Nucleic Acids Flashcards
What is the monomer of a nucleic acid
Nucleotides
Are proteins usually acidic or basic
Basic
Are Nucleic acids acidic or basic
Acidic
What are the types of nucleic acids
DNA and RNA
What is the function of nucleic acid
To store genetic information and to retrieve genetic information
What are some modified nucleotides
ATP, NADH and cAMP
What makes up the sugar of a nucleotide
Phosphate and a pentose (furan)
Are nucleic acids negatively charged
yes
What is the difference between ribose and deoxyribose
Deoxyribose has a H in 2’ for deoxyribose and OH in 2’ for ribose
Do we have a furan in ribose
Yes
What carbon does the phosphate bind to
the 5’ and 3’ carbon
What are the shapes of nitrogenous bases
Pyramidine and purine
How many rings does pyramidine have
1
How many rings does purine have
2
What does the 1’ carbon bind to for pyramidine
The carbon 1 (N carbon)
What does the 1’ carbon bind to for purine
The NH carbon
What are the members of purines
A (adenine) and G (Guanine)
What are the members of pyramidine
C (Cytosine), Uracil and Thymine
What base is exclusive to DNA
Thymine
Are Nucleic acid bases hydrophobic or hydrophillic
Hydrophobic
What is resonant (in chemistry)
Electron ring causing partial double bond
What wavelength can Nucleotides absorb easily
260nm wavelength (UV light can be absorbed)
What is a nucleoside
Nucleotide with no phosphate
What is the nomenclature for nucleoside purines
add Osine
What is the suffix for for nucleoside pyrimidines
add Idine
What do you do for nucleotide purines
add ylate
What do you do for nucleotide pyramidines
idylate
What is deoxyribonucleotides
deoxyribonucleoside monophosphate
How are bases modified so transcription of Dna into RNA terminates
Through methylation
Are there modified nucleotides
yes
How are nucleotides joined
Phosphodiester bonds
What is the direction of the DNA
From the Phosphate end to the 3’ end
What is the backbone made of
Sugars and phosphates
What component of DNA is inherited from the parents
The bases
What is the difference between DNA and RNA in terms of structure
DNA is double helix, RNA is single helix
What makes DNA acidic
It is negatively charged
What does phosphate look like in DNA code
P with a circle
What is the primary structure of DNA
Sequence of bases from 5’ to 3’ end
what is the secondary structure
DNA involves 2 strands running in opposite directions (antiparallel)
Do the antiparallel DNA helixes have the same primary structure
No, they have complimentary structures
What is always equal in DNA bases
The sum of purines = sum of pyramidines
Are DNA in cells of the same specimen identical
yes
Does base composition change with age
NO
What did Franklin measure with X rays
DNA helix size and secondary structure
What is transformation
Bacteria changing their own DNA from the environment
What is DNA
The carrier of genetic information
How does DNA associate with each base
Hydrogen bonds
Why does the number of pyramidines = number of purines in DNA
Because of the complimentary nature of double helix structures
What does adenine bond with
Thymine
What does cytosine bond with
Guanine
How many hydrogen bonds are between A and T
2
How many hydrogen bonds are between C and G
3
Are other base pairings possible
Yes, but not as stable
Can purine purine bonds and pyramidine pyramidine bonds occur
No
How is the double helix stabilised
By the base pairs
Is DNA amphiphatic
Yes
Can DNA transcribe into RNA
Yes
What are viruses that infect bacteria
phages
What are viruses made of
50% proteins and 50% nucleic acids
Does virus use their own DNA
No, they use the host cell’s DNA
How was viruses not using their own DNA but using their own proteins proven
Trough radioisotopes of phosphorous (DNA) and Sulphur (proteins)
What is a turn under watson and crick’s model
Right handed (clockwise) helix with a major and minor groove
What does DNA look like on top
Sugars and phosphates on the edge and bases in the middle
Why do we need to have an even diameter DNA
Because it needs to be stable, and if it wasn’t even it would be unstable
What is the humn form of DNA
B form and Z form occasionally
What is a N-O bond
Glycosidic bond
How would we denature DNA
Splitting the strands into two
What happens if denatured dna renatures
Annealed
Can hybrid DNA form
Yes, but only partially
What is hybridisatation
When short DNA sequences or RNA bind to separate DNA sequences
Why are some genes so similar
Because some genes are essential to life
What happens on a macro scale when DNA denatures
Decreasing viscosity
What kind of DNA has higher absorbtion at 260nm UV light than the other
Denatured DNA
What happens when you denature DNA
A hyperchromic (absorbance) shift
What is the melting temperature
Where half of the DNA has denatured
What increases melting point
Long DNA with lots of Cytosenes and Guanines
What base pair usually gets replicated first
the A’s and T’s
What can stabilize the double helix and why
Cations because DNA is negatively charged due to the phosphates
Why does DNA denature at extreme PH’s
Becuase DNA is held with hydrogen bonds which protonise as acids and deprotonise as bases
What bonding force allows denaturing temperatureto be low
Hydrogen bonds
What is a pallindrome in DNA
Inverted repeats
What happens if there are self complimentary sequences
It can form H bonds with each other
How many molecules of nuclear DNA are there per cell
46
What does mitochondrial DNA look like
Circular
What can DNA do in terms of making stuff
Copy itself and transcribe RNA
What is involved in the elongation phase of DNA replication
Synthesizing and attatching the okazaki fragments to the lagging strand with DNA polymerase delta (5’ to 3’ on lagging strand so backwards)
What is the enzyme for polymerizing DNA
DNA polymerase
What is nucleophillic attack
Where the OH donates an electron to the phosphate
Why is magnesium important
Attracts phosphates and aspartines
What direction do we synthesize
5’ (PO4) to 3’ (OH)
Which polymerases the most important to replicate nuclear DNA
Alpha, delta and epsilon
How often do DNA make errors
1 in 1000000000
What happens after polymerization
3’ to 5’ proofreading
What makes the leading strand
DNA polymerase epsilon
Where are the RNA primers
at the end
What are the RNA primers for
to stop the polymerization)
What is the leading strand made of
Continuous strands
What is the lagging strand made of
Okazaki fragments (small little bits which continur into RNA primers sometimes
What synthesises the lagging strands
Delta
What does DNA ligase do
glue 2 okozaki fragments together
What does the primase do
Every okozaki fragment and end of the strands rna primers
What is the gyrase
Cuts the DNA into 2 and relieve contortional stress (prevents dna from overwinding)
What is the RPA protein
Kepps the DNA denatured
What is PCNA
Holds DNA polymerase delta and epsilon onto the template strands
How fast does replication go
200 nucleotides per second
How is nuclear DNA structured
Linearally
WHat do chromosomes have a role of
Faithful transmission and appropriate expression.
What is a combination of DNA an proteins
Chromatin
What do nuclear proteins do
Bind DNA to the nucleus
What are the centromeres
Constricted central region
What are the telomeres
The edges of the chromosomes
What is the shorter chromosome arm called
p arm
what is the longer chromosome arm called
q arm
What happens where there is two chromatids but one chromosome
There are 2 DNA molecules but one centromere
What happens most of the time in chromosomes
only one molecule of DNA
What numbers chromosomes
Size of the condensed chromosomes
What are the different centromere positons from closest to center to furtherst away
Metacentric, submetacentric, acrocentric and telocentric
What type of chromosome is the most stable
Metacentric
What is the haploid numbers
the number of chromosomes from one parent
what is the haploid number for humans
23
What is C
the mass of each DNA molecule
How much does DNA weigh
3.5*10^-12 cells
What is a karyogram
Visual profile of all chromosomes
What is a homologous pairs
the pairs of identical chromosomes
What do the light and dark reigions show
AT and GC pairs
What is a giesma stain
Bind more effectively to A’s and T’s meaning that the pale reigions are C’s and G’s
What are the types of chromatin
Euchromatin and heterochromatin
What chromatin will be used more often
Euchromatin
What are the proteins in chromatin
Histones
What PH is histones
Basic
What are the types of histone proteins
H1 H2a H2b H3 and H4
How long are haploid genomes
2 m
What does DNA wrap around
an octoma of histome
What joins the octoma
the H1 protein
How many octom are there wrapping DNA
2
What does DNA do after it wraps around the 2 octomer
it bends around the scaffold protein
How many proteins are in the nucleosome octomer
2 H2a 2 H2b 2 H3 and 2 H4
What does the chromatosome
the H1 protein
What are genes
Functional units of DNA
where does RNA in the body come from
complement of one of the DNA strands
What percentage of the genes encode protein
5%
What happens when DNA turns into messenger RNA
transmission
What is the coding strand
the strand being converted into RNA, except the T’s become U’s
What does helicase do
It unzips the DNA by breaking H bonds
What phase does DNA replication occur in
S phase
Do we need to replicate histones while replicating DNA
yes
What protein is required to transport histodones to the replication fork
Chromatin assembly factor 1
During the replication of DNA, are all histones transported in DNA replication newly synthesized
no, only some are
How was this experimentally proven
Cells were first replicated using a heavy amino acid base, then when transferred to a light amino acid base and replicated again, the DNA of the cell was at mixed densities as seen with centrifugation
Why are there multiple origins of replication
Due to the DNA being too long for one origin of replication
What do the telomeres have a pattern of
TTAGGG
What elements are needed for a replicated chromosome
Centromere, telomere and arms
What is the order of replication
Telomeres to Centromere
What is chromosome regulation regulated through
Control of location of initiation of replication (origin points), where the leading strand and lagging strand switch
Are origins usually telomeres
No due to origins being rich in Adenine and thymine
What is the ORC protein
A protein complex which recognises the location of DNA replication origins, binds to the origin and separates the strands
Is DNA replication unidirectional in eukaryotic cells
no
What is needed to initiate replication
For origins to be licenced which can only happen once per origin. This means that they are separated and ready for replication. This is the binding of the ORC and recruitment of the helicase
How many proteins are in DNA helicase
6
Why cannot proteins initiate twice
because the helicase hexomer denatures
What can help the ORC find the origin
ATP
What does CDC6 do
It combines with the ORC to be able to recruit the helicase only available in s phase
What does CDT1 do
loop the DNA around and attach DNA to the helicase, finishing the licensing process
What goes away after licensing occues
CDC6 and CDT1
What is DNA polymerase Alpha used for
Initiation of DNA replication at the origin
What happens at the end of replication
3’ overhand
What does telomerase do
Add extra TTAGGG to the end of the DNA after the removal of primers
What does Messenger RNA do
encode proteins
What is the difference in the the backbone of RNA to DNA
RNA has OH meaning it has ribose, but DNA has deoxyribose
Is RNA or DNA more stable
DNA
What is RNA secondary structure like
It can wind back onto itself and can form unique structures because of the single helix
Can RNA form unusual base pairs
Yes, U-U and G=U (GU is weak)
What is a ribozyme
RNA that can catylyse a reaction
What way does the RNA helix go
Clockwise
What are the 2 RNA classes
Coding and noncoding
What does coding RNA do
read and synthesize proteins, use code to make proteins
What is the tRNAs for
Transfer amino acids to ribosome
What is the rRNA for
structures the ribosomes
What is lncRNA
long noncoding RNA
What are most RNA’s used for
Ribosomes
What happens when protein synthesis….
Trnas and mRNA associate with ribosomes
What is the coding RNA
mRNA
What is ribosomes made of by mass
50% rna and 50% rna
What is S (Svedberg unit)
an indication of size due to sedimentation due to centrifuge
What is the ribozyme
28S rna
How many genes is rRNA synthesised from
2 genes with 4 different rRNAs
What is from a separate gene
the 5S rRNA (short one)
What is from the other gene
18, 5.8 and 28S RNA (longer 3)
What is the tRNA strtucture
Amino acids binds to the 3’ end of RNA, the anticodon loop has 3 nucleotides. The anticodon and the 3’ end is specific to which amino acid bonds to it
What is the codon on
mRNA
What is a notable difference in nucleus between females and males
Holds one of the X chromosomes and covers it with lncRNA, genes are only inherited on one x chromosome
What happened first in evolution
RNA
What are regulatory regions important for
control of transcription of rna
What happens if the reg region is close to the transcribe region
promotion
What happens if the reg region is not close to the transcribe region
enhance
What is an exon
directily transcribed into mRNA
what is a promoter
it is at the 5’ end of the transcription region and synthesised rna
What must be made before any proteins can be synthesised
RNA
Can both strands be used as the template
no, only one known as the template strand, aka antisense, the other one is the sense gene or coding strand
What happens when rna polymerises
the triphosphate becomes a phosphate and the OH becomes an OPO4
Does RNA have directionality
yes, from 5’ to 3’
Does initiation of transcription require a primer
no
What happens when RNA transcribes
DNA unwinds, polymerase goes through and preceding DNA reqineds, going backwards relative to the RNA
Where is the transcription start site
just after the promoter most of the time
What does the promoter do
determine template, transcription direction and where the transcription will start
Is the transcription termination site transcribed
yes, but it tells the primer to stop transcribing after
What is the transcription start site denoted as
+1
Is there a 0 for the transcription of RNA nucleotide numebrs
no, just goes to -1, upstream of the start site
Is the coding strand the exact same as the strand of rna
no, there are u’s instead of t’s, troloololoolooloooloolol
Hoe simple are rna polymerases
not simple at all, they have 10 common subunits and 7 unique subunits
What does rna polymerase 2 have
CTD which han be phosphorylated or dephosphorylated
What does the death cap mushroom do
stop transcription of rna
WHat happens first in transcription
polymerase binds
the start site forms a bubble, allowing the RNA polymerase to add rna, what process does this describe?
transcription
What is a nascent RNA
RNA during transcription
What polymerase transcribed genes have a core promoter
RNA polymerase II
What elements are common
TFIIB recognistion, TATA box, initiator element, downstream core promoter element
What is a y
c or t (pyramidines)
what is an R
a or g (purines)
What do tata boxes do
rapidly transcribe genes
What does tbp and tata binding proteins do
bind to the tata box and bends dna
What happens after the dna is bent in transcription
tfiif and polymerase binds to dna
what adds on after
tfiie and tfiih which has helicase activity
what does tfiih do
unwinds the dna
What does the carboxyl terminal end do in polymerase ii
activates and move away from the promoter, takes away the transcription factor and polymerises rna
What is the regulatory promotors function
bind transcription factors
What are econic and intronic sequences
extrons are real rna bits, introns are leftovers
What is the consensus sequence
tells when its cleavaged
When does the RNA get rid ov exxons
when transcription occurs
How does RNA capping work
RNA capping attaches 7-methylguanosine to the 5’ end to the rna. The 5’ cap protects rna from exonuclease. It forms a triphosphate bond
What is the polyadenylaition for
protects RNA from decomposing on the 3’ end
What does the AAUAAA sequence identify in rna
shows cleavage point 10-30 nucleotides ahead
What is at the 5’ end of the intron
GU
What is at the 3’ end of the intron
AG
What is the branch point of the intron
What does a splicosome do
splices exxons and introns and catylyzes the splicing reactions
Why does the intron loop
5’ end of the g nucleotide and the 2’ of the branch point attatch through phosphate
What is a spliceosome
Complex of snRNPs, ENA lariat formed
How does splicing form
2’ OH of A forms covalent bond via nucleophillic attack with 5’P of intron G, then the intermeddiate bits are removed, then it loops
Does splicing of RNA skip exons when it gets spliced together
yes
Do all genes have the same splicing structure
no
Are introns always small
no
What are codons
code what an amino acid is
What states a protein in RNA
3 digit combination of RNA
Does genetic code overlap for proteins
no (DUH)
What does the TRNA do
binds the aino acid
What soes aminoacyl-trna synthetase
Alloes the TRNA to bind to the amino acid
What are the binding sites for trna
E site (exit), P site,(peptide bonds) and A site (Entrance site)
Is mrna in the large or small ribosomal unit
small
What is an APE
A black person troloolooll or the order of the trna’s from entry to exit
WHat attatches to the peptide site
the proteins
What does elongation factor g do
accept the new trna, where the anticodon is the same as the codon for mrna
What is the wobble position
the unusual base pairings for rna
What wobbles
the GU bond
What does not wobble at the 5’ end of the anticodon
A and c
What initiates most proteins
methianine
What dissociates when the met dinds the initiation part of RNA
the initiation factors dissociate
What moves first in ribosomes
large subunit, then small subunit, then exit exits and then the new a enters
What is a stop codons function
Markes as UAA UAG or UGA, the transfer rna has no amino acid attatched meaning that they all exit after no amino acid is found.
How many neuromuscular junctions do muscle fibers have
1
Does a nerve control one muscle fiber
no
What does the number of junctions per neuron tell us about the muscle
lots = big and powerful, few = small and precice
Where do motor neurons come from
straight out the spinal chord
What controls muscle
primary motor cortex and corticospinal tract
What is the upper motor neuron in
CNS
How quick are the lower motor neurons
very
What controls most subconscious actions
reflex
how many synapses is a monosynaptic reflex
2 bc science …..
What are the synapses
sensoryneuron -> motor -> neuromuscular junction
What is the polysynaptic reflex for
it involves modular neurons as well, extra motor neurons
What is the point for PSR (NOT PULSARS)
To make movement inhibitory
What is the fertilised eggs
A zygote
What changes the gene expression of cells
differentiation
What establishes polarity
the egg
What influences gene expression
cell contact, hormones, morphogens
Where is the receptors of hormones
In the nuclear membrane
What can polarity do
It can allow shapes of animals/plants to become distinct
What is needed for different cell types
different transcription factors, meaning there are cell or tissue specific transcription factors
What differentiates with cells to differentiate cell types
difering phenotype
What is pluripotent
Most cells have the same nuclei
do genes change
no
What is special about B cells
they synthesise antibodies , meaning their dna is special
What is beta actin
Cytoskeletal protein, needed for all cells
What does tyrosine aminotransferase do
transfer tyrosine to amino acids
Are genes expressed in all cells
no
What is a sign of differentiation
rapid proliferation
What happens when replicates end
3’ overhang at the ends for stability
What makes DNA more active
increased accessibility
What is less active euchromatin or heterochromatin
heterochromatin
What causes gene expression
proteins
What is DNase 1
Something that allows access to dna
Does DNAse 1 change where it accesses dna throughout the creatures life
yes
What can aceytylisation do to basic amino acids
This neutralises the basic amino acid, detacthing the dna from the histone octomer
What does the HAT do
They add acetyl groups to the histone proteins, decreasing the affinity of histone proteins
What does HDAC do
remove acetyl groups
What makes euchromatin
hyperacetylated regions
what makes heterochromatin
hypoacetylated regions
Where do we modify the histone proteins
at the end
What is methylation, phosphorylation and ubiquination
the other codes for the histone proteins
What can effect from histone modification
Diseases, cancers and neurological disorders
Do we maintain the location of dnase 1 intergenerationally
yes
What is SWI/SNF
An ATP dependent complex, pushes the dna around nucleosomes to access the TATA box
What can we do with SWI/SNF
Allow transcription to happen
What is methylation
Adding a methyl group to the base. This promotes against transcription. This is used with CPG islands, where C’s alternate with G’s
Why does methyltion of c’s and g’s stop the DNA from opening
It recruits deacetylase protins, getting rid of acetyls to stop transcription to occur
What is fragile x syndrome
There are lots of C’s and G’s in the DNA, stopping transcription of proteins
What is epigenetics
Non-sequence changes to DNA, the histone access is differnet
What is cis acting control
sequence on the dna
What is an enhancer and repressor
promote or demote the quantity of transcription of that protein
What is a promoter proximal element
promoters
Are there trans-acting transcription factors
yes
What is cooperative binding
TF’s bind to each other to bend the dna which can increase transcription speed
What is a transcriptional activator
increases gene expression
what is a transcriptional repressor
decreases gene expression
What is a protein domain
Functional part of a protein which can fold to give a specific structure
Is there only one transcription factor for activators/repressors
not always
What does the cap and tail do to the messenger rna
It stops the messenger RNA from being degraded through signalling that it hasn’t been damaged
Why do genes have introns
because you can make many proteins from one region
What is the process of exporting rna
It is delayed until processed completely
Do ribosomes move to MRNA
sort of
What are the three ways of MRNA to go
directed transport to anchor proteins on cytoskeleton, random diffusion and degredation
What charge is to the center of the cell for cytoskeleton
-ve
What is dyesin for
moving to the center
what is kinesin for
moving away from the center of the cell
What causes development of humans anterior and posterior
protein polarity
What is the median half life of mrna
10 hours
What is the effect of a longer half life
you can translate more proteins
What causes mrna to degrade
the shortening of the poly-a tail by nuclease
What happens when the poly a tail less than 25 exists in mrna
decapping then there is rapid forward degredation or continued degredation
What is eIF
Binds to the 5’ cap to prevent degredation
what is the poly-a tail binding protein
it is a protein that bings to the a cap
What is the effect pf having the cap and the polytail
it causes it to be ready for translation
What causes the a tail to go
the deadenylase competing with the binding protein
How many genes do we have for each thing
2
Where does mitochondrial DNA come from
mother
What is a genomes
complete composition of an organism
what is identical within all humans
99.9% of all the genomes
When is the human genome completed
2003
What is the percentage of genes that are exons
1-2%
What percentage is non coding DNA
92%
What is over 50% of our genome
repeditive DNA
What is the non coding DNA for
that make non coding RNA, centromeres, telomeres
What decreases when the organism increases in complexity
fewer coding DNA
What does not correlate with complexity
number of nucleotides and number of chromosomes
What percentage of our genome is actually teanscribed
90%
how many protein coding genes are there
20000
What is the length of protein coding genes
53600
What is the gene density
1 per 120000 bases
What is relationship of proteins determined by
amino acid bases
What is a homolog
gene related to antother gene by descent from ancestry
What are paralogs
derived from a same species but different genes
what are orthologs
different species but same gene
What is highly conserved during evolution
histones
What is a pseudogene
duplication of genes with one functioning and one not functioning
how many pseudogenes are there
10000
What caused mutations in the pseudogenes
it not being necessary to function
what is the symbol of the pseudogene
trident
what is the alpha globin gene on
16
what is the beta gene on
11
are there multiple genes being expressed for haemoglobin
yes
what are microsatelites
1 to 6 base pair repetition
What is replicative slippage
where the dna bends onto itself and skups a number during replication
what is an example of a mistake with microsatelites
huntingtons and fragile x
What is a minisatelite
big microsatelite
What are the chromosome variations
Duplication of gene, deletion of genes, translocation (replace), inversion (switch), missing chromosome, extra chromosomes
What is naked dna like
highly recombinogenic, it can switsch around easily
What will allow survival of cells
one centromere + 2 telomeres
What is the chromoseome abbreciations
letters for genes and dots for centromere
What are the effects of deletionds
deletion of centromere, homozygous lethal deletions, heterozygous defective deletion, pseudominance recessive allele epressed, haploinsufficient gene, only one copy where 2 are needed
what is a tandem duplication
duplication next to each other
What is a wild type chromosome
natural chromosomee
What causes dupliction of gene sequences
misalignment
what is a paracentric inversion
inversion not including the centromere
what is a pericentric inversion
inversion including the centromere
what is formed when duplicationg inversion of genes
inversion loop
what is the unusual structure of inversions whem duplicatefd
there having one with 2 centromeres and one with no centromeres
What does the dicentric bridge do eventually
split in two
What is a reciprical translocation
where genes sqitch between chromosomes
what is a non recirprocal rare translocation
where one gene is transferred into another where the other is kept the same
what does the transloction of the philadelphia chromosome do
lukemia, the chromosomes are swapped between chromosome 22 and chromoseome 9
what does the ge e fusion do
promote a kinase
what is a robertsonian transocation
2 acrocentric chromosomes, one on 14 and one of 21, where you get a long chromosome and a small chromosome
