C2: Molecular Biology Flashcards
Class 2
what is a point mutation?
single base pair substitution
what is a gene rearrangement?
how many types of gene rearrangements are there?
add, delete or move nucleotides around
- 5 types
what is a transition mutation?
- what does it effect?
- what kind of mutation is it?
- when you pair one pyrimadine with another pyrimadine (or purine w purine)
- effect on nucleotide
- point mutation
what is a transversion mutation?
- what does it effect?
- what kind of mutation is it?
- when you swap one of the pyrimidines for one of the purines (or vice versa)
- effect on nucleotide
- point mutation
what is a nonsense mutation?
- what does it effect?
- what kind of mutation is it?
- what happens if this mutation happens early in the protein coding region?
- a codon is changed to a stop codon
- effect on AA
- point mutation
- the protein will be severely shortened
what is a missense mutation?
- what does it effect?
- what kind of mutation is it?
- codon is changed to a diff codon, one AA is switched to another
- effect on AA
- point mutation
what is a silent mutation?
- what does it effect?
- what kind of mutation is it?
- codon is changed to a diff codon, no change in AA bc genetic code is degenerate (ex: GGU to GGG, both still code for glycine)
- effect on AA
- point mutation
what is a conservative point mutation?
a type of missense mutation that leads to little change
what is a conservative point mutation?
- what type of point mutation is it?
- does this change the protein structure/ function?
- AA is changed to a diff but similar AA
- type of missense mutation
- no
what is an insertion mutation?
- what type of mutation is this?
adds nucleotides, can shift reading frame or will not if there are 3 insertions
- gene rearrangement
what is a deletion mutation?
- what type of mutation is this?
deletes nucleotides, can shift reading frame or not if there are 3 deletions
- gene rearrangement
what is an inversion mutation?
- what type of mutation is this?
chromosome section is flipped
ex: if the code is FED, it is flipped to DEF
- gene rearrangement
what is an amplification/ duplication mutation?
- what type of mutation is this?
chromosome section is duplicated, increases copy #
ex: if gene 1 has 2 copies, after amplification/ duplication it will have 3 copies
- gene rearrangement
what is a translocation mutation?
- what type of mutation is this?
chromosome segment is swapped w another (non- homologous) chromosome
- gene rearrangement
in DNA replication, it is a ____ process that requires a ____ and a ____. Polymerization happens in the ____ direction and is read in the _____ direction.
semiconservative, template, primer, 5’ to 3’, 3’ to 5’
DNA is held together by a variety of molecular bonds. which of the following types of bonds is NOT found in a molecule of double stranded DNA?
a. covalent
b. hydrogen
c. N- glycoscidic
d. peptide
e. phosphodiester
D
what is the function of helicase?
unwinds DNA (which causes tension), uses ATP
what is the function of topiomerase?
decreases tension
what is the function of ssBP?
stabilize ss DNA that was caused by unwinding
what is the function of primase?
build RNA primer, it is an RNA polymerase enzyme
what is the function of DNA polymerase?
replicates, proofreads, edits DNA, removes primer, actually builds DNA
what is the function of ligase?
links fragments of DNA called Okazaki fragments
are okazaki fragments present on the leading or lagging strand of DNA?
leading strand
what does prokaryotic replication look like?
- what shape is the bacterial genome?
- what is he chromosome made of?
- theta because of one origin of replication per chromosome
- circular and contains one chromosome
- dsDNA
what does eukaryotic replication look like?
replication bubbles up and down linear chromosomes
in prokaryotes,
what is elongation?
- what direction is it in?
- is DNA polymerase 1 fast or slow in this process?
- what about DNA polymerase 2?
- polymerase activity, elongates and builds DNA
- 5’ to 3’
- slow
- fast
in prokaryotes,
what is proofreading?
- is DNA polymerase present in this process?
- what about DNA polymerase 2?
- 3’ to 5’, exonuclease goes backwards to fix mistakes by cutting out nucleotides
- yes
- yes
in prokaryotes,
what is repair and primer removal?
- in what direction does this happpen?
- is DNA polymerase present in this process?
- what about DNA polymerase 2?
- exonuclease removes a mistake on the primer
- 5’ to 3’
- yes
- no
in prokaryotes,
where is DNA polymerase 1 located?
- what about DNA polymerase 2?
- starts at the primer
- takes over wherever DNA pol 1 leaves off
in prokaryotes,
what happens to mRNA?
it is NOT processed
what is the central dogma?
- what happens between each one?
- what happens in the reverse of the first step?
DNA > RNA > Protein\
- DNA > RNA: transcription
- RNA > Protein: translation
- RNA > DNA: reverse transcription
what enzyme allows reverse transcription to happen?
- what does it make?
- ____ doesn’t contain any ____ so genes are ____ and easier to work with in the lab
- reverse transcriptase
- makes complementary DNA (cDNA)
- cDNA, introns, shorter
what is the first step of DNA transcription?
- where does it start?
- what enzyme helps with this and what does it do?
- what happens after this?
- what is the DNA strand that this occurs on called?
initiation
- promoter
- RNA polymerase, binds to template strand on 3’ end
- RNA polymerase starts making RNA at the start site
- template, noncoding strand, antisense strand, transcribed strand
what is the 2nd step of DNA transcription?
- what enzyme is moving along the template strand?
- what direction is it moving?
- what is coming out of this enzyme?
- what does this mean for the coding strand?
elongation
- RNA polymerase
- to the right, 3’ to 5’
- RNA transcript that is 5’ to 3’ and contains a nucelotide (ex CAT) which is transcribed to its RNA sequence (ex: GUA)
- it codes for the RNA sequence from the template strand (ex: GTA)
what is the last step of DNA transcription?
- what strand does it happen on?
termination
- RNA polymerase stops at the termination signal and dissociates, RNA is released
- coding strand, sense strand
what are the similarities between DNA replication and DNA transcription in regard to:
- requires template?
- driving force?
- building direction?
- yes
- removal and hydrolysis of pyrophosphate (PPi)
- 5’ to 3’
what are the differences between DNA replication and DNA transcription in regard to:
- requires primer?
- does polymerase repair?
- starts at?
- stops?
- R: yes, T: no (promoter, not primer)
- R: yes, T: no
- R: origin of replication, T: start site
- R: when fragments overlap and all DNA has been replication, T: termination signal
where does transcription occur in eukaryotes?
- prokaryotes?
- do transcription and translation occur simultaneously?
- nucleus
- cytoplasm
- only in prokaryotes
both prokaryotes and eukaryotes have ____ DNA
double stranded
what is mRNA?
read by ribosomes, template for making proteins
what kind of mRNA is monocistronic? what does this mean?
what kins of mRNA is polycistronic?
what does this mean?
- eukaryotic
- there are as many different mRNAs as there are proteins
- prokaryotic
- codes for more than one polypeptide
what is a 5’ cap?
a tag on the mRNA of eukaryotes that is stuck on the 5’ end of the mRNA and is essential for translation and preventing digestion of the mRNA by exonucleases
what is a 3’ poly A tail?
a tag on the mRNA of eukaryotes that is stuck on the 3’ end of the mRNA and prevents digestion of the mRNA by exonucleases
what is rRNA?
major component of ribosome
what is tRNA?
- where does it bind the AA?
- what enzymes do this?
- how is it decided which AA will be brought into the mRNA
binds AA’s and brings them to the ribosome
- 3’ end
- aminoacyl tRNA synthetases, they pair an AA w a tRNA
- by the 3 base pair anticodon that is complementary to the mRNA codon (IF CONFUSED SEE SLIDE * Translation Machinery: tRNA *)
what is tRNA loading/ amino acid activation?
when an AA is attached to its tRNA molecule
what is siRNA?
- what falls under this category?
small interfering RNA
- mRNA, tRNA, rRNA
what is hnRNA?
- where can this type of RNA be found?
heterogeneous nucelar RNA, precursor to mRNA
- only in the nucleus
what is the small ribosomal subunit in prokaryotes?
- eukaryotes?
- 30s
- 40s
what is the large ribosomal subunit in prokaryotes?
- eukaryotes?
- 50s
- 60s
what is the total ribosomal in prokaryotes?
- eukaryotes?
- 70s
- 80s
are eukaryotic and prokaryotic translation different? if so, how?
mostly same steps BUT prokaryotic translation happens on 70S ribsosome, eukaryotic on 80S
what is the first step in RNA translation called?
- what is the first step?
- what is the name of the site in which this happens on the mRNA?
- where does assembly happen?
- what goes into this site?
initiation
- assemble ribosome
- APE (but it is assembled backwards on the mRNA) and stands for:
A: aminoacyl
P: peptide
E: exit
- P site
- tRNA- Met goes into the P site
during RNA translation, what are the sites that methionine can occupy on the ribosome?
A or P site
what is the second step in RNA translation called?
- what is the first step?
- second step?
- third step?
- this process ____
elongation
- tRNA AA#2 goes into the A site
- peptide bond is formed between the Met and AA#2
- ribosome shifts 3 nucleotides AKA 1 codon
- repeats
what is the third step in RNA translation called?
- how is the mRNA read?
- what direction is the peptide chain made?
- how does this process end?
- what are the 3 stop codons?
termination
- 5’ to 3’
- N terminus to C terminus
- ribosome dissociates and peptide is released
- UGA, UAG, UAA
(u go away, u are gone, u are away)
what is a nuceloside made up of?
a 5C sugar and an aromatic base
what does truncated mean?
smaller/ shortened
in eukaryotes, 1 molecule of ____ makes ___ ATP.
glucose; 30
how many hydrogen bonds does C-G contain?
A-T?
3; 2
is there proofreading in both DNA replication and transcription?
no, only in DNA replication
what does hemizygous mean?
- it is often used to describe ____ genes in ____
- ____have ____ chromosomes and are NOT ____
a diploid individual who has only one member of a chromosome pair rather than the usual 2
- X linked; males
- females; 2 X, hemizygous
what are homologous chromosome pairs?
contain the same genes in the same order but may have different alleles of the same genes
in the human karyotype, chromosomes are in order from ____ to ____
- the last chromosome pair is the ____ chromosome, ____ or ____
- ____ chromosome is similar in size to chromosome ____ (____), and the X chromosome is 3 times ____ and similar in size to chromosome ____.
1 (largest); 22 (smallest)
- sex; XX; XY
- Y; 19; small
- larger; 7
x chromosome inactivation and ____ are mediated by ____
genetic imprinting; epigenetics
true or false:
genomic components include genes that code for proteins and genes that do not code for proteins
true
true or false:
genomic components include large regions with no known function
true
true or false:
genomic components include repeating sequences
true
what is an epigenetic modification?
modifications to DNA that regulate whether genes are turned off or on
what are the 3 types of epigenetic control?
- DNA methylation
- histone modification via acetylation
- RNA interference
- what is DNA methylation?
- can prokaryotes or eukaryotes do this?
- what does it do?
- histone acetylation?
- can prokaryotes or eukaryotes do this?
- covalently modifies DNA by adding a methyl group
- both
turns gene expression off - turns gene expression on
- only eukaryotes, prokaryotes supercoil their genome
transcriptionally active parts of the genome have ____ levels of DNA methylation and ____ levels of histone acetylation. what about inactive parts of the genome?
- low; high
- opposite, high and low
can a single gene only be regulated by a single type of epigenetic modification or various?
various
what is methylation?
an epigenetic modification that silences genes
to silence gene expression, ____ can be bound by interfering ____ and targeted for ____.
mRNA; RNA; degradation
histone acetyltransferases upregulate ____
gene expression
the lac operon is ____ since the enzymes it codes for are part of the ____
inducible; lactose catabolism
gene expression is influenced by how DNA is ____
- it can do this in 2 ways which are…
- packaged in chromosomes
- euchromatin: loosely packaged
- heterochromatin: densely packaged
- euchromatin: loosely packaged
the way that DNA is packaged is controlled by ____
methylation
X chromosome inactivation is an example of ____
methylation
methylation can lead to deamination which leaves behind a ____, methylated cytosines are therefore prone to ____
thymine base; mutations
what does a permease protein do?
- what gene codes for it?
- transports lactose into the cell
- Y genes
what genes code for the lac operon?
A, Y and Z genes
what does a CAP protein do?
- what codes for it?
- helps turn the lac operon on when lactose is present
- CPR gene
what gene(s) code for histone acetylation?
I
bacteria methylate ____ nucleotides via the enzyme ____
adenine; DNA adenine methylase
eukaryotes methylate ____ nucleotides in ____ by a family of DNA ____ enzymes
cytosine; CpG motifs; methyltransferase
both prokaryotes and eukaryotes methylate ____ nucleotides
thymine
the trp operon codes for…
mediate tryptophan biosynthesis or anabolism, it is anabolic
the lac operon is ____
catabolic
post translational modifications of a protein can involve 3 things…
- covalent linkage of phosphate or carbohydrate groups
- cleavage of zymogens to turn inactive proteins into active proteins
- ensuring the protein is folded correctly (this is mediated by a chaperone)
out of the following options, which would cause a downstream response within a pathway and why?
- double stranded RNA
- single stranded DNA
- single stranded RNA
- yes bc its degraded by RNA interference and is not considered normal
- yes bc ssDNA is very unfavorable
- no bc most RNA molecules are single stranded
the lac operon promoter has a binding site for…
CAP-cAMP and RNA polymerase
