Nucleic acid structure, chromosomal structure, genomic organization
Quiz yourself by thinking what should be in
each of the black spaces below before clicking
on it to display the answer.
Help!
|
|
||||
|---|---|---|---|---|---|
| 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
🗑
|
Review the information in the table. When you are ready to quiz yourself you can hide individual columns or the entire table. Then you can click on the empty cells to reveal the answer. Try to recall what will be displayed before clicking the empty cell.
To hide a column, click on the column name.
To hide the entire table, click on the "Hide All" button.
You may also shuffle the rows of the table by clicking on the "Shuffle" button.
Or sort by any of the columns using the down arrow next to any column heading.
If you know all the data on any row, you can temporarily remove it by tapping the trash can to the right of the row.
To hide a column, click on the column name.
To hide the entire table, click on the "Hide All" button.
You may also shuffle the rows of the table by clicking on the "Shuffle" button.
Or sort by any of the columns using the down arrow next to any column heading.
If you know all the data on any row, you can temporarily remove it by tapping the trash can to the right of the row.
Embed Code - If you would like this activity on your web page, copy the script below and paste it into your web page.
Normal Size Small Size show me how
Normal Size Small Size show me how
Created by:
JaneO
Popular Biochemistry sets