Lecture Exam 4 Flashcards
Phenotype
visible property; a gene was defined as a portion of a chromosome that determines or affects a single phenotype
Gene
all the DNA that encodes the primary sequence of some final gene product (polypeptide or RNA with a structural or catalytic function)
Mutation
Mutation
What is the relationship between DNA, RNA, and protein?
-Each amino acid of a polypeptide chain is coded for by three consecutive nucleotides in a single strand of DNA (“codon”)
-a polypeptide chain of 350 amino acid residues (an average-size chain) corresponds to 1,050 base pairs (bp) of coding DNA
How large are bacterial cells and viruses in comparison to the length of the DNA/RNA molecule contained within them?
-DNA viral genomes vary greatly in size and tend to be circular for at least part of their life
-The contour lengths of their DNA are typically hundreds of times longer than the long dimensions of the viral particles that contain them
-an E.coli cell contains ~100x as much DNA as a bacteriophage particle
-the E. coli chromosome is a single, double-standard circular DNA molecule of 4,641,652 bp; the genome is ~850 times the length of the cell
How much DNA is in a diploid human cell?
-Total: 3,096,649,726
-46 chromosomes
-20,454 protein-coding genes
-2m of DNA in each human cell
What are introns and exons in a gene?
-Introns: nontranslated, intervening DNA segments that do not code for the amino acid sequences of the polypeptide product
-Exons: coding DNA segments; makes up only ~1.5% of human DNA
What are repeat sequences? Where are these located on a chromosome typically?
-Highly repetitive sequences: short sequences, generally less than 10 bp long, that are sometimes repeated millions of times per cell
-make up ~3% of the human genome
-do not encode proteins or RNAs
-associated with centromeres and telomeres
What is the telomere? How does it influence cell aging and the ability to replicate and divide?
-Telomeres: sequences at the ends of eukaryotic chromosomes that help stabilize the chromosome; shortened after each round of replication; end with multiple repeated sequences of the form
What is DNA supercoiling? What is relaxed DNA?
-Supercoiled: neutralizing the negative charges of the phosphoryl groups in the DNA backbone with cations and polyamines
-underwound DNA: state where DNA has fewer right handed turns per given length of DNA than B-form DNA; places structural strain on the DNA causing it to twist upon itself (supercoiling)
-most cellular DNAs are supercoiled; this is an intrinsic property of DNA tertiary structure
-Relaxed DNA: state where there is no net bending of the DNA axis upon itself
What enzymes remove (relax) supercoils?
Topoisomerases
What is linking number and how does it quantify supercoiling?
-Linking Number: the number of times the twisting strand penetrates a surface; topological property of double-stranded DNA
-always an integer
-positive strands interwound in a right-handed helix
-the linking number is negative for strands interwound in a left-handed helix; not encountered in DNA
-Lk=number of bp/number of bp per turn
How do topoisomerases change linking number?
-Topoisomerases: enzymes that increase or decrease the extent of DNA underwinding
-change the linking number; play an important role in replication and DNA packaging
What is a general mechanism for type I topoisomerases?
-act by transiently breaking one of the two DNA strands, passing the unbroken strand through the break, and rejoining the broken ends
-change Lk in increments of 1
What is a general mechanism for type II topoisomerases?
-break both DNA strands
-change Lk in increments of 2
What is a catenane, how are they formed, and what topoisomerases can remove them?
-Catenanes: DNA circles that are topologically linked
-Type II Topoisomerases can pass one duplex DNA segment through a double-stranded break in another duplex; allows these enzymes to untangle catenanes
What components make up chromatin?
-Chromatin: eukaryotic chromosomal material composed of DNA ,RNA, and proteins
How is the DNA packaged in a nucleus? What are the roles of histones?
-Histones: proteins that are tightly associated with chromatin and function to package and order the DNA
-Nucleosomes: the fundamental structural unit of chromatin; composed of core histone proteins bound to DNA
What are the roles of histone tails?
-Play a key role in forming contacts between nucleosomes in chromatin
What are the differences between the active and inactive compartments in the nucleus?
-Active Compartments: have reduced chromatin condensation
-Inactive Compartments (heterochromatin): highly condensed
Describe the roles of the SMC proteins cohesins and condensins.
-SMC proteins (structural maintenance of chromosomes): responsible for maintaining the structure and integrity of chromosomes following replication; consist of 5 district domains
-Cohesions: link sister chromatids together after replication and keep them together as the chromosomes condense to metaphase
-Condensins: essential to chromosomal condensation as cells enter mitosis; create positive supercoils
-as DNA is compacted to form tighter and tighter loops, condensins stabilize the loops by binding at the base of each one
How does gene and protein naming differ between prokaryotes and eukaryotes?
-Prokaryotes:
-Genes: typically names using three italicized letters reflecting a function; capital letters added to abbreviation reflect order of discovery, not enzymatic order
-Proteins: often named after their genes using nonitalcized, roman types with the first letter capitalized
-Eukaryotes:
-Genes: no single convention exists for all eukaryotic systems, three gene names are three italicized uppercase letters followed by an italicized number
-Proteins: complex and variable; in yeast, some proteins have long common names; other yeast proteins have the same name as the gene, with one uppercase and two lowercase letters in roman type, followed by a number and the letter “p”
What is semiconservative DNA replication?
-Semiconservative replication: each DNA strand serves as a template for the synthesis of a new strand; produces two new DNA molecules.\, each with one new strand and one old strand
What are the lagging and leading strands during replication?
-Lagging Strands: 5’–> 3’ synthesis proceeds in the opposite direction that the replication fork moves; discontinuous synthezise through the synthesis of Okazaki fragments
-Leading Strands: 5’–>3’ synthesis proceeds in the same direction that the replication fork moves; synthesized continuously
What is the difference between an endonuclease and an exonuclease?
-Exonuclease: degrade nucleic acids from one end of the molecule; many operate in only one direction (either 5’–>3’ or 3’–>5’)
-Endonuclease: degrade nucleic acids at specific internal sites in the molecule
What is a DNA polymerase? What is does proofreading enable a polymerase to do?
-DNA polymerase: complex enzymes that can synthesize DNA; many have additional activities
-the reaction is a phosphoryl group transfer
-the 3’-OH of the nucleotide at the 3’ end of the strand (the nucleophile) attacks the alpha-phosphorous of the incoming dNTP
-Proofreading: DNA polymerase activity that involves the replacement of the incorrect nucelotide; improves accuracy by 100-1000 times
-permits the enzyme to remove a newly added nucleotide
How accurate is DNA replication?
-DNA polymerases insert one incorrect nucleotide for every 10,000-100,000 correct nucleotides; this may occur because a base is in a tautomeric form
What are the main classes of proteins/enzymes involved in replication?
-Helicases: enzymes that move along the DNA and separate the strands
-require chemical energy from ATP
-Topoisomerases: relieve topological stress created by strand separation
-DNA-binding proteins: stabilize short segments of RNA to serve as primers
-Primases: synthesize short segments of RNA to serve as primers
-Ligases: seals nicks in the DNA backbone following removal and replacement of an RNA primer
What are the main phases of replication?
-Three stages:
-Initiation
-Elongation
-Termination
What are Okazaki fragments?
-Okazaki Fragments: short DNA fragments that are synthesized in the replication of one of the new DNA strands
What are mismatch and base excision repair?
-Mismatch: mismatches are corrected to reflect template strand information
-distinguished from the newly synthesized strand by the presence of methyl group tags on the template DNA
-Base Excision Repair: recognize common DNA lesions and remove the affected base by cleaving the N-glycosyl bond in the process of base-excision repair; generally specific for one lesion type
WHat is recombination in meiosis?
What is nonhomologous end-joining?
-process by which broken chromosomes ends are processed and ligated back together
-occurs when recombinational DNA repair is not feasible because replication is not occurring and sister chromatids are not present; mutagenic process; does not randomly join ends
How is recombination used to make diverse antibodies?
What is a ribozyme?
-Ribozyme: catalytic RNAs that act as enzymes
What is transcription? And what is the transcriptome?
-Transcription: process by which an enzyme system converts the genetic information in dsDNA into an RNA strand with a complementary base sequence
-the entire chromosome is usually copied during replication; transcription is more selective
-Trascriptome: the sum of all the RNA molecules produced in a cell under a given set of conditions
-~76% of the human genome is transcribed into RNA
-most products are ncRNAs
What are the major classes of RNAs and what do they do?
-mRNA: encode the amino acid sequences of polypeptides
-tRNA: read the mRNA and transfer the appropriate amino acid to a growing polypeptide chain during protein synthesis
-rRNA: constituents of ribosomes, the cellular machines that synthesize proteins
-ncRNA: have a variety of catalytic, structural, and regulatory functions
What are the relationships between the template DNA, nontemplate DNA, and the transcript sequence?
-Template strand: DNA strand that serves as a template for RNA synthesis
-Nontemplate strand (coding strand): DNA strand that is identical in base sequence to the transcribed RNA, with U in RNA in place of T in DNA
What are the three types of RNA polymerases in eukaryotes and what do they transcribe?
-RNA polymerase I: responsible for the synthesis of a transcript called pre-ribosomal RNA; pre-rRNA contains the precursor for the 18S, 5.8S, and 28S rRNAs
-RNA polymerase II: responsible for synthesis of mRNAs and many ncRNAs; can recognize 1000s of promoters
-RNA polymerase III: responsible for the synthesis of tRNAs, the 5S rRNA, and other ncRNAs; are well characterized
What is the difference between the terms transcription factors and general transcription factors?
-Transcription factors: an array of proteins that work with Poly II form the active transcription complex
-General Transcription Factors: those required at every Poly II promoter
What are the main phases of transcription?
-Elongation: elongation factors bound to RNA poly II enhance processivity and coordinate posttranslational modifications; some are bound to phosphorylated CTD
-termination: Poly II CTD is dephosphorylated and transcription machinery is recycled
-release
What are the main modifications made to eukaryotic mRNAs?
-At the 5’ end, a 5’ cap (a modified nucleotide structure) is added
-At the 3’ end, cleavage occurs and 80 to 250 A residues are added to create a poly (A) tail
What is the 5’ cap made from?
-a residue of 7-meethylguanosine linked to the 5’-terminal residue of the mRNA through an unusual 5’-5’-triphosphate linkage
What is a self-splicing intron?
-Group II intron: catalytic RNA; maturase and reverse transcription proteins; self splicing using a nucleophile within the intron to form a lariat; primarily found in the mitochondria and chloroplast genes of fungi, algae, and plants. Can be found in bacteria
What is the spliceosome and what are snRNAs and snRNPs?
-Spliceosome: a large complex made up of multiple specialized RNP complexes called small nuclear ribonucleoproteins (snRNPs) and dozons of other proteins
-Small nuclear RNAs (SnRNAs): 100-200 nucleotide RNAs that make up snRNPs
-snRNP: small nuclear ribonucleoproteins
What is alternative splicing?
-Alternative splicing: process in which a particular exon may or may not be incorporated into the mature mRNA transcript; occurs in >95% of human genes
What are some roles of nucleoside modifications?
-Conversion of uridine to pseudouridine
-adoMet-dependent nucleoside methylation
-Slide 59, 62,63
What are miRNAs?
-Micro RNAs (miRNAs): a special class of non-coding RNAs that promote mRNA degradation and suppress translation to fine-tune gene expression
-22 nucleotides long
-complemetary in sequence to particular regions of mRNA
-found in plants and animals
What are reverse transcriptases and what types of reactions do they catalyze?
-Reverse transcriptase: an RNA-dependent DNA polymerase
-contained within certain RNA viruses called retroviruses
-discovery showed genetic information can flow “backward” from RNA to DNA
-catalyzes conversion of viral RNA to dsDNA, which is often integrated into teh host genome
-Reactions: RNA-dependent DNA synthesis, RNA degradation, DNA-dependent DNA synthesis
How are transposons, retroviruses and introns similar?
-Slide 70 and beyond
-Retroviruses have a genome that is desiggned to integrate into a host
-In our cells, we already have tag elements (transpospons) like retroviruses do
What is telomerase and how does it extend telomeres?
-Telomerase: a ribonucleotideprotein that synthesizes the telomere endsd of linear chromosomes; act as a specialized reverse transcriptase; contains an internal RNA repeat sequence that serves as a template for synthesis of the TG strand of the telomere
What are ribozymes? Why do some people believe that these are critical to the origin of life?
-Ribozymes: RNA enzymes
-RNA world hypothesis: proposal that the evolution of life on Earth may have included an “RNA world”, RNAs not proteins act as catalysts; the discovery of ribozymes gave life to the RNA world hypothesis; the parent of all life on this planet might have been a self-replicationg RNA, or a polymer with equivalent chemical characteristics
