b11 Flashcards
what type of bond connects a base pair (ex A and T)
hydrogen bond
what do nucleosides consist of?
sugar + nitrogenous base
what do nucleotides consist of?
nucleoside + phosphate group (s)
what are the four nucleosides?
AdenoSINE, thrymidINE, guanoSINE, cytiDINE
true or false: purines and larger than pyrimidines
true, purines are double ringed and pyrimidines and single ringed
what are the purines and what are the pyrimidines
Purines: G and A
Pyrimidines: T, C, U (in RNA)
in a nucleotide, where is the phosphate group bonded to the sugar
5’ carbon of sugar
in a nucleotide, where is the nitrogenous base bonded to the sugar?
1’ carbon of sugar
nucleotides are joined together by:
3’ - 5’ phosphodiester linkages (3’ hydroxyl on carbon 3 joins to 5’ phosphate on carbon 5 of anther nucleotide)
- 3’ end is a sugar of one nucleotide
- 5’ is a phosphate of one nucleotide
thats why it is a SUGAR PHOSPHATE backbone!
how many hydrogen bonds are between nitrogenous bases
A and T: 2 hydrogen bonds
G and C: 3 hydrogen bonds
DNA to RNA
transcription
RNA to protein
translation
the complex of DNA and its tightly bound proteins
chromatin!
highly conserved means what
highly important
codes for the amino acid sequence of proteins
exons
spliced out during RNA processing
introns
changes in the nucleotide sequence of DNA can be caused by errors in what?
DNA replication OR DNA repair
change in the DNA sequence
mutation
switching one nucleotide for another
point mutation
who has a higher error rate? bacteria or humans
bacteria!
bacteria: 3 per 10^10 nucleotides copied
human: 1 per 10^10 nucleotides copied
addition of one or more nucleotide into a segment of DNA
insertions
removal of one or more nucleotide in a segment of DNA
deletions
addition of one or more copies of any piece of DNA into a segment
duplications
when a segment breaks off and reattaches within the same chromosome, but in reverse orientation
inversions
RNA that has catalytic activity
ribozymes
rearrangement between two chromosomes
interchromosomal rearrangements
rearrangement within 1 chromosome
intrachromosomal rearrangements
translocations where there is a swap of material without any net loss or gain to the genome
reciprocal translocation
translocations where there is a loss or gain or material
non-reciprocal translocation
defines the presence of two or more genes on the same chromosome of a given species
synteny
sequences that repeat over and over without interruption
Tandem repeats
what are the three types of tandem repeats
satellite DNA, minisatellite DNA, microsatellite DNA
5-500 bp in tandem repeats and repeats up to 100kb that can form very large clusters
satellite DNA
10-100bp with up to 3000 repeats
minisatellite DNA
1-5 bp in clusters of 10-40 bo scattered quite evenly throughout the genome
microsatellite DNA
present as a single copy per haploid set of chromosomes
Includes the genes for almost all proteins
non-repetitive DNA
are repetitive DNA sequences stable?
NO
repetitive sequences can be expanded or destroyed by
SLIPPAGE events causing misalignment
2 different forms of the same gene
alleles
DNA that moves from one place to another in the genome
Mobile DNA
what does it mean to say plants and animals have low gene density
- we have lots of non-coding regions in our DNA
- lots of unimportant stuff
- lots of space due to HUGE genome
when does crossing over happen
prophase of meiosis I
similar genes with similar but distinct function
multigene families
one of two or more genes that are similar in sequence as a result of derivation from the same ancestral gene.
homolog
genes in two separate species that derive from the same ancestral gene in the last common ancestor of those two species.
ortholog
genes or proteins that are similar in sequence because they are the result of gene duplication event occurring in an ancestral organism.
paralog
a DNA strand is synthesized in what direction
5’ to 3’
what adds new nucleotides to a growing DNA strand
DNA polymerases
what two sites does DNA polymerization have
polymerization site (to add nucleotides) and an editing site (when there is a mistake)
The ability of the two DNA strands to unwind and separate into two individual strands
Denaturation
complementary single stranded DNA molecules can re-associate
Renaturation or reannealing or hybridization
true or false:
double stranded DNA absorbs more UV light than single stranded DNA
false
The higher the ____content of DNA, the higher the Tm the melting temperature
G/C
where does DNA replication initiate
at sequences rich in A-T base pairs
why?
- because they have 2 hydrogen bonds and are easier to break apart than G-C which have 3 hydrogen bonds
1 replication bubble contains how many replication forks?
2 replication forks
points where a pair of replicating segments come together
replication forks
prokaryotic replication forks move in ________ direction(s)
opposite
enzyme that separates two strands of DNA in DNA replication, unwinds two strands of DNA
helicase
what makes sure that single stranded DNA does not fold/reanneal on itself
SSBPs
what does the RNA primer do in DNA replication
creates a 3’ OH in which DNA polymerase can build on
what adds the RNA primer in DNA replicaiton
DNA primase a type of RNA polymerase
produces a transient (short lasting) SINGLE STRAND break that allows rotation of DNA strands
topoisomerase I
Produces a transient double strand break in the helix , reduces supercoiling, detangles DNA
topoisomerase II
when does sliding clamp releases DNA polymerase from DNA
when a double stranded region is encountered
covalently connected the okazaki fragments into a continuous strand
DNA ligase
what direction does DNA polymerase move on the template strand
3’ –> 5’
which DNA pol replaces RNA primers
DNA pol I
describe the exonuclease activity of DNA pol III and DNA pol I
DNA pol III: 3’ to 5’ exonuclease activity to proofread
DNA pol I: 3’ to 5’ and 5’ to 3’ to proofread and remove RNA primers
which polymerase extends RNA primers
DNA pol III
in eukaryotes when does the nucleus/cell divide
M phase (mitosis)
in eukaryotes when does DNA synthesis take place
S phase (lasts 40 mins to 8hours)
eukaryotic cells replicate their DNA in small portions called
replicons
initiation of DNA synthesis in a replicon needs
ORC (origin of replication complex)
which enzyme is responsible for maintaining chromosome ends
telomerase
what is something interesting about telomerase
it is a reverse transcriptase: is can make DNA from RNA template
also it contains its own RNA template
what does telomerase do in terms of replicating the ends of eukaryotic chromosomes
telomerase extends the template strand (this is a source of repetitive DNA)
- one telomerase extends the template strand primase and DNA pol extend the LAGGING strand
Distortions of the double helix is used for recognition of mismatched base pairing
Can distinguish which strand is newly synthesized and target that strand for correction (using other strand as the template)
strand directed mismatch repair (MMR)
what does UV radiation cause in terms of DNA damage
pyrimidine dimers (when C or T pair together or C and C or T and T)
what does ionizing radiation cause in terms of DNA damage
breaks in DNA backbone
what does thermal energy do in terms of DNA damage
causes A/G to come off the sugar backbone
what are the purines and pyrimidines
Purines: A, G (double ringed)
Pyrimidines: C, T (single ringed)
removes purines (A, G) from DNA
depurination
converts cytosine to uracil
Deamination
removes bulky bad things/lesions (ex. Pyrimidine dimers, chemical alteration)
NER: nucleotide excision repair
patients are unable to repair damage caused by exposure to UV light
Xeroderma pigmentosum (XP) result of defects in NER
which enzymes would be most useful for detecting and/or repairing a depurination
AP endonuclease
initiated by DNA glycosylase enzymes that recognize specific alternations (different versions of DNA glycosylase for different alternations)
Base excision repair (BER)
is important for rescuing stalled/broken replication forks
Homologous recombination
Highly active pathway in humans for rapid repair of double strand breaks in DNA
NHEJ, non homologous end joining
the intermediate between DNA and protein- used as a template for protein synthesis by ribosomes in cytoplasm.
mRNA
provide structural support in the ribosome and catalyzes the chemical reaction in which amino acids are covalently linked to each other
rRNA
required for translation of mRNA information into polypeptide sequence i.e. convert the language of nucleotides to the language of amino acids
tRNA
true or false: mRNA are long lived
false: mRNA have shorter half lives
direction of transcription is determined by what in DNA
orientation of promoters sequence in the DNA at the beginning of each gene
what are the three stages of transcription?
- initiation
- elongation
- termination
RNA polymerase binds to the promoter sequence
initiation: STEP 1 of transcription
DNA strand temporarily unwinds allowing synthesis of complementary RNA
Ribonucleotides are linked together by phosphodiester bonds (5’ to 3’ like DNA synthesis!)
elongation: STEP 2 of transcription
WHICH Strand?
5’ to 3’ sequence of the gene; it matches the 5’ to 3’ sequence of the RNA
sense, coding or nontemplate strand of DNA
3’ to 5’ sequence of the gene used to make the RNA
template, antisense, noncoding strand
increases the RNA polymerases affinity for promoter sequences
sigma factor
RNA polymerase (5 subunits) + sigma factor is called the
RNA polymerase holoenzyme
one promoter and multiple genes
polycistronic mRNA (prokaryotic)
one promoter and one gene
monocistronic mRNA (eukaryotic)
what synthesizes all eukaryotic mRNA precursors (pre-mRNA)
RNA polymerase II
recognizes TATA box and other DNA sequences near the transcription start point
TFIID
unwinds DNA at the transcription start point, phosphorylates Ser5 of the RNA polymerase C-termal domain (CTD); releases RNA polymerase from the promoter
TFIIH
site of assembly of preinitiation complex (PIC) that contains general transcription factors and RNA polymerase
TATA box
are RNA sequences that do not encode protein but play important regulatory roles
Untranslated regions (5’ UTR or 3’UTR)
expressed sequences
exons
intervening sequences
introns
what removes introns from pre-mRNA
RNA splicing
splicing of introns as lariats are carried out why what
5 snRNA (small nuclear RNA) and 100s of proteins
what are the sequences required for intron removal?
5’ splice site, branch point, 3’ slice site
sites of RNA biosynthesis
nucleoli
5S rRNA is made by which RNA pol and where
RNA pol III, not in the nucleolus
change in ___________ cell DNA can be passed to offspring
germline
________ cells make up the tissues of the body
somatic
name three things supercoiling does
- increases stability
- makes DNA more compact
- allows unwinding of sections
which protein enzymes regulate/relive supercoiling
topoisomerases
helix is overwound
positive supercoils
helix is underwound
negative supercoils
any of a group of basic proteins found in chromatin.
histones
eukaryotic DNA associates with histones and other proteins to form
chromatin
histones packages DNA into repeating units called
nucleosomes
repeating subunit of DNA + histones
nucleosomes
histones are _______ charged
positively
where does the negative charge of DNA come from
phosphate
Regulates how tightly these nucleosomes pack together, without this nucleosomes would look like beads on a string
histone H1
DNA that is less compacted and functionally active (accessible for protein binding and transcription) genes here can be expressed
euchromatin
DNA that is highly compacted and has little to no functional activity
heterochromatin
what connects one nucleosome to another
histone H1 (linker histone) binds linkner DNA
phenomenon in which a gene is either expressed or not expressed in the offspring depending on which parent it is inherited from.
genomic imprinting
covalent modifications (ex. methylation) of DNA and histones
epigenetic
does epigenetics influence heterochromatin or euchromatin
heterochromatin
causes compaction/repression
methylation
leads to more open structure, more transcription
acetylation
DNA methyltransferase can add the methyl group to DNA at sites where
a C is followed by a G
some (very few) methylation patterns are passed from parents to offspring what is this called
genomic imprinting
can histone tail modifications be passed on to daughter cells during cell division
yes
can DNA methylation patters be passed on to daughter cells during cell division?
yes
what are examples of ribozymes
spliceosomes and ribosomes
how many possible reading frames for every nucleotide sequence
3
splicing is carried out by what
5 snRNA (small nuclear RNA) molecules and 100s of proteins
