
original strand by the enzyme DNA Polymerase

59. DNA
Transcription

60.  During replication, an enzyme called helicase “unzips” the
DNA molecule along the base pairing, straight down the
middle.
 Another enzyme, called DNA polymerase, moves along the
bases on each of the unzipped halves and connects
complementary nucleotides.

61. From Gene to Protein
Synthesis of DNA
from RNA is
reverse
transcription.
Viruses that do
this are
Retroviruses.

62. Differences between DNA and RNA
DNA
RNA
 Structure:
 Structure:
 Double stranded
 Single-stranded
 Sugar: Deoxyribose
 Sugar: Ribose
Bases:
Bases:
 Adenine
 Adenine
 Guanine
 Guanine
 Cytosine
 Cytosine
 Thymine
 Uracil

63. ow do you get from DNA to Proteins?
TRANSCRIPTION – the synthesis of RNA under the direction of
DNA
TRANSLATION – the actual synthesis of a protein,
which occurs under the direction of mRNA

64. Splicing
Each gene has it own promotor
Each gene is widely spacied
The information is fragmented
Exon = expressed gen
Intron = intervening part
Alternative splicing: A regulatory mechanism by which
variations in the incorporation of a gene’s exons, or coding
regions, into messenger RNA lead to the production of more
than one related protein, or isoform.
Alternative splicing is a source of genetic diversity in
eukaryotes.
Splicing has been used to account for the relatively small
number of genes in the human genome.

65. mRNA Splicing
The entire gene is transcripted into a message. Some of
the message is
Junk (introns) and is removed before exiting the nucleus.
A spliceosome is a complex of specialized RNA and protein
that removes introns from a pre-mRNA This process is
generally referred to as splicing.
Introns typically have a ―GU‖ nucleotide sequence at the 5' end
splice site, and an AG at the 3' end splice site.

66. Guttmacher and Collins , NEJM, 347 (19): 1512, Figure 2 November 7, 2002

68. Translation- the Ultimate Goal!
•Going from mRNA to the final product

69. Transcription- how RNA is made
 Just as DNA polymerase makes new DNA, a similar
enzyme called RNA polymerase makes new RNA.
 RNA polymerase temporarily separates the strands of a
small section of the DNA molecule. This exposes some of
the bases of the DNA molecule.
 Along one strand, the RNA polymerase binds
complementary RNA nucleotides to the exposed DNA
bases.
 An exposed thymine on the DNA strand hooks up with
an RNA nucleotide with an adenine; an exposed cytosine
on the DNA hooks up with an RNA nucleotide with a
guanine base; an exposed adenine DNA base will hook up
with URACIL!

70.  As the RNA polymerase moves along, it makes a
strand of messenger RNA (mRNA).
 It is called messenger RNA because it carries DNA’s
message out of the nucleus and into the cytoplasm.
 mRNA is SINGLE STRANDED!
 When the RNA polymerase is done reading the gene
in the DNA, it leaves.
 The separated DNA strands reconnect, ready to be
read again when necessary.
 mRNA moves out of the nucleus and finds a ribosome
 On the ribosome, amino acids are assembled to form
proteins in the process called translation.

71. Translation: Protein Synthesis
1)mRNA is transcribed in the nucleus and leaves
the nucleus to the cytoplasm
2) mRNA attaches to the ribosome
3) tRNA carries the anticodon which pairs up
with the codon on the mRNA
4) tRNA brings the correct amino acid by reading
the genetic code
5) The amino acids are joined together to form a
polypeptide (protein)
6) When a stop codon is reached (UAA, UAG,
UGA) protein synthesis stops

72. Translation
mRNA
GUA UCU GUU ACC GUA
•mRNA carries the same message as DNA but
rewritten with different nitrogen bases.
•This message codes for a specific sequence of
amino acids
•Review..Amino acids are the building blocks
of…
•PROTEINS

73. SO:
 Say the mRNA strand reads:
 mRNA (codon) AUG–GAC–CAG-UGA
 tRNA (anticodon) UAC-CUG-GUC-ACU
 tRNA would bring the amino acids:
 Methionine-Aspartic acid-Glutamine-stop

74. Translation
mRNA
GUA UCU GUU ACC GUA
•Codon: a sequence of 3 nitrogen bases on
mRNA that code for 1 amino acid
•It’s a TRIPLET code
•Example: This strand of mRNA has 5
codons, so it would code for 5 amino acids.

75. Translation
mRNA
GUA UCU GUU ACC GUA
•These codons are universal for every
bacteria, plant and animal on earth
•There are 64 codons which code for all 20
amino acids on earth.

76. The genetic code: specifies which amino
acids will be used to build a protein
Codon: a sequence of three bases. Each
codon specifies a particular amino acid.
Start codon: AUG—initiation signal for
translation
Stop codons: stops translation and
polypeptide is released

77. Codons match
up with
anticodons to
create a
protein

78. Figure 12.6 The Genetic Code

79. Translation
mRNA
GUA UCU GUU ACC GUA
Ribosome
•The mRNA molecule travels to the ribosomes
where the mRNA codes are ―read‖ by the
ribosomes
•Ribosomes hold the mRNA so another type
of RNA, transfer RNA (tRNA) can attach to the
mRNA

80. Translation
mRNA
GUA UCU GUU ACC GUA
Ribosome
CA U AG A

81. Translation
mRNA
GUA UCU GUU ACC GUA
CA U A G A CA A

82. Elements of translation
 Ribosomes
 rRNA
 Large and small subunits  Initiation
 Codons  Chain Elongation
 Initiator or start codon  Peptide bonds
 Methionine (AUG)  Chain termination
 Stop codons  Polysome
 tRNA

83. RNA
Ribonucleic acid
Single-stranded helix
Sugar is ribose
Thymine is replaced by URACIL

84. Major RNAs
mRNA
messenger RNA carries the genetic information that will be
expressed ultimately as proteins. (carries information from
DNA to ribosome)
tRNA
transfer RNA is the adapter molecule. It recognizes the codons
of the mRNA on the one hand, and it can be covalently bonded
to the appropriate amino acid, on the other. (Carries amino
acids)
rRNA
ribosomal RNA is found in the ribosomes (Makes up
ribosomes)

85. RNA-Coding Genes
A. Ribosomal RNA (rRNA) genes
B. Transfer RNA (tRNA) genes
C. Small Nuclear RNA (snRNA) genes
D. Small Nucleolar RNA (snoRNA) genes
E. Regulatory RNA genes
F. XIST RNA-Coding Genes
G. MicroRNA (miRNA) genes
H. Antisense RNA genes
I. Riboswitch genes

86. RNA
can be
Transfer
Messenger Ribosomal RNA
RNA RNA
also called which functions to also called which functions to also called
Bring
Combine
Carry rRNA tRNA amino
mRNA with proteins
instructions acids to
ribosome
from to to make up
DNA Ribosome Ribosomes

88. Processing the RNA transcript into mRNA
1. Mono-cistronic
2. Maturation
a) RNA capping
b) RNA polyadenylation
c) RNA splicing
Cistron = Gene

89. Maturation of Eukatriotic mRNA
 Intron: not founded in cytoplasm
Cap: 7-Methyl-Guanosine cap, protect mRNA
from degradation and serve as a ribosome
binding site
Poly-A tail: AAUAAA (200 A’s) to protect the
message from degradation
 Splicing: remove of introns
Lariat structures: introns removed from hnRNA
(heterogeneus nuclear RNA) are degraded in
nucleus

92. Transfer RNA

93. The conformation (three-dimensional
shape) of tRNA results from base
pairing (H bonds) within the molecule.
3' end is the amino acid attachment
site—binds covalently. Always CCA.
Anticodon: site of base pairing with
mRNA. Unique for each species of
tRNA.

94. Hydrogen bonds form between the
anticodon of tRNA and the codon of
mRNA.
Small subunit rRNA validates the
match—if hydrogen bonds have not
formed between all three base pairs,
it must be an incorrect match, and
the tRNA is rejected.

95. Example:
DNA codon for arginine: 3'-GCC-5'
Complementary mRNA: 3'-CGG-5'
Anticodon on the tRNA: 3'-GCC-5' This
tRNA is charged with arginine.
TAC - ___ ____ ____ - TAC

96. Wobble: specificity for the base at the 3'
end of the codon is not always
observed.
Example: codons for alanine—GCA,
GCC, and GCU—are recognized by the
same tRNA.

98. Protein formation
 Amino acids link
together to form a
protein
 The new protein
could become cell
part, an enzyme, a
hormone etc.

100. Ribosomic RNA
50S
Prokaryotic ribosomes
have 3 rRNA
molecules:
23S, 16S and 5S. 30S
2 Subunits: 50S+30S
Eukaryotic ribosomes
have 4 rRNA
60S
molecules:
28S, 18S, 5.8S and 5S
2 Subunits: 60S+40S
40S

101. Ribosome: the workbench—holds mRNA and
tRNA in the correct positions to allow
assembly of polypeptide chain.
Ribosomes are not specific, they can make any
type of protein.

102. Prokaryotes
Small Subunit 30s Large subunit 50s
16s 5s
21 proteins 23s
34 proteins
Eukaryotes:
Small 40S Large 60S
5S
18S 28S
33 proteins 5.8S
49 proteins
**The numbers are not additive – based on centrifugation rates

103. Subunits are held together by ionic and
hydrophobic forces (not covalent
bonds).
When not active in translation, the
subunits exist separately.

104. Figure 12.10 Ribosome Structure

105. Large subunit has three tRNA binding
sites:
• A site binds with anticodon of
charged tRNA.
• P site is where tRNA adds its amino
acid to the growing chain.
• E site is where tRNA sits before
being released.

109. RNA polymerases
catalyze synthesis of
RNA.
RNA polymerases are
processive—a single
enzyme-template
binding results in
polymerization of
hundreds of RNA
bases.

110. Figure 12.4 RNA Polymerase
What are the bonds called that
form between ribose bases?

111. Transcription occurs in three phases:
• Initiation
• Elongation
• Termination
http://vcell.ndsu.edu/animations/transcription/movie.htm

112. Initiation requires a promoter—a special
sequence of DNA.
RNA polymerase binds to the promoter.
Promoter tells RNA polymerase where to start,
which direction to go in, and which strand of
DNA to transcribe.
Part of each promoter is the initiation site.

114. DNA Is Transcribed to Form RNA (A)

115. http://www.biostudio.com/demo_freeman_pro
tein_synthesis.htm
STEP 1
Step 2

116. Start codon is AUG; first amino acid is
always methionine, which may be
removed after translation.
The large subunit joins the complex, the
charged tRNA is now in the P site of the
large subunit.

117. Elongation: RNA polymerase unwinds
DNA about 10 base pairs at a time;
reads template in 3' to 5' direction.
The RNA transcript is antiparallel to the
DNA template strand.
RNA polymerases do not proof read and
correct mistakes.

118. Elongation: the second charged tRNA
enters the A site.
Large subunit catalyzes two reactions:
1. Breaks bond between tRNA in P site
and its amino acid.
2. Peptide bond forms between that
amino acid and the amino acid on tRNA
in the A site.

123. Termination: specified by a specific DNA
base sequence.
Mechanisms of termination are complex and
varied.
Eukaryotes—first product is a pre-mRNA
that is longer than the final mRNA and
must undergo processing.

124. Termination: translation ends when a
stop codon enters the A site.
Stop codon binds a protein release
factor—allows hydrolysis of bond
between polypeptide chain and tRNA on
the P site.
Polypeptide chain—C terminus is the last
amino acid added.

128. Table 12.1

129. Several ribosomes can work together to
translate the same mRNA, producing
multiple copies of the polypeptide.
A strand of mRNA with associated
ribosomes is called a polyribosome or
polysome.

132. Figure 12.14 A Polysome (Part 1)

133. Figure 12.14 A Polysome (Part 2)

136. Stabilizing the message
Posttranslational aspects of protein synthesis:
1. 5’ cap added to N side of new protein
 How is a message
(mRNA) stabilized
to get enough
protein…at the
right time?

137. 5’ cap can enhance translation – go faster

138. 2. Polyadenylation is the synthesis of a poly(A) tail, a stretch
of adenines at the end of the mRNA molecule.
At the end of transcription the last 3’ bit of the newly made
RNA is cleaved off by a set aof enzymes. The enzymes then
synthesize the poly(A) tail at the RNA's 3' end.
The poly(A) tail is important for the nuclear export, translation
and stability of mRNA. The tail is shortened over time and
when it is short enough, the mRNA is degraded.
In a few cell types, mRNAs with short poly(A) tails are stored
for later activation

139. Processing the protein (product)
3. TARGETING:
Polypeptide may be moved from synthesis site to an
organelle, or out of the cell.
Amino acid sequence also contains a signal sequence—an ―address label.‖
i.e. – proteins targeted to ER 5-10 hydrophobic amino acids
on the N-terminus.

140. Destinations for Newly Translated Polypeptides in a Eukaryotic Cell

141. A Signal Sequence Moves a Polypeptide into the ER (Part 1)

142. Figure 12.16 A Signal Sequence Moves a Polypeptide into the ER (Part 2)
Folding chaperones (proteins)
in RER fold proteins appropriately.
Mis-folding diseases:
Altzheimer’s
Creutzfeld–Jakob disease (CJD) (prion disease)
P53 – cancer from misfolded ―watchdog‖

143. What Happens to Polypeptides after Translation?
4. Glycosylation: addition of sugars to form
glycoproteins Sugars may be added in the
Golgi apparatus—the resulting
glycoproteins end up in the plasma
membrane, lysosomes, or vacuoles.
Diseases: incorrect addition of sugars to
specific amino acids – shows in infancy-
almost always involves nervous system
development.

144.  All proteins inserted into or associated with
the cell membrane have sugars attached to
them. They aid in recognition of other
molecules.
 What would be some consequences of
incorrect glycosylation at the cell
membrane?

145. What Happens to Polypeptides after Translation?
Protein modifications:
5. Proteolysis: cutting the polypeptide
chain by proteases. Degradation of
protein message.
6. Phosphorylation: addition of phosphate
groups by kinases. Charged phosphate
groups change the conformation.
Generally makes protein into enzymes!

146. Posttranslational Modifications of Proteins