155 terms

DAT Bootcamp - Molecular Genetics

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the _____ is a theory that states that, in cells, information only flows from DNA to RNA to proteins
central dogma
a _____ is the basic unit of DNA
nucleotide
a nucleotide is composed of a _____ bonded to both a _____ _____ and a _____ _____
sugar, phosphate group, nitrogenous base
what are the two classes of nitrogen bases found in nucleic acid?
purines, pyrimidines
the purines include _____ and _____
adenine, guanine
the pyrimidines include _____ and _____
cytosine, thymine, uracil (replaces thymine in DNA)
antiparallel DNA strands are held together by _____ _____ between the bases oriented toward the center
hydrogen bonds
in DNA, thymine forms 2 hydrogen bonds with _____
adenine
in RNA, _____ forms 2 hydrogen bonds with adenine
uracil
in DNA and RNA, guanine forms 3 hydrogen bonds with _____
cytosine
1 side of the DNA helix runs in the opposite direction to the other (5' to 3' and 3' to 5') - this is known as the _____ _____ of DNA
antiparallel arrangement
the DNA structure was discovered by _____ and _____
Watson, Crick
what is the enzyme that breaks the hydrogen bonds between nitrogenous bases during DNA replication?
DNA helicase
the _____ is a Y-shaped region where the parental strands of DNA are being unwound
replication fork
DNA replication is _____, meaning that each daughter strand will have 1 new and 1 old strand
semiconservative
_____ is the enzyme that reads the parent DNA strand and creates a complementary, antiparallel daughter strand
DNA polymerase
DNA polymerase always reads the template strand in the _____ direction
3' --> 5'
DNA polymerase creates the complimentary strand in the _____ direction
5' --> 3'
the _____ is the DNA strand that is continually synthesized by DNA polymerase
leading strand
the _____ is the DNA strand that is synthesized discontinuously, due to a limited reading direction of DNA polymerase
lagging strand
_____ are short fragments that result from the discontinuous synthesis of the lagging strand
Okazaki fragments
in RNA, thymine is replaced with _____
uracil

(both are pyrimidines)
DNA is transcribed into mRNA and arranged into triplets known as _____
codons
codons are translated from mRNA into _____
amino acids
most amino acids have more than one codon coding for them - this is known as _____ or _____
degeneracy, redundancy
_____ carries the complement of a DNA sequence from the nucleus to the ribosomes for protein synthesis
messenger RNA (mRNA)
_____ assists in translation by bringing amino acids to the ribosomes during protein synthesis
transfer RNA (tRNA)
in tRNA, triplet sequences of nucleotides that are complementary to mRNA codons are called _____
anticodons
the nucleotide structural component of ribosomes is _____
ribosomal RNA (rRNA)
mRNA sequences pass through _____ ribosomal subunits during translation
2
what is the process where DNA gene sequences are copied into mRNA?
transcription
the promoter region is where _____ binds to DNA during transcription
RNA polymerase
the _____ is a short DNA sequence found upstream from the site where transcription of a specific RNA is going to take place
promoter region
what is the typical human promoter region?
TATA box
RNA polymerase is the enzyme that binds to DNA and initiates _____
transcription
RNA polymerase recruits and adds complementary _____ based on the DNA sequence during transcription
RNA nucleotides
RNA polymerase synthesizes a daughter strand of RNA in the _____ direction
5' --> 3'
_____ are extra sequences of nucleotides that are not necessary to create the corresponding protein
introns
_____ are the nucleotides necessary to make the protein
exons
the introns are _____ out by the _____ leaving only the exons behind
spliced, spliceosome
the spliceosome is only found in _____
eukaryotes

(most prokaryotes lack introns (archaea have them))
a 5' _____ _____ and a 3' _____ _____ are post-transcriptional modifications to mRNA, which provide protection against enzyme degradation after the mRNA leaves the nucleus
guanine cap, poly-A tail
translation occurs in the _____, and it is the process through which mRNA codons produce a _____
cytoplasm; polypeptide
what are the 4 distinct stages of translation?
initiation, elongation, translocation, termination
initiation is the stage of translation in which the ribosome binds to the mRNA near its _____
5' end
in translation initiation, the ribosome scans the mRNA until it binds to the _____
start codon (AUG)
the start codon is the codon that signals the start of translation - what is it and what amino acids does it code for?
AUG = methionine
the initiator aminoacyl-tRNA complex, _____, base pairs with the start codon during translation initiation
methionine-tRNA
_____ is the stage of translation in which hydrogen bonds form between the mRNA codon in the A site of the ribosome and its complementary anticodon on the incoming aminoacyl-tRNA complex
elongation
a _____ is formed between the amino acid attached to the tRNA in the A site and the amino acid attached the tRNA in the P site of the _____ during elongation
peptide bond; ribosome
after the peptide bond formation of elongation, a ribosome caries unbound tRNA in the _____ and peptidyl-tRNA in the _____
P site; A site
_____ is the stage of translation in which the ribosome advances three nucleotides along the mRNA in the 5' --> 3' direction
translocation
the unbound tRNA from the P site is expelled at the _____ and the peptidyl-tRNA from the A site moves into the _____ during translocation
E site; P site
a _____ is a group of several ribosomes attached to, and translating, the same messenger RNA molecule
polyribosome
_____ is the stage of translation in which 1 of 3 special mRNA codons, or stop codons, arrives in the A site
termination
_____ do not code for amino acids; rather, they signal the ribosome to stop translation (termination)
stop codons
what are the 3 stop codons?
UAG, UAA, or UGA

(they do not code for amino acids)
what is the machine that carries out translation?
ribosome
the ribosomal _____ binds to the next incoming aminoacyl-tRNA complex
A site
the _____ is the ribosomal binding site for peptidyl-tRNA
P site
the _____ for releases empty tRNAs from the ribosome
E site
a _____ is a unit of chromatin consisting of a DNA strand wrapped around histone proteins
nucleosome
histone proteins are not found in _____ DNA
bacterial
each nucleosome contains _____ histone proteins
9
which histone protein keeps the DNA wrapped around the histone core in a nucleosome?
H1
_____ represents parts of DNA that consist of "loosely-packed" nucleosomes
euchromatin
euchromatin is _____ for RNA polymerases to access and transcribe
easy
_____ represents parts of DNA that consist of "tightly-packed" nucleosomes
heterochromatin
heterochromatin tends to be _____ in transcription
inactive
histones are _____ charged
positively
DNA is _____ charged
negatively
acetylation of histones increases _____ levels and therefore increases _____
euchromatin; transcription
deacetylation of histones increases _____ levels and therefore decreases _____
heterochromatin; transcription
histone methylation _____ DNA transcription levels
decreases
each single strand of DNA is made of a chain of nucleotides, which are linked together by _____ bonds
phosphodiester
the ______ end of DNA has the terminal phosphate group
5'
the _____ end of DNA has the terminal hydroxyl group
3'
origins of replication tend to occur at _____ rich segments
A=T
after helicase unzips DNA during replication, _____ attach to each strand of uncoiled DNA to keep them separated
single-strand binding proteins
_____ creates small nicks within the DNA double helix ahead of the replication fork, to relieve tension created by DNA helicase
topoisomerase
_____ is a subtype of DNA topoisomerase found in bacteria and plants
DNA gyrase
_____ are sequences of repeated nucleotides at the end of a chromosome that don't code anything
telomeres
telomeres are only necessary in ______ organisms
eukaryotic
telomeres are not necessary in prokaryotes because they have _____ chromosomes
circular
_____ is an enzyme that catalyzes the lengthening of telomeres in eukaryotic cells
telomerase
DNA polymerase can only add DNA nucleotides off an existing _____
3' hydroxyl group
_____ provides a 3' hydroxyl group for DNA polymerase to attach new nucleotides to
primase
a _____ is a protein that helps to hold DNA polymerase to the template strand
DNA sliding clamp
_____ is an enzyme that covalently links DNA ends together, which is important for connecting Okazaki fragments
DNA ligase
DNA replication takes place during the _____ phase of the cell cycle
S
if the cell does not meet the criteria for entrance into the S phase, it will remain in _____ (cell cycle arrest)
G0
in prokaryotes, transcription occurs in the _____ (location)
cytosol
prokaryotic core RNA polymerase combines with _____ to form _____, which has the ability to target the promoter region of bacterial DNA
sigma factor; RNA polymerase holoenzyme
what are the 2 types of transcriptional termination in bacteria?
rho dependent, rho independent
an _____ is when a group of related genes are under the control of 1 promoter site, and they function to make sure the cell conserves its resources
operon
the _____ is an inducible operon that aids in control of transcription of lactose metabolizing genes in E. coli
lac operon
an _____ operon is one that is usually inactive, unless it is made to become active
inducible
a gene that is always being transcribed and translated is _____ expressed
constitutively
cAMP is _____ related to glucose levels (lac operon)
inversely
a _____ operon is one that is usually active, unless turned off somehow
repressible
the trp operon is an example of a _____ operon
repressible
in eukaryotes, transcription of DNA into mRNA occurs in the _____
nucleus
which class of RNA polymerase is responsible for transcribing most eukaryotic genes?
RNA polymerase II
in eukaryotic cells, RNA polymerases cannot directly detect and bind to the promoter region - they require the binding of _____
transcription factors
_____ are regulatory proteins that bind to promoter DNA and affect the recruitment of RNA polymerases in eukaryotes
transcription factors
_____ occurs when transcription factors increase rates of transcription
up-regulation
_____ occurs when transcription factors decrease rates of transcription
down-regulation
_____ proteins bind _____, and they work to increase transcription
activators; enhancers
_____ proteins bind _____, and they work to decrease transcription
repressor; silencers
in eukaryotes, the terminator sequence for protein coding genes involves a _____ signal
poly A
in eukaryotes, processed mRNA is able to exit the nucleus and enter the _____, which is where translation occurs
cytoplasm
different mRNA molecules are produced from the same pre-mRNA primary transcript due to _____
alternative splicing
in eukaryotes, ribosomes are composed of small (_____) and large (_____) subunits, which come together to form a _____ ribosome
40S, 60S, 80S
rRNA is synthesized and attached to proteins in the _____, which produces eukaryotic ribosomal subunits
nucleolus
eukaryotic ribosomal subunits are made in the _____, but they are assembled in the _____
nucleolus; cytosol
In prokaryotes, ribosomes are composed of small (_____) and large (_____) subunits, forming a _____ ribosome
30S, 50S, 70S
in prokaryotes, rRNA is synthesized and attached to proteins in a region called the _____
nucleoid
the _____ is a region within prokaryotic cells that contains most of the cell's genetic material
nucleoid
how many different codon combinations are there?
64 (444)
_____ codon combinations code for amino acids
61

(3 of the 64 codons are stop codons, which do not code for amino acids)
when tRNA binds to an amino acid, it is referred to as _____
aminoacyl-tRNA
_____ are enzymes that "charge" tRNAs into aminoacyl-tRNAs
aminoacyl-tRNA synthetases
a _____ mutation occurs when the change in the DNA code results in the codon now coding for a different amino acid
missense
a _____ missense mutation occurs when the mutated amino acid has the same properties as the unmutated amino acid, so the function is often maintained
conservative
a _____ missense mutation occurs when the mutated amino acid does NOT share the same properties as the unmutated amino acid, so the protein function is often changed
non-conservative
a _____ mutation occurs when the codon is mutated to a stop codon
nonsense
_____ are another name for viruses
phages
are viruses living cells?
no
viral coats are made up of a series of protein subunits called _____
capsomeres
in viruses, capsomeres come together to form a protective protein coat called the _____
capsid
a _____ has no cell wall, no plasma membrane, nor any organelles - it only has nucleic acid and proteins
virus/phage
name the two cycles possible for a virus
lysogenic; lytic
in the _____ stage, the viral nucleic acid will insert itself into the host's genome, and it's nucleic acid will be replicated whenever the host's DNA is replicates
lysogenic
the virus is considered _____ and _____ harm the host while in the lysogenic stage
dormant; does not
in the lytic cycle, a virus takes over the _____ and _____ harm the host
host cell's machinery; does
viruses exist as both _____ and _____ viruses
DNA, RNA
a _____ is a virus that stores its genetic material as RNA; therefore, they infect host cells with RNA
retrovirus
retroviruses carry an enzyme called _____, which allows them to convert their RNA into complementary DNA
reverse transcriptase
HIV is a common example of an RNA _____, which carries the enzyme _____
retrovirus, reverse transcriptase
the host cells affected by HIV are the _____ cells
T helper (CD4)
bacteria are asexual, and they reproduce via _____
binary fission
bacteria increase their genetic diversity via _____
horizontal gene transfer
in _____ gene transfer, genes are not being passed from parents to offspring - they are being passed within a generation
horizontal
what are the 3 methods by which bacteria can accomplish horizontal gene transfer?
conjugation, transformation, transduction
_____ is the process where bacteria transfer DNA between each other via a cytoplasmic bridge called a pili
conjugation
a _____ is a small ring of DNA that carries accessory genes separate from those of the bacterial chromosome
plasmid
a _____ is a tube made of protein that is used to pass messages from one bacteria to another during conjugation
pili
the _____ is a special plasmid that contains the necessary DNA for producing a pilus
F plasmid
_____ occurs when a bacterial cell takes up extracellular DNA from it's environment and incorporates it into their chromosome
transformation
if a bacterial cell is able to take up extracellular DNA through transformation, it is referred to as _____
competent
for experimental purposes, bacteria can be made competent in a lab via _____
electroporation
______ is when brief electrical impulses are applied to a cell membrane to create temporary holes through which foreign DNA can pass
electroporation
_____ occurs when virus particles transfer bacterial DNA between different bacterial hosts
transduction
transduction occurs when a bacteriophage infects a bacterium and enters the _____ cycle
lysogenic
a _____ is a virus that infects bacteria
bacteriophage