Chapter 10: From DNA to Protein: Gene Expression Flashcards
Is the one gene-one protein hypothesis completely accurate?
no it is an oversimplification
Is the one gene-one polypeptide hypothesis complete accurate?
Whiel this is very useful, it is still a little simpler than real life (some genes do not code for polypeptides)
Molecular Biology
study of nucleic acids and proteins, often focuses on gene expression
True or false: genes are expressed as RNA
true
True or false: all RNA is translated into proteins
false
Transcription
the information in a DNA sequence (a gene) is copied into a complementary RNA sequence
Translation
the RNA sequence is used to create the amino acid of a polypeptide
Messenger RNA
the modified RNA that came from the complimentary DNA strand
Where does mRNA travel in eukaryotic cells?
from the nucleus to the cytoplasm
gets translated into a polypeptide
nucleotide sequence of it determines the sequence of the amino acids
Ribosomal RNA
rRNA
catalyzes peptide bond formation between amino acids to form a polypeptide
ribosome
protein synthesis factory
multiple proteins and rRNAs
Transfer RNA
tRNA
mediates between mRNA and protein
can bind a specific amino acid and recognize a specific sequence in mRNA
figures out which amino acid should be added to the growing polypeptide
What does DNA expression start with?
transcription to RNA
Transcription
tue formation of a specific RNA sequence from a specific DNA sequence
What factors are required for transcription?
A DNA template for complementary base pairing
the appropriate nucleoside triphosphates (ex ATP) to act as substrates
an RNA polymerase `
RNA polymerases
catalyze the synthesis of RNA from the DNA template
all have common structure
do not require primer
Are RNA polymerases processive?
Yes
a single enzyme-template binding event results in the polymerization of hundreds of RNA nucleotides
what are the three steps in transcription?
initiation
elongation
termination
Initiation (transcription)
needs a promoter
RNA polymerase binds to the promoter
Promoter
a special DNA sequence to which the RNA polymerase can bind to very tightly
tell RNA polymerase where to start transcription and which of the two strands to transcribe
orients the RNA polymerase
Tom Haverford
transcription initiation site
part of the promoter
where transcription begins
upstream
5’ on the non-template strand and 3’ on the template strand
Are all promoters identical?
no
Elongation (transcription)
the RNA polymerase unwinds the DNA and reads in the 3’ to 5’ direction (copying in the 5’ to 3’)
RNA polymerase uses the ribonucleoside triphosphates as substrates and catalyzes the formation of phosphodiester bonds
True or false: RNA polymerases and crew have more efficient proofreading mechanisms than DNA
false they are less efficient
True or False; RNA errors are more harmful than DNA ones
false
lots of RNA copies are made/they aren’t around for very long, less potential for harm in copying errors
Termination (transcription)
occurs at specific sequences
Coding reigons
sequences within a DNA molecule that are expressed as proteins
introns
intervening regions
interrupt the coding region
exons
expressed regions
transcribed regions
pre-mRNA
exons and introns (basically the whole section complementary to the DNA)
mature mRNA
just exons, no introns
Nucleic Acid Hybridization
DNA that you want analyzed denatured and hydrogen bonds broken to separate the pairs
probe incubated within the DNA if it has a base sequence complementary to the target DNA, double helix forms
prode
a single-stranded nucleic acid from another source
Do introns scramble the DNA sequence of a gene?
no they interrupt it
RNA splicing
removes the introns and splices the exons together
Consensus sequences
short stretches of DNA that appear with little variation in different genes that acts as borders between introns and exons
snRNOs
small nuclear ribonucleoprotein particles
surround the consensus sequences
has RNA with complementary sequences to the consensus sequences
spliceosome
RNA protein complex
large
cuts pre-mRNA releases introns and joins the ends of the exons
Are all exons included in every mRNA?
no they aren’t
5’ cap
added to the 5’ end of the pre-mRNA as it is transcribed
chemically modified GTP
facilitates binding of mRNA to ribosome and protects the mRNA from degradation
poly A tail
added to the 3’ end of the pre-mRNA at the end of transcription assists in export of mRNA from the nucleus and is important for stability
True or false: transcription and translation are coupled in prokaryotes
true
no nucleus and ribosomes bind to mRNA as it is being transcribed
Codons
three letter “words”
sequential
nonoverlapping
specify amino acids
How many variations could triplet codons code for?
64
Start codon
AUG
codes for methionine
Stop codons
UAA UAG UGA termination signals for translation once the machinery arrives here, translation stops and the polypeptide is released from the copmlex
True or false: The genetic code is redundant
true
True or false: The genetic code is ambiguous
false
each only codes for one
Is the genetic code universal?
nearly
very few exceptions
Silent mutations
occur because of the redundant of the genetic code
Missense mutatiosn
change in the amino acid sequence
Nonsense mutatiosn
result in a premature stop codon
Frame-shift mutations
result from the insertion or deletion of one or more base pairs within the coding sequence
new triplets are read
What key events must take place to ensure that the protein made is the one specified by mRNA?
a tRNA must chemically read each mRNA codon correctly
the tRNA must deliver the amino acid that corresponds to the mRNA codon
What molecule links the information contained in each mRNA codon with a specific amino acid?
tRNAs
True or false: tRNAs bind to specific amino acids
true
When is the tRNA charged?
when it is carrying an amino acid
Anticodon
a triplet of bases on the tRNA (t for antiocodon and tRNA)
which is complimentary to the mRNA codon for the particular amino acid that the tRNA has
What bonds hold the codon and anticodon together?
hydrogen of course
Does tRNA interact with ribosomes?
yes
noncovalently
Wobble
the specificity for the base at the 3’ end of the codon is not always observed
doesn’t always occur
ex. GCA GCC and GCU all are recognized bt the same tRNA
True or false; each mRNA codon binds to just one tRNA species, carrying a specific amino acid
true
What family of enzymes is responsible for the charging of tRNA?
aminoacyl-tRNA synthetases
Are aminoacyl-tRNA synthetases specific for amino acids?
yup and the tRNA
How does the reaction that aminoacyl-tRNA synthetases catalyze work?
use ATP to form a high energy cone between the amino acid and tRNA
What is recognized the amino acid or the anticodon on the tRNA?
the anticodon on the tRNA
How many subunits does the ribosome consist of?
two
In eukaryotes, what do the large subunits and small of the ribosome consist of>
rRNA and proteins
they also interact noncovalently
When the ribosome isn’t translating DNA, are the subunits together?
nope
What order does a charged tRNA traverse the ribosome sites in?
A P E
A site
amino acid site
charged tRNA anticodon binds to the mRNA codon, living up the correct amino acid
P site
polypeptide site
tRNA adds amino acid to the polypeptide chain
E site
exit site where the tRNA resides before being released from the ribosome and heading up to the cytosol to pick up another amino acid
fidelity function
ribsosome has this
ensures that a charged tRNA with the correct anticodon bings to the right codon
hydrogen bonds form when proper binding occurs, the rRNA makes sires that these hydrogen bonds have formed
What three steps occur in translation?
initiation, elongation, and termination
look familiar?
Initiation (translation)
initiation complex binds to mRNA
small subunit moves until it reaches start codon (AUG)
methionine is first in amino acid sequence
at the end of initiation the methionine charged tRNA is in the P site
Initiation complex
charged tRNA and small ribosomal subunit (both bound to mRNA)
Initiation factors
translation
mRNA
ribosomal subunits and methionine charged tRNA
Elongation (translation)
chraged tRNA with anticodon complementary to the second mRNA codon enters the A site
large subunit catalyzes two reactions (breaks bond between methionine and tRNA in P site and catalyzes the formation of a peptide bond between methionine and the amino acid on the tRNA in the A site)
first tRNA moves to E site and leaves second tRNA moves to P site
rinse and repeat (in the 5’ to 3’ direction)
Peptidyl transferase activity
large ribosomal subunit has this because it can break bond between tRNA and amino acid and form peptide bonds between different amino acid)
True or false: polypeptides grow in the amino to carboxyl direction
true
alphabetical order
termination (translation)
elongation ends when a stop codon enters the A site
bond between polypeptide chain and tRNA in P site broken
amino acid separate from the ribosome
release factor
part of termination (in translation)
allows hydrolysis of the bond between the pole peptide chain and the tRNA in P site
Polyribosome
polysome
the strand of mRNA with multiples ribosomes and their polypeptide chains
Can several ribosomes simultaneously translate a signal mRNA molecule?
yup
true or false: the site of a polypeptide’s function in the cell may be far away from its point of synthesis at the ribosome
true
True or false: polypeptides are rarely modified by the addition of new chemical groups that contribute to the function of the mature protein
false
they often are
Where is the default location for a protein?
the cytosol
Signal sequence
short stretch of amino acids that indicates where in the cell the polypeptide should go
Where does a signal sequence bind?
to a receptor protein on the surface of an organelle
What happens if a polypeptide has a signal sequence of 5-10 hydrophobic acids at its N terminus ?
it will be directed to the rough endoplasmic reticulum
Proteolysis
the cutting of a polypeptide chain
PROTEASES
CUT POLYPEPTIDE CHAINS
Polyproteins
long polypeptides containing the primary sequences of multiple distinct proteins
these are cut into final products by proteases
Glycosylation
addition of carbohydrates to proteins to form glycoproteins
Phosphorylation
addition of phosphate groups to proteins
catalyzed by protein kinases
cell signaling
