CELL 120 Unit 3
Central Dogma of Biology
DNA -> RNA -> Protein. DNA encodes RNA in the nucleus, RNA leaves the nucleus and RNA encodes polypeptides in the cytoplasm at the ribosome
bidirectional replication
DNA strands unwind, begins outward from the two replication forks, continues in both directions
Hurwitz and Furth
Discovered RNA polymerase, which transcribes RNA. Discovered in a blunt force experiment.
Avery experiment
Follow up on Griffith experiment. Found out that DNA was the transforming factor when they used enzymes to break it down; discovered that DNA stores and transmits genetic information from 1 generation of bacteria to the next.
Base pairing in DNA
occurs through hydrogen bonding, C-G (3 hydrogen bonds) A-T (2 hydrogen bonds). Less reactive than RNA b/c H instead of OH on 2' carbon.
subunits
one gene one enzyme explanation is a little bit simplified. In some cases, multiple genes code or polypeptides that combine to form one enzyme
Beadle and Tatum experiment
one gene one enzyme hypothesis. If a gene is mutated or defective- will affect the protein
3 parts of nucleic acids
phosphate group, pentose (5-C) sugar, Nitrogenous bases
polysaccharide
polymer (glycogen)
macromolecules
polymers- large molecules that are made up of smaller molecules or monomers
termination of translation
polypeptide freed from ribosome when stop codon reached. Synthesis is from N-terminus to C-terminus
open reading frame in translation
portion of DNA that corresponds to the part of the RNA that encodes the translated
exons in eukaryotes
portion of gene that codes for amino acids. processing involves "capping" at 5' end and poly-A tail at 3' end
Structures that determine shape and function
primary, secondary, tertiary, quaternary structures
Level that determines protein shape and function
primary- all levels affects function but primary starts it
nitrogenous bases
purines and pyrimidines
dispersive replication
replication results in both original and new DNA dispersed among the two daughter strands
tertiary structure
secondary structures and other coiled regions fold into 3-D shapes. This is when a polypeptide may become functional protein. Defines quaternary
DNA replication can be
semiconservative, conservative, dispersive
primary structure
sequence of amino acids, linear sequence, and defines secondary structure
okazaki fragment
short sequences of DNA nucleotides which are synthesized discontinuously and later linked together by the enzyme DNA ligase to create the lagging strand during DNA replication.
types of DNA mutations
silent, missense, nonsense, frameshift
DNA
storage molecule of genetic information in all organisms except some viruses. Double stranded and antiparallel. Reads 3'-5'. Base-pairing occurs between antiparallel strands.
leading strand
strand that is getting read for replication
chirality
structure and its mirror image are not identical. Molecules are chiral- lift or right handed- amino acids are chiral
polysaccharides (polymer)
sugar subunits (monomer)
A site
tRNA enters
RNA primer
that serves as a starting point for DNA synthesis. Required for DNA replication-enzymes that catalyze this process
Non-template strand
the strand of DNA that is not transcribed into RNA during transcription. Coding; sense strand.
treatment 4 of Griffith's experiment
control: injected living R and heat killed type S bacteria into mouse living type R cells have been transformed into virulent type S cells by a substance form the heat killed type S cells
Treatment 1 of Griffith's experiment
control: injected living S bacteria into mouse Conclusion: type S cells are virulent
Treatment 2 of Griffith's experiment
control: injected living type R bacteria into mouse conclusion: type R cells are benign
"heat-killing" bacteria
denatures proteins, but DNA is still intact
Replication
double stranded and replicated in nucleus. Before cells divide, they need to double the amount of DNA so resulting daughter cells contain correct amount of DNA.
DNA polymerase 3
duplication of the chromosal DNA
ligase
joins the okazaki fragments and DNA synthesized after replacing the RNA primer
protocol for hershey and chase experiment
label protein of DNA of bacteriophages, let bacteriophages infect bacteria, remove "ghosts" from outside of bacteria see what the bacteriophages injected protein or DNA.
translation =
mRNA > polypeptide
DNA replication
1. DNA is unwound (5'-3' top, with 3-5' bottom- anti parallel) breaking the hydrogen bonds between nitrogenous bases 2. RNA primers are inserted- primase (protein that acts like an enzyme) lays down the RNA primer. Lays down a shorter version of RNA on top of parts of the DNA with its opposite 3. DNA synthesized 5'-3'- mixes DNA and RNA together 4. DNA is unwound (leading and lagging strand) 5. more RNA primers are inserted 6. DNA replication continues 7. DNA replication continues, primers are removed, fragments are joined- okazaki fragments
translation at the ribosome
3 Sites E, P, A
tRNA is read
3'-5'
DNA is read
5'-3'
mRNA is read
5'-3'
nonsense mutation
A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.
aminoacyl-tRNA synthetase
An enzyme that joins each amino acid to the correct tRNA. Amino acid is activated by the covalent binding of AMP and pyrophosphate is released. Correct tRNA binds to synthetase, and amino acid is covalently attached and AMP is released. The charged tRNA is released. Protein loads amino acids onto tRNA, then used at the ribosome to translate a mRNA transcirpt into amino acids
DNA repair mechanisms
Any of several processes by which enzymes repair DNA damage. DNA polymerase 1 & 3- proofread and correct point mutations during replication
Nirenberg and Leder experiment
Made codons in a "soup" applying product rule. Codon probability: proportion (normalizing the data) the probability is compared to 1.00
semiconservative replication
Method of DNA replication in which parental strands separate, act as templates, and produce molecules of DNA with one parental DNA strand and one new DNA strand - how DNA actually replicates
basic (alkaline)
R groups attract H+ ions out of solution
hydrophobic
R groups do not interact with water- associated with membranes
aromatic
R groups have ring structures
hydrophilic
R groups interact readily with water
Acidic
R groups lose H+ ions to solution
3 polymerases in eukaryotic transcription
RNA polymerase 1 - makes large rRNA transcripts RNA polymerase 2- makes mRNA transcripts RNA polymerase 3- makes tRNA and small rRna transcripts
Pentose (5-C) sugar
Ribose (in RNA) and deoxyribose (in DNA)
Key components of Avery experiment
S-strain bacteria; virulent R-strain bacteria; non-virulent DNA from S strain bacteria DNase= enzyme that "chews up" all DNA present RNase= enzyme that "chews up" all RNA present Protease= enzyme that "chews up" protein
template strand
The DNA strand that provides the template for ordering the sequence of nucleotides in an mRNA transcript. anti-coding, non-sense strand. 3'-5'
Thymine Dimer formation
Ultraviolet exposure can commonly result in DNA damage. Which causes a mutation.
Biochemical pathway
a gene code for protein that has a function in the cell.
purines
adenine (A) and guanine (G)
4 deoxyribonucleotides
adenine, guanine, cytosine, thymine. Doesn't have 2 prime hydroxyl group (H not OH-)
4 ribonucleotides
adenine, guanine, cytosine, uracil- have 2 prime hydroxyl group (OH-)
silent mutation
alters a base but does not change the amino acid
protein or polypeptide (polymer)
amino acid subunits (monomer)
Initiation of translation
mRNA is attached to a subunit of the ribosome, the first codon is always AUG. tRNA binds to start codon of mRNA. Large ribosomal subunit binds
translation continued
mRNA sequence "interpreted" 5'-3' RNA message is "translated" by tRNAs (complementary recognition sequences or anticodons, are read 3'-5')
transcription orientation
mRNA sythesized 5'-3'. Made off the template strand of DNA- exact copy of non-template strand.
monosaccharide
monomer (glucose)
Nucleic Acid (polymer)
monomers are nucleotides. Formed from condensation/dehydration reactions. Building blocks of nucleic acids- DNA and RNA
frameshift mutation
mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide
introns in eukaryotes
not in prokaryotes. are spliced out in the mRNA processing- there until transcription
Griffith's experiment
an experiment carried out by Griffith using the heat-killed bacteria in mice to discover that a factor in heat-killed, disease-causing bacteria can "transform" harmless bacteria into ones that can cause disease
topoisomerase/gyrase
any of a class of enzyme that reduce supercoiling in DNA by breaking and rejoining one or both strands of the DNA molecules
Single stranded binding protein
binds to single-stranded regions of DNA
How genes work
biochemical pathway, and subunits
phosphodiester bond
bond formed in nucleic acid synthesis
amino acids
building blocks of proteins
DNA + proteins =
chromosomes. if RNA transcription is happening
Hershey-Chase Experiment
confirmed that DNA is the genetic material because only radiolabeled DNA could be found in bacteriophage-infected bacteria
sulfur
containing
Treatment 3 of Griffith's experiment
control: injected heat killed type S bacteria into mouse conclusion: heat killed type S cells are benign
nucleic acid (polymer)
nucleotide subunits (monomer) RNA: Ribonucleotide subunits DNA: deoxyribonucleotide subunits
DNA is located in
nucleus
missense mutation
A base-pair substitution that results in a codon that codes for a different amino acid.
conservative replication
Conservative replication is a theoretical method of replication where the original strands of DNA are left intact and two new strands are formed bonded together.
pyrimidines
Cytosine (C), Uracil, (U) and thymine (T)
Initiation of bacterial transcription prokaryotes
Initiation: promotor functions as recognition site for sigma factor. RNA polymerase is bound to sigma factor, causing it to bind to promotor. Elongation/synthesis of RNA transcript: sigma factor is released, and RNA polymerase slides along the DNA is an open complex to synthesize RNA Termination: RNA polymerase reaches the terminator, it and the RNA transcript dissociates from the DNA
Helicase
enzymes that bind and may even remodel nucleic acid or nucleic acid protein complexes
E site
exit site
polymerization
formation of a polymer from monomers- occurs through dehydration (condensation) reaction and hydrolysis reaction
formation of polypeptides
formed though condensation reactions, forms peptide bond. In polypeptide chain- letter code- and synthesized from N-terminus to C-terminus
lagging strand
has the same DNA as the leading strand but is not used in replication -just chillin
secondary structure
hydrogen form to alpha-helices and B-pleated sheets. Defines tertiary structure
types of amino acid categories
hydrophobic, hydrophilic, basic (alkaline), Acidic, Sulfur, aromatic
DNA polymerase 1
to fill DNA gaps that arise during DNA replication, repair and recombination
transcription
to make a written copy of, to transfer (data) from one recording form to another-DNA is transcribed
translation
to turn into one's own or another language. To transfer or turn from one set of symbols to another- RNA is translated
Quaternary structure
two or more polypeptides join together to form a functional protein
Initiation of Eukaryotic Transcription
variable promotors bind to DNA "TATA" box at -30. The "TATA" signals to promotor. 3 RNA polymerases
dehydration (condensation reaction)
water is formed in the creation of bonds
hydrolysis reaction
water is used up in breaking up bonds
P site
where the new amino acids are connected to the polypeptide chain
Ribosome
where translation occurs- rough ER- made up of a small and large subunit