Molecular Exam Flashcards
lectures
what is a palindromic/ inverted repeat
a single stranded sequence of nucleotides followed downstream by its reverse compliment
on its own what is a palindrome
a sequence that is read the same way in either direction
what is non palindromic inverted repeat
a repeat that is not palindromic because it is interrupted
what is another name for a mirror repeat?
hairpin loop or cruciform
what forces does a cruciform repeat have
hydrophobic interactions (double stranded)
what type of duplex is not possible for RNA. why
B-type duplex because of steric crowding
what helical structure does RNA form
A form
what does a RNA sequence encode for
protein to serve as a binding site for single-stranded binding proteins or interacting RNAs
what are secondary structures
helices that create functional motifs on their own and function as switches that alter the accessibility of constituent sequences
what are tertiary structures
multiple secondary structures that form higher-order (tertiary) motifs that function as catalysts, ligand-binding domains, switches, and environmental sensors
what is the secondary structure of tRNA
partially double helical single-stranded regions with loops that form complicated structures
what functions do the loops have in tRNAs
contains anti-codons and carries amino acids
what is a pseudoknot
an element where the first and third bond and the second and fourth bond
what happens more frequently in RNA than in DNA
non-watson-crick base pairing
what are very modifiable
ribonucleosides
what is a genome
the complete haploid genetic complement of the typical cell
what is genomics
the study of DNA at the genome level
what is the E. coli genome like
has 4.6x10^6 base pairs and codes for 3,000 different proteins
how mant sets of chromosomes are in haploid, diploid, and polyploid
haploid - 1 set
diploid - 2 sets
polyploid - many sets of the same chromosomes
what does the c-value refer to
the total amount of DNA in an unreplicated haploid or gametic nucleus of an organism (refers to the haploid size)
what does the g value refer to
the number of protein-coding genes
what is complexity
the number of instructions necessary to have an organism
what is the c-value paradox
genome size does not correlate with the organismal complexity in eukaryotes
what is the number of protein-coding genes in Homo sapiens
19,900 (~20,000)
what is the number of protein-coding genes in S. cerevisiae
6,600
what is the number of protein-coding genes in E. coli
4,300
what are tandem clusters
long DNA regions with short sequences that repeat in tandem
what are transposable genetic elements
described DNA sequence that can occasionally move (transpose) from one position on a chromosome to another
who discovered transposable elements
Barbara McClintoele in 1940’s from corn study
what are the two basic types of transposable elements in the human genome
class 1 - retrotransposons
class 2 - dna transposons
what is a retrovirus
a retrotransposons RNA based virus
what type of polymerase do retroviruses possess
RNA-dependant DNA polymerase with reverse transcriptase (allows them to synthesize DNA from RNA transcript)
what is the difference between DNA and RNA
DNA -> DNA = DNA polymerase
DNA -> RNA = RNA polymerase
how are retrotransposons transposed
through an RNA intermediate
what do retrotransposons and retroviruses have in common
they both have the gene to make DNA from RNA (no longer a virus)
what retrotransposons are currently transpositionally active
Li line and ALV sine retrotransposons
what is a gene
the locatable region of genomic sequence, corresponding to unit of inheritance
what is a locus
specific location of gene/ DNA sequence on chromosome
what is an allele
variant of DNA sequence at given locus
what are genes like in prokaryotes
regular coding sequences where transcript happens at same time as transcription
what do most eukaryotic genes have their coding info interrupted by
non-coding sequences called introns. coding sequences are then called exons
what is an intron present in and absent from
present in gene, absent from mRNA
introns have to be removed for what to occur
for mRNA to be translated to produce protein
what is the genome size in humans
3.1648 x 10^9 bp
what is the average size gene
~50,000 bp
what is the size of the average intron
~3,330 bp
what is the size of exons
~100 bp
what is the size of coding sequences
~2,000 bp
how long is human DNA
~1.8m
how long is the largest human chromosome
~3x10^8 bp
what is a chromatin
the complex of DNA and protein found in eukaryotic cells
what is the H1 unit of DNA packaging
linker histone outside the nucleosome
in a cell at the mitotic stage, right before cell division, how many copies of any particular gene except for the sex chromosome in men?
4 - homologous chromosomes
what is the structure of nucleosome core particles
146 bp of DNA wrapped in 1.67 left-handed superhelical turns around the histone octamer, consisting of 2 copies each of the core histones
how are adjacent nucleosomes joined
stretch of free DNA termed “linker DNA” (rage of 20-100 bp)
what do N-terminal histone tails do
contact DNA in the phosphodiester backbone and minor grooves
how many pairs of chromosomes do women have
23
what is the structure of eu chromatin
chromosomes are outside and are organized into factors
what is heterochromatin
regions of chromatin that remain highly condensed and transcriptionally inactive during interphase
what is karyotyping
looking to see if you have any abnormalities in your genome
how do you see large mutations in kayrotyping
banding
what is metaphase
two identical copies of one chromosome
what chromosomes are homologous and which one are not
sex chromosomes are NOT homologous and the other 22 pairs are homologous
what is a karyotype
the number, sizes, and shapes of the metaphase chromosomes
how is DNA packaged in eukaryotic cells
in the form of chromatin
what do deletions of histone tails result in
transient unwrapping of DNA, an increase in nucleosome sliding rate, and a decrease in nucleosome stability
what are the core domains of histones formed by
three a-helices connected by short loops, mainly composed of positively charged residues
how many histone tails are there per nucleosome
ten histone tails which contain approx. 30% of total histone mass
what does the flexibility of glycerines do
facilitates change in the local curvature of nucleosomal DNA
what is nucleosome sliding
a process in which DNA gradually repositions itself around histones, while maintaining contact with the histone core.
what do histone tails have a high degree of
conformational flexibility
what is one of the most prevalent modes of interaction between histone tails and DNA
insertion of arginine and, in some cases, lysine side chains into the DNA minor and major grooves serving as anchors
what does ATP-dependant chromatin remodelling complexes do
move, eject, or restructure nucleosomes
what does trans regulations mean
there is an outside regulating factor that is not in the chromatin
what does cis regulations mean
the process is intrinsic to the chromatin
what are the three processes that histones can go through at numerous sites
acetylated, methylated, and ubiquitylated
where are modifications most common
N-terminal
what is acetylation associated with
gene activation
what is neutralized upon acetylation
positive charge on lysine
what does not eliminate the positive charge on lysine
mono-, di-, or trimethylation
what 4 amino acids are histone tails particularly rich in
G (glycine), K (lysine), S (serine), R (arginine)
what happens when dna is methylated
inactivation
what happens when histone proteins are methylated
activation
what is genomic imprinting
an epigenetic phenomenon in which a segment of DNA is imprinted, or marked during egg or sperm formation in a way that results in the monoallelic expression of a gene depending on the parental origin of throughout the life of the individual who inherits that DNA
who is always silenced in dwarf genes
the mother
what are glucocorticoids (GCs)
steroid hormones widely used for treatment of inflammation, autoimmune diseases, and cancer
what does histone acetylation influence
chromatin structure and transcription through recruitment proteins
what is a histone code
different patterns of histone modifications are ‘read” by various proteins to produce an effect on gene expression
what is a bromodomain
an approximately 110 amino acid protein domain that recognizes acetylated lysine residues, such as those on the N-terminal tails of histones
what is type 1 topoisomerase activity
catalyze changes in DNA topology via transient single-stranded breaks in DNA
what is type 2 topoisomerase
catalyze changes in DNA topology via transient double-stranded breaks in DNA. ex, Gyrase
what is SSB activity
single-stranded DNA binding protein
what is the SSB activity complex for DNA replication of eukaryotes called
replication protein A (RPA)
what is a primosome
a complex where DnaG is bonded to DNA helicase
how is primase activated
by the helicase where it then synthesizes a short RNA primer
what do polymerase detect
whether or not a mistake was made in DNA replication
what happens when polymerase detects a mistake
a different type of domain is invoked where the polymerase can go in reverse
how is proofreading in exonuclease activity is read
3’ - 5’
can a ligase produce phosphates
no
what is a klenow fragment
– a proteolytic product of E. coli DNA Polymerase I which retains polymerization and 3’→ 5’ exonuclease activity, but has lost 5’→ 3’ exonuclease activity
how many nucleotides in distributive synthesis
ten nucleotides
how many nucleotides in processive synthesis
thousands nucleotides
what are internal RNA primers removed by
exonuclease
what is a telomere
tandem repetitive sequence at the ends of linear chromosomes in humans
what is telomerase
reverse transcriptase. RNA dependant DNA polymerase
what does telomerase do
carry its own template and copies that instead of other templates.
what is a template
template is something that codes for a specific pattern
what does a reverse transcriptase carry
its own RNA sequence with it and copies that when it extends the end of the 3’ hydroxy.
what subunit of Core POL III has polymerase activity
α subunit (encoded by the dnaE gene)
what Core POL III subunit has 3’-5’ exonuclease activity
ε subunit (dnaQ)
what does the θ subunit of Core POL III do
stimulates the ε subunit’s proofreading and maintains the heterodimer structure
how many subunits does 3 B clamps have and what are the function(s)
2 subunits - sliding clamp(s)
what is Pol α responsible for
the initiation of DNA at origins of replication (on both the leading and lagging strands) and during the synthesis of Okazaki fragments on the lagging strand
what are the 4 subunits in pol α
catalytic subunit POLA1
regulatory subunit POLA2
small primase subunit PRIM1
large primase subunit PRIM2
what happens once primase has created the RNA primer
pol α starts replication elongating the primer with ~20 nucleotides
eukaryotes do not have what type of clamp and what is it replaced with
do not have beta clamps, have PCNA instead
what are mutations
changes in the genetic material (sequence) that can be irreversibly passed from cell to cell and/ or from parent to offspring
what are mutagens
a physical or chemical agent that permanently changes genetic material, usually DNA, in an organism
what are the two types of mutations
point (gene level) mutations and large scale (chromosomal level) mutations
what is a point mutation
small-scale mutation that causes nucleotic substitutions, insertions, or deletions in DNA or RNA sequence
what does the term frameshift mutation indicate
the addition or deletion of nucleotides (that change the reading frame)
what is a transition
a pyrimidine to a pyrimidine or a purine to a purine
what is a transversion
a switch in base pairs or pyrimidine to pyrimidine/ purine to purine
what is a mutation
two strands separate and the incorrect pairing is fixed in the second generation. this second generation is the mutation
what is a lesion
a mismatch in base pairing that causes a mutation (ex. A - G)
what are the 3 stop codons
UAA, UAG, UGA
what are the three types of point mutations
silent, missense, nonsense
what is a frameshift
change of reading frames
what is the start codon that allows us to figure out what three bases give us a codon
AUG
what do insertions of 3 do
they do not change the reading frame
what is a missense
a change in amino acids
what is a nonsense
a base substitution mutation that changes the codon for the amino acid into a stop codon
what do you call the mutations that convert a codon for an amino acid into a stop codon?
nonsense
what are the three types of single chromosome mutation
deletion, duplication, inversion
which one of our chromosomes has more telomeres than it should and has telomeric sequences in the middle where a centromere has atrophied
chromosome 2
what are the 4 damage repair pathways
mismatch repair
base excision repair
nucleotide excision repair
recombination repair
what is a molecular lesion
damage to the structure of a biological molecule such as DNA, RNA or protein
what is a mutagen
chemical or physical agent capable of inducing changes in DNA called lesions and ultimately mutations
what is a mutation
changes in the genetic material (sequence) that can be irreversibly passed from cell to cell and-or from parent to offspring
what can mutagens be
physical, chemical, or biological
what does methylation of cytosine give
uracil and damage to the base
what is deprivation
if you hydrolyze the base out, there is nothing there anymore
what is ROS
reactive oxygen species
what is alkylation
addition of CnH2n+1
what is an adduct
a product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all components
what does cross linking do
links 2 bases together
what is difference between genotoxic and cytotoxic
cytotoxic is used to kill cells and genotoxic is used to kill genomes
what initiates melanin production
fragment of DNA with the crosslink
what does a tan mean
tan means your system is repairing the damaged crosslinked region
what does CH3 mark
the parental strand in bacteria
what is the function of MutS
binds mismatch
what is the function of MutL
links MutH and MutS
what is the function of MutH
binds 7-meGACT
what is the function of DNA ligase
binding DNA fragments together to form 2 new daughter DNA strands. It does so by facilitating the formation of a phosphodiester bond between two DNA monomers at a time
what does AP endonuclease do
enzyme that breaks phosphodiester bonds in DNA to repair damage and is found in both prokaryotic and eukaryotic organisms:
function of UrvA
processes and recognizes DNA lesions
function of UvrB
interacts with both the UvrA and UvrC proteins in addition to binding, bending, and incising DNA.
functions of UvrC
cleaving the nucleotides either side of the DNA damage
function of UvrD
functions within the TCR by using its inherent ATPase activity for backtracking the stalled RNAP without displacing it altogether
what is a consensus sequence
a nucleotide or amino acid sequence consisting of the residues that most commonly occur at each position in a set of similar sequences
what happens during the initiation phase of transcription
RNAP/ σ recognizes the promoter and starts the transcription
what happens during the elongation phase of transcription
the RNA strand is continuously growing (50-70rNTPs /s)
what do RNAP core enzymes do
carries out all steps of transcription except promoter-specific initiation that requires an accessory σ factor
what happens during the termination phase of transcription
the rNAP stops synthesis and the nascent RNA is separated from the DNA template
what is the ρ factor (Rho factor)
a hexameric helicase involved in the termination of transcription of some genes
what are the 5 RNA polymerases in eukaryotes and what do they do
1) RNAP I: makes rRNA in the nucleolus
2) RNAP II: makes mRNA and sRNA in nucleoplasm
3) RNAP III: makes rRNA and tRNA in nucleoplasm
4) mRNAP: mitochondria
5) cRNAP: chloroplast
how much of each type of RNA are contained in a cell?
- about 75% rRNa
- about 15% tRNA
- less than 10% mRNA
what does tRNA code for
methionine and its start codon
can you only base pair with one thing at a single time
no, possible to base pair with two things at once
what is the wobble hypothesis
codon variation for a particular amino acid is greatest in the third position
what did crick and brenner propose about a single tRNA molecule
can recognize codons with different bases at the 3’- end owing to non-Watson-crick base pair formation with the third base in the codon-anticodon interaction
what does the term wobble hypothesis indicate
that a certain degree of flexibility or “wobbling” is allowed at this position in the ribosome
how many tRNAs recognize how many codons
~40 tRNAs recognize 61 codons
in order for translation to happen what do we need
polypeptides, tRNA with amino acid, ribosomes, and aminoacyl-RNA-synthetase
what does aminoacyl-RNA-synthetase do
catalyzes attachment of amino acids to tRNA
what is called the second genetic code
the ability of aminoacyl-tRNA synthetase to recognize appropriate tRNA
what is a ribosome
the site where translation takes place
what are ribosomes a mixture of
RNA and proteins on the end
in E. coli, how much of its dry weight is ribosomes
25% (around 15,000)
what is a polyribosome (polysome)
a complex of an mRNA molecule and is translated by multiple ribosomes to form polypeptide chains during translation.
when does translation of mRNA begin
on ribosomes that are free in the cytosol
where does a lot of synthesis happen
in the rough endoplasmic reticulum
what are the three sites on a ribosome and what do they do
- A.site (acceptor site): holds the newest tRNA carrying the next amino acid to be added to the chain
- P.site (peptidyl-tRNA site): holds tRNA carrying growing polypeptide chain
- E.site (exit site): empty tRNA leaves ribosome
what is the transcription factor II D (TFIID)
a general transcription factor that participates in the RNA polymerase II preinitiation complex
what does the TFID complex do before the start of transcription
binds to the TATA box in the core promoter of the gene
what is TFIID composed of
TBP and several subunits called TATA-binding proteins associated factors (TBP-associated factors (TAFs))
what is TATA-binding proteins (TBP)
is a general transcription factor that binds specifically to a DNA sequence called the TATA box
what is BRE
TFIIB recognition element
what percent of human promoters have TATA boxes
10-20%
what occurs concurrently
transcription and translation
where does transcription happen
in the cytoplasm
what is heterogeneous nuclear RNA (hnRNA)
primary transcript - what comes out of the transcript machinery
what happens due to heterogenous nuclear RNA (hnRNA)
puts on a 5’ cap, removes introns and splices together exons, then puts on poly-A this
where does transcription happen in eukaryotes
nucleus
what does 5’ capping (Pol II) do
cap blocks the 5’ end of mRNA and can be methylated at several positions
what does 7-methylguanylate residue do
attaches to the first nucleotide of the pre-mRNA by a 5’-5’ linkage
what are the 4 functions of 7-methylguanylate residue
- enable transport of mRNAs out of the nucleus
- protect mRNA from degradation
- enhance efficiency of splicing mRNAs
- enhance translatability of mRNAs
what do most eukaryotic mRNAs have
chain of AMP residues about 250 nucleotides long at their 3’ ends
what is polyadenylation
the process of adding poly (A) to RNA
when is poly (A) is added and by what
added post-transcriptionally by polyadenylate (poly (A)) polymerase
what is the polyA signal and what does it do
5’-AAUAAA-3’
signal to remove part of the transcript
what is the function of poly(A)
protects from degradation and is involved in the translation of mRNA
the ends of nuclear introns are defined by what
the GU-AG rule
introns often begin and end with what
begin with GU and end with AG (GU 5’, AG 3’)
what is a lariat
a form that an intron is removed in
what is a splicosome
a large complex molecular machine found primarily within the cell nucleus of eukaryotic cells
what are spliceosomes composed of
5 small nuclear RNAs (snRNAs) and a range of associated protein factors
what creates a snRNP
an RNA-protein complex where snRNAs and protein factors are combined
what does snRNP so
identify splice site, branch site and 3’ splice site. the 3’ gets cut and lariat is made
what does DNA polymerase need to work and why
Mg - extremely important and can change the fidelity
what will DNA polymerase never get
base pairing or phosphodiester bonds
what can DNA polymerase never do
initiate a new strand
what is the easiest genome to replicate
a circular genome found in mitochondria
what is an origin of replication
a bubble formed due to circular DNA duplex having no beginning or end
what happens in DNA replication in a circular genome
both strands are replicated and at the end, ligase joins the newly synthesized strands
what is an Okazaki fragment
a short segment of DNA that is synthesized discontinuously during DNA replication on the lagging strand:
what does helicase do
melts DNA and opens up DNA duplex
what does topoisomerases do
untying knots and unwinding DNA
what is helicase activity
will load leading or lagging strands and will use ATP hydrolysis to break up H bonds
