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Structure of DNA

• Are large molecules consisting of long chains of repeating monomer units known as nucleotides

Nucleotides consist of

 Pentose sugar
 Base-adenine, quanine, cytosine, and thymine
 Phosphate

Bases in DNA

 Cytosine (C)
 Guanine (G) Same in both DNA
 Adenine (A) and RNA
 Thymine (T) Found in DNA only

RNA contains the bases

 Cytosine (C)
 Guanine (G) Same in both DNA
 Adenine (A) and RNA
 Uracil (U) Found in RNA only

Primary Structure of DNA

Nucleic acids consist of polymers of many nucleotides the 3'-OH group of the sugar in one nucleotide bonds to the phosphate group on the 5'-carbon atom in the sugar of the next nucleotide

phosphodiester bond

• Phosphate link between the sugars in adjacent nucleotides

which direction do nucleotides attach?

only at the 3' end

how many hydrogens hold the bases on one side of the helix to another base on the other side

A-T: 2 hydrogens..................C-G:3 hydrogens

what directions do the strands of DNA run to each other

opposite directions and contain the same information
 One strand goes from the 5' to 3' direction
 Other strand goes in the 3' to 5' direction

DNA Functions

 1. Store genetic information
 2. Copy that information for future generations of cells
 3. Express that information
 4. Occasionally change its message (mutate)

Storage of Genetic Information

• Genetic information in a DNA molecule resides in the sequence of nucleotides, expressed by the bases

• Genome

the term for the sum total of DNA in an organism's chromosomes

DNA replication

 Genetic information is maintained each time a cell divides
 The DNA strands unwind
 Each parent stand bonds with new complimentary bases
 Two new DNA strands form that are exact copies of the original DNA
 DNA polymerase (enzyme) bonds to parent strand and is used to add nucleotides for the new strands being created
 After DNA replication each DNA strand contains one old strand and one new strand. Each half old half new strand is like the parent molecule.

Expression of information (2nd function

Each cell in a multi cellular plant contains the same DNA information, but different subsets of the master plan are read in each cell type

1. Transcription -

 converting a gene to RNA

2. Translation -

RNA to proteins

RNA Differs from DNA by

• The sugar in RNA is ribose rather than the deoxyribose (no oxygen on two prime) found in DNA
• The base uracil replaces thymine
• RNA molecules are single, not double stranded----DNA: ATCG
• RNA molecules are much smaller than DNA molecules-------RNA: AUCG

RNA

• RNA is involved with transmitting the genetic information needed to operate the cell
• Three types of RNA
 Messenger RNA (mRNA)
 Ribosomal RNA (rRNA)
 Transfer RNA (tRNA)

mRNA(can go into translation)

• Carries genetic information from the DNA in the nucleus to the ribosomes in the cytoplasm for the synthesis of particular proteins
• 3 bases form a codon (codes for a particular amino acid or stop signal) specifying an amino acid or a stop signal
• Transcription makes this RNA.
• Transcription for protein synthesis (in nucleus: DNAmRNA) (in cytoplasm: mRNAprotein)

rRNA

• Is the most abundant type of RNA
• Is combined with proteins to form ribosomes
• Cells that synthesize large numbers of proteins have thousands of ribosomes

tRNA

Smallest of the RNA molecules
• Delivers amino acids one by one to ribosomes in the order specified by mRNA
• There are one or more different tRNAs for each of the 20 amino acids

Transcription (going from DNA to RNA)

• The types of RNA are made by transcription
• Only one strand of DNA is used to make the RNA in Transcription
• 3 steps
• 1. Initiation - RNA polymerase binds to a promoter region (TAC-signals this is the start of the protein) on the DNA and assembles an RNA strand using complementary base pairing
• 2. Elongation - RNA polymerase moves along the DNA strand in a 3' - 5' direction
• 3. Termination - A sequence of DNA at the end of each gene signals the transcription enzymes to fall off the DNA molecule

Genetic Code

 In sets of three nucleotide bases known as codons
 Three nucleotide bases make one amino acid
• Collectively, the codons constitute the genetic code
• Also contains start and stop codons
• 64 different codons used

Translation

• At the end of transcription, if a mRNA strand is made, it will move into the cytoplasm for the second stage to make a protein!
• mRNA specifies amino acid order via codons
• tRNA takes the amino acids coded for in the mRNA to the ribosome
• Ribosomes is made up of two rRNA strands and structural proteins
• tRNA binds to an amino acid via an anticodon (KNIW)which has complementary base pairs to the codon on the mRNA
 3 prime end carries amino acid to ribosome (accepting end)

Translation 3 steps

3 steps
 1. Initiation - small ribosomal subunit binds to the mRNA. The tRNA brings the first amino acid. The large ribosomal subunit binds with the small ribosomal subunit
 2. Elongation - the ribosome assembles a polypeptide chain as it moves along the mRNA strand. Other tRNA deliver amino acids to the ribosome. The ribosome joins each amino acid via a peptide bond
 3. Termination - Occurs when the ribosome encounters a STOP codon on the mRNA strand. The mRNA and new polypeptide chain detach from the ribosome

Why did gregor mendel choose peas

• Reproduces quickly
• Lots of offspring produced from one breeding
• Lots of traits that appear in two easily distinguishable forms
• Easy to grow
• Develop quickly
• Easy to control which plants mate with which

Mutations

• Are changes in DNA sequence and happens every time DNA replicates
• DNA repair enzymes can often find and correct damaged DNA, but if left uncorrected, it results in a permanent change in DNA sequence
• Most are silent, with no visible consequence of the DNA alteration
• Are either somatic or germ-line

• Somatic mutation

occurs in a body cell and will exist in all cells produced by mitosis of the mutant cell
 These are sometimes the source of new types of horticultural plants

• Germ-line mutation

occurs in tissue that will produce gametes, or sex cells
 Will be passed on to future generations through seeds
 Mutation has now become a permanent feature of that plant's lineage

• Gene

 Units of Information on heritable traits. Each gene has a specific location (locus; loci pl.)

• Mutation

 A process that alters a gene's molecular structure and its message about a trait. It may cause a trait to change

• Alleles

 All molecular forms of the same gene

• Pure breeds

 When offspring inherit identical alleles for a trait generation after generation, they typically are a true-breeding lineage

• Hybrids

 Offspring of a cross between two individuals that breed true for different forms of a trait are hybrids; each one has inherited nonidentical alleles for the trait

• Dominant allele

 When the effect of an allele on a trait masks the effect of another allele (denoted by capital letters)

• Recessive allele

 The allele whose trait is masked by another allele (denoted by lowercase letters)

• Homozygous Dominant

 Has a pair of dominant alleles (AA)

• Homozygous Recessive

 Has a pair of recessive alleles (aa)

• Heterozygous

 Has a pair of nonidentical alleles (Aa)

• Genotype

 The particular alleles that an individual carries, i.e., an individual's genetic makeup

• Phenotype

 An individual's observable traits

• P

 True breeding parents

• F1

 The first generation offspring

• F2

 The second generation offspring of self-fertilized or intercrossed F1 individuals

Mendel's Theory of Segregation

• Monohybrid experiments (termed the theory of segregation)
• Two homozygous parents differ in a trait that is governed by alleles of one gene
• They are crossed to produce F1 offspring that are all heterozygous
• F1 individuals are then encouraged to produce an F2 generation
• Mendel crossed plants that breed true for a trait (ex.-flower color) Purple x pink.
• All of F1 offspring looked like the parents (purple)
• Some of the F2 offspring looked like the parents but some were purple
• Homologous chromosomes have pairs of alleles which are separated from each other during meiosis, so they end up in different gametes

Probability

• The chance that each outcome of an event will occur is proportional to the number of ways in which and outcome can be reached
• Can use the Punnett-square method to show the possibilities

Punnett-Square Method

• If half of a plant's sperm or eggs are "a" and half are big "A," then the outcomes are:
• Sperm A meets Egg A ¼ AA offspring
• Sperm A meets Egg a ¼ Aa offspring
• Sperm a meets Egg A ¼ Aa offspring
• Sperm a meets Egg a ¼ aa offspring
• You can see that the probable phenotypic ratio is 3:1

Mendel's theory of independent assortment

• Mendel used dihybrid experiments (cross between true breeding that differ in 2 genes)to explain how two pairs of genes are sorted into gametes independently of each other
• Dihybrid crosses start with a cross between true-breeding homozygous parents that differ in two traits governed by alleles of two genes

• Organic evolution

- The accumulation of genetic changes in populations of living organisms through many generations

• Aristotle

-arranged organisms from simplest to most complex
- Implied that organisms were static and did not evolve

• Leonardo da Vinci

-reviewed fossils and observed that they were parts of previously existing organisms that had become extinct

• Count de Buffon

-described plants and animals. Presented evidence of descent with modification in organisms, but did not provide any theories on how evolution might take place

• Georges Curvier-

used comparative anatomy to classify animals. But did not believe that organiss changed over time

• Carolus Linnaeus

-created our current classification system and classified all known plants and animals based on relationship of organisms

• Jean Baptiste Lamarck-

supported the idea that hereditary changes in populations over long periods of time occurred as a result of the inheritance of acquired characteristics

• Charles Darwin-

Theory of evolution by natural selection

• Alfred Wallace-

looked at animal geography. Teamed up with Darwin

• Mutations!

• A sudden change in a gene or a chromosome
• Most mutations are harmful, but some (1%) are silent or have a favorable effect on the affected organism
• Mutations are heritable! This is VERY important! This is the essence of evolution!

 A fossil is

a remnant of past life uncovered from the crust of the earth

Common Descent

• Darwin proposed that all plants and animals have descended from an ancestral form into which life was first breathed

phylogeny

• Life is depicted as a branching tree

Homologous Structures

• -Structures that are shared from a common ancestor (divergent evolution) based on bone structure

• Analogous Structures

• Analogous Structures-Although the bones in the wings of bats and birds are homologous, the actual WINGS are analogous because they evolved INDEPENDENTLY in two different groups of non-flying animals (convergent evolution)

Darwinian Evolutionary Theory

 The living world is neither constant nor perpetually cycling, but always changing

divergent evolution

when two or more species sharing a common ancestor become more different over time

Convergent evolution

when two or more species NOT descended from a common ancestor develop similar traits

vestigial structures

remnant of a structure that may have had an important function in a species' ancestors, but has no clear function in the modern species

Microevolution

• Evolution that occurs within a species
• Natural Selection
• Descent with modification

Four Principles of Micro evolution

1) Overproduction (many organisms produce more offspring than can survive)
• A single maple tree produces thousands of seeds each year. Most are capable of becoming a new tree but only a few survive to maturity
• 2) Struggle for Existence (competition for resources)
• All seeds and mature plants are going to compete for moisture, light, mates, nutrients, and space.
• 3) Inheritance and Accumulation of Favorable Variation (favorable traits increase over time, unfavorable traits decrease over time)
• Ex. Coloration changes when those best adapted to the environment survive and reproduce (Pepper moths)
• 4) Survival and Reproduction of the Fittest (those best adapted to an environment have the best chance to survive and reproduce)
• Ex. A tree with thicker bark may have a higher probability of surviving cold temperatures and reproduce more often than one with thinner bark

How does micro evolution happen?

Mutations!
• A sudden change in a gene or a chromosome
Migration
• Gene flow between populations occurs when individuals or gametes migrate from one population to another
• How large the population is and how far apart populations are from each other are important
• Genetic Drift
• A change in the genetic makeup of a population due to random events

MacroEvolution

• How Species evolve
• If new genes are spread through an interbreeding population, they may gradually change the nature of the entire population
• If a barrier divides a population, the two new populations may become distinct from each other

How does Macro Evolution happen

Reproductive Barriers
• Biological features that prevent different species from interbreeding
• These barriers typically evolve gradually
• In order for reproductive barriers to evolve, diverging populations must be kept physically separate for long periods of time
• May require 10,000-100,000 years or more
• Geographic isolation-species occur in different places
• Ecological isolation-species utilize different resources
• Behavioral isolation-species perform different courtship behavior (seen in animals)
• Temporal isolation-species breed at different times
• Mechanical isolation-structural differences prevent sperm or pollen transfer

• Theophrastus (4th Century B.C.)

- Classified plants based on leaf characteristics
• 13th century, monocots and dicots were distinguished
• 18th century, details of fruit and flower structure, form and habit were considered in classification
• European herbariums were overflowing in plants and things were getting hectic

Development of the Binomial System...

• Latin was being used in schools and universities
• All organisms were grouped into Genera but still had very long and descriptive names
• Carolus Linnaeus (father of taxonomy) started abbreviating these preposterously long names
- He limited the Latin phrases to 12 words and put a single word in the margin that, when paired with the Generic name would form an individual species name tailored for that particular plant
- Linnaeus published a book (2 volumes) called species planetarium on plant names and classification

Binomial Nomenclature

• This abbreviated name, consisting of two parts (binomials), was termed the Binomial System of Nomenclature
- Today, this is how all organisms are named

International Code of Botanical Nomenclature

- Uses Linnaeus's Species Plantarum as a starting point for scientific names of plants and fungi
- A similar code has been developed for zoology as well

How to name your new species

• Prepare a Latin description of the plant and publish it in a journal or other publication that is circulated and available to the public
• Prepare an annotated herbarium specimen of the plant, designated by the author as a type specimen, and deposit it in a public herbarium
• The author's name follows the species name

Cladistics

• A method of examining natural relationships among organisms, based on features shared by those organisms

cladograms

• Relationships are portrayed in straight line diagrams (evolutionary trees)

character state

• The value or form of a feature - Hypotheses are derived to determine which character states are primitive and which are derived
- In a feature such as flower color the character would be the flower color and the state could be purple or red.

Occam's razor

- In trying to choose the best of several cladograms, taxonomists use the principle of parsimony
- Parsimony is based on a principle of logic called Occam's razor. Which states that one should not make more assumptions than the minimum needed to explain anything
- The best cladogram is usually interpreted as that which requires the fewest evolutionary changes in the taxa involved to arrive at the present situation

• Domain Archaea

- Kingdom Archaea
• Lack muramic acid in their cell walls, RNA bases, metabolism, and lipids are different from Bacteria

• Domain Eubacteria

- Kingdom Bacteria
• Have muramic acid in their cell walls, RNA bases, metabolism, and lipids are different from Archaea

• Domain Eukarya

- Kingdom Protista
- Kingdom Fungi
- Kingdom Plantae
- Kingdom Animalia

what separates the 3 domains

• Based on cellular structure

what separates the 3 kingdoms

• Three of the Kingdoms are based on how the organisms get their nutrition (photosynthesis, ingestion of food, and absorption of food in solution)
- Plantae, Fungi, Animalia
• Three of the Kingdoms are based on cellular structure
- Protista, Archaea, Bacteria

water are the 6 kingdoms

Animilia, Plantae, fungi, protista, bacteria, archaea

Plant Life Cycle

• The Life cycle alternates between a sporophyte and a gametophyte stage
o The sporophyte stage is diploid and makes sexual spores by way of meiosis
o Each spore is haploid and remains dormant until conditions are right when it forms into a gametophyte.
o The gametophyte stage is haploid and produces gametes that need to join with other gametes to form a diploid zygote they then grow into a mature sporophyte

Non vascular plants-

• plants that do not have a vascular system (xylem and ploem)
o Have no roots stems or leaves
o Some nonvascular plants possess tissues specialized for the internal transport of water.
o Include the only plants that have a dominant gametophyte generation.

Bryophytes

• The bryophytes are nonvascular plants
• Include the mosses, liverworts, and hornworts
• Found in various habitats
o Damp banks, trees, rocks, logs, bare soil, bones, dung, insect wings
• Have mycorrhizal fungi associated with their rhizoids

Phylum Hepaticophyta: Liverworts

• There are 8000 species of liverworts
• The most common and widespread liverworts have flattened lobed somewhat leaflike bodies called thalli (thallus)
• The most numerous liverworts are the leafy liverworts which superficially resemble the mosses
• Thalloid liverworts have smooth upper surfaces with various marking and pores, and the corners of the cell walls are thickened
• Liverworts differ from moss: Thalli and reproductive structures
• Leafy liverworts are abundant in tropical forests and fog belts
• They contain two rows of partially overlapping leaves that contain oil bodies
• These leaves have no midribs and they have folds and lobes unlike mosses
• Rhizoids develop from a stem like structures that holds a third layer of leafy structures underneath the top two layers

• Have mycorrhizal fungi

associated with their rhizoids

Structure of Broyophytes

• Do not have true xylem or phloem
o May have hydroids (water conducting cells) and leptoids (food conducting cells)
• Must have external water present to reproduce
• Water is absorbed through the surface of the plant
• The leafy part of a bryophyte is the gametophyte and the sporophyte is very small

Mosses: Phylum Bryophyta

• The most diverse of the bryophytes with 15000 species known worldwide
• The leafy structures of moss gametophytes have no mesophyll tissue, stomata, or veins
• The blades are nearly always one-cell thick and are never lobed or compound
• There is no petiole (seta)
• The midrib consists of hydroids
• Moss plants grow in clustered pattern
• There is no stem just an axil that may have a central strand of hydrois
• Rhizoids are rootlike structures that help anchor the moss to the ground but are not specialized to absorb water or nutrients

Phylum Anthocerophyta- Hornworts

• The smallest division of bryophytes with 100 species worldwide
• Mature sporophytes look like miniature greenish to blackish rods that may curve slightly have gametophytes that resemble filmy versions of thalloid liverworts
• They are usually less than 2 cm in diameter and thrive on moist earth in shaded areas although some do occur on trees
• They differ from liverworts and mosses in that they have only one large chloroplast in each cell (a few species have up to eight) and each chloroplast has pyrenoids like algae
• The thalli have pores and cavites filled with mucilage in contrast to the airfilled pores and cavites of thalloid liverworts
• Nitrogen fixing cyanobacteria often grow in the mucilage
• Have rhizoids to anchor the plant
• Paranoid- are protein bodies in the chloroplast of various lower organisms that are involved in starch synthesis and deposition
• Mucilage- gelatinous substance that contains proteins and polysaccharides and is similar to plant gums (like sap)

Bryphytes are seperated into 3 phlya based on what

structure and reproduction. Bryophyta, Hepaticophyta, and anthocerophyta

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