mod 7: Molecular Genetics Flashcards
nucleic acid
weakly acidic, phosphorus-containing substance from the nucleus. two types are DNA and RNA
deoxyribonucleic acid (DNA)
also known as deoxyribose nucleic acid. the nucleic acid molecule that governs the process of all heredity in all cells
transforming principle
the phenomenon discovered by Fredrick Griffith where dead pathogenic bacteria pass on their disease-causing properties to living non-pathogenic bacteria, transforming the living bacteria into disease-causing.
nucleotide
repeating unit of DNA. two strings of nucleotides joined in the middle by a hydrogen bond form a DNA molecule. each is made up of deoxyribose sugar, a nitrogenous base (of which there are four types), and a phosphate group
what are the four bases found in DNA nucleotides?
adenine (A), guanine (G), cytosine (C), and thymine (T)
adenine
a nitrogenous base of the purine (double ring structure) group. complementary base pairs with thymine (double hydrogen bond)
thymine
a nitrogenous base of the pyrimidine (single ring structure) group. complementary base pairs with adenine (double hydrogen bond)
guanine
a nitrogenous base of the purine (double ring structure) group. complementary base pairs with cytosine(double hydrogen bond)
cytosine
a nitrogenous base of the pyrimidine (single ring structure) group. complementary base pairs with guanine (double hydrogen bond)
Chargaff’s rule
in any sample of DNA, there is a a constant relationship in which the amount of A is roughly equal to the amount of T and the amount of G is roughly equal to the amount of C
complementary base pairs
A-T and C-G pairs held together by hydrogen bonds. these combinations fit together perfectly and are the only way to organize the bases while also maintaining the constant radius of DNA’s 3D structure
Hershey-Chase experiment
- proved that DNA is responsible for heredity and not protein. two parts:
the protein part of a virus (which attaches to cells and injects genetic materials into them, causing them to produce more viruses) was labelled with radioactive sulfur and allowed to infect a cell. no radioactivity was found inside the cell, only outside.
the DNA part of the virus was labelled with radioactive phosphorus and allowed to infect a cell. radioactivity was found inside the cell, not outside.
Friedrich Miescher
- coined the term “nucleic acid” to describe a weakly acidic, phosphorus-containing substance he’d isolated from the nucleus of white blood cells.
Phoebus Levene
early 1900s. isolated RNA and DNA. showed that chromosomes are made up of a combination of DNA and proteins. determined that both DNA and RNA are made up of long chains of individual units (nucleotides), of which there are four types.
concluded incorrectly that nucleotides were present in equal amounts and that they appeared in chains in a constant repeating sequence, leading scientists to believe that DNA was too simple to be the molecule of heredity
Fredrick Griffith
- discovered and named the transforming principle.
Erwin Chargaff
late 1940s. determined the Chargaff’s rule that nucleotides are not present in equal amounts but are present in varying but characteristic proportions. adenine and thymine are always roughly equal and cytosine and guanine are always roughly equal.
Rosalind Franklin
1950s. used x-ray tech to analyze the 3D structure of DNA. was able to conclude that DNA has a helical structure with two regularity occurring patterns. concluded nitrogenous bases were located on the inside of helical structure, and sugar phosphates on the outside.
James Watson and Francis Crick
- first to produce a structural model of DNA that could account for all the experimental evidence. this model is the ones currently used
why was protein believed to be the substance responsible for heredity and variation?
because proteins are made of many amino acids but DNA is only made up of four bases. DNA seemed too simple to account for all the variation within a species and between different species
Oswald Avery, Colin Macleod, and Maclyn McCarty
- continued with Griffith’s studies. aimed to find the material responsible for the transforming principle.
took DNA, RNA, proteins, lipids, and carbohydrates from the dead pathogenic bacteria and combined it with non-pathogenic bacteria to see which would turn it pathogenic and cause it to kill the mice. only the bacteria that had been cultured with DNA killed the mouse.
also tried treating the pathogenic heat-killed bacteria with a protein destroying enzyme. it still cause the transformation to occur and the mouse to die. treating the pathogenic heat-killed bacteria with a DNA destroying enzyme prevented the transformation from occurring and the mouse lived.
polynucleotide
many nucleotides bonded together in a chain
deoxyribose sugar
the five carbon sugar in DNA. called this because it lacks an oxygen atom that is normally found in the ribose sugar molecule.
what causes the coiling of DNA strands?
hydrogen bonds between bases
mutation
change in sequence of bases on the DNA molecule
DNA replication
process of creating an exact copy of a molecule of DNA
genome
the sum of the entire DNA carried in an organism’s cells. includes all genes as well as regions of “non-coding” DNA that may play various roles in gene expression
gene
functional sub-unit of DNA that directs the production of one or more polypeptides (protein molecules). not spaced regularly along chromosomes (some chromosomes may have less base pairs but more genes than others). encodes proteins, tRNA, or rRNA, or regulates the transcription of such a sequence.
semi-conservative (DNA replication)
each new molecule of DNA contains one strand of the original complementary DNA and one new daughter strand. each new DNA molecule conserves half of the original molecule
replication origin
specific nucleotide sequence where replication begins. prokaryotes may have just one while eukaryotes may contain thousands
helicases
group of enzymes that bind to DNA at the replication origin, cleaving the double helix (removing the hydrogen bonds between bases, therefore also uncoiling the DNA structure). creates the replication bubble and replication fork structures.
replication bubble
oval-shaped area created by the unwound double helix
replication fork
Y-shaped areas on each end of the replication bubble. consists of two unwound DNA strands that branch out into two unpaired (but complementary) single strands. the point where new strands develop. it constantly moves along DNA until the two original strands are entirely separate
DNA polymerase
adds new nucleotides to the 3’ OH group of an existing nucleotide strand. dismantles the RNA primer. “proofreads base pairings”—if hydrogen bonds do not form between the parent and new strand, then the base pairing must be incorrect, so the faulty base is replaced with the correct base based on the parent strand
primer
short strand of RNA that serves as a starting point for the attachment of new nucleotides by DNA polymerase
leading strand
replicated continuously in the 5’ to 3’ direction by DNA polymerase. runs in the 3’ to 5’ direction. antiparallel to the lagging strand
lagging strand
replicated in short segments called Okazaki fragments. runs in the 3’ to 5’ direction, antiparallel to the leading strand. nucleotides are still added in the 5’ to 3’ direction but since the fork is moving the other way (along the leading strand), the synthesizing needs to constantly catch up and form new fragments that begin closer to the fork. think of back stitching in embroidery
Okazaki fragment
short segments of DNA synthesized by the lagging strand. spliced together afterwards by DNA ligase
DNA ligase
splices together Okazaki fragments in the lagging strand
primase
enzyme that synthesizes an RNA primer to begin the elongation process, so that DNA polymerase has something to work off of
replication machine
the complex of polypeptides and DNA that interact at the replication fork
elongation (simple definition)
the process of joining nucleotides to extend a new strand of DNA
what are the two conditions of elongation?
- elongation can only take place in the 5’ to 3’ direction
- a primer must serve as the starting point for the attachment of new nucleotides (because DNA polymerase cannot build a starting point itself and needs something it can build off of)
elongation (description of process, excluding proofreading)
primase constructs a primer. DNA polymerase extends the DNA strand by adding nucleotides. this is a continuous process in the leading strand.
in the lagging strand, many primers are needed because the strand is essentially backstitching to keep up with the movement of the fork. a primer is created, DNA polymerase builds off of it and removes it, DNA ligase replaces it with nucleotides, and another primer is created, the DNA polymerase again extends it towards the just-finished segment and the process repeats itself. each segment like this is called an Okazaki fragment.
this repeats until the two new DNA strands are separate from each other. as soon as they are complete, they rewind into their chemically stable helix structure
elongation (finishing up, proofreading)
after each nucleotide is added to a new DNA strand, DNA polymerase can recognize whether hydrogen bonding is taking place. absence of hydrogen bonding indicates a mismatch between bases. DNA polymerase removes the incorrect base and replaces it with the correct one, using the parent strand as a template
termination
the completion of the new DNA strands and the dismantling of the replication machine
DNA sequencing
the process of identifying the precise nucleotide sequence of a DNA fragment
5’ carbon (5’)
read “fifth prime carbon”. attached a phosphate group
3’ carbon (3’)
read “three prime carbon”. attached to is is OH
where are bonds between adjacent nucleotides formed?
between the hydroxyl group of the 3’ carbon of one nucleotide and the phosphate group of the 5’ carbon of the following nucleotide
genetic code
the order of base pairs in a DNA molecule
transcription (simple definition)
the process of producing a strand of messenger RNA (mRNA) that is complementary to a segment of DNA.
mRNA
“messenger RNA”. linear strand of RNA that carries information from DNA in the nucleus to the protein synthesis machinery in the cytoplasm of the cell.
sense strand
the strand of DNA that is transcribed during the process of transcription
anti-sense strand
the strand of DNA opposite to the one being transcribed during the process of transcription
RNA polymerase
an enzyme that catalyzes the synthesis of RNA. in eukaryotes, each RNA polymerase has a specific function.
promoter region
sequence of nucleotides in DNA that tell the RNA polymerase complex where to bind during transcription.
transcription (process)
RNA polymerase complex binds to the sense strand of the DNA molecule (in the promoter region), it opens a section of the double helix. enzymes then work their way along the DNA molecule (5’ to 3’) and synthesize a string of mRNA that is complementary to the sense strand (but since it’s RNA, thymine is instead uracil). a specific nucleotide sequence in the template DNA signals to stop transcription. mRNA is released and the DNA double helix reforms
codon
set of three bases that code for an amino acid or termination sequence. (see table 18.3 on p637 for which codon corresponds with which amino acid). UAA, UAG, and UGA are terminator codons. always interpreted based on the mRNA rather than template DNA. the start codon is AUG and also codes for the amino acid methionine
tRNA
“transfer RNA”. made up of a single strand of RNA that folds into a characteristic shape. one lone contains the anticodon and the opposite end of the molecule has a binding site for the amino acid that corresponds to the codon
ribosomes
main structures of protein synthesis. bring together mRNA, tRNA, and enzymes necessary to build polypeptides. contains rRNA
anticodon
stretch of three nucleotides on tRNA that is complementary to the mRNA codon
rRNA
“ribosomal RNA”. linear strand of RNA that remains associated with the ribosomes
translation (process)
mRNA molecule binds to an active ribosome complex in such a way that two adjacent codons are exposed. tRNA carrying methionine base-pairs with the first exposed mRNA codon: AUG. translation follows a cycle of these steps:
- second loaded tRNA molecule arrives at the codon adjacent to the first tRNA
- amino acid carried by first tRNA joins to the amino acid carried by second tRNA through chemical bond (w/ enzyme catalysts). amino acid chain transferred from the first tRNA to the second one
- ribosome moves one codon down mRNA strand. first tRNA detaches and leaves (replenishing it’s amino acid supply). second tRNA is now in the spot the first one was in and a third tRNA arrives at the spot adjacent to it, and the cycle repeats (with the second tRNA now being referred to as the first and the third being referred to as the second, so each new tRNA gets the whole polypeptide chain transferred to it each cycle)
these steps are continued until the stop codon is reached. completed polypeptide chain is released and the ribosome assembly comes apart
adaptive advantage
a difference in structure, physiology, or behaviour that gives an organism a better chance of survival
somatic cell mutation
mutation that occurs in body cells and is passed on to daughter cells but not to offspring of the organism
germ line mutation
mutation of a gamete cell. passed on to the next generation. source of genetic variation
what are the two types of mutation?
point mutation and chromosomal mutation
point mutation
chemical change that affects just one or a few nucleotides (substitution of one for another, addition of extra nucleotides, deletion of nucleotides)
effects of substitution (point mutation)
- due to the fact that different sequences can code for the same protein, sometimes mutation has no effect
- can change the amino acid in a protein and make it function different or create a new type of protein that meets different needs altogether
- can cause no protein to be built at all (if the start codon is changed or a stop codon is made prematurely)
frameshift mutation
caused by insertion or deletion of nucleotides. the entire reading frame to be altered and to shift, causing series of new codons for different amino acids and causing leftover nucleotides
chromosomal mutations
crossing over and nondisjunction are both chromosomal mutations. part of the chromosome is duplicated or lost doing DNA replication
what kind of mutations are passed on to the next generation?
only mutations affecting gametes are passed down
silent mutation
mutation that has no effect on the cell’s metabolism
mi-sense mutation
mutation that results in an altered protein. can be harmful (sickle cell anemia) or helpful (antibodies in the immune system)
nonsense mutation
mutation that renders the gene unable to code for a functional protein (due to deleted start signal or creation of a premature stop signal)
spontaneous mutation
mutation caused by molecular interactions that take place naturally within the cell.
what is a source of spontaneous mutation?
incorrect base pairing by DNA polymerase during DNA replication
rate of spontaneous mutation
varies in different organisms and even among different genes in the same cell. can be increased by exposure to certain factors in the environment
induced mutation
caused by mutagen outside the cell
mutagen
substance or event that increase rate of mutation. two categories are physical and chemical
physical mutagens (examples?)
mutagens that cause physical changes to the structure of DNA. (ex: X rays, UV rays,
chemical mutagen (examples?)
can enter the nucleus of a cell and induce mutations by reacting chemically with DNA. (ex: nitrites (found in food preservatives), gasoline fumes, compounds from cigarette smoke). most are carcinogenic.
carcinogenic
mutagens associated with one or more forms of cancer
biotechnology
the use of natural biological systems to create new technologies and products. includes genetic engineering
genetic engineering
manipulation of genetic material to alter genes and to blend plant, animal, and bacterial DNA
DNA microarray (definition)
chip (usually glass) that contains a grid of thousands of microscopic cells, where each cell contains a DNA or RNA sequence that can bind with one of the mRNA molecules transcribed during gene expression
DNA microarray (usual steps)
- mRNA extracted from cell(s) to be studied
- each mRNA sample used to make cDNA (copy DNA, artificial form of DNA), marked by a fluorescent tag for easy identification
- cDNA samples are incubated with the microarray and binds to corresponding areas of cells’ DNA
- microarray is scanned and analyzed to compare patterns to gene expression in each cell sample
cDNA
“copy DNA”. artificial form of DNA
recombinant DNA
molecule of DNA that includes genetic material from different sources (ex: the DNA of the spider goats)
restriction enzyme
enzyme that cuts DNA at specific nucleotide sequences
target sequence
short sequence of nucleotides with a strand of DNA recognized and cut by restriction endonuclease. they are organized in such a way that they are the same on both strands, but going in different directions (ex: GAATTC on one strand and CTTAAG on the other)
restriction endonuclease
type of restriction enzyme that recognizes a target sequence (short sequence of nucleotides) within a strand of DNA and cuts the strand at that point (the restriction site), producing two restriction fragments (with sticky ends)
restriction site
specific location within a short sequence of nucleotides (the target sequence) in a strand of DNA where restriction endonuclease will cut
restriction fragments
small segment of DNA cut from a DNA molecule by restriction endonuclease
sticky end
staggered cuts leave a few unpaired nucleotides on a single strand at each end of the restriction fragment. the part of the strand with the unpaired nucleotides is the sticky end and can form base pairs with complementary sticky end strands (even from other organisms)
DNA ligase (in genetic engineering)
splices together DNA fragments that have formed base pairs with each other
what is it about the target sequence that makes sticky ends occur?
the target sequence is the same on both strands of DNA but, since it is complementary, it goes in a different direction on one strand. the nucleotides between which the restriction endonuclease cuts are usually not in the centre, and since they’re antiparallel, this causes the cut to be staggered.
chimera
genetically engineered organism that contains DNA from unrelated species
plasmid
small self-duplication loop of DNA in a prokaryotic cell that is separate from the main chromosome and contains from one to a few genes
bioremediation
use of living cells to perform environmental clean-up tasks (ex: using bacteria to clean up oil spills)
transgenic organism
produced by incorporating the DNA from one organism into another to create a new genetic combination
process of cloning
- unfertilized eggs are collected from a donor animal and the nuclei are removed. somatic cells are collected from the genetic donor and cultivated in medium that stops cell division.
- nuclei of genetic donor’s somatic cells are transplanted into the egg cells
- the cells are traced with an electrical correct to restart the cell cycle.
- resulting cells are cultured. some being to produce early embryos
- embryos implanted into uterus of surrogate mother. one embryo survives to produce a clone of the genetic donor
gene replacement therapy
process of changing the function of genes to treat or prevent genetic disorders
DNA vector
a carrier of foreign DNA that will transplant it into target cells in the patient. some are made by genetically altering viruses to carry the target DNA
what do DNA microarrays allow scientists to do?
analyze the activity of thousands of genes at once
gel electrophoresis (process)
- a solution containing many DNA fragments (DNA must be amplified: copied many times to produce a large number of identical DNA molecules) is applies to one end of a gel.
- an electric current is passed through the gel, causing the end farther from the DNA to develop a positive charge and the closer end to develop a negative one.
- because DNA has a negative charge, it moves towards the positive end, but small molecules move through the gel faster, causing the fragments to separate into a pattern of bands: the DNA fingerprint
gel electrophoresis (definition)
technique used to separate molecules according to their mass and charge. can be used to separate fragments of DNA
DNA fingerprint
pattern of bands formed during DNA electrophoresis. unique for every individual except genetically identical siblings (such as identical twins)
what can DNA fingerprints be used for in society?
to solve crimes: a DNA fingerprints is created of the suspect and DNA found at the scene
to determine parentage: DNA is inherited equally from both parents so a child’s DNA fingerprint must show some matches with the DNA fingerprint of each parent
mtDNA (definition)
“mitochondrial DNA”. genetically identical to that of the mother because the cytoplasm of the organism (which contains the mitochondria) is derived from the egg.
mtDNA (uses)
variation in this DNA can only be derived from mutation so comparing mtDNA can give an idea of how closely two people are related
cpDNA
“chloroplast DNA”. circular molecules of DNA found in chloroplasts that codes for the function of photosynthesis
endosymbiont theory
theory that eukaryotic cells developed by one species of prokaryote engulf another so that organelles are formed
