Lecture Exam 5

Question 1

What is the adapter hypothesis?

Answer 1

-Adapter Hypothesis: postulation that a small nucleic acid could act as an adaptor, binding to both a specific amino acid and the mRNA sequence encoding that amino acid; verified with the discovery of the tRNA

Question 2

Translation

Answer 2

the overall process of mRNA guided protein synthesis; the tRNA adaptor translates the nucleotide sequence of an mRNA into the amino acid sequence of a polypeptide

Question 3

aminoacyl-tRNA

Answer 3

tRNA attached to an amino acid

Question 4

aminoacyl-tRNA synthetases

Answer 4

catalyze the formation of aminoacyl-tRNA

Question 5

What does it mean that the DNA/RNA sequence is a nonoverlapping code?

Answer 5

-Codons are found in triplets to allow every codon to code for a single amino acid; once used none of the amino acids are used again

Question 6

What is a reading frame?

Answer 6

-Reading Frame: method of dividing nucleotides such that a new codon begins every three nucleotide residues; established by the first codon; no punctuation between codons

Question 7

How does a mutation affect reading frame (frame shift)? What types of mutations would be expected
to cause a frame shift?

Answer 7

-Insertions/Deletion adds or deletes a nucleotide from the reading frame which will shift the reading frame

Question 8

How is the genetic code degenerate?

Answer 8

-Degenerate: an amino acid may be specified by more than one codon and is not uniform
-each codon specifies only one amino acid

Question 9

How is the code optimized to decrease the impact of mutations?

Question 10

What is RNA editing and what effect does it have on proteins?

Answer 10

-RNA editing: the addition, deletion, or alteration of RNA nucleotides in a manner that affects the meaning of the transcript during translation
-posttranscriptional editing inserts four U residues; revises the reading frame

Question 11

What are the main stages of protein synthesis?

Answer 11

Activation of amino acids: the tRNA is aminoacylated
Initation: the mRNA and the aminoacylated tRNA bind to the small ribosomal subunit. The large subunit then binds
Elongation: successive cycles of aminoacyl-tRNA binding and peptide bond formation occur until the ribosome reaches a stop codon
Termination: translation stops when a stop codon is encountered. The mRNA and protein dissociate, and the ribosomal subunits are recycled.
Protein folding and posttranslational processing

Question 12

What is the ribosome made from?

Answer 12

-Bacterial Ribosomes: contain ~65% rRNA (forms the core and catalyzes peptide bond formation) and ~35% protein and have two unequal subunits

Question 13

How do aminoacyl-tRNA synthetases “charge” tRNAs?

Answer 13

-tRNAs are “charged” when attatched to their amino acid (aminoacylated)
-Step 1: forms the enzyme bound intermediate ( aminoacyl-AMP)
-Step 2: transfers the aminoacyl group from enzyme-bound aminoacyl-AMP to its corresponding specific tRNA; the mechanism depends on the enzyme class

Question 14

What is the initiator codon? What is the amino acid associated with it?

Answer 14

-AUG is the initiation codon
-Methionine is the amino acid residue associated with it

Question 15

What are the terminator codons?

Answer 15

-UAA, UAG, UGA

Question 16

What are the energy costs of peptide bond formation?

Answer 16

-At least four high energy phosphate equivalents are required to generate each peptide bond
-aminoacyl-tRNA formation uses two high energy phosphate groups
-a GTP is cleaved during the first elongation step
-a GTP is cleaved during translocation
-a ATP is consumed each time an incorrectly activated amino acid is hydrolyzed during proofreading
-the energy investment is required to guarantee fidelity

Question 17

What are some post-translational modifications of proteins? What kinds of effects do they have?

Answer 17

-Ubiquitination: adding ubiquitin to protein to mark for degradation
-Phosphorylation
-Acetylation
-Methylation

Question 18

How are proteins targeted for specific destinations in a cell? How are they targeted for degradation?

Answer 18

-Signal Sequence: a short sequence of amino acids that directs a protein to its appropriate location in the cell
-removed during transport or after arrival at final destination
-located at the amino terminus of proteins slated for transport into mitochondria, chloroplasts, or the ER
-Ubiquitin: a protein that is covalently linked to proteins slated for destruction via an
ATP-dependent pathway; highly conserved protein
-The ATP dependent pathway includes three enzyme types:
-E1: activating enzyme
-E2: conjugating enzyme
-E3: ligase

Question 19

Promoter

Answer 19

sites on the DNA template that are generally found near points at which RNA synthesis begins

Question 20

Repressor

Answer 20

restrict access of RNA polymerase to the promoter; block RNA polymerase binding or its movement along DNA

Question 21

Activator

Answer 21

enhance the RNA polymerase-promoter interaction

Question 22

Housekeeping Gene

Answer 22

genes for products that are required at all times and are expressed continuously

Question 23

Constitutive Gene Expression

Answer 23

expression of a gene at approximately constant levels

Question 24

Heterochromatin

Answer 24

more-condensed form of chromatin that is transcriptionally inactive
-10% of chromatin in a typical eukaryotic cell
-generally associated with chromosome structures, such as centromeres

Question 25

Euchromatin

Answer 25

less condensed form of chromatin

Question 26

What are the lncRNAs and what do they do?

Answer 26

-long noncoding RNAs: noncoding RNAs more than 200 nucleotides long that lack an open reading frame that encodes a protein
-non-protein coding would be a better term here
-Known Functions Include:
-regulation of nucleosome positioning and chromatin structure
-control of DNA methylation and posttranscriptional histone modifications
-transcriptional gene silencing
-multiple roles in transcriptional activation and repression

Question 27

What are negative and positive regulation?

Answer 27

-Negative Regulation: regulation by means of a repressor protein that blocks transcription; gene regulation by a repressor is less common in eukaryotic cells; the binding site for a repressor may be some distance from the promoter
-more common in lower eukaryotes such as yeast
-Positive Regulation: regulation by means of an activator protein that induces transcription

Question 28

What is the lac operon and how does it function?

Answer 28

-Operon: a gene cluster and promoter, plus additional sequences that function together in regulation
-the lac operon is repressed in the absence of lactose

Question 29

How do proteins interact with specific DNA sequences? What amino acids are involved?

Answer 29

-regulatory proteins generally bind to specific DNA sequences
-have discrete DNA-binding domains containing characteristic structural motifs that interact with the DNA
-most of the chemical groups that differ among the four bases are hydrogen-bond donor and acceptor groups exposed in the major groove of DNA
-permits discrimination between base pairs
-most of the protein-DNA contacts that impart specificity are hydrogen bonds

Question 30

What is catabolite repression?

Answer 30

-Catabolite Repression: a regulatory mechanism that restricts expression of the genes required for catabolism of other sugars in the presence of glucose
-mediated by cAMP as a coactivator and an activator protein, cAMP receptor protein

Question 31

What is transcription attenuation and how does it work?

Answer 31

-Transcription attenuation: a regulatory process in which transcription is initiated normally but is
abruptly halted before the operon genes are transcribed

Question 32

What is mRNA regulation in trans or cis?

Answer 32

-a separate RNA molecule may bind to the mRNA “in trans” and affect its activity
-a portion of mRNA itself may act “in cis” and regulate its own function

Question 33

What are the key features of eukaryotic gene regulation?

Answer 33

-access to eukaryotic promoters is restricted by the structure of chromatin; transcription requires chromatin remodeling
-positive regulation mechanisms are more prominent and are required for transcription
-eukaryotic transcriptional regulation commonly involves lncRNAs
-eukaryotic cells have larger, more complex multimeric regulatory proteins
-transcription (in the nucleus) and translation (in the cytoplasm) are separated in space and time

Question 34

How does chromatin remodeling work and what are the key proteins and enzymes involved in opening of closing access to the DNA?

Answer 34

-Chromatin remodeling: transcription-associated structural changes in chromatin
-Chromatin remodeling to yield transcriptionally active genes involves:
-repositioning nucleosomes
-the presence of histone variants
-covalent modification of nucleosomes
-Enzyme Complexes:
-SWI/SNF complexes: remodel chromatin so that nucelosomes are ejected near transcription start sites; involved in a cycle that replaces nucleosomes with transcription factors
-ISWI Complexes: optimize nucleosome spacing to allow chromatin assembly and transcriptional silencing

Question 35

What are enhancers and activators in eukaryotic transcriptions?

Answer 35

-Activators: proteins that enhance the RNA polymerase-promoter interaction; positive regulation by activators is common in eukaryotes
-Enhancers: DNA sites that bind activators and are distant from the promoter

Question 36

How does RNAi work?

Answer 36

-RNA interference: gene silencing technology where Dicer cleaves a duplex RNA molecule inro small interfering RNAs (siRNAs)
-siRNAs bind mRNA and silence it

Question 37

What are morphogens and how do they participate in development?

Answer 37

-Morphogens: proteins that cause the surrounding tissue to take up a particular shape or structure; function through changes in local concentration or activity
-Morphogens are the products of pattern-regulating genes: maternal genes, segmentation genes, and homeotic genes

Question 38

What are stem cells and what types of stem cells are there? How do they differentiate?

Answer 38

-Stem Cells: cells that can differentiate into various tissues
-Totipotent Cells: cells that can differentiate into any tissue or a complete organism
-Pluripotent Cells: cells that can give rise to cells of all three germ layers and many tissue types; cannot differentiate into a complete organism
-Unipotent Cells: cells that can develop into only one type of cell and/or tissue
-Embryonic stem cells: pluripotent cells of the blastocyst; used in embryonic stem cell research
-Adult Stem Cells: have more limited potential than embryonic stem cells; considered multipotent; have a niche, microenvironment that promotes stem cell maintenance while allowing differentiation of some daughter cells