ch. 4 Flashcards
DNA and RNA are what and made up of what? what does this monomer consist of?
DNA and RNA are nucleic acids made up of nucleotides. nucleotides are made up of 1) sugar (deoxy for DNA and ribose for RNA) 2) nitrogenous base (A, G, T, C), and 1-3 phosphate groups.
what is the main building block of DNA that isnt nucleotides
dNTP where N stands for one of the four nitrogenous bases
what are the purines? the pyrimidines?
the purines are G and A and the pyrimidines are the C, U, T “cut the py”
what are nucleosides?
they are nucleotides but without the phosphate groups so just the sugar and nitrogenous bases
what are nucleosides with three phosphates called?
nucleoside triphosphate or NTP
what is the backbone of DNA
the sugar and phosphate groups
how are the nucleotide linked by
phosphodiester bonds between 3’ hydroxy group to 5’ phosphate group of next nucleotides
what does the WC model indicates
right handed double helix held together by hydrogen bonds between bases and is complementary to each other
AT bonds have how many hydrogen bonds, GC bonds have how many hydrogen bonds
AT has 2 H bonds and GC has 3 H bonds
binding of 2 complementary strands of DNA is called
annealing or hybridization
what is a genome? chromosome?
genome is the sum total of organisms genetic info and chromosomes is each piece of double stranded DNA
how many chromosomes do humans have? how many come from each parent?
humans have 26 chromosomes and they get 23 from each parent
prokaryotes have what kind of DNA? to protect the DNA, what do bacteria do? what enzyme does this?
single circular chromosome, this DNA is super coiled and this is done by DNA gyrase and it uses ATP
what is the DNA= packaging (big to small)
nucleus to chromosome to chromatin to nucleosomes to histones to sugar phosphate backbone
heterochromatin
more dense and its darker stained
euchromatin
less dense and lighter strained
what does density of these two chromatin have to do with gene activity
less dense areas have high transcription therefore high gene activity due to less density and easier to access than more densely packed.
centromeres
middle part of chromosome where spindle fibers in cell division attach to 1) the fibers attach to proteins called kinetochores that act like anchors 2) small p arms 3) long q arms
what is a chromosome with equal parts of long arms and short arms?
metacentric
what is a chromosome with no short arms?
telocentric
what is a chromosome with minimal top arms?
acrocentric
what is a chromosome with a less arms than the metacentric chromosome?
submetacentric
telomeres make up
they are the ends of linear chromosome and they are guanine rich with many nucleotide sequences repeats.
what do telomeres do
it stabilizes chromosome and prevents chromosome deterioration from replication
do prokaryotes have telomeres?
no they do not because they have circular DNA
human genomes have how many different chromosomes? how many are autosomal and how many are sex?
we have 24 different chromosomes with 22 autosomal and 2 different sex chromosomes
the genomes have what two regions?
the region with high transcription rates are the coding regions and these are separated by the intergenic regions which are the noncoding DNA
what is the intergenic regions mostly made up of ?
tandem repeats and transposons
gene
a DNA sequence that encodes a gene product and it includes both regulatory regions and protein coding.
what are the kinds of genomic variations
single nucleotide polymorphism (SNP), copy # variation (CNV’s), Tandem repeats
what are single nucleotide polymorphism
single nucleotide changes in every 1000 base pairs
what are copy number variation
structural variations in genome that lead to different copies of DNA sections, these large regions of genome can be duplicated or deleted
the number of copies of a particular gene varies from one individual to the next.
what are tandem repeats
where short sequences of nucleotides are repeated one right after the other from as little as 3 or to 100 times
what is transcription? what kind of RNA is created?
reading DNA and writing it into RNA, you can make noncoding rna (rRNA and tRNA) or coding rna mRNA
after the mRNA is created, what does the mRNA do? what is this process called?
the mRNA goes to a ribosome and the tRNA brings the right AA to the ribosome to make the polypeptide, this is called translation
what is the central dogma of biology
where inherited info is used to create actual objects, DNA to RNA to proteins
what is the genetic code
the language used by mRNA and DNA to specify which building blocks are used to make what proteins
what is the genetic code made up
codons: 3 nucleotide letters that code for a specific AA
when DNA gets transcribed, how is the RNA written?
RNA is complementary
how many codons are there? what are the stop codons? what are stop codons also called?
there are 64 codons and there are three stop codons, UAA, UAG, and UGA. they are called nonsense codons because they dont code for an AA
what are synonyms
2 or more codons coding for the same things
how can some viruses transcribe DNA from RNA
using enzyme called reverse transcriptase (retrovirus)
what is DNA replication and in what phase in mitosis does it occur
duplication of DNA, it occurs in S phase
what is the new strand dna called? what was the strand that was used to create new dna called?
the new strand is called the daughter strand and the old strand is called the parent strand
what are the three theories of dna replication and which one do we agree with?
conservative: parent DNA would remain as is, dispersive: both copies of DNA had scattered pieces of new and old, and the one we agree with is semiconservative: semiconservative: one strand comes from parents and other is new strand
what is the enzyme that unwinds DNA to get ready for replication? where does it begin to unwind and how does it find it
helicase unwinds DNA at the origin and it has proteins that marks the origin for helicase
as helicase unwinds dna, what other enzyme cuts the strands in half? what are two separated DNA strands called? what does two strands start?
topoisomerases and two separated strands are called an open complex which begins dna replication
what is weaker a single strand of DNA or two strands together? any enzymes that help with this?
single strands are weaker so theres single stranded binding protiens that protect the DNA in that form
what enzyme thats the actual replication process after helicase and topo. and how is this done
replication starts once RNA primer is placed on each strand and its placed by proteins called primosomes
what enzyme elongates the dna strands? in what direct does parent strand go? the daughter?
DNA pol binds to RNA primer and ALWAYS adds to the 3’ direction of the new strans. PARENT STRAND on TOP is in the 3’ to 5’ direction while DAUGHTER strand is in the 5’ to 3’ direction
what are the conditions for dna pol to work
- it needs to occur ing the 5’ to 3’ direction
- it needs a template (parental DNA)
- it needs a primer (RNA primer)
where the dna continues to unwind is called the
replication fork
what part of the DNA is considered the leading strand? the lagging strand?
the leading strand is replicated in the 3’ – 5’ direction toward the replication fork while the lagging strand is replicated in the 5′ – 3′ direction (opposite direction to the replication fork). DNA is added to the lagging strand in discontinuous chunks called ‘okazaki fragments’.
leading/lagging strand is (con/discon)?
leading strand is continuous while lagging strand is discontinuous creating okazaki fragments
how are okazaki fragments binded together
enzyme called DNA ligase
Prokaryotes have how many DNA Pol? what does each do?
they have five pol, DNA POL 3: super fast addition and has exonuclease activity both 5 to 3 and 3 to 5,DNA POL 1: adds bases slower and also have exonuclease activity, DNA POL 2: is back up for DNA POL 3, DNA 4 & 5 error prone but helps other DNA pol’s
what is exonuclease activity
reading in the 5’ to 3’ to proofread to check for errors and has the ability to correct back bases at the end of the strand
what does high processive/low processive mean
high processive means speedy addition of bases
what is endonuclease activity
proofreading and cuts bases in the middle of the chain
Prok vs Euk replication
Prok: have only one circular chromosome so they only have one origin and replication for them is called theta replication
Euk: each chromosome has its own origin therefore there are many replication forks that widen to make replication bubbles.
why does the end of chromosomes shorten after each replication? what is the name of the ends?
the ends are telomeres and they shorten because there isnt enough DNA to place RNA primer and DNA pol needs a primer
what two things can occur if telomeres get too short
- the enter a senescent state where they no longer replication 2. start apoptosis
what enzyme can add bases on telomere? what is the hayflick limit?
telomerase can had repetitive bases to base telomeres longer, the hayflick limit is how many times a chromosome can replicate
where is telomerase usually located in what cells
germ, cancer, stem, white blood cells
what is a genetic mutation, what are the two general types
genetic mutation is any change in DNA sequence, and some can be germline mutations that can be passed onto kids or somatic mutations that arent passed on
what are the three causes of mutations?
- physical mutations: radiation that causes pyrimidine dimers, two pyrimidines bound together
- reactive chemicals: chemicals that can alter bases or cause crosslinks between other bases
3.biological agents: DNA pol mistakes or viral integration of DNA transposons as well
what are point mutations? what are the three types?
point mutations are single base pair substitutions, 1)missense: replace one AA with another AA 2)nonsene: a stop condon replaces normal codon 3)silent: still codes for same AA
what are insertions, deletions, and inversions
insertions: addition of one or more extra bases,
deletions: removal of bases
inversion: chromosome rearranges itself (can be caused by transposons)
what is a frameshift mutations and what kind of mutations cause this?
frameshifts mutations: shifts in the reading frame and this can be caused by deletions and insertions
what is chromosome amplification? translocations?
amplification: when a segment of chromosome is duplicated and translocation is when recombination occurs between nonhomo chromosomes: two gene parts make one new gene
translocations can have be two things?
balanced: no genetic info is inserted or unbalanced where genetic info is inserted
what are transposons? what are the three kinds
transposons are jumping genes with transpoase that moves them to new places in genome; 1) there IS element: transposon with inverted repeat 2) complex: transposons with additional genes 3)composite: have 2 similar or identical IS elements with a central region inbetween
what is loss of heterozygosity? what does it cause
its causes deletion of a normal gene where theres two chromosomes but now theres only one copy called hemizygous
haploinsufficiency
a diploid animal has only one func copy of a gene and this one gene isn enough to support a normal state
what are good mutations
what are bad ones
good: sickle cell is resistant to maleria, missing genes in CCk5 that is resistant to HIV,, bad: cancer is mutation accumulation where oncogenes (cancer causing gene) and inborn errors of metabolism which cause metabolic disorders
what phase does most DNA repair occur
in G1/S transition and G2/M transition
what are the three types of DNA repair
- direct reversal, 2.homology-dependent repair 3. double stranded break repair
direct reversal
most DNA damage cant be reverse but some can through things like photoreactivation for UV induced dimers that directly repairs the bases
homology dependent repair
using the okay strand to fix the bad strand and can be divided by excision repair: removes bad bases and replaces them or post replication repair: the mismatch repair targets mismatched pairs
double strand break repair
a) homologous recombination: sister chromatid can help repair a break b)nonhomologous end jointing: if sister chromatids arent available, broken ends are stabilized by just joining them together by ligase
what is gene expression? transcription?
gene expression is the process where genes begins to have effects in the cell. transcription is genetic info written in RNA info
what are the characteristics of RNA
- single stranded 2. has uricil instead of thymine 3. pentose ring with ribose instead of 2’ deoxyribose
what is a coding RNA
the only coding RNA is the mRNA as it carries genetic info to the ribosome to be translated into AA
mRNA is —-cistronic in euk and —-cistronic in prok
euk mRNA is monocistronic where one gene gives to one protein so #of mrna= #of proteins, prok mRNA is polycistronic where one gene can code for multiple proteins
what is the first mRNA made called?
hnRNA
what are the two noncoding RNA
tRNA: responsible for translating the genetic code, it carries AA’s from cytoplasm to ribosome to build proteins
rRNA: we have rRNA types and they make up parts of the ribosome
replication vs transcription
both: start at an origin and the sequences that starts it is called the promoter, both go to 5 to 3’, template driven polymerization
different: replication needs a primer while transcription doesnt, RNA has no proofreading
the strand that is the template is called the — and the other one is called? toward the 3’ is called —stream and toward the 5’ is called the —stream
the one that is a template is called the antisense and the other one is the coding or sense strand. toward the 3’ is called downstream (+) and toward the 5’ is upstream (-)
prok RNA pol has how many subunits and what makes it start transcription
RNA pol has 5 subunits called the core enzyme with an additional subunit called sigma factor or holoenzyme that tells the core enzyme to start the process
prok transcription has three stages
initiation: RNA pol binds to promoters by scanning the strand
elongation: the core enzyme elongates RNA to create bubbles
termination: RNA pol falls off DNA releasing the RNA strand created and bubble closes
Prok vs Euk Transcriptions
prok: occurs in cytoplasm, mRNA is ready to be used
Euk: transcription occurs in nucleus and is sent out to cytoplasm to do translation. primary mrna (hnrna) isnt ready to be used until splicing occurs
what is splicing and what enzyme does it? define the region it deals with
splicing is when introns get removed and extrons get joined together and its done by spliceosome. introns are noncoding regions and extrons are coding regions
how does hnrna get activated to mRNA
hnrna has a 5 cap and a 3 tail that is essential for translation
what are the three RNA pol we need to know in humans?
RNA pol 1: transcribes rRNA
RNA pol 2: transcribes hnRNA
RNA pol 3: transcribes tRNA
what is translation
the creation of the polypeptides (AA’s) according to the RNA sequence dictated by codons by mRNA
what is the overall process of translation
mRNA attaches to a ribosome at a specific location and the first AA is delivered by tRNA to the ribosome ,the 2nd AA is delievered to the ribosome by another tRNA, the ribosome binds the 2 AA’s together and continues until its done
each trna is made by and how does it get the right AA? where does the AA go on the ribosome
transcription by RNA pol 3 and it gets right AA by reading the anticodon which is three bases that codes for an AA. the AA then goes to the AA acceptor site where its attached to the tRNA
most organisms have less than 45 diff types of tRNA? why
because anticodons (AA) have more than one tripair of bases that codes for the same thing
what is the wobble hypothesis
the first two nucleotides in an anticodon obeys normal base pairing while the third one is more flexible
if 5’ base anticodon is this, what is its 3’ codon pair
G
C
A
U
I
C or U(wobble)
G
U
A or G (wobble)
A, U, C (all wobble bases)
peptide bond making is spon or nonspon
nonspon meaning it needs ATP to occur and it has slow kinetics so it uses rxn coupling
how is AA activated?
AA binds to AMP to make amino acyl amp, a phosphate group leaves, and aa loads to ribosome because its favorable to break amino acyl amp bond
AA actvation needs how many atps each
2 atps
each AA has what enzyme that binds it to the tRNA
aminoacyl-trna synthetase
ribosomes have how many binding sites? what do they do?
they have 3: A) where each new tRNA delivers the AA P) where the growing peptide chain thats still attached to the tRNA is located E) where a new empty tRNA sits prior to its release from ribosome
where is important to note about mRNA is prokaryotes? where does transcription and translation occur in prokaryotes?
the first mRNA created is ready to use immediately after it is made unlike hnRNA. transcription and translation both occur in the cytoplasm of prokaryotes
mRNA in prokaryotes dont need a promoter but rather they have? what does this site do?
a ribosome binding site called shine-dalgarno sequence in the upstream area. it acts as the initiation site.
prokaryotes have a 3 stage translation process, describe each one
initiation: subunits of ribosome join together and the initiator tRNA joins as well. The start codon and the ribosome site is needed to start process.
elongation: tRNA brings AA to A site and 1 ATP is used. peptidyl transferase binds new and first AA together. translocation occurs when empty tRNA moves to the E site
termination: when stop codon appears in a site
how many phosphate bonds need to break to make a polypeptide where n is # of AA
4n
difference between prok and eu translation
- ribosome is bigger 2. Eu mRNA needs to be processed before its used 3. initial amino acyl tRNA is met not fmet 4. eu mRNA must be transported from nucleus to cytoplasm
Eu translation process steps:
- formation of initiation complex where subunits come tigether with met tRNA and mRNA is scanned to find start codon.
- elongation and termination are the same in prok and euk.
what is cap dependent translation? cap independent translation?
cap dependent: using 5’ end of RNA to start translation. cap independent: starts translation in the middle and this mRNA needs a internal ribosome entry site
why would cap independent translation need to occur?
in sub optimal cell conditions
what is the principal site for gene expression regulation? what can it be affected by?
transcription is the main site for gene expression regulation since the amount of each protein is based on the mRNA made in transcription. epigenetics can affect gene expression through heritable and long term effects and NOT by dna sequence changes
how are four ways to regulate gene expression?
1) DNA methylation and chromatin remodeling: can block gene from transcription proteins or change winding around histones
2. Gene dose: to increase gene expression, increase copy number of gene by amplification
3.imprinting: when only one allele of a gene is expressed
4. x chromosome inactivation: females have two x’s and one is activated while the other is not.
in prok. how do they regulation gene expression
through regulation of transcriptions by inhibiting (repressible) or activating (inducible) certain enzymes
the lac operon is used for what? is it inducible or repressible
it is used in lactose catabolism and it is inducible
the trp operon is used for what? is it inducible or repressible
it is used in coding for trp biosyn/anabolism, it can be repressible
the lac operon has how many coding proteins? what do they do?
5 coding proteins:
P: promoter where RNA pol starts
O: operator where lac repressor binds
Z: codes to cleave lactose
Y: codes for transport of lactose into cell
A: codes for enzyme that deals with another enzyme that breaks lactose
POZYA!!!
how many regulatory sequences does lac operon have? what do they do?
we have two where the crp gene: codes for catabolite activator and I: codes for lac repressor
increased glucose causes what in lac operon? decreased glucose causes what in lac operon?
increase glu: means decreased cAMP which causes lac operon to be off
decreased glu: means increased cAMP which causes lac operon to be on
lac and trp operons are only found in
bacteria
trp operon
when bacteria can make trp they turn it off but when it cant it turns it on
when does gene expression regulation occur in Eu most of the time? how do they do this?
this occurs usually in initiation using enhancer sequences (noncoding seq that activate the expression of genes) or use gene repressor proteins to repress transcription
beside gene regulation during initiation, cells can use
- RNA translocation: doesnt let mRNA go to wrong part of the cell
- mRNA surveillence: cells monitor mRNA to make sure defect ones dont go
- RNA interference: a way to silence gene expression after transcript has been made
how can we affect gene expression at protein level?
- using chaperones to make sure proteins are folding correctly
- covalent modifications
3.cleaving zymogens
RNA transcription has what parts?
the open reading frame that has start and stop codon and 5 to 3 UTR regions
signal to get ready for replication, transcription, and translation
replication: ORI
transcription: promoter
translation: shine-dalgarno seq (prok)
kozak seq (eu)
signal to start for replication, transcription, and translation
replication: ORI
transcription: start site
translation: AUG start codon
key synthesis enzymes for repli, transcrip, and transla
replication: DNA pol
transcription: RNA pol
translation: ribosome
build direction for repli, transcrip, transla
replication: 5’ to 3’
transcription: 5’ to 3’
translation: n term to c term
