NUCLEIC ACIDS + DNA REPLICATION Flashcards
what is a nucleotide?
Fundamental biochemical building block of DNA and RNA
what does a nucleotide consist of?
3 components
nitrogenous base, pentose sugar, phosphate sugar
what are nitrogenous bases?
Pyrimidine (C, T in DNA, U in RNA)
Purine (G, A)
what is pentose sugar?
deoxyribose in DNA, ribose in RNA
what is phosphate group?
acts a bridge between adjacent ribose/deoxyribose groups
what is adenosine?
nucleoside (sugar+base)
what is AMP?
nucleoside monophosphate
what is ADP?
nucleoside diphosphate
what is ATP?
nucleoside triphosphate
how are the bases on complimentary strands held together?
Hydrogen bonds
what bases pair up with what base?
C-G 3-H bonds
T-A/U-A 2-H bonds
where are the hydrophobic bases found?
in the centre od the duplex away from water, stabilised by H bonds
how is the hydrophilic sugar-phosphate backbone stabilised?
by electrostatic and H-bonding interactions with water
what is the interaction between stacked bases like?
weak transient electrostatic interactions
van der Waal’s forces (pi-pi interactions)
what is the structure of RNA?
Single-stranded, adopt secondary structures through base-pairing
how are nucleic acids define by?
size and direction
how are polymers described by?
sequence and the number of bases
where are nucleotides added?
to the 3’- end of a polynucleotide chain
how is a 3-5’ phosphodiester bond formed?
the alpha-phosphate of the new nucleotide reacts with the 3’-OH group of the polymer
how does the polypeptide chain grow?
in a 5’ to 3’ direction
what does the nucleus contain?
DNA and proteins which help compact the DNA
what is chromatin?
histone-bound DNA
what is the order of organisation of DNA by increased complexity?
DNA duplex, nucleosome, chromatosome, chromosomes
what is a nucleosome?
DNA wrapped around 8 histones, basic unit of compacted DNA
what does a nucleosome contain?
Octamer with 2 copies four histone proteins (H2A, H2B, H3, H4)
high arg/lys content (+ve ) to bind to DNA backbone (-ve)
what is core DNA?
146 bp wrap around histone core
what is linker DNA?
60-80 bp leads to adjacent nucleosome
what does a replicating chromosome contain?
2 chromatids linked by a centromere
what does a chromatid contain?
1 single DNA molecule compacted as chromatosomes
what are chromosome territories?
nuclear regions in which specific chromosomes are localised
what is DNA replication?
several steps that involve multiple proteins called replication enzymes and RNA
where does DNA replication occur?
in the S phase of interphase during the cell cycle
why is DNA replication important?
vital for cell growth, repair, and reproduction
what is semi-conservative replication?
the parent strand is separated, creating two single strands used as a template for the complimentary strand
what Step 1: Replication Fork Formation?
Double stranded DNA “unzipped” into two single strands, base pairs broken by DNA helicase
strands form a Y shaped replication fork which is the template for replication to begin
proteins bind and stabilise unwound single stranded DNA
how is the replication fork bi-directional?
One strand oriented 3’ to 5’ direction,leading strand
Other oriented 5’ to 3’, lagging strand
is each side of the stand replicated differently?
Each side is replicated by different processes to accommodate the directional difference
what is Step 2: RNA primer binding?
A short piece of RNA (primer) binds to the 3’ end of the strand. The primer is the replication starting point, primers generated by the enzyme DNA primase
what is Step 3: Elongation?
DNA polymerase alpha binds to the strand at the site of the primer, adds new complementary base pairs to the strand during replication
extends approx 20 base pairs, then elongation taken over by
DNA pol epsilon
DNA pol delta and epsilon have proofreading 3’->5’ exonuclease activity
what does Step 3: Elongation prevent?
Prevents incorporation of incorrect nucleotides
what does Step 3: Elongation result in?
the synthesis of one continuous replicated DNA strand in the 5’-3’ direction
what happens to the lagging strand?
Multiple RNA primers needed, DNA pol delta generates complimentary DNA (Okazaki fragments) to the strand between the RNA primers
Replication discontinuous as the new fragments are not joined
what is Step 4: Termination?
RNA primers degraded and filled by action of RNAse H and DNA pol delta
DNA ligase joins any breaks in the leading and lagging strands to generate continuous double stranded DNA
why does DNA replication occur at multiple sites?
Replication cannot just originate from 1 site per chromosome as it would take too long
how many origins of replication are needed?
Multiple origins of replication with replication forks proceeding in opposite directions necessary
replication bubble
how is a replication bubble formed?
the enzyme helicase is used to separate the 2 strands. the separated DNA strands form a little open pucker-replication bubble
what is a replication bubble?
an unwound and open region of a DNA helix where DNA replication occurs
what happens in the replication bubble?
Histones removed in front of the bubble
H3/H4 tetramers remain intact adjacent to the DNA after synthesis
New H3/H4 tetramer cores bind followed by H2A/H2B.
what is epigenetics?
heritable changes in phenotype/cell behaviour or gene expression in cells caused by changes other than in the DNA base sequence that control the activity of genes
give examples of changes in DNA
Histone modifications
E.g. acetylation of Lys, methylation of Lys and Arg
DNA modifications
E.g. methylation of cytosine
what does epigenetic modifications alter?
alter chromatin structure to control accessibility of transcription factors and co-activators necessary for gene transcription
how are epigenetic marks altered?
by environmental stimuli
E.g. smoking, nutritional status
what do epigenetic markers provide?
provides a mechanism for environmental factors to be imprinted genetically
what is dutch famine?
Fetuses prenatally exposed to famine during 1944-45 had, >50 years later, less DNA methylation on the IGF2 gene compared with unexposed same sex siblings
what was the effect of dutch famine?
children developed obesity and schizophrenia later in life
Children born to these women 20-30 years later suffered from the same problems despite being conceived and born in a normal dietary state
what did dutch famine suggest?
Association for exposure just after conception is important in establishing epigenetic marks that persist for generations
what are the application of DNA replication?
Polymerase chain reaction (PCR)
DNA sequencing
Precision/personalised medicine
