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WVSOM - Molecular
Nucleic acid structure, chromosomal structure, genomic organization
| Question | Answer |
|---|---|
| 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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