Chapter 13: Meiosis and Sexual Life Cycles

13.1: Offspring acquire genes from parents by inheriting chromosomes

• Genes: What parents endow offspring with, the hereditary unites that information is coded in

• Heredity: Transmission of traits from one generation to the next

• Variation: Happens along with inherited similarity

• Genetics: Study of both heredity and variation

• Gametes: Vehicles that transmit genes from one generation to the next

• Somatic Cells: All body cells other than gametes (and their precursors)

• Locus: Gene’s specific location along the length of a chromosome

• Asexual Reproduction: Single individual is the sole parent, copying all of its genes and passing them on to the offspring without fusing gametes

  • Clone: Genetically identical to parent, from asexual reproduction

• Sexual Reproduction: Parents give rise to offspring with unique combinations of genes inherited from both parents

13.2: Fertilization and meiosis alternate in sexual life cycles

• Life Cycle: Generation to Generation sequence of stages in reproductive history of organism

  • Includes conception all the way to production of offspring

• In humans, each somatic cell has 46 chromosomes, set of 23 from mom and set of 23 from dad

• Karotype: Images of chromosomes arranged in pairs, starting with the longest

• Homologous Chromosomes (Homologs): Chromosomes with same length, centromere position, and staining patterns

• Sex Chromosomes: X and Y Chromosomes

  • XX female, XY male

  • Autosomes: Other chromosomes

• Diploid Cell: A cell with two chromosome sets and a diploid number of chromosomes (Abbreviated 2n)

• Haploid Cell: Single set of chromosomes, such as in gametes, with a haploid number of chromosomes (Abbreviated n)

  • For humans, n = 23

• Fertilization: Union of gametes, causing fusion of their nuclei

  • Zygote: Resulting fertilized egg, diploid

• Meiosis: Cell division that causes gamete formation

• Three main timing variations of meiosis and fertilization

  • In humans and most other animals, gametes are the only haploid cells

  • In plants and some algae, exhibit alternation of generations

    • Alternation of Generations: Includes both diploid and haploid stages, which are multicellular

      • Sporophyte: Multicellilar diploid stage

      • Spores: Haploid cells produced by meiosis in the sporophyte

      • Gametophyte: the haploid stage, since haploid spore divides mitotically

      • Sporophyte generation produces gametophyte offspring, gametophyte produces sporophyte

13.3: Meiosis reduces the number of chromosome sets from diploid to haploid

• Meiosis preceded by interphase (including S phase)

  • Followed by two consecutive cell divisions, meiosis I and II, and four daughter cells all with one set not two

• During prophase I:

  1. Two members of a homologous pair associate along their length

     1. Each gene is alligned presicely with the corresponding alleles of that gene on the other homolog

     2. DNA of two nonsister chromatids broken by specific proteins at precisely matching points

  2. Formation of synaptonemal complex (zipper like structure) which holds one homolog tightly to the other

     1. Synapsis: When synaptonemal complex holds one homolog tightly to the other ^^

  3. DNA breaks closed up so each broken end is joined to the corresponding segment of the nonsister chromatid

  4. Points where crossing over has occured are visible as chiasmata after synaptonemal complex disassembles and homologs move slightly apart

• There are a few things unique to meiosis not in mitosis

  • Synapsis and crossing over

  • Alignment of homologous pairs at metaphase plate, instead of individual chromosomes

  • Seperation of homologs

• Meiosis I is called reductional division since there is ½ the number of chromosomes per cell

• Meiosis II is called equational division, since sister chromatids seperate, producing haploid daughter cells

13.4: Genetic variation produced in sexual life cycles contributes to evolution

• Three things contribute to genetic variation from sexual reproduction

  • Independent Assortment: First mieotic division means each pair sorts maternal and paternal homologs into daughter cells

    • There are a lot of combinations which the cells can be in, independent of each other

    • During metaphase I

    • In metaphase II, there is random orientation

  • Recombinant Chromosomes: Individual chromosomes carrying genes from two different parents, caused by crossing over

  • Random fertilization, there are 70 trillion possible diploid combinations

    • 16 square punnett square, using FOIL for the mother and father as top and side

Chapter 14: Mendel And The Gene Idea

14.1: Mendel used the scientific approach to identify two laws of inheritance

• Character: Heritable feature which varies among individuals (ex. color of flower)

  • Trait: Variant for a character (ex. purple flower)

• True Breeding: Offspring from self pollination are all the same variant

• Hybridization: Mating/crossing of two true breeding varieties

  • P Generation: True breeding parents

  • F₁ Generation: Hybrid offspring

  • F₂ Generation: Second filial generation

• Mendel’s model has four concepts.

  1. Alternative versions of genes account for variations in inherited characters.

  • Alleles: Alternative versions of a gene (ex. purple vs white flower)

  2. For each character, an organism inherits two versions (that is, two alleles) of a gene, one from each parent.

  • Each somatic cell in diploid organism

  3. If the two alleles at a locus differ, then the dominant allele determines the organism’s appearance; the other, the recessive allele, has no noticeable effect on the organism’s appearance.

  4. The Law of Segregation: The two alleles for a heritable character segregate during gamete formation and end up in different gametes

  • An egg or sperm only gets one of the two alleles present in the diploid cells of the organism

  • If identical alleles for particular character, the allele is present in all gametes.

• Punnet Square: A diagram to predict the allele composition of offspring

• Homozygote: Organism with pair of identical alleles (homozygous for that gene)

• Heterozygote: Two diff alleles for a gene (heterozygous for the gene)

• Phenotype: Appearance (ex. purple)

• Genotype: Genetic makeup (ex. Pp)

• Testcross: Breeding organism of unknown genotype with recessive homozygote

• Monohybrids: Heterozygous for one particular character being followed in the cross

  • Monohybrid Cross: Cross between monohybrids

• Mendel crossed YYRR and yyrr

• Dihybrids: Heterozygous for two characters being followed in the cross (YyRr)

  • Dihybrid Cross: Cross between two F₂ dihybrids

• Law of Independent Assortment: 2+ genes assort independently, meaning they segregate independently of any other pair of alleles during gamete formation

14.2: Probability laws govern mendelian inheritance

• Multiplication Rule: Multiple probability of one event and other event for probability of both to occur

• Addition Rule: Probability that at least one of two mutually exclusive events will occur by adding their probabilities

14.3: Inheritance patterns are often more complex than predicted by simple Mendelian genetics

• Complete Dominance: One allele in a pair makes the F₁ variety only show it over the other

  • Incomplete Dominance: Intermediate phenotype results

  • Codominance: Both phenotypes exhibited by heterozygotes

• The observed dominant/recessive relationship of alleles depends on the level we examine the phenotype on

• Pleiotropy: Most genes have multiple phenotypic effects

• Epistasis: Phenotypic expression of gene at one locus alters that of a gene at a second locus

• Quantitative Characters: Characteristics that vary based on a scale (like skin color)

• Polygenic Inheritance: Additive effect of 2+ genes on a single phenotypic character, indicated by quantitative characters

  • ex. height

• Multifactorial: Many factors (genetic and environmental) collectively influence phenotype

14.4: Many human traits follow Mendelian patterns of inheritance

• Pedigree: Tree with info about a family’s history for a particular trait

• Carriers: Heterozygotes that transmit the recessve allele to offspring in recessive diseases

• Human diseases are multifactorial

• Aminocentsis: Procedure to see if a developing fetus has a recessive disease, needle inserted into uterus, extracting aminiotic fluid which is tested

• Chronic Villus Sampling (CVS): Tube inserted into uterus, takes small amount of placenta tissue, tested

Chapter 15: The Chromosomal Basis of Inheritance

15.1: Mendelian inheritance has its physical basis in the behavior of chromosomes

• Chromosome Theory of Inheritance: Mendelian genes have specific loci along chromosomes, and the chromosomes undergo segregation and independent assortment

• Wild Type: Phenotype most commonly observed in natural populations

  • Mutant Phenotypes: Alternatives to the wild types, due to alleles assumed to have originated as mutations in the wild type allele

• Thomas Hunt Morgan found evidence associating genes with a specific chromosome

  • Chose a species of fruit flies, with only 4 pairs of chromosomes which are easy to distinguish under a light microscope. 3 pairs of autosomes, 1 pair of sex chromosomes. Female XX, male XY

  • Red eye wild type, white eye mutant type. Mated white eye male with red eye female. At F₁ it had red eyes, so red is dominant. In F₂, there was a 3 : 1 ratio (red : white), and white eyes only in males.

15.2: Sex linked genes exhibit unique patterns of inheritance

• Sex Linked Gene: Gene located on either sex chromosome

  • X linked and Y linked genes

• If X linked trait is recessive, female only expresses if she is homozygous for it. Males will express the trait if it’s from their mother

  • Hemizygous: Since males only have one locus, if receiving recessive allele from mother

• Duchenne Muscular Dystrophy: X Linked progressive muscle weakening, loss of coordination, and eventual death

• Hemophilia: X Linked recessive disorder defined by absence of one or more proteins required for blood clotting

• Almost all of one X chromosome in each cell in female mammals becomes inactivated during embryonic development

  • Males and females have only one active copy of most X linked genes

• Barr Body: Compact object inactive X chromosome condenses into

15.3: Linked genes tend to be inherited together because they are located near each other on the same chromosome

• Linked Genes: Genes located near each other on the same chromosome, inherited together during genetic crosses

• Genetic Recombination: Production of offspring with combos of traits that differ from those found in either parent

• Parental Types: Same phenotype as either of the parents

• Recombinant Types/Recombinants: New combinations different from parents

• Crossing over occurs for the recombination of linked genes

• Chi square has two types, goodness of fit (how close is it to what i expected?) vs independence (are these two things related?)

• Genetic Map: Ordered list of genetic loci along a particular chromosome

• The further apart two genes are, the higher probability a crossover will occur between them and the higher the recombination frequency

  • Recombination frequency is percentage of recombinant offspring

• Linkage Map: Genetic map based on recombination frequencies

  • Map Units: Distances between genes, one is 1% recombination frequency

15.4: Altercations of chromosome number or structure cause some genetic disorders

• Nondisjunction: Pair of homologous chromosomes don’t move apart properly during meiosis I or fail to separate during meiosis II

  • One gamete gets two of the same type of chromosome, the other doesn’t get any

  • Aneuploidy: Zygote has abnormal number of a chromosome. If either abnormal gamete unites with a normal one at fertilization, zygote will have this

• Monosomic: 2n-1 chromosomes, missing a copy

• Trisomic: 2n+1 chromosomes, extra copy of chromosome

• Nondisjunction in meiosis I

• Nondisjunction in meiosis II

• Polyploidy: More than two complete chromosome sets in all somatic cells (triploidy and tetraploidy), common in plants

  • Bananas triploid, wheat hexaploid, strawberries octaploid

  • Few fishes and amphibians are polyploids

• Four types of changes in chromosome structure

  • Deletion: Chromosonal fragment is lost

  • Duplication: Lost fragment is reattached as an extra segment to sister or nonsister chromatid

  • Inversion: Fragment reattaches to original chromosome but in reverse orientation

  • Translocation: Fragment joins a nonhomologous chromosome

• Down Syndrome: Trisonomy 21, extra chromosome 21 so each body cell has 47 chromosomes

• Sometimes there are extra X and Y chromosomes

  • XXY, Klinefelter syndrome, testes are small with little to no sperm, but have male sex organs

    • Taller height, less muscle mass, bigger breasts

  • XYY just taller than average

  • XXX, Trisonomy X, just taller than average

  • Monosomy X, sex organs don’t mature, so they are sterile unless they take estrogen

15.5: Some inheritance patterns are exceptions to standard Mendelian inheritance

• Genomic Imprinting: When the allele inherited depending on which parent (male or female) changes the phenotype

  • Imprints are formed during gamete production. The result is that one allele is not expressed in offspring

  • Inheritance of traits controlled by genes present in mitochondria and plastids depend solely on the material parent (since zygote’s cytoplasm containing these organelles come from the egg)

  • Diseases affecting nervous and muscular systems are caused by defects in mitochondrial genes which prevent cells from making enough ATP

Chapter 16: The Molecular Basis of Inheritance

16.1: DNA is genetic material

• The two components of chromosomes are proteins and DNA

  • Until the 1940s, people thought proteins were genetic material because they were a class of macromolecules with good diversity and function specificity

    • Nucleic acids were also mostly unexplored and too uniform

• In 1928, Griffith was trying to make a vaccine for pneumonia. He had two strains of bacteria, pathogenic (disease causing, S strain) and nonpathogenic (harmless, R strain).

  • When he killed the pathogenic bacteria and then mixed the remains with the nonpathogenic, some of the nonpathogenic bacteria became pathogenic, inherited by the descendants of the originally nonpathogenic bacteria

• Transformation: A change in genotype and phenotype due to assimilation of external DNA by a cell

• 1944, Avery, Macleod, and McCarty found when they destroyed the DNA of

• Bacteriophages/Phages: Viruses that infect bacteria

• Virus: DNA (Sometimes RNA) enclosed by a protective coat (usually protein)

• In 1952, Hershey and Chase used radioactive sulfur to tag phage’s protein in one batch, and radioactive phosphorus in the other

  • Sulfur is in protein but not DNA, phosphorus is in DNA but not protein

  • Phage DNA entered host cells, protein did not, so DNA must carry genetic information, not proteins

• DNA is a polymer of nucleotides, each with a nitrogenous base, a deoxyribose (pentose sugar) backbone, and a phosphate group

  • Nitrogenous base can be Thymine (T), Guanine (G), Cytosine (C), and Adenine (A)

  • Pyrimidines: 1 ring, T & C (& Uracil in RNA)

    • CUT ✂

  • Purines: 2 rings, A & G

    • Pure as gold (AG)!

• Chargaff’s Rules:

  1. DNA base composition varies between species

  2. For every species, the % of A and T are equal, same with C and G

• Franklin took a picture of a DNA strand, showing us the double helix structure of DNA

  • Used X-Ray Crystallography, using pure DNA instead of mixed forms

• Watson and Crick found sugar phosphate backbones are antiparallel (subunits run in opposite directions)

• A and T pair, C and G pair

• 2 hydrogen bonds between A and T, 3 between C and G

1. You need to know which side has the phosphate group (5’) and which one has the OH group of the sugar (3’)

2. He was expecting the mouse to be healthy, since, unaware of the concept of transformation, Griffith most likely assumed the result would be the same as in the other two trials.

16.2: Many proteins work together in DNA replication and repair

• DNA Replication: Copying of DNA

  • Hydrogen bonds first broken, so the two sides unwind and separate. Since they’re complementary, they serve as templates for the other side

• Semiconservative Model: Daughter molecules each have one old strand and one new strand (Predicted by Watson and Crick)

• Conservative Model: Two parental strings come back together after the process

• Dispersive Model: All 4 strands have a mixture of old and new DNA

• Origins of Replication: Where replication starts

  • Proteins that initiate replication recognize it and make a replication bubble

  • Replication Forks: Form at each end of the bubble, y shaped region where parental strands are being unwound

• Helicase: “Unzips” the double helix at the forks and separates them

• Single Strand Binding Proteins: Bind to the unpaired strands and keeps them open

• Topoisomerase: Relieves strain of untwisting double helix by rejoining DNA strands

• Primase: Places RNA primer to guide synthesis

• DNA Polymerase III: 5’ to 3’, can only add nucleotides to free 3’ end of primer

• Leading Strand: One primer for entire leading strand

• Lagging Strand: Series of segments, called Okazaki Fragments

• DNA Polymerase I: Removes RNA Primers from 5’ end and replaces them with DNA nucleotides added to 3’ end of adj fragment

• Ligase: The “glue”

• Mismatch Repair: Other enzymes remove and replace incorrectly paired nucleotides

• Nuclease: “Cuts” DNA

• Nucleotide Excision Repair: Detect damaged DNA, nuclease cuts the damaged DNA, repair synthesis by polymerase, and it’s sealed by Ligase

• Telomeres: Become shorter after replication. “Buffer zone” against organism gene shortening, and prevent staggered ends (can trigger cell death) of daughter molecule from activating cell’s systems for monitoring DNA damage

1. It means it can be used as a template

2. Synthesizes, idk second

16.3: A chromosome consists of a DNA molecule packed together with proteins

• DNA has two polynucleotide strands, and is 2 nm across

• Histones: Main proteins for packing DNA into chromosomes in interphase

  • >1/5 of histone’s amino acids are + charged, and bind tightly to DNA (- charge)

  • 4 types most common in chromatin, and are all very similar among eukaryotes

• Unfolded chromatins are ~10 nm in diameter, and looks like beads on a string

  • Nucleosome: The “beads”, basic unit of DNA packing

    • DNA wound 2x around core (8 histones, 2 of each of the 4 types)

      • Histone tail (the amino end of each histone) involved in regulation of gene expression, extends outward

  • Linker DNA: The “string”

• Euchromatin: Less compacted/loosely arranged, more dispersed interphase chromatin, DNA is accessible to proteins to be expressed

• Heterochromatin: Densely arranged, genes usually not expressed

• Chromatin: Complex of eukaryotic DNA and protein

1. It is DNA wound twice around a core of 8 histone proteins with histone tails sticking out

2. Euchromatin is more loosely arranged and its DNA is easy to access for gene expression. Heterochromatin isn’t used for gene expression and is more tightly bound

3. can’t

Chapter 17: Gene Expression—From Gene to Protein

17.1: Genes specify proteins via transcription and translation

• Gene Expression: Process in which DNA directs synthesis of proteins

  • Two stages, transcription and translation

• In prokaryotes transcription and translation occur together and sometimes at the same time

• In eukaryotes RNA must be processed first to make

• One gene one enzyme hypothesis states that the function of a gene is to dictate production of a specific enzyme

  • Has been modified since. Genes code for polypeptide chains or RNA molecules

• Transcription: Synthesis of RNA using information from the DNA

  • Produces mRNA

    • Messenger RNA (mRNA): Carries genetic message from DNA to protein synthesizing machinery of cell

  • Takes place in nucleus

• Translation: Synthesis of polypeptide using info from mRNA. Translates mRNA into amino acid sequence of a polypeptide

  • Takes place in cytoplasm

  • Ribosomes: Site of translation

  • Primary Transcript: Initial RNA transcript from any gene

• Central Dogma: Genetic info only flows one way, DNA → RNA → Protein

• Triplet Code: Genetic instructions for a polypeptide chain are written in DNA in three nucleotide words

• Template Strand: The strand that is used as a template for replication

  • Codons: mRNA nucleotide triplets, how genetic information is coded, = 3 ribonucleotides = 1 amino acid

• Coding Strand: Nontemplate DNA strand

• Reading Frame: Reading symbols in correct groupings

• AUG represents methionine amino acid or “start”

• UAG, UAA, or UGA is “stop”

17.2: Transcription is DNA directed synthesis of RNA

• RNA Polymerase: Pries two strands of DNA apart, joines RNA nucleotides complementary to DNA template strand

  • Catalyzes RNA synthesis

• Promoter: DNA sequence where RNA polymerase attaches and begins transcription

  • Region where proteins bind and begin synthesis, start point

  • TATA Box: In some (~25-33%) genes, promoter DNA sequence that helps eukaryotic RNA polymerase to recognize promoter sequences

• Terminator: Sequence that ends transcription

• Transcription Unit: Stretch of DNA that is transcribed into RNA

• Start Point: Nucleotide where RNA polymerase actually begins synthesizing

• 3 stages of transcription

  1. Initiation: After polymerase binds to the promoter, the polymerase unwinds DNA and starts RNA synthesis at the start point on the template strand

  2. Elongation: Polymerase keeps moving, unwinding and adding to the RNA 5’ to 3’

  3. Termination: RNA transcript is released and polymerase detaches from DNA

17.3: Eukaryotic cells modify RNA after transcription

• RNA Processing: Enzymes in eukaryotic nucleus modify pre mRNA before the message is dispatched to the cytoplasm

  • Both ends of primary transcript are altered

  • Interior sections of RNA are cut out and remaining parts are spliced for ever to make it ready for translation

• 5’ Cap and Poly-A Tail share important functions

  • 5’ Cap: Modified form of Guanine nucleotide added onto 5’ end after transcription of the first 20-40 nucleotides

  • Poly-A Tail: Added to 3’ end, a string of 50-250 adenine nucleotides

  1. Facilitate export of mature mRNA from nucleus

  2. Help protect mRNA from hydrolysis

  3. Help ribosomes attach to 5’ end of mRNA once it reaches the cytoplasm

• RNA Splicing: Large portions of RNA primary transcript molecules are removed and remaining portions are reconnected.

  • Removes introns (non coding material) and joins exons (stuff read by ribosome)

    • Introns/Intervening Sequences: Non coding material

    • Exons: Stuff read by ribosomes, parts that are eventually expressed and translated

  • Carried out by spliceosomes

    • Fold it in and “pop out” the introns

  • Ribozymes: Catalytic RNA molecules that function as enzymes and splice their own RNA, such as removing introns on their own

• Alternative RNA Splicing: Which segment is considered an exon can vary, so genes may give rise to 2+ different polypeptides

• Domains: Discrete structural and functional regions of proteins

  • Make up modular architecture of proteins

  • Different exons code for different domains

17.4: Translation is the RNA direcred synthesis of a polypeptide

• Transfer RNA (tRNA): Translator of a genetic message of codons along an mRNA molecule

  • Not all identical

  • Each has a specific amino acid on one end and an anticodon on the other

    • Anticodon: Particular nucleotide triplet that base pairs to a specific RNA codon

  • Single RNA strand ~80 nucleotides long, L shaped

• Accurate translation of a genetic message requires two things

  1. tRNA that binds to an mRNA codon specifying a particular amino acid that must carry that amino acid only to the ribosome

     1. Aminoacetyl-tRNA Synthetases: Family of related enzymes that correctly match up tRNA and amino acid

        1. 20 different synthetases one for each amino acid, active site only fits a specific combo of amino acid and tRNA

  2. Pairing of tRNA anticodon with appropriate mRNA codon

• Wobble: Third base of mRNA can pair with more than one kind of base in the tRNA anticodon

• Ribosomal RNA (rRNA): + a protein to make a ribosome

• Ribosome has three binding sites for tRNA, a P, A, and E site

  • P(eptidyl tRNA binding) Site: Holds tRNA carrying the growing polypeptide chain

  • A(minoacetyle tRNA binding) Site: Holds tRNA carrying the next amino acid to be added to the chain

  • E(xit) Site: Where discharged tRNAs leave the ribosome

• Initiation stage brings together mRNA, tRNA, and two subunits of a ribosome

• In elongation, amino acids are added one by one onto the previous

• Termination happens when a stop codon is read

• A number of ribosomes can simultaneously bond to the same mRNA molecule

• Signal Peptide: Marks polypeptides of proteins destined for the endomembrane system or secretion

• Signal Recognition Particle (SRP): Recognizes signal peptide as it emerges from the ribosome, protein RNA complex

• Polyribosomes: Strings of ribosomes that translate an mRNA at the same time

17.5: Mutations of one or a few nucleotides can affect protein structure and function

• Mutations: Changes to genetic information of a cell.

• Point Mutations: Changes in a single nucleotide pair of a gene

  • If occurs in a gamete or cell that gives rise to gametes, may be transmitted to offspring

• Nucleotide Pair Substitution: Replacement of one nucleotide and its partner with another pair of nucleotides

  • Silent Mutation: Change in nucleotide pair transforms one codon into another that is translated into the same amino acid

  • Missense Mutation: Substitution that changes one amino acid into another

  • Nonsense Mutation: Codon for amino acid changed into a stop codon, causing the polypeptide to be shorter than usual

• Insertion: Addition of nucleotide pairs in a gene

• Deletion: Loss of nucleotide pairs in a gene

  • Frameshift Mutation: Number of nucleotides inserted or deleted is not a multiple of three

• Mutagens: Physical and chemical agents that cause mutations in DNA

• Gene Editing: Altering genes in a specific, predictable way

  • CRISPR-Cas9 System: New technique for gene editing

    • Cas9 is a bacterial protein that helps dfend bacteria against viruses that infect them

Chapter 18: Regulation of Gene Expression

18.1: Bacteria often respond to environmental change by regulating transcription

• Operon: DNA required for enzyme production and the tryptophan pathway + operator + promoter

  • Operator: Segment of DNA that acts as an on-off switch for transcription units

    • Genes of related function are grouped into a transcription unit

    • Repressor: Binds to the operator to prevent RNA polymerase from transcribing genes and acting as the “off switch” of an operator

      • Regulatory Gene: Encodes the repressor protein, among bacterial genes that are expressed continually

      • Corepressor: Small molecule that cooperates with the repressor to turn an operon off

    • Inducer: Binds to the operator and inactivates the repressor

• Cyclic AMP (cAMP): Small orgamic molecule, interaction with allosteric regulatory protein stimulates transcription

  • Activator: Protein that binds to DNA and stimulates transcription

18.2: Eukaryotic gene expression is regulated at many stages

• Differential Gene Expression: Expression of different genes by cells with the same genome

  • Causes differences between cell types

• Histone Acetylation: Addition of an acetyl group to an amino acid in a histone tail, promotes transcription by opening up chromatin structure

• DNA Methylation: Methylating the DNA on certain bases, usually cytosine

• Epigenetics: Study of inheritance of traits transmitted by mechanisms not involving nucleotide sequence itself

• Control Elements: Segments of noncoding DNA that serve as binding sites for proteins (transcription factors, which bind to control elements and regulate transcription)

• Enhancers: Groupings of distal control elements, may be thousands of nucleotides up or downstream of a gene or within an intron

  • Gene may have multiple, but an enhancer is only associated with that gene

• Alternative RNA Splicing: Different mRNA molecules are produced from the same primary transcript depending on which parts are considered exons example of regulation at RNA processing level

18.3: Noncoding RNAs play multiple roles in controlling gene expression

• MicroRNAs (miRNAs): Small, single stranded RNA molecules capable of binding to complementary sequences in mRNA molecules

• Small Interfering RNAs (siRNAs): Class of small noncoding RNAs similar in size and function to miRNAs

• RNA interference (RNAi): Blocking of gene expression by siRNAs

• Long Noncoding RNAs (lncRNAs): Long and noncoding strings of RNA

18.4: A program of differential gene expression leads to the different cell types in a multicellular organism

• Differentiation: Process by which cells become specialized in structure and function

• Morphogenesis: Deveopment of form of an organism and its structures

• Cytoplasmic Determinants: Maternal substances in the egg that influence course of early development

• Induction: Signals conveyed to an embryonic cell from other embryonic cells in the vicinity causes changes in target cells

• Determination: Point at which an embryonic cell is irreversibly committed to becoming a particular cell type

• Pattern Formation: When cytoplasmic determinants and inductive signals both contribute to spatially organizing the tissues and organs of an organism in their characteristic places

• Positional Information: Molecular cues that control pattern formation

• Homeotic Genes: Regulatory genes that control pattern formation

• Embryonic Lethals: Mutations with phenotypes causing death at the embryonic or larval stage

• Maternal Effect Gene: Gene when mutation in the mother results in a mutated phenotype in the offspring

• Morphogens: Gradients of substances that establish an embryo’s axes and other features of its form

18.5: Cancer results from genetic changes that affect cell cycle control

• Oncogenes: Cancer causing genes in certain types of viruses

  • Proto Oncogenes: Normal versions of the oncogenes

• Tumor Suppressor Genes: Genes whose products inhibit cell division

• Ras Gene: G protein that relays a signal from a growth factor receptor on the plasma membrane to a cascade of protein kinases. Encodes the ras protein

• p53 Gene: Tumer suppressor gene named for molecular weight of the protein product

Chapter 19: Viruses

19.1: A virus consists of nucleic acid surrounded by a protein coat

• Virus: Infectious particle with mostly just genes packaged in a protein coat

• Capsid: Protein shell enclosing the viral genome

  • Can be rod shaped, polyhedral, or more complex in shape

• Viral Envelopes: Membranous envelope surrounding capsids of any viruses, derived from membranes of the host cell

• Bacteriophages/Phages: Viruses that infect bacteria

19.2: Viruses replicate only in host cells

• Host Range: The limited number of host species each virus can infect cells of

1. Virus enter the cell and is uncoated, releasing viral DNa and capsid proteins

2. Host enzymes replicate the viral genome

3. Host enzymes transcribe the viral genome into mRNA, used by host ribosomes to make more capsid proteins

4. Viral genomes and capsid proteins self assemble into new virus particles which exit the cell

• Lytic Cycle: Phage replicative cycle that culminates in the death of the host cell

  • Virulent Phage: Phage that only replicates by a lytic cycle

• Lysogenic Cycle: Allows replication of phage genome without destroying the host

• Temperate Phages: Phages able to use both lytic and lysogenic cycle to replicate

• Prophage: Viral DNA integrated into the bacterial chromosome by viral proteins that break both circular DNA molecules and join them to each other

  • One prophage gene codes for a protein that prevents transcription of most of the other prophage genes

• Restriction Enzymes: Cellular enzymes cut up phage DNA since it is identified as foregin, and restrict the phage’s ability to replicate within the bacterium

• Retroviruses: RNA animal viruses with the most complicated replicative cycles

  • Reverse Transcriptase: Transcribes RNA → DNA, in retroviruses

  • Includes HIV and AIDS

• When virus enters a host cell its reverse transcriptase molecules are released into the cytoplasm

  • Provirus: Integrated viral DNA, enters cell nucleus, integrates into the DNA of the chromosome, and never leaves the host’s genome

19.3: Viruses and prions are formidable pathogens in animals and plants

• Vaccine: Harmless derivative of a pathogen stimulates the iune system to mount defenses against the harmful pathogen

• Epidemic: Widespread outbreak

• Pandemic: Global epidemic

• Outbreaks of emerging viral diseases in humans are usually not new but caused by existing viruses that expand past their host territory

• Viruses enter plant cells through damaged cell walls or are inherited from a parent

• Prions: Proteins that appear to cause degenerative brain diseases

Chapter 20: DNA Tools and Biotechnology

20.1: DNA sequencing and DNA cloning are valuable tools for genetic engineering and biological inquiry

• DNA Technology: Techniques for manipulating DNA]

• Genetic Engineering: Direct manipulation of genes, uses nucleic acid hybridization

  • Nucleic Acid Hybridization: Base pairing of one strand of nucleic acid to complimentary strand (Can be DNA or RNA)

• DNA Sequencing: Using complimentary base pairings to find nucleotide sequence of DNA

  • First automated procedure called dideoxy sequencing, developed by Frederick Sanger

• DNA Cloning: Isolate the segment of DNA carrying a gene and copying it

  • First isolates plasmids from bacterial cells and alters them using genetic engineering. It becomes a recombinant DNA molecule, which is then returned to the bacterial cell, making a recombinant bacterium

  • Cell repeatedly does cell division until full population of copies (gene cloning)

    • Plasmids: Small, cicular DNA molecules with only a small number of genes, which many bacteria have

    • Recombinant DNA Molecule: Molecule with DNA from 2 sources (Usually different species)

    • Gene Cloning: Production of many copies of single gene. Used to either amplify (make copies of) a gene or produce a protein product from it

• Cloning Vector: DNA that carries foreign DNA into a host cell, replicating there

  • In above picture, the plasmid is one. TBacterial plasmids are often used as cloning vectors, because they’re easy to obtain, manipulate, and introduce into bacterial cells

• Restriction Endonucleases/Enzymes: “Cut” DNA at a number of specific locations.

  • Restriction Site: Where restriction enzymes recognize a short DNA sequence (cuts both ends). DNA sequence usually four-eight nucleotide pairs, and most restriction sites are symmetrical (read same way from 5’ to 3’ direction)

  • Restriction Fragments: The multiple fragments resulting from cuts of DNA, the same every time

• Sticky End: Single stranded end

20.2: Biologists use DNA technology to study gene expression and function

• Nucleic Acid Probe: Cloned short single straded nucleic acid complementary to mRNA of interest

• In Situ Hybridization: Solution containing probe molecules is applied and allows the probe to hybridize specifically any complementary sequences on the mRNAs in embryonic cells in which the gene is being transcribed

• Reverse Transcriptase Polymerase Chain Reaction (RT-PCR): Method used to detect mRNA

  1. Turns sample sets of mRNAs into double stranded DNA

     1. Transcriptase enzyme is used to synthesize a complementary DNA to each mRNA in the sample

     2. The mRNA is degraded by addition of a specific enzyme

     3. Second DNA strand complementary to the first is synthesized by DNA polymerase

     4. Complimentary DNA (cDNA): Resulting double stranded DNA

  2. PCR step, quantitative RT-PCR

  3. Gel electrophoresis

• RNA Sequencing/RNA Seq: Rapid inexpensive DNA seqiencing method, sequencing cDNA samples from different tissues or embryonic stages

• DNA Microarray Assays: Large number of single stranded DNa fragments representing different genes fixed to a glass slide in an array

• In Vitro Mutagenesis: Specific mutations are introduced into a cloned gene, and the mutated gene is returned to the cell and disables the normal cellular copies of the same gene. Used to edit genetic material in a predictable way

• Gene Drive: Introduces a modified gene, biased inheritence of gene makes it spread rapidly in the population

• RNA interference (RNAi) is used to silence expression of selected genes, synthetic double stranded RNA molecules matching the sequence of a particular gene are used to trigger breakdown of the gene’s mRNA or to block its translation

• Genome Wide Association Studies: Analyze genomes of large numbers of people and look for genetic markers (DNA sequences that vary in the population)

• Single Nucleotide Polymorphism (SNP): Single base pair site where variation is found in at least 1% of the population

20.3: Cloned organisms and stem cells are useful for basic research and other applications

• Stem Cells: Relatively unspecialized cell that can both reproduce indefinitely and deffrentiate into specialized cells of 1+ types

  • Embyronic from animal embryos, adult from adult tissues, can reproduce and diffrentiate both in the lab and the organism

• Totipotent: Capable of generating all tissues of a complete new plant

  • Usually single diffrentiated cells from plants are

• Pluripotent: Capable of diffrentiating into many different cell types

20.4: The practical applications of DNA based biotechnology affect our lives in many ways

• Biotechnology: Manipulation of organisms or their components to make useful products

• Personalized Medicine: Type of medical care where each person’s specific genetic profile can provide information about diseases or conditions for which the person is especially at risk

• Gene Therapy: Introduction of genes into an afflicted individual for therapeutic purposes

• Transgene: Gene transferred from one organism into another

  • Transgenic Organism: Embryo developed by being surgically implanted in a surrogate female

• Genetic Profile: Person’s unique set of genetic markers

Chapter 21: Genomes and Their Evolution

21.1: The Human Genome Project fostered development of faster, less expensive sequencing techniques

• Genomics: Studying whole sets of genes and their interactions

• Human Genome Project: The project to find the sequencing of the human genome in 1990, completed in 2003

  • Still several gaps, but 99% complete

• Reference Genome: Full sequence that best represents the genome of a species

• Whole Genome Shotgun Approach: Starts with cloning and sequencing of DNA fragments from randomly cut DNA, which are them assembled using computer programs into a continuous sequence

• Metagenomics: DNA from entire community of species is collected and sequenced

21.2: Scientists use bioinformatics to analyze genomes and their functions

• Gene Annotation: Process to identify all protein coding genes in a long DNA squence and their functions

  • First computers are used to search for patterns that indicate the presence of genes

  • Uses software to scan stored sequences for start and stop signals, RNA splicing sites, and other signs of protein coding genes

• Proteomics: Systematic studies of sets of proteins and their properties

• Systems Biology: Aims to odel dynamic behavior of whole biological systems based on the study of interactions among a system’s parts

21.3: Genomes vary in size, number of genes, and gene density

21.4: Multicellular eukaryotes have a lot of noncoding DNA and many multigene families

• Pseudogenes: Former genes that have accumulated mutations over a long time and no longer produce functional proteins, unique noncoding DNA

• Repetitive DNA: Sequences that are present in multiple copies in the genome

• Transposable Elements: Stretches of DNA that can move from one location to another within the genome. In eukaryotic, two types, transposons and retrotransposons

  • ~75% of human repetitive DNA

  • Transposons: Move within a genome using a DNA intermediate. Either a “copy and paste” or “cut and paste” method using transposase

  

  • Retrotransposons: Move by means of an RNA intermediate, a transcript of the retrotransposon DNA, and always leave a copy at the original site

• Simple Sequence DNA: Stretches of DNA that contain many copies of tandemly repeated short sequences

  • Short Tandem Repeat (STR): Series of repeats in a unit

• Multigene Families: Collections of 2+ identical or very similar genes

  • Ones with identical DNA sequences, they’re clustered tandemly and have RNAs as their final products

  • Ones with nonidentical genes enclode globins, a group of proteins that include the a and B polypeptide subunits of hemoglobin

21.5: Duplication, rearrangement, and mutation of DNa contribute to genome evolution

• Errors in cell division leads to extra copies of all or part of entire chromosome sets which may diverge if one set accumulates sequence changes

  • Polyploidy occurs more often among plants than animals and contributes to speciation

• Chromosonal organization of genomes can be compared among species to provide info about evolutionary relationships

• Genes encoding various relaed but different globin proteins evolved from one common ancestral globin gene which duplicated and diverged into a globin and B globin

• Rearrangement of exons within and between genes during evolution has led to genes containing multiple copies of similar exons and/or different exons derived from other genes

• Movement of transposable elements or recombination between copies of the same element generate new sequence combinations

  • These are beneficial to the organism

21.6: Comparing genome sequences provides clues to evolution and development

• Evo-Devo: Evolutionary developmental biology

• Homeobox: 180 nucleotide sequence that codes for homeodomain (amino acid) in the encoded proteins