chapter 14 Flashcards
Model Organisms
- Easy to grow in the lab
- short generation times
- easy to manipulate
- produce large numbers of progeny
examples: pea plants, E. coli, bread mold
central dogma of molecular biology
the ways in which intro flows in a cell
mRNA
Messenger RNA: one strand of DNA is copied to a complementary mRNA strand
In eukaryotes, mRNA moves to the cytoplasm where it is translated into a polypeptide. The nucleotide sequence determines the amino acid sequence
rRNA
Ribosomal RNA
Ribosomes are made up of proteins and rRNA
rRNA catalyzes peptide bond formation between amino acids to form a polypeptide
tRNA
Transfer RNA
a.) binds specific amino acids (amino acid binding site) and
b.) recognizes specific sequences in mRNA (codon with its anti-codon)
tRNA recognizes which amino acid should be added next to a growing polypeptide chain
retroviruses
Retroviruses make a DNA copy of their RNA genome (reverse transcription by reverse transcriptase)
RNA polymerase
catalyze RNA synthesis
- nucleotides are added in a 5’ to 3’
-processive-one enzyme-template binding results in the polymerization of hundreds of RNA bases
- they do not need primers
transcription occurs in 3 steps
- initiation
RNA polymerase binds to a DNA promoter sequence.
-promoters (specific sequences) tell the enzyme where to start and which strand of DNA to transcribe.
-promoters have an initiation site where transcription begins. - elongation
-RNA polymerase unwinds DNA about 10 base pairs at a time; reads template in 3’ to 5’ direction
- the transcript (which is the processed mRNA) is antiparallel to the DNA template strand
- RNA polymerases do not proofread and correct mistakes - termination
specified by a specific DNA sequence
-for some genes, the transcript forms a loop and falls away from the DNA
-for others, a protein binds to the transcript and causes it to detach from the DNA
sigma factors & transcription factors
proteins that bind to DNA sequences and to RNA polymerase
Help direct polymerase onto the promoter and help determine which genes are expressed at particular times
introns vs exons
the noncoding regions (introns) get transcribed, but then sliced out of pre-mRNA in the nucleus
Only the coding sequences (exons) reach the ribosome
Splicing out the introns is one of the steps in RNA processing
RNA splicing
removes introns and splices exons tg
specific sequences commonly found in introns (consensus sequences) allow the splicing machinery to identify and remove introns
splicing machinery includes proteins and small nuclear ribonucleoproteins (snRNPs)
genetic code
specifies which amino acids will be used to build a protein
types of codons
AUG is the start codon—initiation signal for translation; also codes for methionine
Stop (or nonsense) codons — termination signals, including UAA, UAG, and UGA. the other 61 codons are sense codons
Translation uses mRNA to synthesize a polypeptide
Transfer RNA (tRNA) links mRNA codons with specific amino acids
There is at least one specific tRNA molecule for each of the 20 amino acids
tRNA has three functions
- binds to a specific enzyme that attaches it to only one amino acid at the amino acid binding site—it is then “charged”
- binds to mRNA at a triplet called the anticodon, which is complementary to mRNA codon
- interacts with ribosomes, noncovalently
aminoacyl-tRNA synthetases
tRNAs are charged by aminoacyl-tRNA synthetases
each enzyme is specific for one amino acid and its corresponding tRNA
Charging requires ATP; a high-energy bond forms between the amino acid and the tRNA–its energy is later used to form the peptide bond
Where is translation
Translation occurs at a ribosome
it holds mRNA and charged tRNAs in the correct position to allow polypeptide assembly
Ribosomes can make any type of protein and can be used over and over. most cells have thousands of them
Ribosomes
Ribosomes have two subunits, large and small, held together non-covalently
in eukaryotes, the large subunit has 3 different molecules of rRNA and 49 different proteins
the small subunit has 1 rRNA and 33 proteins
The large subunit has 3 binding sites
- A (aminoacyl tRNA) site–binds w the anticodon of charged tRNA
- P(peptidyl tRNA) site–where tRNA adds its amino acid to the growing chain
-E (exit) site–where tRNA sits before being released from the ribosome
Ribosomes have a fidelity function
when proper binding occurs, hydrogen bonds form between base pairs of the anticodon and the mRNA codon
small subunit rRNA validates—if H bonds haven’t formed between all three base pairs, the tRNA must be an incorrect match, and it is rejected
translation occurs in 3 steps
1.) initiation
a charged tRNA and small ribosomal subunit, both bound to mRNA, for an initiation complex
In prokaryotes, rRNA binds to the Shine-Dalgarno sequence on the mRNA. in eukaryotes, it binds to the 5’ cap
2.) Elongation
another charged tRNA enters A site; the large subunit catalyzes 2 reactions
- the bond between tRNA in P site and its amino acid is broken
- a peptide bond forms between that amino acid and the amino acid on tRNA in the A site
3.) termination
-translation ends when a stop codon enters the A site
- a protein release factor hydrolyzes the bond between the polypeptide and the tRNA in the P site
- the polypeptide then separates from the ribosome
peptidyl transferase activity
RNA was shown to be catalyst by:
-removing the proteins from the large subunit—it still catalyzed peptide bonds
- modifying rRNA, which destroyed peptidyl transferase activity
when the first tRNA has released its methionine, it moves to the E site and dissociates from the ribosome
the tRNA can be charged again
Elongation occurs as the steps are repeated, assisted by proteins called elongation factors
polyribosome, or polysome
several ribosomes can work together to translate the same mRNA, producing multiple copies of the polypeptide
A strand of mRNA with associated ribosomes is called a polyribosome, or polysome
signal sequences
after translation, a signal sequence is added to the polypeptide, indicating where in the cell it belongs
If there is no signal sequence, it remains where it was synthesized
Signal sequences bind to receptor proteins on the surface of an organelle
protein synthesis
protein synthesis always begins on free ribosomes
some polypeptides have a signal that stops translation and sends the ribosome to the rough ER
It binds to the RER and translation resumes, The polypeptide moves into the RER lumen, and may move to other areas of the endomembrane system
Mitochondria DNA
Mitochondria and chloroplasts have some DNA, specific RNA polymerase, and specialized ribosomes
The DNA encodes proteins involved in the electron transport chain and photosynthesis
Other proteins are imported from the cell’s protein synthesis systems
Most polypeptides are modified after translation
Proteolysis: polypeptide is cut by proteases (e.g. signal sequence is removed)
Glycosylation: addition of sugars to form glycoproteins: The sugars can act as signals: others form membrane receptors
Phosphorylation
Phosphorylation: addition of phosphate groups catalyzed by protein kinases
The charged phosphate groups change the conformation and may expose active sites or binding sites
