Nucleic Acids Flashcards
how is the ribose sugar different from the deoxyriboses sugar?
deoxyribose sugar does NOT have OH on 2’ carbon
what are the key structural features of DNA
B-DNA
double helix thats righthanded 10 bp per turn 2 complementary antiparallel strands complementary base pairing major and minor grooves (stable)
what are the key structural features of DNA
A-DNA and Z-DNA
11bp per turn
forms when DNA is dehydrated
12bp per turn
Left handed helix
what is the directionality of DNA molecule
runs in 5’ to 3’ direction
what bond maks up the sugarphosphate backbone
phosphodiester bond makes up the backbone
> dna is negatively charged due to the prescence of phosphate groups
how are adjacent nucelotides linked together?
they are linked together by phosphodiester bonds between the 5’ and 3’ carbons
How can you measure denaturation of a DNA moelcule? When can DNA be resisitant to denaturation ?
(its melting point will increase as a result)
when DNA is unwound/denatured, it can absorb more U.V light (260nm) in its single stranded form.
>If DNA has large amounts of G—C bonds it can be resistant as it takes more energy to break the bonds
>also is there are cations+ they can reduce the ELECTROSTATIC repulsion between phosphate groups
what are some roles of RNA
RNAs are highlt variable and their strucutural flexiblity means they have many roles •enzymatic/catalyst •carrier of information •transportation •regulation of gene expression microRNA
DEFINITION
genome and gene
chromosome and chromatin
complete set of genes in an organism/cell/organelle
sections of DNA that code for a polypeptide/RNA
long DNA molecule asscoiated with histones
DNA-protein complex in eukaryotic cells which condenses into chromosomes
features of bacterial chromosomes/genomes
(multiple copies of) single, circular chromosome made of double-stranded DNA.
they are negatively supercoiled by and achored to a protein to form nucleoid
Plasmids may also be present and NO introns
properties of plasmids
smaller than the circular chromosome they carry non-essential genes and
they can pass from cell to cell via pilli in process conjugation
features of eukaryotic chromosomes/genomes
DNA packaged into long and linear chromosomes only visible in mitosis/meiosis where
DNA is supercoiled and associated with histones.
genes are split into introns and exons
when are scaffold proteins useful?
(condensind and topoisomerases)
POOP
A visible (mitotic/meiotic) chromosome is made from loops of the nucleosomes attached to a scaffold made of non-histone protein.
how do epigenetics and histone proteins relate?
Covalent modification of histone proteins can be used as a mechanism for regulating genes.
>acetylation of Lysine residues removes the postive charge and WEAKENS DNA-histone interaction so its morelikely the gene will be transcribed– switched on
what are the 3 main features of genetic code?
degenerate
non overlapping
universal - some variation in mitch, protist and mycoplasma e.g UGA = tryptophan instead
what are the key codons in translation?
Not all of an mRNA is translated into protein.
the initiation codon: translation starts with AUG
the termination codons: UGA, UAG and UAA
➡ AUG encodes methionine (so all newly made proteins begin with methionine)
what is meant by a reading frame?
An mRNA has three possible reading frames, only one of which is “open” and used.
spams from the intiation codon to the stop codon
features of tRNA
short with a “clover leaf” secondary structure
have an anticodon, complementary to codon,
an amino acid binding site at their 3′ end (unpaired CCA)
its tertiary structure is inverse L shapes
name given for aminoacid + tRNA
aminoacyl tRNA
are the base pairing rules the same for tRNA
NO! Some tRNAs can recognise more than one codon due to “base wobble” – reduced base-paring specificity aR the 3rd position of the codon
mitochondrial genome facts
may be spread over several circular molecules instead of a single linear one
genome also in chloroplast and nucleus
DNA REPLICATION -
comparison between pro and euk
✓ semiconservative, bi-directional
✓ semidiscontinuous (leading and lagging)
✕ only one origin if replication in prokaryotes, multiple in eukaryotes
✕ because of this, eukaryotic DNA polymerases are slower, but overall, DNA replication is faster as there are more working at once
how is DNA stable
POOP
base stacking and hydrogen bonds
DNA REPLICATION
where would the sequence of bases be for the origin of repliaciton in bactera?
bacterial replication begins at a SINGLE/ONE AT-rich origin
>easier to unwind as fewer hydrogen bonds
DNA REPLICATION what enzyme synthesises DNA, and what are their requirements to synthesise? RNA polymerase Reverse transcriptase DNA ligase DNA polymerase RNA primase
DNA polymerases. They require deoxynucleoside triphosphates (dAMP, dCMP. dGMP, dTMP), a single-stranded template, and a primer with a free 3′-OH to attach nucleotides to
DNA REPLICATION
decribe the exonuclease activtiy of DNA polymerase
a 3′→5′ exonuclease activity (allowing them to proofread).
ONLY DNA polymerase I from E. coli has 5′→3′ exonuclease activity allowing it to “overtype” existing DNA or RNA (nick translation).
DNA REPLICATION
step by step the process
- helicase, gyrase counteracts supercoiling, protesin binds to single strands
- primase synthesizes the RNA primers
- Synthesis of DNA by DNA polymerase III, some okazi fragments made
- removal of RNA primers and Nick translation by DNA polymerase 1
- DNA ligase synthesises the missing phosphodiester bonds/ covelently links fragments(gap fill)
DNA REPLICATION
why does DNA polymerase III makes most of the DNA
it has high speed, effciency and processivity (can stay attacthed to chain for long time before it detaches)
