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Biochemistry > Exam 3 > Flashcards

Exam 3 Flashcards

1
Q

Define Translation

A
  • process where an mRNA molecule is read by the ribosome to make a protein
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2
Q

The mRNA is read in pairs of three nucleotides called______

A

Codons

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3
Q

Each codon encodes one of (how many) amino acids

A

20

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4
Q

Ribosomes reads the codons and links the amino acids together in the correct order by forming _________

A

Peptide Bonds

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5
Q

Define tRNA

A
  • RNA molecules that read the mRNA in groups of three and bring in the correct amino acid
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6
Q

What two things the tRNA molecule contains?

A
  1. Amino acid attachment site
    1. amino acid covalently attached (via an ester bond)
      1. amino acid covalently attaches to either the 2’ or 3’ -oh of the ribose
  2. Anticodon region
    1. a group of three nucleotides that will base pair with the codon it is reading
      1. there is at least one tRNA for each amino acid
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7
Q

When an amino acid is attached to a tRNA it is called an _____________

A

aminoacyl-tRNA

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8
Q

Define Genetic Code

A
  • relationship between the sequence of bases in DNA and the sequence of amino acids in proteins
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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 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
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10
Q

There are (how many) total codons?

A
  • 64
    • 61 codons for amino acids
      • 3 are stop (termination) codons
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11
Q

Define Synonyms

A
  • codons that encode for the same amino acid
    • most differ at the 3rd position of the codon (wobble position)
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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
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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
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14
Q

Translation Powerpoint

A

Slide 13

Question

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15
Q

True of False

The genetic code is universal

A

False

The genetic code is Nearly universal but there are differences

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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
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17
Q

What type of RNA structure is located in the 30S?

A

16S

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18
Q

True or False

RNA makes up approx. 2/3 of the total ribosoma mass

A

True

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19
Q

True or False

mRNA passes through the cleft formed by the two subunits

A

True

Translation PP

Slide 17

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20
Q

What is the basic steps/overview of translation?

A
  1. ribosome reads the codons in an mRNA transcript in the 5’ to 3’ direction
  2. amino acids arrive at the ribosome covalently linked to a tRNA
  3. the tRNA anticodon region base pairs with the correct codon in the mRNA
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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
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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

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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
  • 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
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24
Q

What are the three active sites in a ribosome during translation?

A
  • A (aminoacyl)
  • P (peptidyl)
  • E (exit)
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25
Q

How does creating a peptide bond work in a ribosome?

A
  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
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26
Q

What is RF1 and what is it used for?

A
  • 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
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27
Q

True or False

A ribosome reads the mRNA in the 3’-5’ direction to make a polypeptide

A

False

ribsome reads the mRNA in the 5’-3’ direction

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28
Q

True or False

Proteins are synthesized from N-terminal to C-terminal

A

True

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29
Q

True or False

Proteins are the most versatile of the macromolecules and perform functions in essentially all biological processes

A

True

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30
Q

True or False

Every protein has a unique 3D shape that dictates its function

A

True

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31
Q

Proteins can be classified based on their ________

A

function

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32
Q

Proteins are ________ _________ made up of ________called _____ ______

A

organic polymers; monomoers; amino acids

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33
Q

What properties allow proteins to perform diverse activities?

(5)

A
  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
Q

Name all componants of an amino acid

A
  • 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
Q

Are protiens made from the L-amino acids or D-amino acids?

A

L-amino acids

  • 19 out of 20 amino acids have a chiral alpha carbon
  • L-amino acids have the S absolute configuration
36
Q

At what pH does most of the amino acids reside in?

A

pH = 7

  • exists as zwitterions
    • protonated amino group, deprotonated carboxylate group = overall neutral charge
37
Q

True or False

Protonation states change with pH

A

True

pH < 1.0 = Overall +1 charge

pH > 10 = Overall -1 charge

38
Q

What are the three groups that the 20 amino acids can be broken down into?

A
  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
Q

Are the polar charged groups ionized at neutral pH?

A

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
Q

What is the pH of the Histidine side chain if the pka = 6?

A

pH < 6.0 = more protonated

pH > 6.0 = less protonated

41
Q

Draw the amino acids aspartic acid (Asp, D) and Lysine (Lys, K) at the following pH values:

pH = 1

pH = 7

pH = 12

42
Q

Peptide Bond

A
  • 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
Q

A peptide or protein always has an __________ end with a free amino group and a __________ end with a free carboxyl group

A

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
Q

Define Residue

A
  • each amino acid in a peptide/protein
45
Q

Main Chain (backbone) of Peptide

A
  • the constant component that is the same in all the amino acids
    • contains all the atoms except those in the side chains
46
Q

Side Chains (R groups) of Peptide

A
  • the variable component of the polypeptide chain
47
Q

What is the Primary Structure of Proteins?

A
  • the order of amino acids linked by peptide bonds, listed from N-terminal to C-terminal
48
Q

Important Points about Primary Structure

A
  • 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
Q

True or False

Protein main chains contain both rigid and flexible regions

50
Q

Explain the cis and trans arrangements

A

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
Q

What is the Ramachandran Plot?

A
  • 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
Q

Define Secondary Structure

A
  • alpha helices, beta strands, and loops
  • hydrogen bonding that occurs between the main chain N-H and C=O groups
53
Q

Define Tertiary Structure

A
  • role of amino acid side chains in protein structure
    • can be attractive or repulsive forces
54
Q

Define Quaternary Structure

A
  • 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
Q

What are the two types of secondary structures that can form without steric clashes?

A

Alpha Helices and Beta Sheets

Beta Sheets are more common

56
Q

Alpha Helix

A
  • 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
Q

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

58
Q

Why is Proline known as a “helix breaker?”

A
  • because it lacks an NH group and forms a ring with the main chain
59
Q

What would you expect to be different about the side chains in helices found in memberane proteins compared to helices in water soluble proteins?

A

In membrane proteins, the side chains neet to be hydrophobic to interact with the hydrophobic lipids

61
Q

Define Enzymes

A
  • catalyst in biological systems
    • most but not all enzymes are proteins
    • RNA can also catalyze chemical reactions
      • ribozymes
62
Q

True or False

Enzymes are known for their high substrate specifity and their catalytic power

A

True

enzymes have a unique 3D fold that allows them to selectively bind a substrate

63
Q

Define Substrate

A
  • the compound the enzyme binds to
64
Q

Define Active Site

A
  • the site in the enzyme where the chemistry occurs
    • makes up a very small portion of the enzyme
65
Q

What are Proteolytic enzymes (Proteases)?

A
  • they are a type of enzyme that are designed to specifically cleave peptide bonds via the addition of water (hydrolysis)
66
Q

Define Cofactor

A
  • metals or small organic molecules (called coenzymes) that facilitate chemical reactions
67
Q

An Enzyme without a cofactor is called an _______

68
Q

An Enzyme with a cofactor is called a _________

A

Holoenzyme

69
Q

What is a tightly bound coenzyme called?

A

Prosthetic Group

  1. remain tightly bount to the enzyme through multiple rounds of catalysis
    1. usually are required for proper protein folding
70
Q

What are loosely bound conenzymes called?

A

Cosubstrate

  • like substrates, these cofactors bind and are released from the enzyme during a catalytic cycle
71
Q

Do enzyems obey the laws of thermodynamics?

A

Yes

They convert energy from one form to another

72
Q

A chemical reaction can take place spontaneously only if deltaG is ________

73
Q

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

A

True

The pathway of getting from the reactants to the products does not matter

74
Q

True or False

Delta G can tell me how fast a reaction occurs

A

False

something that is spontaneous could still take years or centuries to occur

75
Q

True or False

Enzymes accelerate a chemical reaction if and only if the reaction has an overall negative delta G

76
Q

Define Transition State

A
  • 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
Q

Define Activation energy

A
  • 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
Q

What is Carbonic Anhydrase

A
  • 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
Q

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?

A
  1. help maintain the unique 3D shape of the protein
  2. Function as regulatory sites
  3. serve as sites of interaction with other proteins

Biochemistry (5 decks)

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