Chapter 10 Flashcards
what are the physiological roles of nucleotides
-energy currency (ATP)
-signalling molecules (cAMP)
-enzyme co-factors (NAD, FAD)
-building blocks of nucleic acid
what are the physiological roles of nucleic acids
-genetic information (DNA, RNA)
-all stages of protein synthesis (DNA, mRNA, tRNA, rRNA
what are the building blocks of nucleic acids
nucleotides
what are the components that nucleotides share
-ribose sugar (ribose or deoxyribose)
-nitrogenous base (purine or pyrimidine)
-phosphate(s)
what back bone do all nucleotides contain
a ribose backbone
what form is ribose in within nucleotides
it is in cyclized form (B-D-ribofuranose)
in ribose what carbon is where you can see if its oxy or deoxy form
on C 2’
RNA contains ____; DNA contains ____
ribose, deoxyribose
what are the two families of nitrogenous bases
purines and pryimidines
how can you differentiate purines and pyrimidines
pyrimidines have a singular ring purines have a two ring system
what are two characteristics of nitrogenous bases
they are plainer and relatively non-polar
what are the five standard nitrogenous bases
adenine, guanine and cytosine in both DNA and RNA. the fourth base differs; DNA has thymine and RNA has uracil
how are nitrogenous bases linked to ribose
through N-glycosidic bonds
what carbon are nitrogenous bases linked to
all are linked to C1’ of the sugar
what N is the N-glycosidic bond to of the nitrogenous base in purines
N9 of nitrogenous base
what N is the N-glycosidic bond to of the nitrogenous base in pyrimidines
N1 of nitrogenous base
how do nucleotides and nucleosides differ
-they differ in whether they are phosphorylates at the C5’ position
where do nucleotides ave phosphates
nucleotides have 1-3 phosphates of the 5’ position: (one (NMP) two (NDP) three (NTP)
nucleotides are phosphorylated…
nucleosides
for nomenclature of nucleotides and nucleosides what are the three things to look at
1) which nitrogenous base is present (base name)
2) whether the sugar is ribose of deoxyribose (deoxy prefix)
3) whether there are phosphoryl groups (suffix of osine from nuclosides; ylate for nucleotides)
what is an alternative method for naming nucleotides
to specify the number and position of the phosphoryl groups
i.g adenosine 5’-triphosphate rather then adenylate
what is the energy transfer for nucleotides
-anhydride linkages in ATP are high energy bonds
-the energy released form the hydrolysis of these bonds drives many biochemical reactions
how what is signal transduction for nucleotides
-cyclic AMP, formed form ATP in reaction catalyzed by adenylyl cyclase
-common intracellular messenger produced in response to hormones
how do nucleotides from linear nucleic strands
through 3’-5’ phoshodiester linkages
are 3’-5’ phoshodiester bonds the same in RNA and DNA
yes they are identical
are 3’-5’ phoshodiester bonds different depending on the nucleotides being joined
yes they are identical independent of nucleotides being joined
what is the back bone of nucleic acid
strands of sugars linked by phosphodiester bridges
what is it that uniquely characterizes a nucleic acid
the sequence of bases
what is the direction nucleic acid strand sequences are presented in
5’—>3’
sequences of bases is a form of…
linear information (blueprint)
how does RNA differ from DNA
-RNA contains ribose rather than deoxyribose
-RNA contains uracil rather then thymine
-RNA is single stranded but can adopt complex 3D structures
what is ribosomal RNA
an integral part of ribosomes~ 80% of RNA in cells
what is transfer RNA
carry activated amino acids to ribosomes for protein sysnthesis (small molecules 73-95 nucleotides long)
what is messenger RNA
code for proteins; contains triplet codons that specify the amino acid sequence of a protein
what is micro RNA (miRNA)
short oligonucleotides (22-24 nts in length) that function in transcriptional and post-transcriptional regulation of gene expression
what is more stable DNA or RNA
DNA
what makes RNA more reactive
the 2’ hydroxyl group of RNA increases its susceptibility to base hydrolysis at the phosphodiester linkage
why does it make sense DNA would me more stable the RNA
the greater stability of DNA is consistant with its role as a long term information storage molecules
what is RNAase
and enzyme the body produces to destroy RNA
how was double helix descovered
-watson and crick postulated the structure of DNA in 1953
-rosalind and wilkins btained the X-ray difraction data that showed DNA is a helix
-they set the stage for watson and crick
-watson, crick, and willson shared the 1962 nobel prize in medicine
what is the specificity of watson-crick base pairing largely determines by
they hydrogen bonding groups of the nitrogenous bases
what is chargaffs rule
A+G=T+C
what is the number of pyridines equal to in duplex DNA
pyrimidines
what are the A-T and G-C hydrogen bonded pairs like
they are planar and have the dame dimentions
what base pairs are more stable? G-C or A-T
G-C=3H bonds so more stable
A-T only have 2H bonds
what weak forces help to stabilize the double helix
-hydrophobic effects
-stacking interacrtions
-hydrogen bonds
-charge-charge interactions
what does the hydrophobic effects do in a double helix
they bury purine and pyrimidine rings in the interior of the helix
what do the stacking interactions do in a double helix
stacked base pairs form van der waals contacts
where do hydrogen bonds from in the double helix
between base pairs
how do charged charges interactions work in the double helix
electrostatic repulsion of neg charged phosphate groups os decreased by cations (e.g. Mg2+) and cationic proteins
a double helix has two grooves of uneven width what are these
major groove and minor groove
within each groove base pairs are—-and are——-
exposed and are accessible to interactions with other molecules
how do DNA binding proteins read specific sequences
because within each groove base pairs are exposed and can interact with other molecules. through these interactions DNA binding proteins can “read” specific sequences
how much of of our genome represents genes
and very small precent
what does restriction endonuclease do
it recognizes and cleaves specific DNA sequences
how do bacteria protect themselves against viral invasions
-using restriction endonuclease
-the host cell protects there own DNA by covalent modifications of bases at the restriction site (e.g methylation)
what does the name of restriction enzyme reflect
the origins i.g…
-BamHI is the first restriction enzyme characterized from bacillus amyloliquefaciens strain H
- EcoRV is the fifth restriction enzyme characterized form Esherichia coli strain R
what sequence do restriction enzymes cut at
palindrome sequence
what can using restriction enzymes do when used as “molecular scissors”
manipulation of DNA
what does treating DNA from different individuals with restriction enzymes do to the DNA
it breaks it into pieces
how do different peoples DNA react to restriction enzymes
due to difference in genome sequences DNA from different people will break down into a different number of fragments and fragments of different sizes
duplex DNA contains two complementary…
anti parallel strands
in duplex DNA because the strands are complementary…
they sequence of one strand determines the sequence of the other strand
what is the complementary nature of the DNA strand important for
-replication and repair
-as the nucleotide sequence of one strand determines the sequence of the other each strand can be used as a template to produce the other
-resulting two DNA duplexes will be identical
what is denaturation
the complex separation of double stranded DNA by heat of chemical agents
denaturation of DNA is a ____ process
cooperative
what is annealing
reforming the double stranded helix form single strands
what is the melting point for denaturalization of DNA/what does it reflect
-the temperature at which half the DNA has become single stranded
-it reflects the sequence compositions; the higher the GC content the higher the Tm
what are the primary enzymes for synthesizing nucleic acids
DNA and RNA polymerases
what are substrates for the synthesis of nucleic acids
nucleotide triphosphate
what direction does polymerase synthesize nucleic acids
-all polymerases synthesize nucleic acids in the 5’ to 3’ direction
what way are incoming residues added during the synthesis of nucleic acids
incoming residues are added to the 3’ end of the growing strand
how are incoming residues selected in the synthesis of nucleic acids
they are selected to be complementary to the template strand
what is polymerase chain reaction
it takes advantage of the ability for each DNA strand to serve as a template for production of a complementary strand
what does polymerase chain reaction use to make new DNA
heat stable enzymes
what does PCR allow for
exponential amplification of short regions of DNA very quickly
what did PCR revolutionize
molecular biology, diagnostics and forensics
the amount of eukaryotic DNA necessitates its packaged into…
higher order structures
what does a first level of DNA packaging involve for packing of eukaryotic DNA
formation of nucleosomes
what are nucleosome “beads” for packing of eukaryotic DNA
that are DNA-histone complexes on a “string” of double-stranded DNA
what are histones
-DNA packaging proteins
-they are highly conserved and positively charged
-there is 5 histone proteins
what are the 5 histone proteins
H1, H2A, H2B, H3 and H4
which of the 5 histone proteins represent the core for packing of eukaryotic DNA
H2A, H2B, H3, H4
what region does histone H1 bind for packing of eukaryotic DNA
the region of linker DNA
histones are reversibly modified to regulate…
there interaction with DNA
what is a gene
a segment of DNA containing information for production of a functional biological product (like a protein)
how can the size of a gene be estimated
from the size of the corresponding protein
what does 3 nucleotides=
3 nucleotides= 1 codon= 1 amino acid
where are genes contained
within the chromosome
how many chromosomes do virus and bacterias have
they have a single chromosome
how many chromosomes do eukaryotes have
they will have multiple
what is the genome of a bacteria like
-millions of base pairs
-closed circular genome
-no interruptions (intons)
-have additional genetic information in the form of plasmids
what are plasmids
-non chromosomal DNA
-many encode information for resistance to antibiotics
-they may be isolated and manipulated
in eukaryotes billions of ___ divided among numerous____
nucleotides, chromosomes
do all organisms have the same number of chromosomes
no they have different numbers
each chromosome has a characteristic…
set of genes
what shape are eukaryotic chromosomes what problems does this bring
-they are linear
-presents problem for replication ends of chromosomes
what do ends of chromosomes containing repeating sequences called
telomers
can stomatic cells be imortal
no. only cancer cells
in eukaryotes what are genes interrupted by non-coding regions
introns
what organelles may contain additional DNA distinct from the nucleus
the mitochondria and the chloroplast
because the mitochondria and chloroplast can contain additional DNA what does this inducate
that these at one point were separate organisms
most eukaryotic genes interrupted by…
non coding intervening sequences (introns)
what do exons contain
protein coding information
how can introns vary
in size, number and position
are introns on mRNA during translation
no they are removed prior to translation
what is one functional advantage of introns
that multiple mRNAs of different sequences can be generated from a single gene
what do conventional genetics suggest about inheritance
that individuals inherit genetic material which they pass to their offspring; that we are carriers rather then editors of genetic info
what does epigenetic refer to
the functionally relevant changes to the genome that do not involve a change in the nucleotide sequence
in response to environmental influences how else can our genetic material be modified
-it can be covalent modified
-modifications can include methylation of cytosine residues
can the covalent modifications of DNA be heritable
yes it can be passed to offspring
what does epigenetics do
the changes can alter patterns of gene expression (and phenotypes) without altering the underlying DNA sequence
