2.1. Chemical Basis of Heredity Flashcards
• DNA as the Genetic Material • DNA Structure • DNA Organization in Chromosomes • RNA as Genetic Material
what characteristics should a molecule possess for it to serve as the genetic material?
(1) replication
(2) storage of information
(3) expression of information
(4) variation by mutation
what is replication?
a fundamental property of all living organisms; part of cellular reproduction
explain what storage of information is about
the molecule acts as a repository of genetic information wherein it has the ability to encode diverse information
true or false: a molecule always expresses the genetic information it stores.
false. information may or may not be expressed. while most cells contain a complete copy of the organism’s genome, they express only a part of this genetic potential at any point in time. example: bacteria “turn on” specific genes in response to specific environmental conditions; when conditions change, they “turn it off”
what is considered to be the underlying basis of the process of information flow within cells?
expression of (stored genetic) information
detail the process of information flow in cells
(1) transcription of DNA
(2) three main types of RNA are synthesized:
🔸messenger RNA (mRNA)
🔸ribosomal RNA (rRNA)
🔸transfer RNA (tRNA)
(3) translation : mRNA directs the construction of a chain of amino acids, called a polypeptide, which then folds into a protein
explain variation by mutation
🔸mutation, a change in the chemical composition of DNA, is the source of variability among organisms
🔸alterations may be reflected during genetic expression (transcription and translation)
🔸if mutation is present, it may be passed to future generations and with time, become distributed throughout the population
🔸genetic variation provides the raw material for the process of evolution
how are the evidences that DNA is the genetic material classified?
direct
indirect
direct evidences that DNA is the genetic material
(1) avery-mcleod-mccarty experiment
(2) hershey-chase experiment
(3) recombinant dna technology
(4) phage DNA-mediated infection
explain the avery-mcleod-mccarty experiment. how is it a direct evidence?
(1) heat-killed IIIS were used to see if they could transform non-virulent IIR cells into virulent ones
(1) the filtrate was treated with enzymes: DNAse, RNAse, and protease
(2) protease and RNAse treatment: when the heat-killed IIIS cells were treated with protease and RNAse respectively and then mixed with IIR cells, transformation still occurred.
(2) DNAse Treatment: when the heat-killed IIIS cells mixed with IIR cells were treated with DNAse, no transformation occurred.
conclusion : dna is the transforming substance given that no transformation occurred when the dna from the s strain was broken down during the DNAse treatment
species: streptococcus pneumoniae
explain the hershey-chase experiment. how is it a direct evidence?
(1) DNA of the T2 bacteriophages was labeled with radioactive phosphorus-32 (^32P), since DNA contains phosphorus
(2) the protein coat was conversely labeled with radioactive sulfur-35 (^35S), since proteins contain sulfur
(3) the labeled bacteriophages were allowed to infect ecoli. during infection, the phages attach to the bacterial cell and inject their genetic material into it.
(4) after the injection, the mixture was agitated in a blender to separate the phage coats from the bacterial cells and was centrifuged to separate the heavier bacterial cells from the lighter phage coats
(5) radioactive DNA (^32P) was found in the bacterial pellet, indicating that DNA had entered the bacterial cells
(6) radioactive protein (^35S) was found only in the surface, indicating that the protein coats did not enter the bacterial cells
conclusion : the genetic material in T2 phage is DNA
explain how recombinant DNA technology is a direct evidence of DNA being the genetic material
recombinant DNA technology involves splicing together DNA sequences from different organisms. for example, a recombinant DNA molecule is produced when u combine the DNA coding for human insulin with bacterial DNA. when introduced into bacteria, the recombinant dna is replicated and expressed, leading to the production of human insulin. this is a concrete evidence that DNA carries genetic information and codes for specific genes.
explain how phage DNA-mediated infection directly illustrates that DNA is the genetic material
the phage DNA carries all the genetic information needed to produce new phages. this shows that DNA is the genetic material responsible for heredity. for example: hershey-chase experiment
what are the indirect evidences that DNA is the genetic material?
(1) DNA absorbs at the wavelength shown to be mutagenic : (mutagenesis)
(2) DNA is found only where the primary genetic function is known to occur : (distribution of DNA)
explain how mutagenesis (DNA absorbs wavelength shown to be mutagenic) is an indirect evidence of DNA being the genetic material
UV light induces mutations in the genetic material. by irradiating simple organisms like yeast and fungi with UV light at different wavelengths, an action spectrum can be created that shows the mutagenic effectiveness of UV light at various wavelengths. when the action spectrum was compared with the absorption spectrum (shows the amount of light a molecule absorbs strongly), it was found that the wavelengths causing the most mutation (around 260 nm) matched the wavelengths where DNA absorbs the most light, in comparison to protein, which absorbs most strongly at 280 nm
explain how the distribution of DNA (DNA is found only where primary genetic function is known to occur) indirectly shows that DNA is the genetic material
DNA is found only in locations where genetic functions occur (nucleus, mitochondria, chloroplasts), whereas proteins are found throughout the cell, supporting DNA as the genetic material.
a long polymer composed of nucleotides
nucleic acid
true or false: DNA is a nucleic acid
true
what are the building blocks of DNA?
2-deoxyribonucleotides
what are the three components of 2-deoxyribonucleotides?
(1) nitrogenous bases
(2) pentose sugar
(3) phosphate group
two kinds of nitrogenous bases
(1) purines (nine-member-double-ring)
(2) pyrimidines (six-member-single-ring)
types of purines and pyrimidines
purines : adenine and guanine
pyrimidines : cytosine, thymine, and uracil in RNA
what are the pentose sugars in RNA and DNA respectively?
ribose; deoxyribose
differentiate ribose and deoxyribose/2-deoxyribose
ribose has a hydroxyl group in carbon 2 whereas deoxyribose only has a hydrogen atom in carbon 2 (hence, 2-deoxyribose)
structure : cytosine vs uracil vs thymine vs adenine vs guanine
cytosine : NH2 at carbon 4
uracil : carbon 4 is double bonded to oxygen
thymine : methyl group at carbon 5
adenine : NH2 at carbon 6; H at carbon 2
guanine : carbon 6 is double bonded to oxygen; NH2 at carbon 2
what is a nucleoside?
nitrogenous base + pentose sugar
what is a nucleotide?
nitrogenous base + pentose sugar + phosphate group
describe the bonding (n-glycosidic bond) between components of a nucleotide when the base is purine and pyrimidine
purine (double ring) : N-9 atom is covalently bonded to the C1 atom of the sugar
pyrimidine (single ring) : N-1 atom is bonded to the C1 atom of the sugar
in deoxyribonucleotides, the phosphate group is usually bonded to what carbon?
carbon 5
nucleotides are also described by the term ____.
nucleoside monophosphate (NDM); the addition of one or two phosphate groups results in nucleoside diphosphate (NDP) and triphosphate (NTP)
what kind of bond is formed when a nitrogenous base is bonded to a phosphate sugar (C1)?
n-glycosidic bond
what kind of bond is formed when a phosphate group is bonded to only one sugar molecule (C5)?
phosphoester bond
what type of bond is formed when the phosphate group is bonded to two (hydroxyl groups in) sugar molecules (in dinucleotides)?
phosphodiester bond or 3’ to 5’ phosphodiester bond
names of the nucleosides and nucleotides of DNA
in deoxyribonucleosides:
(1) deoxyadenosine
(2) deoxycytidine
(3) deoxyguanosine
(3) deoxythymidine
in deoxyribonucleotides:
(1) deoxyadenylic acid
(2) deoxycytidylic acid
(3) deoxyguanylic acid
(4) deoxythymidylic acid
two joined nucleotides; three nucleotides; short chains up to 30 nucleotides; longer chains
dinucleotide; trinucleotide; oligonucleotides; polynucleotides
a simplified notation of DNA using short tandem repeats (STRs), which are short sequences of DNA, typically 2-5 base pairs, that are repeated numerous times in a row at specific lcoations
shorthand method
the basis of watson and crick DNA model; aqueous, low-salt conditions; biologically significant conformation
B-DNA
suggested that the structure of DNA was some sort of helix; confirmed the 3.4 A periodicity, which means that the nitrogenous bases are 0.34 nm apart
x-ray diffraction data; process is called x-ray diffraction analysis
major features of watson and crick DNA model
(1) right-handed double helix
(2) anti-parallel : 5’ to 3’ running in opposite directions
(3) nitrogenous bases are planar, perpendicular to the axis, and stacked on one another
(4) has specific nitrogenous base pairings as a result of hydrogen bonds : adenine and thymine; guanine and cytosine
(5) a complete turn of the helix is 34 angstroms or 3.4 nm long = 10 base pairs
(6) alternating larger major groove and smaller minor grooves in any segment of the molecule
(7) diameter of double helix is 20 angstrom or 2.0 nm
the stability of DNA is due to what?
chemical bonds and and hydrophobic interactions
chemical bonds:
(1) covalent bonds
(2) hydrogen bonds
a type of bond formed by sharing of electrons between atoms found between bases and sugars and in phosphodiester linkages
covalent bond
a type of bond between an electronegative atom and a hydrogen atom that is covalently linked to a second electronegative atom; considered to be weak; occur between the complementary bases across the two strands fo the double helix
hydrogen bond
occurs when nonpolar groups, such as the DNA bases, associate with each other to avoid contact with water. this creates a hydrophobic core within the DNA double helix, where the bases stack on top of each other. these interactions help stabilize the DNA structure by keeping the nonpolar bases away from the aqueous environment
hydrophobic bonds or hydrophobic interactions
scientist who conducted base-composition analysis using chromatographic methods to separate the four bases in DNA samples from various organisms
erwin chargaff
what were erwin chargaff’s findings in his base-composition analysis?
(1) complementary bases have proportional concentrations (A = T and G = C)
(2) sum of purines = sum of pyrimidines (A + G = T + C; based on the proportionality)
(3) %G + C is not necessarily = %A + T
refers to the chemical affinity provided by H bonding between the bases
complementarity
chargaff’s data showed that the diameter of the DNA double helix is ___; and that the AT:GC pairing is the basis for complementarity
2 nm or 20 A
what are the alternative forms of DNA?
(1) A-DNA
(2) C-DNA
(3) D-DNA
(4) E-DNA
(5) P-DNA
(6) Z-DNA
an alternative type of DNA that is prevalent under high salt or dehydrated conditions; right-handed helix; slightly more compact; 9 base pairs per turn; 23 Aor 2.3 nm in diameter; bases are tilted and displaced laterally relative to helix axis
A-DNA
an alternative type of DNA found under even greater dehydration conditions than those observed during the isolation of A-DNA and B-DNA; right-handed helix
C-DNA
a(n) alternative type(s) of DNA that occur in helices lacking guanine in their base composition; right-handed helix
D and E-DNA
an alternative type of DNA that is observed when DNA is artificially stretched; right-handed helix
P-DNA
an alternative type of DNA observed in a small synthetic DNA oligonucleotide containing only G-C base pairs; left-handed double helix
Z-DNA
why is DNA organization important?
(1) solves structural problem : DNA molecules are extremely long. to fit inside the microscopic nucleus, DNA must be efficiently packed, which is achieved through several levels of organization, such as nucleosomes, chromatin, and chromosomes
(2) gene expression regulation : the way DNA is organized is also tied to gene expression regulation as it ensures that genes are expressed at the right time and place (essential for proper cellular function or development)
first level of packing; DNA winding around the histones; 1/3 of original length; 11 nm
nucleosome
second level of packing; six-fold compaction; dependent on H1 (lysine-rich); 30 nm
solenoid
extended form of the chromosome; solenoids are folded into a series of looped domains; 300 nm
chromatin fiber
diameter of chromatid in metaphase chromosome
700 nm
two specialized chromosomes of eukaryotes
(1) polytene chromosomes
(2) lampbrush chromosomes
giant chromosomes ranging from 200 to 600 µm long found in various tissues (e.g., salivary gland, midgut and rectal tubules) in the larvae of some flies and in several species of protozoans and plants
polytene chromosomes
scientist who first observed polytene chromosomes in 1881
E.G. Balbiani
polytene chromosomes can be seen in the nuclei of what type of cells?
interphase cells
why are polytene chromosomes unusual?
(1) they represent paired homologs : PCs are present in somatic cells, wherein most organisms’ chromosomal material is normally dispersed as chromatin and homologs are not paired
(2) large size and distinctive appearance : the DNA of these paired homologs undergo many rounds of replication without strand separation and cytoplasmic division, resulting in large numbers of identical DNA strands (1k to 5k DNA strands)
the bands in polytene chromosomes are arranged in a _____.
linear series of alternating bands and interbands
individual bands in polytene chromosomes; lateral condensations of material along the axis of a chromosome
chromomeres
true or false: the banding pattern in PC is distinctive for each chromosome in any given species
true
result of a localized uncoiling event; visible manifestations of high level gene activity, specifically, transcription
puff
a specialized chromosome resembling a brush used to clean kerosene lamp chimneys in the 19th century; meiotic chromosomes
lampbrush chromosomes
lampbrush chromosomes are known to be characteristic of most vertebrate ____ and ___.
oocytes like salamander and shark; spermatocytes of some insects
lampbrush chromosomes are easily isolated from oocytes in what stage of meiosis?
diplotene stage of prophase I
synapsed pairs in lampbrush chromosomes held together by chiasmata are known to be ___.
homologs
true or false: instead of condensing as most meiotic chromosomes do, lampbrush chromosomes often extend to lengths of 500-800 µm.
true
l.c. are extended, uncoiled versions of the normal meiotic chromosome (15-20 µm).
process of inducing reversible changes in DNA chromatin structure; if DNA is present in several levels of compaction, how is it replicated and how are the genes expressed?
chromatin remodeling; chromatin remodeling is reversible so that the process can be reversed during periods of inactivity
what must the chromatin do to accommodate regulatory protein-DNA interaction and allow replication and gene expression?
chromatin must relax its compact structure
a way to regulate gene expression and maintain chromatin structure
histone modification
what are the different types of histone modification?
(1) acetylation
(2) methylation
(3) phosphorylation
what is acetylation? what enzyme is involved in this modification? what effect does acetylation bring?
(1) type of histone modification wherein there is an addition of acetyl group to lysine in histones
(2) enzyme involved is Histone Acetyltransferase (HAT);
(3) causes gene activation
what is methylation? what enzyme is involved in this modification? what effect does it bring?
(1) type of histone modification wherein there is an addition of methyl group to arginine and lysine residues in histones
(2) enzyme involved is Methyltransferase
(3) causes decreased or increased gene repression
what is phosphorylation? what enzyme is involved in this modification? what effect does it bring?
(1) type of histone modification wherein there is an addition of phosphate groups to serine and histidine in histones
(2) enzyme involved is Kinase
(3) generally associated with gene activation
describe the DNA organization in bacteria vs in viruses
in bacteria:
(1) supercoiled
(2) functionally inert (after packaging)
(3) largely devoid of associated proteins
in viruses:
(1) supercoiled
(2) functionally inert (after packaging inside the capsid)
(3) activation of DNA upon release into host cell
histone-like proteins/DNA structuring proteins that influence DNA compaction such as bridging, wrapping, or bending; helps in gene regulation
nucleoid-associated proteins (NAPs)
long polymer composed of ribonucleotides
ribonucleic acid (RNA)
