Chapter 3- From Genes to Proteins Flashcards
what was Griffith’s experiment?
worked with two forms Pneumococcus, one was an encapsulated bacterium that forms smooth colonies and causes death when injected into mice, the other is a mutant strain that lacks the enzymes needed to synthesize a capsule and forms rough colonies and does not cause death when injected into mice; found that when he heat-treated wild-type did not cause death in mice because it destroyed the capsule; found that when he combined heat-treated wild type and mutant type, the mouse died and he found encapsulated bacteria in the mouse tissue, indicated that the mutant strain had incorporated the virulent element from the heat-treated wild type; concept of “transformation”
what was the Avery , Macleod, and Mccarty experiment?
determined that DNA was the transforming principle, found that transformation still occurred if other bio molecules were destroyed by enzymes, but that transformation would not occur if the sample was given enzymes that destroyed DNA
what was the Hershey and Chase experiment?
When bacteriophages containing 32P (radioactive), were allowed to infect nonradioactive bacteria, all the infected cells became radioactive and, in fact, much of the radioactivity was passed on to the next generation of bacteriophages.
However, when the bacteria were infected with bacteriophages labeled with 35S, and then the virus coats removed (by whirling them in an electric blender), practically no radioactivity could be detected in the infected cells.
because P is in DNA and S is in proteins, indicated that DNA was the molecule of heredity
what was the model developed by Pauling and Corey?
DNA adopts a triple-helical structure, three chains tightly packed together, phosphate on the inside of the triple helix, nitrogenous bases on the outside, stabalized by hydrogen bonds between the interior phosphate groups
which bases are purines?
adenine and guanine
which bases are pyrimidines?
cytosine, thymine, and uracil
which bases does DNA contain?
A,C,T, and G
which bases does RNA contain
A,C,U and G
what forms a nucleoside?
linking atom N9 in a purine or atom N1 in a pyrimadine to a five-carbon sugar at C 1’
what is the sugar in DNA
2’-deoxyribose (2’ C contains a H attached to it instead of an OH
what is the sugar in RNA
ribose
what is a nucloeotide?
nucleoside to which one or more phosphate groups are linked, typically at C5’ of the sugar
what are the functions of nucleotides?
building blocks for DNA and RNA, involved in energy transduction, intracellular signaling, and regulation of enzyme activity
what is the linkage between nucleotides?
phosphodiester bond (single phosphate group forms ester bonds to both C5’ and C3’)
what happens when a nucleoside triphosphate is added to the polynucleotide chain?
a diphosphate group is eliminated
what is a residue?
what a nucleotide is formally known as once incorporated into a polynucleotide
what does the nucleic acid structure look like?
nucleotides consecutively linked by phosphodiester bonds in which the bases project out from a backbone of repeating sugar-phosphate groups
what is the 5’ end?
the end of the polymer that bears a phosphate group attached to a C5’
what is a 3’ end?
the end of the polymer that bears a free OH group
how are base sequences in a polynucleotide read?
from 5’ end to 3’ end
how are the two strands of DNA connected
hydrogen bonds between base pairs
what are Chargaff’s rules?
A=T, C=G; A+C=G=T
how many hydrogen bonds like adenine and thymine?
two
how many hydrogen bonds link guanine and cytosine?
three
why is the sugar-phosphate backbone of the two strands of DNA separated by a constant distance?
all base pairs, consist of a purine and pyrimidine, have same molecular dimensions ( about 11 A wide)
what is the shape of DNA?
double helix, the two strands twist around each other
what does it mean that the two polynucleotide strands are antiparallel?
their phosphodiester bonds run in opposite directions, one strand has 5’ to 3’ orientation, the other has 3’ to 5’ orientation
which was is the DNA latter twisted
in a right hand fashion (if you climbed the ladder, railing would be help with right hand)
what are the major and minor grooves?
the twisting of the DNA helix creates two grooves of unequal width
what defines the exterior of the helix?
sugar-phosphate backbone
what defines the interior of the helix?
base pairs, stack on top of one another
are the base pairs accessible to the solvent?
the planar faces of the base pairs are not accessible, but their edges are exposed in the major and minor grooves, which allows for certain DNA binding proteins to recognize specific bases
what is an oligonucleotide?
a short single-stranded polymer of nucleotides
what are the function of polymerases?
polymerize nucleotides
what are the function of nucleases?
hydrolyze the phosphodiester bonds linking nucleotide residues
what is the function of an exonucleas?
removes a residue from the end of a polynucleotide chain
what is the function of an endonucleuase?
cleaves a reside from some point along the chain not at the end
what is the structure of RNA?
single-stranded, greater conformational freedom, can fold back on itself so that base pairs can form between complementary segments of the same strand, assume intricate 3D shapes
what is an RNA-DNA hybrid double helix?
residues of RNA capable of base-pairing with a complementary single strand of DNA, wider and flatter than typical double stranded DNA, inclined to the helix axis by 20 degrees
what is A-DNA?
DNA helix adopting same structure as the RNA-DNA hybrid double helix
what is B-DNA?
standard DNA double helix
what does the structural stability of a double helix depend upon?
stacking interactions, a from of van der Waals interaction between adjacent base pairs, weak but additive along the length of DNA; doesn’t depend as much on hydrogen bonds between base pairs because the bases could satisfy their hydrogen-bonding requirements by forming hydrogen bonds with water
what stacking interactions are the strongest?
between neighboring GC pairs; double helix rich in GC harder to disrupt
what is the melting temperature of DNA?
temperature at which half the DNA has separated into single strands, midpoint of the melting curve
what is denaturation (melting)?
slowly increasing the temperature, at a high temp the base pairs begin to unstack, hydrogen bonds break, and the strands begin to separate
what is renaturation?
separated strands can reform a double helix by reestablishing hydrogen bonds between complementary strands and by restacking base pairs, occurs when temperature is lowered slowly
what happens is separated DNA is cooled too rapidly?
it may not fully renature becuae base pairs may form randomly between short complementary segments, at low temps the improperly paired segments are frozen in place since they do not have enough thermal energy to melt apart and find their correct complements
what determines the rate of renaturation?
the length of the DNA strand, short sequences come together faster because bases in each strand must locate their partners along the length of the complementary strand
what is the purpose of an oligonucleotide probe?
can be used to detect the presence of a complementary nucleic acid sequence in a complex mixture
what is the central dogma of molecular biology?
a portion of the DNA , a gene, is transcribed to produce a complementary strand of RNA, the RNA is then translated into a protein
what is a genome?
an organism’s complete set of genetic info
what are the other names for the template strand?
the noncoding strand, the antisense strand, the negative strand
what are the other names for the nontemplate strand?
the coding strand, the sense strand, the positive strand
what is the orientation of the template strand?
3’ to 5’
what is the orientation of the nontemplate strand
5’ to 3’
what does the RNA look like that gets transcribed from the template strand?
has same sequence as (except for the substitution of U for T) and the same 5’ to 3’ orientation as the nontemplate strand of DNA
what is the transcribed RNA called?
messanger RNA (mRNA)
what translates the mRNA?
a ribosome
what occurs during translation?
small molecules called transfer RNA (tRNA) which carry amine acids, recognize sequential sets of three bases (called codons) in the mRNA through complementary base-pairing (the tRNA has anticodons), the ribosome covalently links the amino acids carried by successive tRNAs to form a protein
how many codons are there in total?
64
what direction does RNA polymerase read?
3’ to 5’
what does it mean when diseases are polygenic?
many genes contribute to the disease
what does it mean when diseases are monogenic?
only one gene causes the disease
what types of organisms have the least amount of DNA and the fewest genes?
organisms with the simplest lifestyles
how does the proportion of noncoding DNA relate to the complexity of the organism?
in general, the proportion of noncoding DNA generally increases with the complexity of the organism
what are transposable elements?
short segments of DNA that are copied many times and inserted randomly into the chromosome, make up a good portion of the noncoding DNA
what is an open reading frame (ORF)
a stretch of nucleotides that can potentially be transcribed and translated, begins with a start codon: AUG which specifies methionine, ends with stop codon: AUU, AUC, or ACU
