DNA Flashcards
Plasmid and what genes it contains
small, circular DNA molecules that can contain a variety of genes, including those that confer antibiotic resistance, virulence, and the ability to grow in adverse conditions
Rosalind Franklin
Rosalind Franklin prepared crystallography from DNA samples
- Her images suggested a double helix with 10 nucleotides/turn
- 2 nm diameter suggested the sugar‐phosphate backbone must
be on outside
Crick and Watson
used model building, plus physical and
chemical evidence, to solve DNA structure
– Published their results in 1953
Structure of DNA
Biochemists knew DNA is a polymer of nucleotides
– Each nucleotide consists of deoxyribose, a phosphate group, and a nitrogen‐containing base
Four different nucleotides differing only in the bases
Purines: adenine (A) and guanine (G)
Pyrimidines: cytosine (C) and thymine (T), holds DNA together
DNA vs. RNA nucleotides
DNA: Pu. A -> Py. T, Pu. G -> Py. C
RNA: Pu. A -> U (Uracil), Pu. G -> Py. C
DNA structure setup
- Bases are on the inside of each strand
- Sugar‐phosphate groups on outside
- Chains are antiparallel: run in opposite direction
- DNA can be found in the nucleus of the cell
Chargaff’s rule
The amount of adenine is always equal to the amount of thymine found in a sample. The amount of cytosine is always equal to the amount of guanine found in a sample
DNA strands held together by
- hydrogen bonds between complementary base pairs
- Van der Waals forces between adjacent bases on same strand
DNA replication
the process by which cells create two identical copies of DNA from a single original DNA molecule
Semi conservative
each parent strand is a template; new molecules have one old and one new strand
2 step DNA replication
- Double helix unwound, making two template strands
- New nucleotides form complementary base pairs with the template DNA strand and are linked by phosphodiester bonds
origin of replication and replication fork
- Origin of replication (ori): specific region of DNA that indicates the starting point of replication
- In E. coli, DNA is unwound, and replication proceeds in both directions, forming two replication forks
Leading vs. lagging strand and Okazaki fragments
- Leading strand: grows at the 3’ end as the fork opens
- Lagging strand: the exposed 3’ end gets farther from the fork, and an unreplicated gap form
- Okazaki fragments: small, discontinuous stretches of new DNA
3 repair mechanisms
- Proofreading: DNA polymerase recognizes mismatched pairs
and removes incorrectly paired bases - Mismatch repair: newly replicated DNA is scanned for mistakes by other proteins, and mismatches can be corrected
- Excision repair: enzymes scan DNA for damaged bases – they’re excised, and DNA polymerase I adds the correct ones
PCR
Polymerase chain reaction (PCR): an automated process that makes multiple copies of short DNA sequences for genetic
manipulation and research
2 steps of gene expression
- Transcription: DNA sequence is copied to a complementary RNA sequence
- Translation: RNA sequence is template for an amino acid sequence
Central dogma
Proposed by Watson and Crick
DNA -> transcription -> RNA -> translation -> polypeptide
Central dogma exceptions
Some viruses have RNA instead of DNA
- Most replicate by transcribing a complementary RNA strand, which then makes multiple copies of the viral genome
- Retroviruses undergo reverse transcription: making a DNA copy of an RNA genome
Messenger RNA (mRNA)
one strand of DNA is copied to a complementary mRNA strand
- In eukaryotes, mRNA moves to the cytoplasm
Ribosomal RNA (rRNA)
catalyzes peptide bond formation between amino acids to form a polypeptide
- Ribosomes made up of proteins and rRNA
Transfer RNA (tRNA)
binds specific amino acids and recognizes specific sequences in mRNA
- Recognizes which amino acid should be added next to the growing polypeptide chain
Initiation
RNA polymerase binds to a DNA promoter sequence
- Promoters: tell enzyme where to start and which strand of DNA to transcribe
Transcription factors
(eukaryotes): proteins that bind to DNA sequences and RNA polymerase, helping
direct polymerase onto the promote
Elongation
RNA polymerase unwinds DNA about 10 base pairs at a time; reads template DNA strand in 3’ to 5’ direction
Termination
where transcription stops; specified by a specific DNA sequence
- For some genes, transcript forms a loop and falls away from the DNA
- For others, a protein binds to the transcript and causes it to detach from the DNA
Differences between prokaryotic and eukaryotic gene expression
Gene expression is basically the same in prokaryotes and eukaryotes
- Differences in:
- Gene structure
- Location: in eukaryotes, the nucleus separates transcription and translation
Intron
noncoding regions that are transcribed but then spliced out of pre‐mRNA in the nucleus
Exon
coding sequences; reach the ribosome
What happens during pre-mRNA processing
the newly transcribed RNA molecule (pre-mRNA) undergoes modifications including the addition of a 5’ cap, a poly-A tail at the 3’ end, and the removal of non-coding introns through splicing, resulting in a mature mRNA molecule ready for translation into protein; this process occurs primarily in the nucleus of eukaryotic cells
genetic code
specifies which amino acids will be used to build a protein
codon
sequence of three bases, each specifying a particular amino acid
starting codon
initiation signal for translation
- AUG
stop codon
termination signals
- UAA, UAG, UGA
Translation: initiation
a charged tRNA and small ribosomal
subunit, both bound to mRNA
- In prokaryotes, rRNA binds to the Shine‐Dalgarno sequence on the mRNA
- In eukaryotes, it binds to the 5’ cap
Translation: elongation
another charged tRNA enters A site
- Large subunit catalyzes two reactions:
- Bond between tRNA in P site and its amino acid is broken
- Peptide bond forms between that amino acid and the amino acid on the tRNA in the A site
Translation: termination
translation ends when a stop codon enters the A site
Signal sequence
short amino acid sequences that guide newly synthesized proteins to their proper location within the cell
