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67 Cards in this Set

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Within the protein coding genes these nucleotides are organized into three-letter code words called________?
codons
collection of codons makes up the
genetic code.
it is said that the genetic code has 5 qualities, what are they?
The Genetic Code Is 1) Degenerate, 2) Unambiguous, 3) Nonoverlapping, 4) Without Punctuation, & 5)Universal
Three of the 64 possible codons do not code for specific amino acids; are utilized in the cell as termination signals; they specify where the polymerization of amino acids into a protein molecule is to stop, what are they called
these have been termed nonsense codons.
multiple codons must decode the same amino acid, what is this called?
degeneracy
given a specific codon, only a single amino acid is indicated
unambiguous
T/F: given a specific codon, only a specific amino acid will be incorporated—although, given a specific amino acid, more than one codon may be used.
True
What are the two functions of the AUG codon?
Work as the start signal (MET) and specify methionine internally.
What are unique/necessary structural features of tRNA? (4)
1) Secondary structure of tRNA is critical (cloverleaf configuration)
2) CCA @ 3’ end
3) Anti-codon sequence (to recognize mRNA complimentary codon)
4) Phosphorylated 5’ end
ARDS damage to which types?
damage to to type I and II pneumocytes
Arise from a base change that causes incorporation of a different amino acid in a protein
Missense:
Formation of a termination codon from one that encodes for an amino acid; results in premature termination & a truncated protein
Nonsense:
How could a frame shift be caused?
Through the insertion/deletion of 1 or 2 nucleotides
What happens if If 3 bases are added? how does it impact the protein
then a new amino acid is added to sequence without impacting surrounding amino acids – may/may not impact protein
These enzymes form an activated intermediate of aminoacyl-AMP-enzyme complex then the specific aminoacyl-AMP-enzyme complex recognizes a specific tRNA to which it attaches the aminoacyl moiety at the 3'-hydroxyl adenosyl terminal so it binds a specific tRNA to a specific aa
aminoacyl-tRNA synthetases.
How do prokaryotes ensure that the correct reading frame is used?
they use the shine dalgarno sequence 10 nt upstream from AUG to recognize the start codon
How do eukaryotes ensure that the correct reading frame is used?
they use the initiation factor eif 4 to scan the mRNA for the first AUG codon.
Are complex ribonucleoprotein particles made up of 2 dissimilar subunits, each of which contains RNA and many proteins.
ribosome
They are the workbenches for protein synthesis
ribosomes
Structure of euk ribosome
Eukaryote 80S
Small: 40S w/ 34 proteins
18S RNA
Large: 60S w/ 50 proteins
28S, 5.8S, 5S RNAs
Name and briefly describe the 3 steps of ribosomal peptide elongation.
Step 1/Binding: EF-Tu comes into play. It is responsible for the binding of aminoacyl-tRNA to the α-binding site of the ribosome. Ribosomal peptidyl transferase transfers the growing peptide from its carrier tRNA to the α-amino group of the amino acid residue of the aminoacyl-tRNA specified by the following codons.
o Step 2/Transpeptidation: Peptide bond is formed between the aminoacyl group of the aminoacyl-tRNA and the growing peptidyl group.
o Step3/Translocation: EF-G (EF-2) is the main player. Is the movement of mRNA and tRNA along the ribosome.
What is the major energy source in protein synthesis?
GTP
What is the structural basis for the mode of action of the antibiotic puromycin?
Resembles an aminoacyl-tRNA. It binds at the large subunit A site and acts as an acceptor of the nascent peptide in the peptidyl transferase reaction.
Like tRNAs, release factors can recognize certain mRNA codons. Which codons do they recognize and how do they structurally differ from tRNAs?
Prokaryotes:
i. RF-1: UAA and UAG
ii. RF-2: UAA and UGA
iii. NOTE: RF-3 helps RF-1 & 2 bind (it does not catalyze release itself)
o Eukaryotes:
i. eRF (recognizes all of the STOP codons: UAA, UAG, UGA)
Binding of the release factor to stop codon causes _______ ________ to transfer peptidyl group onto________ instead of ___________
peptidyl transferase
water
aminoacyl-tRNA
proteins that reversibly bind hydrophobic regions of the nascent proteins and proteins in an intermediate stage of folding
Chaperones
What are the 5 functions of chaperones?
1)They can stabilize intermediates, 2) maintains proteins in an unfolded state to allow passage through membranes, 3) help unfold misfolded segments, 4) prevent formation of incorrectly folded intermediates & 5) prevent aggregation/other inappropriate interactions with other proteins
What is required for efficient initiation of protein synthesis?
3' poly(A) tail and
How is targeting to specific organelles ensured?
Sorting of proteins for their ultimate destinations occurs in conjunction with their glycosylation and proteolytic trimming as they pass through the cis, medial 7 trans elements of the Golgi apparatus. Families of vesicles and receptor proteins provide specificity for membrane targeting and fusion
Give examples of covalent posttranslational modifications
Phosphorylation: Glycosylation:
Disulfide formation
Acetylation:
Type of posttranslational modification where Kinase activity is a property of many growth factor receptors.
Phosphorylation:
Type of posttranslational modification where u form glycoproteins. It alters the properties of proteins, changing their stability, solubility and physical bulk. The carbohydrate moieties act as recognition signals that can direct protein targeting and influence cell-cell interaction and development of the organism.
Glycosylation:
Type of posttranslational modification where it Prevents unfolding of proteins and their passage across membrane, so it also becomes a means of localization.
Disulfide formation:
Type of posttranslational modification where it Occurs in histones and modulates their interaction with DNA.
Acetylation:
Which characteristics of a peptide would suggest a nonribosomal (rather than ribosomal) biosynthesis?
D-amino acids, unusual amino acids and modified units (like N-methylated)
DNA sequence that enables a gene to be transcribed.
Promoter:
Segment of DNA which regulates the activity of the structural genes of the operon by interacting with a specific repressor or activator.
Operator:
DNA-binding protein that regulates the expression of one or more genes by decreasing the rate of transcription.
Repressor:
Name features of an operon.
The term operon describes the complete regulatory unit of a set of clustered genes. It includes the adjacent structural genes for the related enzymes/associated proteins, a regulatory gene or gene encoding regulatory protein and control elements/sites on the DNA near the structural genes @ which regulator proteins act.
Why is coordinate expression of a biosynthetic pathway important?
Because all the relevant genes for a specific pathway are transcribed @ once.
With respect to gene expression regulation, what do the terms trans and cis refer to?
Cis: Signify the co-location of two or more genes on the same chromosome of a homologous pair and refers to internal factors, for example, a specific promoter sequence.
o Trans: External factors which act on a molecule, for example, proteins which are transcription factors bind to the DNA in trans to modify the rate of RNA transcription
What is the major difference between the repressor of the lactose operon and the repressor of the tryptophan operon?
Lac repressor binds its operator only in the absence of its inducer, while the trp repressor must be complexed to the inducer (2 tryptophan molecules in this case), so it can bind to the operator
How is it ensured that transcription occurs in one direction?
Through the attenuator region, which provides RNA polymerase with a 2nd chance to regulate transcription of the tryptophan operator. Within the attenuator region is the leader sequence, which begins with a methionine codon. The RNA sequence of the attenuator region adopts several secondary structures, which are recognized by the RNA polymerase. In the presence of tryptophan , for example, transcription begins @ the promoter, but it is prematurely terminated @ the end of the attenuator region. In the absence of tryptophan, the attenuator region has no effect on transcription
What is feedback inhibition?
Short-term means of regulating the 1st committed step in a metabolic pathway. For example, tryptophan can bind to an allosteric site on an enzyme and prevent its enzymatic activity. Therefore, as the [tryptophan] increases, the enzyme is inhibited more and more.
Regulation of ribosomal protein biosynthesis is based on affinity to various RNA types. Which and how do the affinities compare?
In some cases, regulation occurs at the level of translation. After the polycistronic mRNA is made, the regulatory ribosomal protein binds to this mRNA and determines which regions are translated. The ribosomal protein that regulates expression of its own operon associates with rRNA in the ribosome. This protein has a high affinity for rRNA and a lower affinity for 1 or more regions of its own mRNA. As the protein accumulates to a higher level than free rRNA, it binds to its own mRNA and prevents protein synthesis @ 1 or more of the coding sequences on this mRNA. As more ribosomes are formed, the excess of this protein is used up and translation of its mRNA can begin again.
Reduces net charge, so there is less electrostatic interaction between DNA and histones.
Acetylation of ε-lysine residue:
Methylation of 5’-CpG-3’. Proteins recognize and bind methylated DNA, which prevents binding of transcription factors.
DNA methylation:
In eukaryotes, which two factors determine whether regions are transcriptionally active?
Acetylation of ε-lysine residue:
DNA methylation:
NF-κB:
This transcription factor is usually kept in the cytoplasm. It is a heterodimers and the way it is regulated is the following. It binds to cytoplasmic repressor proteins (IκB) that, upon phosphorylation releases the transcription factor, which then translocates into the nucleus and activates target-gene transcription.
STAT3:
Oncogenic transcription factor. Like NF-κB, it is also stored in the cytoplasm. Once it is phosphorylated, STAT3 translocates into the nucleus and activate STAT3-dependant genes
w/ NF-kB & STAT3, what is important in their regulation?
In both of these transcription factors, post-translational modification is important in their regulation
Name features of an operon.
The term operon describes the complete regulatory unit of a set of clustered genes. It includes the adjacent structural genes for the related enzymes/associated proteins, a regulatory gene or gene encoding regulatory protein and control elements/sites on the DNA near the structural genes @ which regulator proteins act.
Why is coordinate expression of a biosynthetic pathway important?
Because all the relevant genes for a specific pathway are transcribed @ once.
With respect to gene expression regulation, what do the terms trans and cis refer to?
Cis: Signify the co-location of two or more genes on the same chromosome of a homologous pair and refers to internal factors, for example, a specific promoter sequence.
o Trans: External factors which act on a molecule, for example, proteins which are transcription factors bind to the DNA in trans to modify the rate of RNA transcription
What is the major difference between the repressor of the lactose operon and the repressor of the tryptophan operon?
Lac repressor binds its operator only in the absence of its inducer, while the trp repressor must be complexed to the inducer (2 tryptophan molecules in this case), so it can bind to the operator
How is it ensured that transcription occurs in one direction?
Through the attenuator region, which provides RNA polymerase with a 2nd chance to regulate transcription of the tryptophan operator. Within the attenuator region is the leader sequence, which begins with a methionine codon. The RNA sequence of the attenuator region adopts several secondary structures, which are recognized by the RNA polymerase. In the presence of tryptophan , for example, transcription begins @ the promoter, but it is prematurely terminated @ the end of the attenuator region. In the absence of tryptophan, the attenuator region has no effect on transcription
What is feedback inhibition?
Short-term means of regulating the 1st committed step in a metabolic pathway. For example, tryptophan can bind to an allosteric site on an enzyme and prevent its enzymatic activity. Therefore, as the [tryptophan] increases, the enzyme is inhibited more and more.
Regulation of ribosomal protein biosynthesis is based on affinity to various RNA types. Which and how do the affinities compare?
In some cases, regulation occurs at the level of translation. After the polycistronic mRNA is made, the regulatory ribosomal protein binds to this mRNA and determines which regions are translated. The ribosomal protein that regulates expression of its own operon associates with rRNA in the ribosome. This protein has a high affinity for rRNA and a lower affinity for 1 or more regions of its own mRNA. As the protein accumulates to a higher level than free rRNA, it binds to its own mRNA and prevents protein synthesis @ 1 or more of the coding sequences on this mRNA. As more ribosomes are formed, the excess of this protein is used up and translation of its mRNA can begin again.
Reduces net charge, so there is less electrostatic interaction between DNA and histones.
Acetylation of ε-lysine residue:
Methylation of 5’-CpG-3’. Proteins recognize and bind methylated DNA, which prevents binding of transcription factors.
DNA methylation:
In eukaryotes, which two factors determine whether regions are transcriptionally active?
Acetylation of ε-lysine residue:
DNA methylation:
Protein Translation – Initiation Factors
Antibiotic Agents that target Prokaryotic Protein Translational “Machinery”
Do these affect prok or euk?
all in PROKARYOTES except Cycloheximid)
w/c of the following factors is required for binding of aminoacyl-tRNA during elongation in euk?
a) EF-Tu
b) EF-1alpha
c) EF-G
d) eIF-3
e) RF-1
b) EF-1alpha
w/c 2 statements about release factors are true?
A) they recognize stop codons
B) these are special types of RNAs
C) they release GTP to drive translation
D) There are more release factors in euk than prok
E) There are three release factors in euk
F) they are proteins
A) they recognize stop codons
F) they are proteins
in w/c type of RNA molecule would you expect to encounter dihydrouridin & pseudouridin?
A) mRNA
B) rRNA
C) tRNA
D) siRNA
E) miRNA
C) tRNA
Give 4 examples of posttranslational modifications of protein?
acetylation, phophorylation, proteolytic processing, glycosylation + sulfation, & also protein folding