Exam 2 + 3 Material

Question 1

Genetic Code

Answer 1

• Some codons do not encode any amino acid
• The initiation codon establishes the reading frame for ribosomes
• Every possible codon has some function in translation
• Methionine is only encoded by one codon

Question 2

What is false about genetic code

Answer 2

• All amino acids are encoded by more than one codon
• WRONG because most are but all are not

Question 3

Aminoacyl-tRNA Synthetase functions

Answer 3

• Attachment of amino acid to AMP
• Attachment of amino acid to tRNA
• Proofreading correct amino acid-tRNA linkage

Question 4

Ubiquitylation

Answer 4

• Targets a protein for degradation

Question 5

Random coils

Answer 5

Flexible regions that link secondary structures together

Question 6

What steps of protein synthesis that requires ATP hydrolysis

Answer 6

Attachment of amino acid to tRNA

Question 7

What steps of protein synthesis that require GTP hydrolysis

Answer 7

• Translocation of a ribosome from one codon to another
• Proofreading anticodon-codon pairing
• Binding a release factor to a stop codon
• Ef-Tu
• eIF2

Question 8

Kd value

Answer 8

• Lower Kd = strong binding
• High Kd = weak binding

Question 9

Function of phosphorylation as a post-translational modification

Answer 9

• Adds a negative charge to a protein
• Generates a binding site for proteins containing an SH2 domain

Question 10

How can antibiotics selectively affect prokaryotic cells and why are there side effects on eukaryotic cells

Answer 10

• Affect prokaryotes due to differences in ribosomes
• There are side effects because organelles such as the mitochondria and chloroplasts have similar ribosomes to prokaryotes

Question 11

Where does proofreading occur in protein synthesis

Answer 11

When aminoacyl-tRNA synthetase checks for codon-anticodon pairings to prevent mistakes during protein synthesis

Question 12

Domains

Answer 12

• Independent folding regions within a protein that contains different functions
• The tertiary structure of proteins contains different domains

Question 13

Post-transcriptional modifications

Answer 13

• Addition of 7-methylguanosine cap to the 5’ end of RNA
• mRNA splicing
• Formation of 3’ end poly-A tail

Question 14

Advantage of the addition of a 7-methylguanosine cap to the 5’ end of RNA

Answer 14

This signals that this is an mRNA to be and the 5’ end is intact

Question 15

Advantage of mRNA splicing

Answer 15

• Splicesome removes introns from the codon sequence
• This allows for a diversified production of proteins through alternative splicing

Question 16

Advantage of 3’ end poly-A tail

Answer 16

• The original 3’ end of RNA is cleaved off
• About 200 A’s are added to the 3’ end via poly-A polymerase
• This signals that the RNA is now mature and can be exported to the cytoplasm for translation

Question 17

Introns

Answer 17

• Non-coding sequences
• Interrupts actual coding sequence
• However: They allow many different variations of proteins through alternative splicing

Question 18

Features of 5’ cap on pre-mRNA

Answer 18

• Has 5’ to 7’ methylguanosine
• It is 5’ to 5’
• Has a triphosphate linkage

Question 19

Outer mitochondrial membrane

Answer 19

Contains porins that exchange material between the cytoplasm and mitochondria

Question 20

Inner mitochondrial membrane

Answer 20

• Cardiolipin
• Cristae: site of ETC and provides SA

Question 21

Mitochondrial Intermembrane space

Answer 21

• Cytochrome C
• Factors that program cell death

Question 22

Mitochondrial matrix

Answer 22

• Site of oxidative metabolism
• Contains mDNA and ribosomes

Question 23

Enzyme Catalysis

Answer 23

• Decrease the activation energy for a chemical reaction
• Increase the rate of forward and reverse reactions

Question 24

What can enzymes NOT do

Answer 24

• Do not alter delta G
• No effect on net equilibrium
• No effect on reactant and product concentrations
• Cannot make a reaction occur spontaneously

Question 25

Irreversible inhibitors

Answer 25

- Covalently bind to amino acid residues - Cannot be overcome by increasing substrate concentration - Inactive and remove active enzymes - Lower Vmax

Question 26

Reversible Inhibitors

Answer 26

- Competitive - Non-competitive

Question 27

Non-competitive inhibitor

Answer 27

- Reduces Vmax - No effect on Km - Bind away from the active site

Question 28

Competitive inhibitor

Answer 28

- Increase Km - No effect on Vmax - Compete with the substrate to bind to the active site

Question 29

DNA binding motifs WITH a dimerization region

Answer 29

- Leucine zipper - Helix-loop-helix - Second class of zinc fingers

Question 30

DNA binding motifs WITHOUT a dimerization region

Answer 30

- Helix-turn-helix - Homeodomain - First class of zinc fingers

Question 31

Homeodomain characteristics

Answer 31

- Contains 3 alpha helices - Similar to helix-turn-helix - In contact with major and minor groove of DNA

Question 32

Advantages of cell surface receptors using second messengers

Answer 32

- Signal does not have to travel through the membrane - Difficult signaling pathways can occur from the same signal

Question 33

Examples of second messengers

Answer 33

- cAMP - Ca2+

Question 34

What does a homeobox domain contain

Answer 34

Helix-turn-helix region

Question 35

How can complexes be organized to increase the speed and efficiency of signaling

Answer 35

- Complexes can be organized into scaffolds - Scaffold proteins bind to a cell surface receptor - Intracellular signaling molecules bind to the scaffold protein - When a signaling molecule is bound to a cell surface receptor, the signaling complex is activated - The scaffold sends the signal downstream and further amplifies it - Receptor activation can be used - Once a receptor is turned on, intracellular signaling proteins can assemble near the receptor which can result in downstream signaling occur

Question 36

Advantage of second messengers

Answer 36

Amplifies the signal

Question 37

Types of RNA

Answer 37

- tRNA: responsible for bringing amino acids to ribosomes for translation - snRNA: makes up the splicesome and is responsible for splicing RNA

Question 38

Promoters

Answer 38

- Found upstream of DNA - Bind to RNA polymerase and initiation complexes - Start transcription through binding of TF

Question 39

Enhancers

Answer 39

- Found anywhere on DNA - Do not bind to RNA polymerase or initiation complexes - Enhance transcription through binding of TF

Question 40

Allosteric regulation

Answer 40

- Allosteric regulators bind away from the catalytic site of an enzyme to a regulatory site - This causes a conformational change at the catalytic site which can act as an activator or inhibitor for substrates binding to proteins - Can be competitive or non-competitive

Question 41

How can enzymes stabilize the transition state of a chemical reaction

Answer 41

When 2 substrates bind to the enzyme, it can orient them in a way that encourages a favorable reaction to occur between them

Question 42

Primary structure

Answer 42

Chain of amino acids

Question 43

Secondary structure

Answer 43

- Folding and twisting of the peptide backbone - Held together by weak hydrogen bonding between carbonyl and amine groups - Contain alpha helices and beta sheets - Alpha helices: held together by weak hydrogen bonding between carbonyl and amine groups every 4 amino acids - Beta sheets: held together by weak hydrogen bonding between amine and carbonyl groups on adjacent polypeptide chains (run parallel and antiparallel)

Question 44

Tertiary structure

Answer 44

- 3D arrangement of secondary structure - Results from noncovalent interactions between R groups or R groups and their environments

Question 45

Quaternary Structure

Answer 45

- Arrangement of multiple tertiary structures - Held together by weak bonds and disulfide bonds