Biology- Molecular Genetics Flashcards
nucleotides
consist of 3 parts: phosphate group, sugar, and a nitrogen base
DNA replication
involves separating (unzipping) the DNA molecule into 2 strands.
Each strand then serves as a template to make a new, complementary strand
semiconservative replication
consists of a single strand of old DNA (template strand) and a new, replicated DNA (the complementary)
helicase
unwinds the DNA, forming a Y-shaped replication fork
single-stranded binding proteins
attach to each strand of the uncoiled DNA to keep them separate and prevent them from recombining
topoisomerases
break and rejoin the double helix, allowing the twists to unravel and preventing formation of knots and twists that form as a result of the unwinding done by helicase
(if you unwind a twist, the ends will get extra tight and knot up)
DNA polymerase
enzyme that assembles the new DNA strand, which moves in the 3’-5’ direction along each template strand. A new complement strand grows in the antiparallel direction 5’-3’.
In which direction does replication occur continuously?
3’ => 5’; the DNA polymerase follows the replication fork and assembles a 5’ => 3’ complementary strand
leading strand
complementary strand made in 5’ => 3’ direction (continuous replication)
okasaki segments
short segments of complementary DNA; For the 5’=>3’ template strand, DNA polymerase moves away from the replication fork
*Every okasaki segment has an RNA primer
DNA ligase
enzyme that connects okasaki segments; in all cases of repair, ligase must come in to seal the backbone afterward
lagging strand
for the 5 => 3 template strand the DNA polymerase has to go back to the replication fork and work away from it. complementary strand that requires more assembly time than the leading one, because it is assembled in short okazaki fragments
primase
enzyme that creates a short stretch of RNA to use as a primer during DNA replication; it initiates DNA replication at special nucleotide sequences called origins of replication w/ RNA primers
The small strip of rna primer allows DNA polymerase can work since it can only add to an existing strand
RNA primer
short stretch of RNA nucleotides, later replaced w/ DNA nucleotides by DNA polymerase
elongation
adding of DNA nucleotides to the complement strand; happens when DNA polymerase attaches to RNA primers
Where does the energy for elongation come from?
there are two additional phosphates that are attached to each nucleotide. When the bonds are broken, it provides chemical energy (same w/ transcription). Human rate 50 n/s
Replication of Telomeres (ends of eukaryotic chromosomes)
Two problems can occur:
- When not enough template strand remains to which primase can attach.
- FIX: telomerase comes in - When the last primase is removed, if there is no next okazaki segment to which DNA polymerase can attach, the empty space left by the removal of the primer is left unfilled. RNA is ultimately destroyed by enzymes that degrade RNA left on the DNA, section of the telomere subsequently lost w/ each replication cycle
Prokaryotic DNA is circular so no telomeres or issue.
telomerase
attaches to the end of the template strand and extends the template strand by adding a short sequence of DNA nucleotides over and over again. This allows elongation of the lagging strand to continue. However, at the end it will still be not enough for primase to attach but this loss of unimportant segment will not cause any problem.
Telomerase carries an RNA template: binds to flaking 3’ end of telomeere that compliments part of its RNA template, synthesizes to fill in over the rest of its template
Eventually, telomerase stops the elongation, and ultimately DNA polymerase will be unable to replicate new portions due to the reasons in replication of telomeres. However, the DNA in the extended region of the template is just repeating short segments of nucleotides and merely acts to prevent the loss of important coding DNA that precedes it
one-gene-one-enzyme hypothesis
the gene was defined as the segment of DNA that codes for a particular enzyme
one-gene-one-polypeptide hypothesis
since many genes code for polypeptides that are not enzymes (structural proteins or individual components of enzymes), the gene was redefined as a segment of DNA that codes for a particular polypeptide
protein synthesis
the process that describes how enzymes and other proteins are made from DNA
What are the 3 steps of protein synthesis?
Transcription, RNA processing, and translation
transcription
RNA molecules are created by using the DNA molecule as a template; prokaryotes polycistronic, eukaryotes monocistronic
RNA-processing
modifies the RNA molecule that’s created by deleting or adding
translation
the processed RNA molecules are used to assemble amino acids into a polypeptide
What 3 kinds of RNA molecules are produced during transcription?
messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA)
messenger RNA (mRNA)
single strand of RNA that provides the template used for sequencing amino acids into a polypeptide.
64 possible ways (4x4x4) ways that four nucleotides can be arranged in triplet combinations, there are 64 possible codons. 3 of them are stop codons. There are only 61 codes for amino acids
codon
a triplet group of 3 adj. nucleotides on mRNA, which codes for one specific amino acid
genetic code
provides the decoding for each codon.
How many codons actually code for amino acids?
61 codons, since some signal an end to translation
transfer RNA (tRNA)
a short RNA molecule (consisting of about 80 nucleotides) that is used for transporting amino acids to their proper place on the mRNA template strand
C-C-A-3’ end of tRNA attaches to amino acid, and the other portion is the anticodon which bp with the codon in mRNA. Wobbles: exact bp of the 3rd nucleotide in the anticodon and the 3rd nucleotide in the codon is often not required allowing 45 different tRNA’s base-pair with 61 codons that code for amino acid. Transports AA to its mRNA codon
anticodon
triplet combination of nucleotides found on a portion of tRNA
What happens to the 3’ end of a tRNA molecule?
the 3’ (C-C-A) attaches to an amino acid
What happens to the anticodon during translation?
the anticodon base pairs with the codon of mRNA
wobble hypothesis
exact base-pairing between the 3rd nucleotide of tRNA anticodon and the 3rd nucleotide of the mRNA codon is often not required. This wobble allows the anticodon of some tRNA’s to base-pair w/ more than one kind of codon. As a result, about 45 different tRNA’s base-pair w/ the 61 codons that code for amino acids
Ribosomal RNA (rRNA)
molecules that are the building blocks of ribosomes.
Within the nucleolus, various proteins imported from the cytoplasm are assembled w/ rRNA to form large and small ribosome subunits. Together, the 2 subunits form a ribosome that coordinates the activities of the mRNA and tRNA during translation
nucleolus is an assemblage of DNA actively being transcribed into rRNA. As ribosome, it has 3 binding sites: one for mRNA, one for tRNA that carries a growing polypeptide chain (P site); one for 2nd tRNA that delivers the next aa (A site). Termination sequences include UAA, UGA, UAG. Together with proteins, rRNA forms ribosomes. Ribosome is assembled in nucleolus but large and small subunites exported separately to cytoplasm
How many binding sites do ribosomes have?
3 binding sites: one for the mRNA, one for a tRNA that carries a growing polypeptide chain (P site), and one for a second tRNA that delivers the next amino acid that will be inserted into the growing polypeptide chain (A site)
What are the 3 steps of transcription?
initiation, elongation, and termination
(transcription) initiation
RNA pol attaches to a promoter region on the DNA and begins to unzip the DNA into two strands. A promoter region for mRNA transcriptions often contains the sequence T-A-T-A (called the TATA box)
most common sequence of nucleotides at promoter mRNA is called the consensus sequence; variations from it cause less tight RNA pol binding =>lower transcription rate
(transcription) elongation
RNA pol unzips the DNA and assembles RNA nucleotides using one strand of the DNA as a template; only one strand is transcribed. As in DNA replication, elongation of the RNA molecule occurs in the 5’ => 3’ direction. In contrast to DNA replication, new nucleotides are RNA nucleotides (rather than DNA nucleotides), and only one DNA strand is transcribed
(transcription) termination
when the RNA polymerase reaches a special sequence of nucleotides that serve as a termination point. In eukaryotes, the termination region often contains the DNA sequence AAAAAAA.
transcription is occurring in the 3’ to 5’ direction of the DNA template strand (but synthesis of the RNA strand is , as always, 5’ to 3’
mRNA processing
- A 5’ cap (-P-P-P-G-5’) is added to the 5’ end of the mRNA; Guanine with 2 phosphate groups => GTP; providing stability for mRNA and point of attachment for ribosomes
- A poly-A tail (-A-A-A….A-A-3’) is attached to the 3’ end of the mRNA; Tail consists of 200 A; provide stability and control movement of mRNA across the nuclear envelope (in prokaryotes, poly A tail facilitates degradation
- RNA splicing removes nucleotide segments from mRNA; before mRNA moves into cytoplasm, small nuclear ribonucleoproteins (snRNP’s) and the spliceosome delete the introns and splice the exons. (prokaryotes have no introns!)
- Alternative splicing allows different mRNA’s to be generated from the same RNA transcript; by selectively removing differences of an RNA transcript into different combinations => each coding for a different protein product
note: prokaryotes generally have ready to go mRNA upon transcription. It is only eukaryotesthat you need the above processing. Because prokaryotes don’t need to process their mRNA first, translation can begin immediately / simultaneously. In both prokaryotes and eukaryotes, multiple RNA polymerases can transcribe the same template simultaneously.
exons
sequences that express a code for a polypeptide
introns
intervening sequences that are noncoding
snRNP’s (small nuclear ribonucleoproteins)
delete the introns and splice the exons
aminoacyl-tRNA
amino acids attach to the 3’ end of the tRNA’s
What provides the energy for translation?
energy is provided by several GTP molecules
Translation (Initiation)
small ribosome unit attaches to 5’ end of mRNA; tRNA methionine attaches to start sequence of mRNA AUG, and large ribosome unit attaches to form a complete complex
mutation
any sequence of nucleotides in a DNA molecule that does not exactly match the original DNA molecule from which it was copied
A point mutation includes what?
substitution, deletion, insertion, frameshift
point mutation
single nucleotide error
sustitution
occurs when the DNA sequence contains an incorrect nucleotide in place of the correct nucleotide
deletion
occurs when a nucleotide is omitted form the nucleotide sequence