Chapter 10: Flashcards
What did Archibald Garrod find?
that rare inherited diseases (single gene traits) were due to defects in specific steps of metabolic pathways; correlated one gene with the production of one enzyme
What is Alkaptonuria (black urine disease) due to? Who discovered this?
due to build-up of a chemical intermediate of the metabolism of tyrosine
one gene encodes for ________ ; why?
one-polypeptide; Each gene encodes a piece of a protien
What did Beadle and Tatum do?
used Neurospora (bread mold) to test hypothesis that specific gene expression correlates with specific enzyme activity
What is neurospora?
a simple organism that is haploid for most of its life cycle; all alleles are expressed as phenotypes
How did Beadle and Tatum run their experience?
Treated wild-type Neurospora with mutagens and isolated mutant strains that needed specific nutrient supplements to grow
Conclusions of Beadle to Tatum’s Discoveries
for each mutant strain, the addition of just one compound supported growth; each mutation caused a defect in only one enzyme in a metabolic pathway
Tatum and Beadle; what did having three different arg mutant strains mean?
could have mutations in the same gene – or in different genes that governed steps of a biosynthetic pathway
What was the nutrient path discovered by Tatum and Beadle
Precursor –> Ornithine –> citrulline –> arginine
Gene expression to form a specific polypeptide occurs in two steps:
transcription and translation
transcription
copies information from a DNA sequence (a gene) to a complementary RNA sequence
translation
converts RNA sequence to amino acid sequence of a polypeptide
What is the central dogma of molecular biology?
transcription and translation
What separates transcription and translation in eukaryotes?
the nuclear envelope
Where is the site of transctiption in eukaryotes? translation? What is the intermediate messenger
DNA is in the nucleus which is the site of transcription
Ribosomes in the cytoplasm (ER) are the site of translation
mRNA is the intermediate messenger
Where does translation occur in prokaryotes?
on growing mRNA
How does RNA differ from DNA?
- contains uracil instead of thymine
-the sugar is ribose
-usually differs by a single polynucleotide strand
What are the three kinds of RNA in protein synthesis? How are they made?
Messenger RNA, Transfer RNA, RIbosomal RNA
All types are made by transcription
Messenger RNA
mRNA; carries a copy of a DNA sequence to the site of protein synthesis at the ribosome; has information for the order of amino acids in a protein
Transfer RNA
tRNA; carries amino acids for polypeptide assembly; decodes the information in mRNA; does not hold genetic information for making the protein
Ribosomal RNA
rRNA; catalyzes peptide bonds and provides structure
does not hold genetic information for making the protein
What does the shape of tRNA result from? What is always at the amino acid attachment side?
The 3D structure results from base pairing (hydrogen bonding) within the molecule; always has CCA on the 3’ attachment side
Where is the location of each RNA types activity?
All are in the cytoplasm; rRNA is the ribosomes in the cytoplasm
What does RNA polymerases do?
catalyze the synthesis of RNA from a DNA template
RNA polymerases and DNA polymerases are both processive. What does that mean?
a single enzyme-template binding results in polymerization of hundreds of RNA bases
Where can RNA polymerases add new nucleotides?
It can only add new nucleotides to the 3’ end of a growing strand
What are the differences between DNA polymerases and RNA polymerases
-RNA polymerases can initiate synthesis without an existing 3’-OH group, so do not need primers
-RNA polymerases lack a proofreading function
What are the components of transcription
-DNA template for base pairings – one of the two strands
-nuceloside triphosphates (Atp, Gtp, Ctp, Utp) as substrates
-An RNA polymerase enzyme
-transcription factors (eukaryotes only)
What are the three phases of transcription
Initiation, elongation, termination
Initiation
requires a promoter – a special sequence of DNA – that RNA polymerase binds to. The promoter directs the RNA polymerase to where it should start and in which direction to transcribe
Part of each promoter is the ____________ of transcription
initiation site
Elongation
RNA polymerase unwinds DNA about 10 base pairs at a time; reads template in 3’ to 5’ direction
Where are nucleotides added in elongation? What is this relative to the DNA strand?
Antiparallel to the template DNA strand
Added to the 3’ end
Termination
specified by a base sequence in DNA that destabilizes the transcription complex
What are a few examples of modes of termination
-the transcript falls away from the RNA polymerase and DNA template
-helper protein pulls away the transcript
The _____ of a gene orients the start site and direction of transcription of DNA into RNA
promoter region
The DNA template strand is transcribed _____ by RNA polymerase to produce a _______ transcript (or _____)
3’ to 5’
5’ to 3’
pre-mRNA
What is an intron? Exons?
Introns are transcribed regions that are removed from the pre-mRNA prior to nuclear export; Exons remain
T/F All transcripts of a gene have the same initiation site, or the same exon/intron structure
F; not all transcripts have the same
Eukaryotic genes may have noncoding sequenes, which are called ______
introns
Where do introns appear? Where are they removed?
appear in the primary mRNA transcript and are removed in the nucleus
Where are the coding sequences contained after introns are removed
contained in the exons that remain
What does the spliceosome do?
cuts pre-mRNA, releases introns, and splices exons together to produce mature mRNA
RNA splicing _______ and _____
removes introns and splices exons together
Where is newly transcribed (post-splicing) pre-mRNA bound? By what?
At the ends
By snRNPs (small nuclear ribonucleoprotein particles)
What are consensus sequenes
short sequences at exon/intron junctions; where snRNPs bind and near the 3’ end of the intron
T/F in the eukaryotic nucleus, in the addition to intron removal, one end of pre-mRNA is modified
F; both ends are modified. A G cap at the 5’ end and a Poly A tail at the 3’ end
What is a G cap
modified guanosine triphosphate
added to the 5’ end to facilitate mRNA binding to the ribosome and to protect mRNA from being degraded by ribonucleases
What is a poly A tail
Added to the 3’ end
-An AAUAAA sequence after the last codon which is a signal for an enzyme to cut the pre-mRNA; then another enzyme adds 100 to 300 adenines (the tail)
- may assist in export from nucleus; important for the stability of mRNA
What does UTR stand for?
Untranslated Region
T/F the genetic code is ambiguous and not redundant
F; the genetic code is redundant (more than one codon creates an amino acid) but not ambiguous (each coding only signals for one amino acid)
Somatic mutations
occur in somatic cells – passed on by mitosis but not to sexually produced offspring
Germ line mutations
occur in germ line cells, the cells that give rise to gametes; a gamete passes a mutation on at fertilization
silent mutations
do not change the polypeptide sequence or protein function
loss of function mutation
affect protein function and may lead to structural proteins or enzymes that no longer work - almost always recessive
Gain of function mutations
lead to a protien with altered function
conditional mutations
cause phenotypes under restrictive conditions, but are not detectable under permissive conditions
point mutations
results from the gain, loss, or substitution of a single basepair of DNA; can be silent or alter the sequence of the polypeptide
A missense point mutation at a nonsynonymous site ___________
changes a single amino acid
A nonsense point mutation shortens polypeptide by causing ___________
premature termination of translation
loss of stop mutation
causes read-through translation to a new stop codon
frame-shift
changes reading frame by adding or deleting bases
tRNA
the adapter molecules associates information in mRNA codons with specific amino acids
tRNA functions
binds to an amino acid, and is then “charged”, associates with mRNA molecules, interacts with ribosomes
Anticodon
At the midpoint of the tRNA sequence; The site of base pairing between tRNA and mRNA
What does the 3D conformation of tRNA result from?
base pairing – hydrogen bonding – within the molecules
When end of the tRNA is the amino acid attachment site? How do they attach?
3’ end; binds covalently
What energy source is needed to charge a tRNA molecule?
ATP
What enzymes charge tRNA? What is its specificity? What is it’s three-part active site bind to?
aminoacyl-tRNA; highly specific for one amino acid and it’s corresponding tRNA; binds to a specific amino acid, a specific tRNA, and ATP
What is wobble?
specificity for the. base at the 3’ end of the codon is not always observed; allows cells to produce fewer tRNA species, but does NOT create any ambiguity in the genetic code
What does the ribosomes do?
its the workbench; holds mRNA and charged tRNA in the correct positions to allow assembly of polypeptide chain
What are the subunits of a ribosome?
Large: 3 molecules of rRNA
Small: 1 molecule of rRNA
What are the three tRNA binding sites in the large subunit?
A (amino acid) site, P (polypeptide) site, E (exit) site
What are the three stags of translation?
Initiation, Elongation, Termination
What is RNA initiation
formation of the initiation complex – a charged tRNA and small ribosomal subunit, both bound to mRNA
What is RNA Elongation
charged tRNA enters A site, large subunit acts as peptidyl transferase
What is RNA Termination
a stop codon enters the A site of the ribosome
How do prokaryotes initiate translation?
rRNA binds to mRNA recognition site “upstream” of the start codon
How do eukaryotes initiate translation?
small subunit of a ribosome binds to the 5’ cap on the mRNA and moves until it reaches the start codon
What is the mRNA start codon
AUG
What is the N-terminus
the first amino acid after the mRNA start codon (methionine) which may be removed after translation
Where does the charged tRNA enter the large subunit? Where do the following ones enter? How do they interact?
The first enters the P site; the second enters the A site.
The bond breaks between the tRNA in the P site and it’s amino acid; that amino acid forms a peptide bond with the amino acid carried by the tRNA in the A site
What protiens assist RNA elongation?
elongation factors
What happens to tRNA after it breaks its bond with it’s amino acid
it moves to the E-site where it dissociates from the ribosome; it can become charged again
When does RNA translation end?
when a stop codon enters the A site; this codon binds a protein release factor that allows hydrolysis of the bond between the polypeptide chain and tRNA on the P site
What is the last amino acid added to a polypeptide chain in RNA translation?
C terminus
Where are ribsomes located in a eukaryotic cell? Where is polypeptide chains released after termination?
Located in the membrane of the RER; the chain is released into the lumen of the RER
What are the three types of post-translational modifications?
Phosphorylation, Glycosylation, and Proteolysis
What is phosphorylation?
Adding phosphate groups to the polypeptide chain in post-translational processing to alter the shape of the protien
What is glycosylation?
Adding sugars to the polypeptide chain in post-translational processing that are important for targeting and recognition
What is proteolysis
Cleaving the polypeptide chain in post-translational processing to allow the fragments to fold into different shapes
What are the differences betw4een RNA transcription/ translation in Prokaryotes and Eukaryotes
In prokaryotes, both processes occur at the same time in the cytoplasm; In eukaryotes transcription occurs first in the nucleus then translation occurs in the cytosol
What are the differences between gene structure for Prokaryotes and Eukaryotes
In prokaryotes, DNA sequence is not usually interrupted by introns; in Eukaryotes, transcribed regions (exons) are often interrupted by non-coding introns
What are the difference between the modification of mRNA after transcription but before translation for Eukaryotes and Prokaryotes
In prokaryotes, there is usually no modification; In eukaryotes, introns are spliced out of pre-mRNA, and the 5’cap and 3’ poly-A tail are added to mRNA.
What are the differences between translation initiation in prokaryotes and eukaryotes
In prokaryotes, the small subunit of the ribosomes associates with mRNA at the Shine-Dalgarno sequence; in Eukaryotes, the small subunit of ribosome binds at the 5’ end of mRNa and moves to start codon
