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WVSOM - Molecular

Nucleic acid structure, chromosomal structure, genomic organization

Nucleotides polymerized by a phosphodiester bond? Nucleic acid (RNA and DNA)
Double-stranded polymers of deoxyribonucleotides? DNA (deoxyribonucleic acid)
Single-stranded polymers of unmodified nucleotides? RNA (ribonucleic acid)
Single molecule of DNA, often millions of base pairs long? Chromosome
The entire DNA sequence controlling a specific trait, usually by encoding a polypetide or functional RNA? Gene
A five carbon sugar? Ribose
What positions on a ribose are important for polymerization? 3` (contains an -OH group) and 5` positions
Where are bases attached on a ribose? At the 1` position
Name the pyrimidines Cytosine (has three charges), uracil (has two charges), and thymine (has two charges)
How is thymine different from uracil? It is methylated at the 5` position
Thymine is used for? DNA
Uracil is used for? RNA
Pyrimidines A nucleotide with a base that has ONE ring (i.e. cytosine = C, uracil = U, thymine = T)
Name the purines Guanine (has three charges) and adenine (has two charges)
Purines A nucleotide with a base that has TWO rings (i.e. guanine = G and adenine = A)
What is a nucleoside? A nucleotide precursor; it has a base (i.e. cytosine, uracil, thymine, guanine, adenine) attached at the 1` carbon of ribose and is NOT phosphorylated
What is a nucleotide? NTP: a nucleic acid subunit consisting of a ribose with a 5` phosphorylated carbon and a base at the 1` carbon. Only 1 phosphate = monophosphate; 2 phosphates = diphosphate; 3 phosphates = triphosphate
What do nucleotides with triphosphates carry? Energy
What is the most common form of energy used? ATP = adenosine triphosphate
Deoxynucleotide A modified nucleotide that lacks the 2` hydroxyl (-OH) group from its ribose moiety. Used to produce DNA; RNA consists of unmodified nucleotides; deoxynucleotide is a subclass of nucleotides
Nucleosides Bases attached to ribose at 1` carbon: Cytidine, uridine, guanosine, adenosine
Nucleotide monophosphates Base (attached at 1` carbon) and 1 phosphate (attached at 5` carbon) on ribose (with -OH groups at 2` and 3`): CMP = cytidine monophosphate, UMP = uridine monophosphate, GMP = guanosine monophosphate, AMP = adenosine monophosphate
Nucleotide diphosphates Ribose (with -OH groups at 2` and 3`) with base attached at 1` carbon and 2 phosphates attached at 5` carbon: CDP = cytidine diphosphate, UDP = uridine diphosphate, GDP = guanosine diphosphate, ADP = adenosine diphosphate
Nucleotide triphosphates Ribose (-OH at 2` and 3`) with base at 1` carbon and 3 phosphates at 5` carbon: CTP = cytidine triphosphate, UTP = uridine triphosphate, GTP = guanosine triphosphate, ATP = adenosine triphosphate
Deoxynucleotide monophosphate Ribose (-OH at 3` carbon ONLY) with base at 1` and 1 phosphate at 5`: dCMP = deoxycytidine monophosphate, TMP = thymidine monophosphate, dGMP = deoxyguanosine monophosphate, dAMP = deoxyadenosine monophosphate
T/F: Deoxyuridine exists F
Deoxynucleotide diphosphates Deoxyribose (-OH at 3` carbon ONLY) with 2 phosphates at the 5` carbon and the corresponding base at the 1` carbon: dCDP, TDP, dGDP, dADP
Deoxynucleotide triphosphates Deoxyribose (-OH at 3` carbon ONLY) with 3 phosphates at 5` carbon and corresponding base at 1` carbon: dCTP, TTP, dGTP, dATP
How are nucleotides linked together? Phosphodiester bond between 3` -OH of one nucleotide and 5` phosphate of an incoming nucleotide. Free nucleotides are ALWAYS added to the 3` -OH of a growing chain
In what direction does nucleotide formation occur? 5` - 3`
Where does nucleotide formation get its energy from? The cleaving of the high energy triphosphate bond at the 5` carbon when nucleotides are added to the growing chain
What is one consequence of polymerization? That there is one free 5` phosphate and one free 3` hydroxyl (-OH). The 5` phosphate end is known as the 5` end and the 3` hydroxyl end is known as the 3` end
In what direction would a factor be moving if it moved towards the 3` end? It would be moving in the 3` direction
How is DNA different from RNA at the 2` carbon? DNA does not have an -OH at the 2` carbon making it a deoxynucleotide; RNA does has an -OH at the 2` carbon (it is unmodified; it has 2 -OH groups)
What bases are different between DNA and RNA? DNA has thymidine and RNA has uridine. Thymidine is in the deoxy form and uridine is not in the deoxy form. Thymine is methylated (it contains a methyl group at its 5` carbon)
What size difference is there between DNA and RNA? DNA is millions of base pair long and RNA is about 50-40,000 nucleotides long
What strand differences are there between DNA and RNA? DNA is a double stranded helix while RNA is a single strand (almost always)
What type of bond holds two nucleotides together? Hydrogen bonds hold specific sites on the bases together. Keep in mind that other bonds also exist to hold and stabilize the DNA double helix
How is DNA measured? In base pairs (bp)
How is RNA measured? In nucleotides (because it does not normally form base pairs)
Is RNA easily degraded? Yes
What degrades RNA? RNase
Complementary Two strands have matching, mirror image sequences, so that every A on one strand is paired with a T on another and that every G is paired with a C. Complementary strands will associate with each other into a double helix
Antiparallel Two strands of the double helix are in opposite, 5` - 3` orientations
What does denaturation, deannealing, or melting DNA mean? It means for the double helix to dissociate into single strands due to adverse conditions, such as elevated temperature
What does annealing or reannealing mean? It allows denatured DNA strands to reform double helices. This is most commonly accomplished by allowing a heated solution to cool slowly
Hybridization Two strands from different sources to anneal. Examples include complementary DNA from different species and RNA/DNA hybrids
Antisense RNA RNA with a sequence complementary to DNA or RNA
Will antisense RNA form a double helix? Yes
Place the following in order, from strongest to weakest - RNA/DNA helix, RNA/RNA helix, DNA/DNA helix RNA/RNA helix > RNA/DNA helix > DNA/DNA helix
Why does RNA not normally form a double helix? Because, normally, only one strand of RNA is synthesized
Where do you typically find antisense RNA? Exceptions? Antisense RNA is typically synthesized in a lab; however, there are rare examples in nature of antisense RNA used as a specific repressor of gene expression
What determines base specificity? The hydrogen bonds that form between adenine and thymine (two hydrogen bonds) and between cytosine and guanine (three hydrogen bonds)
What mediates specificity? Steric constraints. Base pairs always form between a purine and a pyrimidine. Therefore, 3 rings span the helix (1 from a pyrimidine and 2 from a purine)
How many oxygens are there in the phosphate groups of a phosphodiester bond? What charge does oxygen carry? What is the significance? 4; oxygen carries a negative charge. The significance is that the negative charges surround the outside of the double helix making DNA (and RNA as well) a negatively charged acid
What is the most common conformation of DNA? B form; characterized by Watson and Crick. It is R-handed double helix with 10 bp/turn. The bases are held together in the core of the helix while the sugar-phosphate backbone wraps around the periphery
The unevenly spaced backbone of DNA results in ...? Major grooves (wide space) and minor grooves (narrow space)
Why is the major groove important? It is important because factors, such as regulatory proteins and various enzymes, bind to it where they have greater access to the bases
A DNA Alternate conformation, more compact than B DNA (11 bp/turn), more tilt to the bp, central hole between strands, forms with DNA/RNA and RNA/RNA hybrids, more stable than B DNA
Z DNA Alternate DNA conformation, L-handed double helix, alternating purines and pyrimidines, regions may be involved in repression of gene expression
Triple helical DNA Forms between one polypurine and two polypyrimidine strands
Chromatin DNA + protein (note that all DNA is bound by protein)
Heterochromatin DNA tightly compacted (not transcribed), darkly staining chromatin, contains more solenoids
Euchromatin Less dense, lightly staining, transcriptionally active chromatin, unraveled DNA, no solenoids
What is one function of supercoiling? Store potential energy
Supercoiling When two strands of DNA are twisted around each other it causes coiling. It is actually negatively supercoiled causing strands to be partly unwound
What proteins form octameric complexes, which eukaryotic DNA wraps around? Histones
Name the types of histones and their functions? H2A, H2B, H3, and H4 = octameric cores; H1 = binds linker regions between octamers; H5 = in fish, birds, reptiles; associates with linkers instead of H1
What is the most abundant protein of chromatin? Histones; mass of histones equals mass of DNA
What amino acid residues are prominent in histones? Why are they important? Lysine and arginine; they are important because they are basic (positively charged), which allows them to bind to negatively charged DNA
T/F: Histones are found in prokaryotes F
Is DNA always bound to histone octamers? Yes, it occurs throughout the cell cycle, interpase, as well as mitosis
Histone octamers + associated DNA, but not including linker regions makes up? Nucleosomes
How many times does DNA wrap around the surface of the octamers? In what configuration? 1.75 times; L-handed superhelix
How many bp does each nucleosome contain? 140 bp wrapped around the octamer
How many bp does each linker region have, on average? ~ 60 bp
How many bp, on average, does the entire repeat contain (nucleosome + linker region)? ~ 200 bp
What arts and crafts project do nucleosomes look like using an electron microscope? Beads on a string
What is a solenoid? Nucleosomes that coil around each other to form a hollow tube
What chromosomal structure is believed to exist during interphase? Solenoid structure, where the heterochromatin is condensed and transcriptionally inactive
Transcriptionally active euchromatin exists as what? Uncoiled nucleosomes (beads on a string)
What chromosomal structure exists during prophase (mitotic or meiotic)? Solenoids, including the euchromatin
When does solenoid tangling take place? During prophase when the solenoids tangle into complex patterns to form the mitotic (or meiotic) chromosomes
What is the 2nd most abundant class of chromatin proteins? Scaffold proteins
What charge do scaffold proteins carry? + charge
How were scaffold proteins demonstrated? Chromatin treated with polyanions, competes with negatively charged DNA, strips histones away, samples stained and viewed with EM, results = halo of DNA loops around central core (scaffold proteins)
Proposed functions of scaffold proteins Tie solenoids together to form condensed chromosomes, maintain supercoiling via scaffold protein topoisomerase II
Structure of scaffold proteins? Heterogeneous, consisting of many different proteins
Centromere Region of chromosome bound to mitotic spindle, recognized by highly constricted region of chromosome (known as primary constrictions), consist of short and repeated sequences (end to end), no functional genes
The 4 centromere positions Metacentric = central centromeres, submetacentric = off center, acrocentric = towards the end, telocentric = at the ends (not in humans)
Two arms of a chromosome p (petite) arm = shorter and q arm (longer); divided by centromere
Telomere Located at either end of a chromsome; constricted in chromosomes; contain repetitive sequences (guanine and thymine); not many genes; repeat sequence for humans = AGGGTT
What stain produces the G bands on a chromosome? On what arm are the bands located? Geimsa stain; q arm
Telomere function Protect chromosome ends from damage; implicated in cancer and aging
Karyotypes Number, size, banding pattern on all chromosomes
Genome All DNA that controls genetics of cellular unit; genomic DNA = DNA of nucleus (separates it from mitochondrial DNA)
When was the Human Genome sequence completed? April 14, 2003
How many bp are in the human genome? 3.2 billion bp
How many bp are there per chromosome? 45 - 280 million bp
The total number of bp in the human genome are spread over how many chromosomes? 23 chromosomes
What portion of the genome is actually transcribed into RNA? 1/3
What percentage of our genome encodes protein? 5%
What does the majority of our genome consist of? "junk" DNA
On average, how many genes are in the human genome? ~ 31,000
What are some general functions of "junk" DNA? They form telomeres, centromeres, make up promoter regions, and act as spacers
What are the three sequence classes of eukaryotic genomes? High repetitive sequences, intermediate sequences, rare sequences
What is the abundance of each sequence? Highly repetitive sequence = up to a million copies per genome; intermediate sequences = a hundred-thousands per genome; rare sequences = one copy per genome
What is the % of genome that each of the sequences makes up? Highly repetitive sequences = 3%, intermediate sequences = >45%, rare sequences = >50%
Highly repetitive sequences 5-15 bp long (can exceed 500 bp), do not encode genes, structural function (telomeres, centromeres, maintain chromosome length), scattered throughout chromosome, tandem arrays (same sequence, repeated over and over, end to end)
Tandem arrays Sequence repeated over and over (thousands of times), end to end; believed to be from duplicaton of single ancestral sequence, slight differences exist (sequence variation, length), differences can be used for genetic markers and DNA fingerprinting
Variations in tandem arrays Cluster within tandem array, one variation may be seen in one region while another is seen in a different region; believed to have risen from one ancestral copy (mutated), then duplicated; analysis may help trace evolutionary construction of chromosome
Transposons Jumping genes; sequence capable of moving from one location in the genome to another
Retroviruses RNA viruses; parasitic DNA molecules capable of moving from on cell to another with the use of an RNA intermediate
Retrotransposons Transposons that move through RNA intermediates; DNA sequences are transcribed into RNA which is then reverse transcribed back into DNA to be reinserted into chromosome; 45% of genome = degenerate retrotransposons; majority = "junk" DNA
Intermediate sequences 100-thousands/genome; majority degenerate transposons (mainly retrotransposons); constitute 45% of genome; serve no apparent purpose; propagate own existence
The most abundant transposon? A specific cause of its transposition? Alu sequences; tumorgenesis
Role of functional intermediate class genes Housekeeping genes involved with basic cellular processes, such as DNA condensation and gene expression
Examples of functional intermediate class genes rRNA (~ 250 copies/human genome), 5S-rRNA (2000 copies/human genome), tRNA (1300 copies/human genome), histones (87 copies/human genome)
Arrangement of intermediate class genes Clusters (similar to tandem arrays); usually present are intervening regions between repeat sequences of clusters; length of clusters is shorter; repeated genes tend to be much longer
Rare sequences Few, usually once/genome; largest of three classes; 50%; scattered throughout genome; most functional; many have no apparent function
Groups of genes classified together because they have similar regions, which aren't necessarily identical Gene families
What proportion of encoding genes belong to gene families? 1/2
Gene families usually contain how many members? Usually <20, but there can be several 100 genes in a family
Are gene families considered part of the rare sequence? Why? Yes; numbers do not reach levels of intermediate class, even though family members have similar sequences they differ from the repetitive / intermediate classes in that they are seldom identical; never arranged in tandem arrays
What does homology mean? It is the estimate of how closely related genes are based on sequence similarity; gene family members are believed to be homologous (evolved from common ancestral gene)
What does conserved domain mean? It refers to the regions on homologous genes where the sequence remains similar; these regions are remained similar because they are very important to the gene's function, so mutations are selected against; sequence conservation = functional importance
What is a sequence similarity? Can be conducted with nucleic acid and protein sequences; computers used to align similar sequences from different genes; most common base at each position is identified to ascertain consensus sequence
Gene families have to contain at least? One conserved region
What is the length of a homologous sequence? It can span the length of the gene or be confined to one small domain. An example is the family of homeotic genes - they share 180 bp consensus sequence known as the homeobox
How are clustered gene families different from gene families? They are grouped closely together on a chromosome; their sequences are not identical, they are not as contiguous, their genes are not necessarily oriented in the same direction
Give two examples of clustered gene families Globins and histones
What two clusters exist for the globin gene family? The a-globin on chromosome 16 and the b-globin on chromosome 11; the sequence of all globin genes is more similar to each other than to those of the other cluster
What are psi-globins? (sigh-globins) They are pseudogenes; have similar sequence to b-globin, but don't express a gene product; evolved from functional genes that were inactivated by mutation
T/F: Histones belong to the intermediate sequence class T
How many histones are there? 5
Where can you find histones? Mammalian histones are scattered throughout their genomes, however, some are clustered. In humans, 5 clusters on different chromosomes; large cluster of 68 histone genes on chromosome 6
Do histones have introns? No
Are histones polyadenylated? No
Histone homology? Most homologous gene family known; sequence of each gene similar to other histones within organism; very little difference from one species to another
Created by: JaneO



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