DNA, RNA, Proteins, and Enzymes (Review #2) Flashcards
DNA structure
-DNA is a nucleic acid (made of nucleotides; 4 of them in DNA, each with a different base)
-Each nucleotide is made of a phosphate group covalently bonded to a pentose sugar (deoxyribose) bonded to a nitrogenous base)
-Nitrogenous bases in DNA: Adenine, Thymine, Cytosine and Guanine
5’ to 3’ binding overview
(Binding nucleotides together in the 5’ to 3’ direction – condensation – removal of water and formation of covalent bonds called phosphodiester bonds – nucleotides can ONLY be added to the 3’ end!!!)
Rosalind Franklin and Maurice Wilkins at King’s College (DNA structure using x-ray diffraction)
-X-ray diffraction/ X-ray crystallography using crystallized DNA molecules
-X-ray beams pass through crystallized DNA (for tens of hours) and diffract (spread) when they hit atoms (or other objects) and their scattering pattern is recorded on a special film
-The scattering pattern produces an image from which a 3D structure can be deduced
Photo 51 by Rosalind Franklin
-DNA is a double helix
-Phosphate groups on outside of molecule (backbone)
-Nitrogenous bases on inside of molecule
Nucleosome
-Core = 8 histone proteins (+ charged) with DNA molecule (- charged) wrapped twice around (“bead on a string”)
-DNA + histone proteins = chromatin
-Fundamental unit of DNA packaging – allows supercoiling of DNA into chromosomes
-Supercoiling prevents certain genes from being accessed by transcription factors/ enzymes (regulates the process)
Sequences of Nuclear DNA that do or do not code for proteins
- Unique (single-copy) sequences = genes (code for proteins)
-2% of genome - Highly repetitive sequences = found
between genes (form barriers of non-
coding regions between genes)
-5 to 45% of genome
-Short-tandem repeats (STR’s): form
polymorphisms (significant variation
between individuals – used to create
DNA profiles)
-Transposable (moveable = shuffle
genes) - Structural Sequences = pseudogenes (highly coiled at centromeres and telomeres)
-20% of genome
Hershey and Chase Experiments Overview
-Used bacteriophages (viruses that infect bacterial cells – made up of
DNA and a protein coat) with radioisotopes (radioactive forms of
elements that decay at a predictable rate – can detect these in cells)
-Used radioactive phosphorus and radioactive sulfur
-Phosphorus found in DNA (phosphate groups)
-Sulfur found in proteins
-Created one type of bacteriophage with radioactive phosphorus and another type with radioactive sulfur
Allowed two different types of phages to infect bacterial cells
-Note: once a virus infects a cell it “takes over” that cell and forces it to make new viruses
Results of Hershey/ Chase Experiments
-Bacterial cells infected with radioactive phosphorus produced new phages with radioactive DNA.
-Bacterial cells infected with non-radioactive phosphorus produced new phages with non-radioactive DNA.
-None of the new viruses had radioactive sulfur (radioactive phosphorus was found in the pellet)
-DNA was passed on to the new viruses, and protein was NOT: Protein is NOT the genetic material and DNA is!
DNA Replication (HPPLP)
Hettie Pooped Poppies Longer Please
- Helicase unzips the parental DNA molecule (breaking H-bonds between bases)
Note: in eukaryotes, gyrase and single-strand binding proteins stabilize unzipped DNA molecules at many sites - Primase adds a sequence of RNA bases (a primer) to each parental DNA molecule at the replication origin (each parental molecule serves as a template)
- DNA polymerase III adds new nucleotides to the RNA primer (at the 3’ end ONLY) to create a new complementary strand (one for each of the parent DNA molecules – A binds to T, C binds to G)
Continuous in the leading strand, as Okazaki fragments in the lagging strand (moves in a 5’ to 3’ direction – adding new nucleotides to the 3’ end only!) - In the lagging strand, DNA
ligase fills the gaps between
fragments (5’ to 3’) - DNA polymerase I removes
the RNA primers and
replaces them with DNA
nucleotides ( 5’ to 3’
direction – DNA bases left
unpaired at the tip of the 5’
end after primers removed)
Semiconservative
DNA Replication process is semiconservative: each daughter molecule produced is half old (parent) strand and half new strand!
Meselson and Stahl Experiments
-Used 2 different isotopes of nitrogen to grow bacteria (E. coli) cells (14N and 15N)
-First, cultured/ grew bacterial cells in medium containing 15N (which is heavier than 14N)
-After many generations, all bacterial cells contained 15N in their DNA
15N bacteria transferred to medium containing 14N
-After 1 generation in 14N medium, bacteria removed and DNA isolated
-Dissolved DNA in solution and centrifuged (spun around very quickly – this separates dissolved contents based on their density – more dense items sink lower in the tube, lighter items stay closer to top of tube)
14N DNA is light, so it would be found at top of tube; 15N DNA is heavy, so it would be found at bottom of tube
Results of Meselson and Stahl Experiments
ALL DNA in F1 (first) generation made up of one strand with 14N and one strand with 15N (all found in middle of test tube) – this shows that DNA replication IS semiconservative
Genes
unique, single copy sequences of
DNA) are made up of specific sequences of
nucleotides that “code” for the sequence/
order of amino acids that are put together
(by ribosomes) to make up each protein
Central Dogma (basic/ fundamental understanding – universal to ALL life) of Molecular Biology:
DNA to RNA to Protein
(Transcription) (Translation)
Transcription Basics
transcribe (writing down a message)= making mRNA (messenger RNA) from DNA
Translation Basics
Translating from one language to another= making a polypeptide chain – a protein - (putting amino acids together) from mRNA
Ribosomes “read” the mRNA code and use it to put amino acids together in the correct order (based on the original DNA sequence) to make a protein
Codon
Set of 3 mRNA base sequences
DNA vs. RNA: Strand
Double vs. Single
DNA vs. RNA: made of
Deoxyribose vs. Ribose
DNA vs. RNA: Bases
Guanine, Cytosine, Adenine, Thymine vs.
Guanine, Cytosine, Adenine, Uracil
Transcription Steps IET + P (In ET and Prince)
- Initiation: (put everything together)
RNA polymerase (IB Student) unwinds DNA strands and binds to promoter on DNA (antisense/ template strand – serves as template for mRNA to be built off of) - Elongation:
RNA polymerase adds RNA nucleotides (nucleoside triphosphates – two phosphates lost to provide energy for binding) to 3’ end of growing mRNA strand based on code in antisense strand of DNA
Works in 5’ to 3’ direction
Bases added using complementary base pairing rules (A + U and C + G) - Termination: (stops, everything detaches)
RNA polymerase continues until terminator sequence reached (passes in eukaryotes)
mRNA molecule detaches from DNA
RNA polymerase detaches from DNA
-Post-transcription:
In EUKARYOTES: Introns removed to form mature mRNA (only exons remain to be translated into amino acids/ protein) – one gene = many polypeptides (many mRNA from one DNA sequence - alternative RNA splicing by spliceosomes and snRNA’s)
Ribosome Structure
-Small subunit (with mRNA binding site) – binds to large subunit ONLY during translation
-Large subunit (with tRNA binding sites – A site, P site, E site)
-Form polysomes (several ribosomes translating mRNA at the same time)
-70S (density) in prokaryotes; 80S in eukaryotes
-Free ribosomes synthesize proteins for use in the cell
-Bound (RER) ribosomes make proteins for secretion/ use in lysosomes
tRNA facilitates translation
Contains anticodons (3 bases – complementary to codons on mRNA – will base pair to mRNA during translation)
Amino acid binding site (3’ end at sequence CCA)
Amino acids bound to tRNA using ATP and tRNA activating enzymes (20 of them)
