Chapter 6: Molecular Genetics [COMPLETE] Flashcards
what is the structure of a nucleotide?
ribose sugar, nitrogenous base, and phosphate group
what is the structure of a nucleoside?
ribose sugar and nitrogenous base
what is DNA - structure and polymer-wise?
polymer of nucleotides that have hydrogen on the ribose sugar’s 2’ carbon
what is RNA - structure and polymer-wise?
polymer of nucleotides that have hydrogen on the ribose sugar’s 2’ carbon
what is the full name of DNA?
deoxyribonucleic acid
what is the full name of RNA?
ribonucleic acid
what are purines and what falls under the category?
double-ringed nitrogenous bases; adenine and guanine
what are pyrimidines and what falls under the category?
single-ringed nitrogenous bases; cytosine, thymine, and uracil
pyrimidine mnemonic
CUT the PYE
C: cytosine
U: uracil
T: thymine
in DNA, what bases bind with each other and how many hydrogen bonds exist between them?
A - T: 2 hydrogen bonds
G - C: 3 hydrogen bonds
in RNA, what bases bind with each other and how many hydrogen bonds exist between them?
A - U: 2 hydrogen bonds
G - C: 3 hydrogen bonds
why is a higher temperature needed to break DNA strands with a larger proportion of G-C bonds?
because G-C bonds have more hydrogen bonds
what are nucleosomes?
complexes of DNA wrapped around histone proteins
how many histones are there per nucleosome?
9 total
what is the histone breakdown for each nucleosome; aka, what are the histones in the central core and on the outside?
central core:
(2) H2A
(2) H2B
(2) H3
(2) H4
outside:
(1) H1
what is the function of the outside histone of a nucleosome?
holds the DNA in place
what is chromatin?
refers to the overall packaging of DNA and histones
what are the two types of chromatin?
euchromatin and heterochromatin
in euchromatin, how are nucleosomes packed and what does this mean for DNA?
nucleosomes are “loosely packed”; so DNA is readily accessible for transcription
in heterochromatin, how are nucleosomes packed and what does this mean for DNA?
nucleosomes are “tightly packed”; so DNA is mostly inactive
what allows proper binding between DNA and histones?
the positive charge on DNA and the negative charge on histones
what occurs when histones go through acetylation and how does it affect transcription?
removes its positive charges, relaxing DNA-histone attractions and allowing for more transcription to happen
what occurs when histones go through deacetylation and how does it affect transcription?
increases its positive charges, tightening DNA-histone attractions and decreasing transcription
what occurs when histones go through methylation and how does it affect transcription?
adds methyl groups, can either increase or decrease transcription
what is the flow of processes that DNA must go through to be translated into proteins?
mnemonic: Roast Turkey Later
replication –> transcription –> translation
what is the origin of replication, in DNA replication, and what is it required for?
it is where the DNA strands first separate, required to initiate DNA replication
how many origins of replication do organisms with circular DNA (bacteria) have?
single
how many origins of replication do organisms with linear DNA (humans) have?
multiple
what does it mean when DNA undergoes semiconservative replication?
each new double helix produced by replication will have one “new” strand and one “old” strand
DNA is antiparallel, what does this mean for the structure?
the 5’ end (terminal phosphate group) of one strand is always next to the 3’ end (terminal hydroxyl group) of the other strand and vice versa
what are the steps of DNA replication?
initiation, elongation, and termination
what occurs in the initiation stage of DNA replication?
origins of replication are created at A-T rich segments of DNA because they only have two hydrogen bonds and are easier to split apart
what occurs in the elongation stage of DNA replication?
new DNA strands are produced using different types of enzymes
[personal mnemonic] how many steps of elongation are there and what is the trigger word for each one?
ten
- helicase
- single-strand binding proteins
- topoisomerase
- primase
- sliding clamp proteins
- DNA polymerase
- leading strand
- lagging strand
- different DNA polymerase
- DNA ligase
what occurs in step 1 of elongation?
helicase unzips DNA by breaking hydrogen
bonds between strands, creating a replication fork. As this occurs, helicase leads to supercoiling (tension ahead of the replication fork)
what occurs in step 2 of elongation?
single-strand binding proteins bind to uncoiled DNA strands, preventing reattachment of the strands to each other
what occurs in step 3 of elongation?
topoisomerase nicks the DNA double helix ahead of helicase to relieve built-up tension and supercoiling
what occurs in step 4 of elongation?
primase places RNA primers at the origin of replication to create 3’ ends for nucleotide addition
what occurs in step 5 of elongation?
sliding clamp proteins hold DNA polymerase onto the template strand
what occurs in step 6 of elongation?
DNA polymerase adds free nucleoside triphosphates to 3’ ends. DNA polymerase can only add nucleotides onto a preexisting 3’ hydroxyl group provided by primase.
what occurs in step 7 of elongation?
the leading strand is produced continuously because it has a 3’ end that faces the replication fork
what occurs in step 8 of elongation?
the lagging strand is produced discontinuously because its 3’ end is facing away from the replication fork. Thus, many RNA primers are needed to produce short DNA fragments called Okazaki fragments
what occurs in step 9 of elongation?
a different DNA polymerase replaces RNA primers with DNA
what occurs in step 10 of elongation?
DNA ligase glues separated fragments of DNA together
what occurs in the termination stage of DNA replication?
replication fork cannot continue, ending DNA replication
what are telomeres?
noncoding, repeated nucleotide sequences at the ends of linear chromosome
why are telomeres necessary in eukaryotes?
because when the replication fork reaches the end of a chromosome, a small segment of DNA from the telomere is not replicated and lost (no RNA primer is present to help produce another Okazaki fragment)
what is telomerase?
an enzyme that extends telomeres to prevent DNA loss
what are the 8 DNA replicating proteins?
DNA helicase, single-stranded binding proteins, topoisomerase, primase, DNA polymerases, DNA sliding clamp, DNA ligase, telomerase
[DNA replicating protein] DNA helicase function:
separates complementary strands at the replication fork
[DNA replicating protein] single-stranded binding proteins function:
proteins that prevent the two strands from coming back together after separating
[DNA replicating protein] topoisomerase function:
relaxes the DNA double helix from the tension and supercoiling the opening helix is creating
[DNA replicating protein] primase function:
provides a 3’ hydroxyl group for DNA polymerase to attach new nucleotides to
[DNA replicating protein] DNA polymerases function:
the class of enzymes that extends DNA in the 5’ to the 3’ direction. several have proofreading capabilities that allow them to catch synthesis errors
[DNA replicating protein] DNA sliding clamp function:
helps to hold DNA polymerase to the template strand
[DNA replicating protein] DNA ligase function:
glues together separate pieces of DNA
[DNA replicating protein] telomerase function:
adds repetitive DNA to the ends of eukaryotic chromosomes, which prevents critical information from being lost
what role do genes play in DNA?
genes are instructions within DNA that code for protein
what must DNA go through before being translate into proteins?
be transcribed into RNA
what is the order sequence in a gene?
the promoter region, then the gene operator, then the gene
what does DNA specifically produce when it undergoes transcription?
single-stranded messenger RNA (mRNA)
in prokaryotes, where do transcription and translation occur simultaneously and why?
in the cytosol, because prokaryotes do not have membrane-closed nuclei
what are the steps of transcription?
initiation, elongation, and termination
what occurs in the initiation stage of transcription?
a promoter sequence (aka promoter) next to the gene attracts RNA polymerase to transcribe the gene
what occurs in the elongation stage of transcription?
transcription bubble forms and RNA polymerase travels in the 3’ → 5’ direction on the template strand, but it extends RNA in the 5’ → 3’ direction
what occurs in the termination stage of transcription?
a termination sequence (aka terminator) signals to RNA polymerase to stop transcribing the gene
what is the template strand used to transcribe the mRNA called?
the template/antisense/noncoding strand
what is the other strand called and why?
the coding/sense strand because it is almost equivalent to the transcribed mRNA
once DNA is transcribed to RNA, what is thymine (T) replaced with?
uracil (U)
in prokaryotes, when RNA polymerase opens up DNA, what does it form?
transcription bubble
before transcription can occur in prokaryotes, what does a sigma factor have to combine with and for what reason?
combines with ‘prokaryotic core RNA polymerase’ to form ‘RNA polymerase holoenzyme’; gives it the ability to target specific DNA promoter regions
what are the two types of termination in bacteria?
rho independent termination and rho-dependent termination
what occurs in rho independent termination?
a termination sequence is reached and the RNA transcript folds into a hairpin loop → RNA polymerase falls off and transcription ends
what occurs in rho-dependent termination?
a rho protein binds to the RNA transcript, moving 5’ → 3’ to catch up and displace RNA polymerase, ending transcription
what is an operon?
a group of genes that function as a single unit that is controlled by one promoter
where is the operator region near?
near the operon’s promoter