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AP Genetics Review Why do cells divide? • The continuity of life is based on the reproduction of cells: cell division • Cells divide to: – Reproduce – Renewal – Repair – Replacement – Make new cells Organization of Genetic Material • DNA: our genetic material, our genes • Chromatin: DNA and proteins • Chromosomes: threadlike structures in the nucleus that are made of chromatin • Genome: all of our DNA Chromosome Duplication • Before a cell can divide, chromosomes must duplicate. • Each duplicated chromosome has two identical sister chromatids, attached at a centromere. Phases of the Cell Cycle • Interphase: 90% of the cell’s life, during which growth, protein synthesis, and chromosome duplication occurs. Has 3 sub-phases: • G1 phase: “first gap” the cell grows • S phase: “synthesis” chromosomes duplicate • G2 phase: “second gap” the cell grows some more and prepares for division Phases of the Cell Cycle • The other phase is the Mitotic Phase (M) during which the cell divides. It has 2 subphases: • Mitosis: when the nucleus divides • Cytokinesis: when the cytoplasm and the rest of the cell divides The Phases of Mitosis • • • • • • Prophase (Prometaphase) Metaphase Anaphase Telophase Cytokinesis Binary Fission • Prokaryotes (bacteria and Archea) reproduce by binary fission, meaning “division in half.” • Bacteria have one chromosome, which is a a big circle, which reproduce starting at the origin of replication. • After DNA is duplicated, the plasma membrane pinches inward and a new cell wall grows between the daughter cells. Kinases and Cyclins • Kinases are enzymes that active or inactive proteins of the cell cycle • Cyclins are proteins that must be attached to kinases to be active; they are cyclin dependent kinases (Cdks) • MPF “maturationpromotion factor” triggers G2 How cells grow • Cells don’t grow if they are over-crowded, which is called density-dependent inhibition • Most cells are anchorage dependent which means that they must be attached to something to grow • Cancer cells are NEITHER of these things, they are cells growing out of control wherever they want. Inheritance of Genes • Genes are segments of DNA. Copies of genes (with some differences due to crossing over) are passed from parents to children. • Gametes are sex cells, eggs and sperm, that carry genes from one generation to the next. • During fertilization, gametes unite to form a zygote, which develops into an embryo, then a fetus, and then a newborn. Karyotypes • A karyotype is a picture of all 23 pairs of chromosomes (duplicated to be 46) arranged in order from 1 23. • Homologous chromosomes are pairs; one from Mom and one from Dad Types of Chromosomes • 22 pairs of our chromosomes are autosomes, non-sex chromosomes. • 1 pair of our chromosomes are called sex chromosomes, and determine gender. • Women = XX • Men = XY Diploid vs. Haploid • • • • • • • Diploid Cells: 2n 46 chromosomes Somatic cells (body cells) 2 sets of chromosomes 2n = 46 Skin, nerve, muscle...all body cells • Zygotes • • • • • • Haploid Cells: n 23 chromosomes Gametes only Egg and sperm 1 set of unduplicated chromosomes • n=23 • Sex cells Meiosis • Meiosis is cell division that reduces the number of sets of chromosomes from two to one, creating gametes (eggs and sperm). • It ONLY happens in the ovaries and testes. The process of meiosis • Meiosis happens in two steps, Meiosis I and Meiosis II. Stages of Meiosis I: Prophase I Metaphase I Anaphase I Telophase I and Cytokinesis Stages of Meiosis II: Prophase II Metaphase II Anaphase II Telophase II and Cytokinesis Prophase I • 90% of meiosis • Chromosomes condense • Crossing over occurs: DNA in non-sister chromatids mix and match; resulting in genetic variation of offspring • Tetrads are held together at chiasmata Crossing Over • Duplicated homologous chromosomes connect, this is called synapsis. • Pieces of DNA swap, called crossing over. • All 4 chromatids together make a tetrad. • Each tetrad has at least one site of chiasma, where crossing over occurs. Anaphase I • The chromosomes begin to move to the poles. • Sister chromatids remain attached! Anaphase II • Centromeres of each chromosome separate, and sister chromatids start moving apart. Mitosis vs. Meiosis Mitosis • Cells divide once • No crossing over • Two daughter cells made • Daughter cells are identical to each other and parents • Daughter cells are 2n • Occurs in somatic cells Meiosis • Cells divide twice • Crossing over (prophase I) • Four daughter cells made • Daughter cells are all different from each other and parents • Daughter cells are n • Occurs in ovaries/testes • Makes gametes Why is crossing over important? • During Prophase I, crossing over occurs and produces genetic variation. • This produces recombinant chromosomes, that carry genes (DNA) from two different parents • Powers natural selection/evolution: all individuals are different and the most fit survive to reproduce • Makes species more “hardy,” if bad things happen, at least some will have adaptations that help them survive. 9.3 Mendel’s principle of segregation describes the inheritance of a single characteristic • From his experimental data, Mendel deduced that an organism has two genes (alleles) for each inherited characteristic – One characteristic comes from each parent!!! Figure 9.3A Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings P GENERATION (true-breeding parents) Purple flowers White flowers All plants have purple flowers F1 generation Fertilization among F1 plants (F1 x F1) F2 generation 3/ of plants have purple flowers 4 1/ 4 of plants have white flowers GENETIC MAKEUP (ALLELES) • A sperm or egg carries only one allele of each pair P PLANTS Gametes – The 2 alleles for a gene separate during gamete formation, and each gamete gets a different one PP pp All P All p F1 PLANTS (hybrids) Gametes All Pp 1/ 2 1/ P P 2 p P Eggs Sperm PP – This is the law of segregation F2 PLANTS Phenotypic ratio 3 purple : 1 white p p Pp Pp pp Genotypic ratio 1 PP : 2 Pp : 1 pp Figure 9.3B Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings Law of Independent Assortment • Another law Mendel discovered is the Law of Independent Assortment which says that each allele segregates independently from another (traits aren’t linked unless they are on the same chromosome) Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings Genotype and Phenotype • A genotype is the genetic make-up of an individual, expressed in letters. (BB, Bb, bb) • A phenotype is the physical appearance of an individual, determined by his or her genotype. (black, brown, short, tall, etc) Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings Purple flowers, P, are dominant to white, p. • Show a Punnett Square crossing a homozygous purple flower with a heterozygous purple flower. • PP x Pp • What are the genotypic and phenotypic ratios? Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings Incomplete Dominance • In incomplete dominance, the heterozygous genotype produces a phenotype that is in between the dominant and recessive ones. • For example, if RR makes red flowers, and rr makes white flowers, then Rr makes PINK flowers (instead of red). Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings Co-Dominance • Co-Dominance- when both alleles are expressed in the phenotype, an example blood type AB. Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings Dihybrid Crosses • Instead of crossing just one trait, dihyrbrid crosses show the crossing of two separate traits. Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings Pedigrees • Pedigrees are used to trace traits through a family tree. • Circles are girls, squares are boys. • Filled in circles and squares represent individuals affected by a disease. • A horizontal line connecting the symbols represents marriage, vertical lines represent offspring. Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings Everything that’s left over… • A testcross is done to figure out an unknown genotype. The mystery genotype is crossed with a homozygous recessive individual. • A carrier is heterozygous for a disease but does not show symptoms. They CAN pass it on to offspring. Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings Other types of inheritance • Pleiotropy: Genes can affect more than one phenotype (sickle-cell and malaria) • Epistasis: One gene affects how a second gene is expressed • Polygenic Inheritance: Many genes affect one phenotype (skin color) Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings Sex-linked diseases • Any gene located on a sex chromosome is called a sex-linked gene. • Examples include color blindness, baldness, hemophilia, and muscular dystrophy. • These recessive diseases usually affect men more than women. Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings The importance of chromosomes • In 1902, the chromosomal theory of inheritance began to take form, stating: genes have specific locations (loci) on chromosomes, and you randomly get one chromosome from each parent. Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings Linked Genes • Genes on the same chromosome tend to be inherited together “linked genes” Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings So why do offspring look different from parents? Independent Assortment • The phenotypes of the parents are called parental types. • The offspring, with new and different phenotypes, are called recombinant types or recombinants. • This happens because offspring receive one chromosome from each parent, and end up looking different. Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings Linkage Mapping • Based on a linkage map, one can assume: the farther apart 2 genes are, the more likely a crossover will occur between them, therefore the recombination frequency is higher. Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings Linkage Mapping • A linkage map is a genetic map based on recombination frequencies. • Units are called map units and show the distance between genes. • 1 map unit = a 1% chance of recombination. • If two genes are 50 map units apart, how likely is recombination? Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings Abnormal Chromosome Number • Nondisjunction is when chromosomes do not separate correctly during meiosis. • This causes an abnormal chromosome number, called aneuploidy • Trisomy is when you have 3 chromosomes instead of 2 (2n + 1) • Monosomy is when you have 1 chromosome instead of 2 (2n – 1) • Polyploidy is having more than one complete set of chromosomes • If any of the above organisms survive to birth, it will have major developmental abnormalities Alterations of chromosome structure • Deletion: chromosomal fragment is deleted • Duplication: a chromosomal fragment is doubled • Inversion: chromosomal fragment gets reversed • Translocation: chromosomal fragments get switched around What is DNA? • DNA stands for deoxyribonucleic acid. • DNA is what makes our genes, and along with protein, makes our chromosomes. • It encodes our hereditary information. • It directs the development of our anatomical, physiological, and behavioral traits. The Structure of DNA DNA is a double helix. It is a polymer made of monomers called nucleotides. Each nucleotide is made of a nitrogenous base, a pentose sugar called deoxyribose, and a phosphate group. The backbone of DNA is called “sugar phosphate” and has bases attached to it like rungs of a ladder. The Structure of DNA DNA is “right handed” and curves to the right. Hydrogen bonds hold the bases together The 5’ end has a phosphate group The 3’ end has an OH group Strands always line up with one 5’ strand face up attached to a 3’ strand Purines Purines are nitrogenous bases with 2 organic rings. G and A are purines Pyrimidines Pyrimidines are nitrogenous bases with only 1 organic ring Cytosine and thymine DNA Replication DNA replicates during the S phase of interphase, prior to cell division (mitosis). DNA replication is semi- conservative, meaning that new DNA strands are made of one new daughter strand attached to one old parent strand. DNA Replication DNA polymerases are special enzymes that add complementary bases to the unzipped DNA. DNA Replication DNA replication can ONLY go from 5’ to 3’ So replication is antiparallel, one strand elongates normally, called the leading strand. The other is going away from the replication fork, called the lagging strand. DNA Replication As the bubble of replication grows, the lagging strand is made bit by bit in fragments, called Okazaki fragments. These are eventually joined by an enzyme called DNA ligase. From Gene to Protein • The “Central Dogma of Molecular Biology” is DNA RNA protein • Meaning that our DNA codes our RNA which provides instructions for making protein • Proteins (you may remember) do many things: structure, support, communication, transportation, enzymes etc. Transcription and Translation • Transcription is the synthesis of RNA from DNA • Translation is the synthesis of a polypeptide (protein) from RNA. Codons • Proteins are made of amino acids. • Each amino acid is coded for by a triplet of nucleotides called a codon. • For example, AGT = serine • There are only 20 amino acids, but 64 codons. Transcription: DNA to RNA • First, RNA Polymerase unzips a strand of DNA. • Transcription can only go from 5’ to 3’ • RNA Polymerase II attaches to DNA at a promoter • The portion of DNA being transcribed is called a transcription unit Transcription: DNA to RNA • RNA is now synthesized, as base pairs are added to the unzipped DNA strand. • RNA is ribonucleic acid. It is a single helix. Instead of T (thymine) RNA has U (uracil). • So every A in DNA now pairs with U (instead of T). • The RNA that is made is called mRNA which stands for messenger RNA. RNA splicing • Some of the RNA isn’t needed to code for proteins, so it is cut out through RNA splicing. • The non-coding regions that are cut out are called introns, the coding portions the cell needs are called exons. • Little molecules called small nuclear ribonucleoproteins, snRNA, join with a molecule called a spliceosome to slice the RNA. Translation: RNA to protein • The mRNA now leaves the nucleus and binds to a ribosome, where protein synthesis occurs. • As it passes through the ribosome, tRNA (transfer RNA) molecules, each carrying an amino acid, begin to form a long chain of amino acids. Translation: RNA to protein • At one end of tRNA is a triplet code called an anticodon which matches the mRNA. • At the other end of the tRNA is an amino acid. Translation: RNA to protein • The ribosome where this all happens has two pieces, and is made of proteins and RNA called ribosomal RNA (rRNA) • The subunits are called “large” and “small” Operons • Genes that can be turned on or off as needed. • The switch that does this is a segment of DNA called an operator. • Along with an operator, there is a promoter and some enzymes that make up the operon. • Repressors turn off an operon • Inducers turn on an operon Trp operon • Tryptophan is an amino acid that is usually produced by the body but can be turned off. This is a “repressible operon” Lac operon • The lac operon is usually off but can be stimulated (induced) and is therefore called an “inducible operon.” • The lac operon functions in the digestion of lactose, milk sugar. Points of control The control of gene expression can occur at any step in the pathway from gene to functional protein 1. packing/unpacking DNA 2. transcription 3. mRNA processing 4. mRNA transport 5. translation 6. protein processing 7. protein degradation AP Biology 1. DNA packing How do you fit all that DNA into nucleus? DNA coiling & folding double helix nucleosomes chromatin fiber looped domains chromosome from DNA double helix to AP Biology chromosome condensed Nucleosomes 8 histone molecules “Beads on a string” 1st level of DNA packing histone proteins 8 protein molecules positively charged amino acids bind tightly to negatively charged DNA AP Biology DNA packing movie DNA packing as gene control Degree of packing of DNA regulates transcription tightly wrapped around histones no transcription genes turned off heterochromatin darker DNA (H) = tightly packed euchromatin lighter DNA (E) = loosely packed H AP Biology E DNA methylation Methylation of DNA blocks transcription factors no transcription genes turned off attachment of methyl groups (–CH3) to cytosine nearly permanent inactivation of genes AP Biology C = cytosine ex. inactivated mammalian X chromosome = Barr body Histone acetylation Acetylation of histones unwinds DNA loosely wrapped around histones attachment of acetyl groups (–COCH3) to histones AP Biology enables transcription genes turned on conformational change in histone proteins transcription factors have easier access to genes RNA interference Small interfering RNAs (siRNA) short segments of RNA (21-28 bases) bind to mRNA create sections of double-stranded mRNA “death” tag for mRNA triggers degradation of mRNA cause gene “silencing” post-transcriptional control turns off gene = no protein produced siRNA AP Biology 6 7 Gene Regulation protein processing & degradation 1 & 2. transcription - DNA packing - transcription factors 5 initiation of translation 4 mRNA processing 5. translation - block start of translation 2 1 initiation of transcription AP Biology mRNA splicing 3 3 & 4. post-transcription - mRNA processing - splicing - 5’ cap & poly-A tail - breakdown by siRNA 6 & 7. post-translation - protein processing - protein degradation mRNA 4 protection