1
Q
Define Translation
A
- process where an mRNA molecule is read by the ribosome to make a protein
2
Q
The mRNA is read in pairs of three nucleotides called______
A
Codons
3
Q
Each codon encodes one of (how many) amino acids
A
20
4
Q
Ribosomes reads the codons and links the amino acids together in the correct order by forming _________
A
Peptide Bonds
5
Q
Define tRNA
A
- RNA molecules that read the mRNA in groups of three and bring in the correct amino acid
6
Q
What two things the tRNA molecule contains?
A
- Amino acid attachment site
- amino acid covalently attached (via an ester bond)
- amino acid covalently attaches to either the 2’ or 3’ -oh of the ribose
- amino acid covalently attached (via an ester bond)
- Anticodon region
- a group of three nucleotides that will base pair with the codon it is reading
- there is at least one tRNA for each amino acid
- a group of three nucleotides that will base pair with the codon it is reading
7
Q
When an amino acid is attached to a tRNA it is called an _____________
A
aminoacyl-tRNA
8
Q
Define Genetic Code
A
- relationship between the sequence of bases in DNA and the sequence of amino acids in proteins
9
Q
What are some features of the genetic code?
A
- 3 nucleotides represent an amino acid
- each of the 20 amino acids are represented by a codon
- the code is nonoverlapping
- the nucleotides are always read in pairs of three without overlap
- ex) the ABCDEF is read ABC DEF NOT ABC BCD CDE etc.
- the nucleotides are always read in pairs of three without overlap
- the code is read continuously
- no nucleotides are every skipped
- the code is degenerate
- mose amino acids are encoded by more than one codon
- exceptions are amino acids Methionine and Trytophan b/c they only have one codon each
- mose amino acids are encoded by more than one codon
10
Q
There are (how many) total codons?
A
- 64
- 61 codons for amino acids
- 3 are stop (termination) codons
- 61 codons for amino acids
11
Q
Define Synonyms
A
- codons that encode for the same amino acid
- most differ at the 3rd position of the codon (wobble position)
12
Q
What are some advantages of having a degenerate genetic code with multiple synonyms for amino acids?
A
- if not defenerate, then we would have 20 codons that encode amino acids and 44 stop codons
- 64 possible triplets from the nucleotide bases
- probability of mutating to a termination codon would be higher leading to a nonfunctional truncated protein
- silent mutation may occur resulting in the same amino acid being produced
13
Q
Silent Mutation
A
- a mutation that results in the same amino acid being produced
- lowers the change of deleterious mutations
- ex) mutation of CCC (encodes proline) to CCA still results in a proline amino acid
- lowers the change of deleterious mutations
14
Q
Translation Powerpoint
A
Slide 13
Question
15
Q
True of False
The genetic code is universal
A
False
The genetic code is Nearly universal but there are differences
16
Q
What is a E. coli Ribosome?
A
- a large complex containing protein and ribosomal RNA (rRNA) that is approx. 2.5 Mdaltons in size
- estimated that the approx. 20,000 ribosomes in an E. coli cell makes up approx. 1/4 of the total cell mass
- ribosome can be broken down into a large subunit (50S) and a small subunit (30S)
- 50S
- 34 proteins and 2 rRNA molecules
- 30S
- 21 proteins and 1 rRNA molecule
- 50S
17
Q
What type of RNA structure is located in the 30S?
A
16S
18
Q
True or False
RNA makes up approx. 2/3 of the total ribosoma mass
A
True
19
Q
True or False
mRNA passes through the cleft formed by the two subunits
A
True
Translation PP
Slide 17
20
Q
What is the basic steps/overview of translation?
A
- ribosome reads the codons in an mRNA transcript in the 5’ to 3’ direction
- amino acids arrive at the ribosome covalently linked to a tRNA
- the tRNA anticodon region base pairs with the correct codon in the mRNA
21
Q
How does the ribosme know where to start in translation?
A
- mRNA contains a purine rich region that pairs with the 16S rRNA of the ribosome
- Shine-Dalgarno sequence
- this region is upstream of the sequence that pairs with the initiator tRNA that starts protein synthesis
- Shine-Dalgarno sequence
22
Q
True or False
The Shine-Dalgarno sequence binds with the 16S rRNA region down steam of the sequence that pairs with the initiator tRNA that starts protein synthesis.
A
False
The region is upstream
not down
23
Q
Translation Initiation has several steps.
Explain in detail the steps.
A
- the 30S subunit binds IF-1 and IF-3 then the mRNA
- the 1st tRNA binds at P site via codon anti-codon binding
- the 16S rRNA binds Shine-Dalgarno to ensure proper alighnment
- the IF-1 and IF-3 binds at A site and E site respectively
- purpose is to not allow the 50S subunit bind yet
- the 1st tRNA binds at P site via codon anti-codon binding
- IF-2 hydrolyzes GTP thus dissociating IF-1, 2, and 3 leaving the initiation complex
- once everything is properly aligned, IF-2 triggers the release of all the IF proteins thus allowing the 50S subunit it bind to the 30s subunit
- ribosome is now ready to start translation
24
Q
What are the three active sites in a ribosome during translation?
A
- A (aminoacyl)
- P (peptidyl)
- E (exit)
25
How does creating a peptide bond work in a ribosome?
1. the first tRNA (initiator tRNA) binds to the P-site
2. tRNA arrives and base pairs with mRNA in the A-site
3. peptide bond is formed between the two amino acids on the tRNAs by the 23S rRNA in the 50S subunit (peptidyl transferase center)
4. once a peptide bond is formed, hydrolysis of GTP provides energy that translocates the mRNA and tRNAs
1. the two tRNAs now occupy the P and E sites
5. tRNA in the E site will dissociate from the ribosome
6. next amino acid can added through same mechanism
1. continues until a stop codon is read
26
What is RF1 and what is it used for?
* release factor
* when a stop codon binds the A site, this protein will bind and trigger the peptide to release
* a water molecule attachks the ester bond between the tRNA and the last amino acid in the P-site, causing peptide release
* hydrolysis
27
True or False
A ribosome reads the mRNA in the 3'-5' direction to make a polypeptide
False
ribsome reads the mRNA in the 5'-3' direction
28
True or False
Proteins are synthesized from N-terminal to C-terminal
True
29
True or False
Proteins are the most versatile of the macromolecules and perform functions in essentially all biological processes
True
30
True or False
Every protein has a unique 3D shape that dictates its function
True
31
Proteins can be classified based on their \_\_\_\_\_\_\_\_
function
32
Proteins are ________ \_\_\_\_\_\_\_\_\_ made up of \_\_\_\_\_\_\_\_called _____ \_\_\_\_\_\_
organic polymers; monomoers; amino acids
33
What properties allow proteins to perform diverse activities?
(5)
1. Proteins are linear polymers that are built of repeating monomer units called amino acids
2. proteins contain a wide range of functional groups, which allow them to perform diverse functions
3. proteins can interact with other proteins as well as other biological macromolecules to form complexes
4. some proteins become actibe when bound to cofactors
1. many proteins use metals to perform their functions
5. some proteins are very rigid, while others can be highly flexible
1. rigid proteins can play structural roles in a cell
2. flexible proteins can move to interact with multiple proteins
34
Name all componants of an amino acid
* alpha carbon
* the central carbon that bonds all of the other groups
* an amino group
* a carboxylate group
* a hydrogen
* one R group
* side chain
* where the 20 amino acids differ
35
Are protiens made from the L-amino acids or D-amino acids?
L-amino acids
* 19 out of 20 amino acids have a chiral alpha carbon
* L-amino acids have the S absolute configuration
36
At what pH does most of the amino acids reside in?
pH = 7
* exists as zwitterions
* protonated amino group, deprotonated carboxylate group = _overall neutral charge_
37
True or False
Protonation states change with pH
True
pH \< 1.0 = Overall +1 charge
pH \> 10 = Overall -1 charge
38
What are the three groups that the 20 amino acids can be broken down into?
1. Hydrophobic amino acids
1. largest group with nine amino acids; all contain a hydrophobic side chain
2. Polar Uncharged amino acids
1. contain polar functional groups but have an overall neutral charge
3. Polar Charged amino acids (5 amino acids)
1. contain polar functional groups that are charged at neutral pH
2. can have a positive or a negative charge
3. play critical roles in stabilizing protein structure due to electrostic interactions (salt bridges)
39
Are the polar charged groups ionized at neutral pH?
yes
* functional groups in amino acids can ionize at different pH values; this is important for protein function
* ability to ionize is dependent on the pka value
40
What is the pH of the Histidine side chain if the pka = 6?
pH \< 6.0 = more protonated
pH \> 6.0 = less protonated
41
Draw the amino acids aspartic acid (Asp, D) and Lysine (Lys, K) at the following pH values:
pH = 1
pH = 7
pH = 12
drawings
42
Peptide Bond
* link the carboxyl group of one amino acid to the amino of a second amino acid
* a water molecule is lost in the reaction
* the peptide bond formed is an amide bond
43
A peptide or protein always has an __________ end with a free amino group and a __________ end with a free carboxyl group
N-terminal
* the first residue of the peptide and would be encoded by the 1st codon
C-terminal
* residue is the last residue of the peptide and would be encoded by the codon just prior to the stop codon
44
Define Residue
* each amino acid in a peptide/protein
45
Main Chain (backbone) of Peptide
* the constant component that is the same in all the amino acids
* contains all the atoms except those in the side chains
46
Side Chains (R groups) of Peptide
* the variable component of the polypeptide chain
47
What is the Primary Structure of Proteins?
* the order of amino acids linked by peptide bonds, listed from N-terminal to C-terminal
48
Important Points about Primary Structure
* the primary structure is different for every protein
* it is the nucleotide sequence in DNA that determines what order amino acids are linked into a primary structure
* the primary structure of a protein will drive the spontaneous folding of a protein into a unique 3-D structure
49
True or False
Protein main chains contain both rigid and flexible regions
true
50
Explain the cis and trans arrangements
Cis
* adjacent R-groups are on the same side of the peptide bond
Trans
* adjacent R-groups are on the opposite side of the peptide
* due to steric clashes, the trans arangement is usually favored
51
What is the Ramachandran Plot?
* diagram that shows all possible allowed phi/psi angles
* due to clashes between atoms in the polypeptide, only certain phi and psi angles are allowed
52
Define Secondary Structure
* alpha helices, beta strands, and loops
* hydrogen bonding that occurs between the main chain N-H and C=O groups
53
Define Tertiary Structure
* role of amino acid side chains in protein structure
* can be attractive or repulsive forces
54
Define Quaternary Structure
* how multiple proteins can assemble into a functional unit
* many proteins are functional by themselves
* most proteins have to assemble with other proteins before they become functionally active
55
What are the two types of secondary structures that can form without steric clashes?
Alpha Helices and Beta Sheets
Beta Sheets are more common
56
Alpha Helix
* a coiled, staircase-like structure
* the backbone (main chain) forms a very tight coil while the side chains (green) extend outward
* can be right or left handed
* right handed helixs are more common
57
Alpha Helix
The C=O group of one amino acid forms a hydrogen bond with the N-H group of an amino acid \_\_#\_\_ residues away
Four
58
Why is Proline known as a "helix breaker?"
* because it lacks an NH group and forms a ring with the main chain
59
What would you expect to be different about the side chains in helices found in memberane proteins compared to helices in water soluble proteins?
In membrane proteins, the side chains neet to be hydrophobic to interact with the hydrophobic lipids
60
61
Define Enzymes
* catalyst in biological systems
* most but not all enzymes are proteins
* RNA can also catalyze chemical reactions
* ribozymes
62
True or False
Enzymes are known for their high substrate specifity and their catalytic power
True
enzymes have a unique 3D fold that allows them to selectively bind a substrate
63
Define Substrate
* the compound the enzyme binds to
64
Define Active Site
* the site in the enzyme where the chemistry occurs
* makes up a very small portion of the enzyme
65
What are Proteolytic enzymes (Proteases)?
* they are a type of enzyme that are designed to specifically cleave peptide bonds via the addition of water (hydrolysis)
66
Define Cofactor
* metals or small organic molecules (called coenzymes) that facilitate chemical reactions
67
An Enzyme without a cofactor is called an \_\_\_\_\_\_\_
Apoenzyme
68
An Enzyme with a cofactor is called a \_\_\_\_\_\_\_\_\_
Holoenzyme
69
What is a tightly bound coenzyme called?
Prosthetic Group
1. remain tightly bount to the enzyme through multiple rounds of catalysis
1. usually are required for proper protein folding
70
What are loosely bound conenzymes called?
Cosubstrate
* like substrates, these cofactors bind and are released from the enzyme during a catalytic cycle
71
Do enzyems obey the laws of thermodynamics?
Yes
They convert energy from one form to another
72
A chemical reaction can take place spontaneously only if deltaG is \_\_\_\_\_\_\_\_
Negative
73
True or False
The delta G of a creation depends only on the free energy of the products minus the free energy of the reactants
True
The pathway of getting from the reactants to the products does not matter
74
True or False
Delta G can tell me how fast a reaction occurs
False
something that is spontaneous could still take years or centuries to occur
75
True or False
Enzymes accelerate a chemical reaction if and only if the reaction has an overall negative delta G
True
76
Define Transition State
* a reaction intermediate that is no longer the reactant by not yet the product
* represents an intermediate that has a higher free energy than the reactans or products
* it is the least stable and least occupied state because it has highest free energy
77
# Define Activation energy
* the difference in free energy between the substrate and the transition state
* not included in the overall delta G calculation b/c the energy required to form the transition state is released once product is formed
* enzymes function to lower the activation energy and promote formation of the transition state
78
What is Carbonic Anhydrase
* brings CO2 and water close together in the active site to promote transition state formation
* lowers activation energy to accelerate the reaction a million fold
79
If the active site of an enzyme makes up a very small part of the overall protein, what is the functions of the rest of the protein?
1. help maintain the unique 3D shape of the protein
2. Function as regulatory sites
3. serve as sites of interaction with other proteins
80
Biochemistry
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