BIOL 218 1st EditionExam # 2 Study GuideChapter 5~M-Phase: where growth stops and cell divides (mitosis then cytokinesis)- DNA is dense, compact & easily visual- Early chromosome has 2 sister chromatids joined together at centromere and also contain telomeres- Occurs after G2- Most M-Cdk activityS-Phase: where chromosomes are copied=DNA replication- Involves long, thin, tangled thread of DNA that is not easily distinguished with light microscope- Loose to allow access for replication but occupy different territories in nucleus, not mixed together- Has heterochromatin on edges and genes in nucleolus- Takes 8 hours- Occurs after G1 with active S-CdkG1: where cell grows and makes proteins- Occurs before s phaseG2: where cell prepares to divide, gap phase where cell grows and makes proteins- Occurs before m phaseNucleotides: building blocks of DNA- Links phosphate to sugar and base- Covalently linked by Phosphodiester linkageDNA: instructions for life- Found in 1940s to be genetic info carrier- Structure determined in 1953 by Watson & Crick which led to discovery of replication and understanding proteinsDNA hybridization: “painting” chromosomes different color- Done by FISH- Fluorescent dyes label DNA/RNA probes & complementarily bind to chromosomes - Allows entire human genome to be sequencedComplementary base pairing: energetically favorable in interior to hold back bones an equal distance apart along DNA- Hydrogen bonded: G—3—C A—2—T - Antiparallel Twisted DNA helix: right handed helix, 2nm - Has 10 base pairs per helical turn- Major groove=wider- Minor groove=smallerChromosomes: functional units of heredity, region of DNA that controls discrete hereditary characteristics of organisms, usually responsible for specifying single protein/RNA molecule- Contains large regions of noncoding DNANucleolus: contains genes for rRNA which are located on multiple chromosomesCentromere: allows one copy of each chromosome to be distributed to each daughter cell Telomere: forms caps at ends of chromatid - Enables ends to be replicated and be identified as not brokenNucleosome: basic unit of chromosomal structure, beadlike structural unit composed of short length of DNA wrapped around core of histone protein to form chromatin- Can be viewed by x-ray crystallography- Either histones/non histone chromosomal proteins included - Converts DNA to 1/3 its initial length (1st level of DNA packaging)- 8 histones: H2A(2), H2B(2), H3(2), H4(2)Heoscht stain: fluorescent dye to identify DNA- In nondividing cell: can’t identify individual chromosomes, DNA is in extended formation- In dividing cell: DNA is visible when cell undergoes mitosis/meiosis, chromosomes visiblewhen condensedKaryotype: display full set of chromosomes of cell arranged with respect to size, shape & numberChromosomal defects: - Example: extra chromosome in 21 => Down’s syndrome- Translocations lead to cancerHistones: used with covalent chemical modifications to communicate opening/closing of DNA- Modifications on tail: - acetyl-methyl-phosphate- Affects ability to recruit certain proteins & access to DNA - Point of regulationHistone H1: 5th histone- Pulls nucleosome together into regular repeating arrayDNA packing levels:**start: short region of DNADNA wraps around histone; chromatin chromatin fiber of packed nucleosomes folds into loops makes up entire mitotic chromosome in this manner- 10000 fold shorter than fully extended lengthChromatin remodeling complexes: use energy of ATP hydrolysis to change position of DNA wrapped around nucleosome - Loosens/tightens DNA- Alters DNA accessibility to proteins- ATP hydrolysis loosens nucleosomal DNA by pushing it along histone core therefore exposing DNA to DNA binding proteins aka decondensesChromatin: complex of DNA & proteins which is used in packaging, repair etc.- Contains DNA repair proteins- Can be heterochromatin/euchromatin through different sets of histone tail modifications in reality both have mixture of structuresHeterochromatin: closed genetic material, gene-poor, usually located around periphery- Highly condensed form therefore doesn’t express genes- Found near centromere/telomeres- Makes up 10% of interphase chromosomeEuchromatin: “open”- Makes up remaining 90% of interphase chromosome- More extended state to allow for replicationH2AX: H2A histone, member x- One of several genes coding for histone H2A- Can be modified to communicate variety of things to cell- It’s phosphorylated by ATM kinase when DNA is damaged- Found flares in nucleiEpigenetic inheritance: transmission of heritable pattern of gene expression from one cell to progeny which doesn’t involve altering actual nucleotide sequence of DNA- Remembers covalent modifications- Remembers which gene was active in parent cell- Critical for establishment & maintenance of different cell types, tissues & organs during development & growth Chapter 6~Replication origins (Ori’s): site at which DNA is first opened - Initiator proteins: break h-bonds, separating nucleotides- Usually in A=T regions because they’re easier to full apart- Replication forks move opposite direction of it, 2 per originReplisome: large protein complex machine- Contains all proteins needed to copy DNA- Moves/walks along DNA at replication fork to open DNA strands & replicate DNA- Bidirectional: moves in opposite directions while “unzipping DNA” - 100 nucleotides/secLeading Strand: made by continuous synthesis in 5’3’ directionLagging Strand: made by discontinuous lengths that are later joined covalentlyOkazaki fragments: small DNA pieces which are later joined together to form continuous strandDNA helicase: separates DNA strands so proteins/enzymes have access to genetic materials - Uses ATP hydrolysis to rip apart double helix- Spins to unravel chromatin structure- Binds to Ori sequence creating bubbleNuclease: breaks apart RNA primer, usually found in lagging strandRepair Polymerase: replaces RNA with DNAPrimase: RNA polymerase which creates short length of RNA (primer)about 10 nucleotides long- Makes base paired 3’ end starting point for DNA polymerase- Usually found in lagging strandDNA ligase: joins Okazaki fragments together after RNA primers are removed - Joins 5’ phosphate of new DNA to adjacent 3’ hydroxyl endSteps in DNA