AP Biology Course Review Part 2

Translation: initiation, elongation, termination

• Ribosome attaches to the mRNA, Ribosome holds everything in place while the tRNAs assist in assembling polypeptides

Initiation

• 3 binding sites: A site, P site, E site 

  • mRNA shuffles through from A>P> E and as mRNA codons are read, the polypeptide will be built 

• The start codon for the initiation of protein synthesis is AUG which codes for methionine

  • Complementary anticodon UAC on the tRNA is the shuttle, when the AUG is read on the mRNA, it delivers the methionine to the ribosome

Elongation

• Addition of amino acids

• mRNA contain many codons and as each amino acid is brought to the  mRNA, it is linked it it neighboring amino acid by a peptide bond>> polypeptide

Termination:

• The synthesis of a polypeptide is ended by stop codons; when the ribosome runs into ⅓ stop codons 

REVIEW:

• Transcription: mRNA is created from a particular gene segment of DNA

• In eukaryotes, the mRNA is processes by having its introns (noncoding sequences) removed

• To be translated, mRNA proceeds to the ribosomes

• Free-floating amino acids are picked up by the tRNA and shuttled over to the ribosome where mRNA waits

• Translation: the anticodon of a tRNA molecule carrying the appropriate amino acid base pairs with the codon on the mRNA

• As new tRNA molecules match up to new codons, the ribosome holds them in place, allowing peptide bonds to form between the amino acids

• The newly formed polypeptide grows until a stop codon is reached

• The polypeptide/protein is released into the cell

Gene Regulation (gene transcription and expression)

• Gene regulation can occur at different times (largest is before transcription: pre-transcriptional regulation; but can also occur post-transcriptional or post-translationally)

• Start of transcription requires the DNA to be unwound + RNA polymerase to bind at the promoter

  • Transcription factors can encourage/inhibit this from happening by making it easier/more difficult for the RNA polymerase to bind/move to the start site

  • Structural genes: genes that code for enzymes needed in a chemical reaction. These genes will be transcribed at the same time to produce particular enzymes

  • Promoter gene: the region where the RNA polymerase binds to begin transcription 

  • Operator: a region that controls whether transcription will occur and is where the repressor binds

  • Regulatory gene: codes for specific regulatory protein called the repressor. The repressor is capable of attaching to the operator and blocking transcription. If the repressor binds to the operator, transcription will NOT occur. If the repressor does not bind to the operator, RNA polymerase moves along the operator and transcription occurs.

• Operon:  the region of bacterial DNA that regulated gene expression

• Example: Lac Operon (controlling the expression of enzymes that break down lactose)

  • INDUCIBLE: OFF UNTIL SWITCHED ON

  • Structural genes: three enzymes (beta galactosidase, galactose permease, and thiogalactoside transacetylase) are involved in digesting lactose coded for

  • Regulatory gene: the inducer, lactose binds to the repressor, causing it to fall off the operator and “turns on” transcription

• Example: trp operon

  • REPRESSIBLE: ON UNTIL SWITCHED OFF

  • Turned “off” in the presence of high levels of amino acid, tryptophan

  • When tryptophan combines with the trp repressor protein, it causes the repressor to bind to the operator that turns the operon OFF, blocking transcription

• Post-transcriptional regulation occurs when the cell creates and RNA but then decides that it should not be translated into a protein; RNAi molecules can bind to an RNA via complementary base bearing that creates a double-stranded RNA- when it is formed, it signals to the destruction machinery that the RNA should be destroyed

  • Prevents it from being translated

• Post-translational regulation occurs when a cell has made protein, but doesnt need to use the protein yet.

  • Common for enzymes b/c when cell needs them, it needs it ASAP; easier to make them ahead of time and then turn them off/on as needed

  • Can involve binding w other proteins, phosphorylation, pH, cleagahe, etc

Mutations

• Mutations: error in the genetic code

• Can occur b/c DNA is damaged and cannot be repaired b/c DNA damage is repaired incorrectly

  • Damage can caused by chemicals/radiation; mistake from DNA/RNA polymerase

  • DNA polymerase has proofreading abilities; RNA polymerase do not (DNA is temporary molecule and is not a problem)

  • DNA is passed on from cell to cell in somatic cells and from parent> offspring

Base Substitution

• Nonsense mutations: these cause the original codon to become a stop codon, which results in the early termination of protein synthesis

• Missense mutations: cause the original codon to be altered and produce a different amino acid

• Silent mutations: happen when a codon that codes for the same amino acid is created; no change in the corresponding protein sequence

Gene Rearrangements

1. Insertions and deletions result in the gain or loss of DNA or a gene

   1. Usually results in a frameshift mutation

2. Duplications can result in an extra copy of genes and are usually caused by unequal crossing during meiosis/chromosome rearrangements

   1. May result in new traits b/c 1 copy can maintain the gene’s original function and 1 copy may evolve a new function

3. Inversions can result when changes occur in the orientation of chromosomal regions

   1. May cause harmful effect if inversion involves a gene/important regulatory sequence

4. Translocations occur when a portion of 2 different chromosomes (or single in 2 dif places) breaks and rejoins in a way that causes the DNA sequence/gene to be lost, repeated, or interrupted

BIOTECHNOLOGY

Recombinant data

• Recombinant DNA is generated by combining DNA from multiple sources to create a unique DNA molecule NOT found in nature

  • Ex. introduction of eukaryotic gene of interest like insulin into a bacterium for production

  • Bacteria can be hijacked and put to work to create proteins

• Genetic engineering: Branch of technology that produces new organisms or products by transferring genes between cells

Polymerase Chain Reaction (PCR)

• Ability to make billions of identical copies of genes within a few hours

  • Process of DNA replication is slightly modified

  • In a small PCR tube, DNA, primers, DNA polymerase, and DNA nucleotides are mixed together

  • In a PCR machine, the tube is heated, cooled, warmed many times; when heated the hydrogen bonds break, separating the double-stranded DNA. when cooled, the primers bind to the sequence binding region of dna we want to copy

  • When warmed, the polymerase binds to the primers on each strand and adds nucleotides on each template strand

• After 1st cycle, there are 2 identical double-stranded DNA molecules (second= 4 segments)

Transformation

• Transformation: the process of giving bacteria foreign DNA

• Genes of interest placed into small circular DNA plasmid; with genes in a vector

  • plasmid vectors usually contain genes for antibiotic resistance an restriction sites

• plasmids/gene of interest are cut with same restriction enzyme, creating compatible sticky ends; when placed together the gene is interested into the plasmid creating recombinant DNA and transforms the bacteria

• Similar: transfection which is putting a plasmid into a eukaryotic cell rather than bacteria cell 

Gel Electrophoresis

• DNA fragments can be separated according to their molecular weight using gel electrophoresis

  • DNA and RNA are negatively charged and migrate toward positive pole of the electrical field

• The smaller the fragments, the faster they move in the gel and further toward + side

  • Used for crime scenes, DNA finger-printing

Cell Communication

1. Reception: receptor digests the molecule/ligand

2. Transduction: relay molecule 1> amplified response

3. Response

Cell Reproduction 

Cell Division: Small part of the life cycle of a cell; most of the time, cells are busy carrying out their regular activities

The Cell Cycle

• Cell’s life cycle is known as the cell cycle

  • Divided into 2 periods: interphase and mitosis

Interphase: the growing phase

• Cell has not yet started to divide

• Cell carries out its regular activities + all proteins/enzymes it needs to grow are produced + every chromosome in the nucleus is duplicated

• Interphase can be divided into 3 stages: G1, S, G2

  • S phase: when the cell replicate its genetic material 

• Original chromosome and its duplicate are still linked like conjoined twins

  • Identical strand of DNA are called sister chromatids

  • Chromatids held together by centromere

Cell Cycle Regulation

• G1 and G2 phases: cell produces proteins and enzymes

  • Ex. during G1, the cell produces all of the enzymes required for DNA replication (DNA helicase, DNA polymerase, and DNA ligase)

• G can stand for “Growth” stages

• The 3 phases are regulated by checkpoints and special proteins called cyclins and cyclin-dependent kinases (CDKs)

• Cell cycle checkpoints: control mechanisms that make sure cell division is happening properly in eukaryotic cells

  • Monitor cell to make sure it is ready to progress through cell cycle and stop progression if not

  • Example of cell signalling pathways inside of cells

• DNA genome has been damaged in some way, cells should not divide (if it did, damaged DNA will be passed onto daughter cells)

  • When damaged DNA is found, checkpoints are activated and cell cycle progression stops

  • Cell uses extra time to repair damage in DNA

    • If not possible to repair, the cell will undergo apoptosis (programmed cell death)

• Cell cycle checkpoints control cell cycle progression by regulating cyclin-dependent kinases(CDKs) and cyclins

  • To induce cell cycle progression, an inactive CDK binds to a regulatory cyclin

  • When together the complex is activated and causes cell cycle to continue

Cancer

• Cell losing control of the cell cycle can result in mutation in a protein that normally controls progression through the cell cycle that causes unregulated cell division and cancer

• Cancer: when normal cells start behaving and growing abnormally an spread to other parts of the body

• Mutated genes that induce cancer are called oncogenes

  • Normally the genes are required for proper growth of the cell and regulation of the cell cycle

  • Oncogenes are genes that can convert normal cells into cancerous cells

  • Normal healthy healthy version: proto-oncogene

• Tumor suppressor genes: produce proteins that prevent the conversion of normal cells to cancer cells

  • They can detect damage to the cell and work with CDK/cyclin complexes to stop cell growth until the damage can be repaired

  • Can trigger apoptosis if the damage is too severe to be repaired

Recap: 

• The cell cycle consists of interphase and mitosis

• During the S phase of interphase, the chromosomes replicate

• Growth and prep for mitosis occur during G1 and G2 stages of interphase

• Cell cycle checkpoints make sure the cell is ready to continue through the cell cycle

• CDK and cyclin proteins work together to promote cell cycle progression

• Oncogenes promote cell growth; tumor suppressor genes inhibit cell growth

Mitosis

• PMAT (Prophase, metaphase, anaphase, telophase)

• Diploid parent cell (2n) and results in 4 haploid daughter cells (1n)

• 
  

Stage 1: Prophase: Prep (the cell prepares to divide)

• Signs: disappearance of the nucleolus (ribosome making area) and the nuclear envelope

• The chromosomes thicken forming coils and becoming visible (during interphase not visible)

  • The dense chromosomes: chromatin 

• Centrioles start to move away from each other toward opposite ends of the cell

  • Will develop microtubules known as spindle fibers

  • Spindle fibers will attach to a structure on each chromatid called a kinetochore (part of centromere)

Stage 2: Metaphase: Middle (chromosomes align in the middle)

• Chromosomes now begin to line up along the equatorial plate/metaphase plate of the cell

• Spindle fibers are attached to the kinetochore of each chromatid

Stage 3: Anaphase: Apart (the chromatids are pulled apart)

• Sister chromatids of each chromosome separate at the centromere and migrate to opposite ends

• The chromatids are pulled apart by the microtubules that begin to shorten

• Each half pair of sister chromatids now move to opposite poles of the cell

• Nonkinetochore microtubules elongate the cell

Stage 4: Telophase: Two (the cell completes splitting in two)

• Nuclear membrane forms around each set of chromosomes and the nucleoli reappear

• Nuclear membrane is ready to divide> splitting process is known as cytokinesis

  • Cells are split along a cleavage furrow produced by actin microfilaments

• A cell membrane forms about each cell and the cell split into two identical daughter cells

• IN PLANT CELLS, CELL DOES NOT FORM CLEAVAGE FURROW BUT INSTEAD A PARTITION CALLED A CELL PLATE IN THE MIDDLE REGION

Stage 5: Interphase

• Once daughter cells are produced they reenter the initial phase, interphase, and the whole process starts over (chromosomes become invisible, genetic material is chromatin again)

Purpose of Mitosis

• To produce 2 daughter cells that are identical copies of the parent cell

• To maintain the proper number of chromosomes from generation to generation

• Happens in every cell except skin cells (ex. Human skin cells make other skin cells”

• Involved in growth, repair, and asexual reproduction

Haploid VS Diploid

• Most eukaryotic cells have 2 full sets of chromosomes, one from each parents (humans have 2 sets of 23 chromosomes, total of 46)

• A cell that has 2 sets of chromosomes is a diploid cell, and the zygotic chromosomes number is 2n (two copies of each chromosomes) (2 copies and 2 alleles per gene)

• If cell has only 1 set of chromosomes, it is haploid; n ( 1 copy of each chronometer and 1 allele per gene)

• Diploid refers to any cell that has 2 sets of chromosomes (46 in humans)

• Haploid refers to any cell that has 1 set of chromosomes (23 in humans)

• Duplicate versions of each chromosomes are homologous chromosomes

  • Make up each pair are similar in size, shape, and express similar traits

Gametes

• Haploid cells called sex cells/gametes

  • An offspring has one set of chromosomes from each of its parents

  • Parents contribute a gamete with on sect that will be paired with set from other parent to produce a new diploid cell-zygote> PRODUCES VARIETY/COMBINATION

Meiosis Overview

• The production of gametes

• Limited to sex cells in species sex organs called gonads

  • Gonads are testes in male; ovaries in females

• The special cells in these organisms (germ cells) produce haploid cells (n) which combine to restore the diploid (2n) number during restoration

• VARIETY; more= selective advantage 

Closer Look at Meiosis

• Meiosis I (prophase I, metaphase 1, anaphase 1, telophase 1) and meiosis II

• Prophase I:

  • nuclear membrane disappears, the chromosomes become visible, the centrioles move to opposite poles of the nucleus

  • Difference from prophase in mitosis:chromosomes line up side by side with their counterparts (homologs): synapsis

  • Synapsis: 2 set of chromosomes that come together to form a tetrad (or bivalent)

    • Consists of 4 chromatids

  • Followed by crossing over, the exchange of segments between homologous 

• IN PROPHASE 1, the chromosomes exchanged by homologous partners> produce genetic variety

  • End of prophase 1, chromosomes will have exchanged regions containing several alleles or different forms of the same gene (from both mom and dad)

• Metaphase I:chromosome pairs (tetrads) line up at the metaphase plate

  • Regular metaphase, chromosomes line up individually

  • Alignment during metaphase is random so the copy of each chromosomes that ends up in the daughter cell is random

• Anaphase I: one of each pair of chromosomes within a tetrad separates and moves to opposite poles

  • Chromatids do not separate at the centromeres, the homologs separate with their centromeres intact

• Telophase I: nuclear membrane forms around each set of chromosomes

  • Cell undergo cytokinesis, leaving with 2 daughter cell (haploid number of chromones)

Meiosis II

• Purpose of 2nd division is to separate the sister chromatids and is identical to mitosis

  • Prophase II: chromosomes condense and become visible

  • Metaphase II: the chromosomes move toward the metaphase plate; lining up as single file (NOT PAIRS)

  • Anaphase II: chromatids of each chromosomes split at the centromere, and each chromatid is pulled to opposite ends of the cell

  • Telophase II: a nuclear membrane forms around each set of chroomes and a total of four haploid cells are produced

Gametogenesis

• Meiosis is also known as gametogenesis

• If sperm cells are produced, meiosis is called spermatogenesis

  • 4 sperm cells are produced for each diploid cell

• If an egg cell or ovum is produced: oogenesis

  • Produces only 1 ovum, NOT 4

  • The other 3 are polar bodies get tiny amount of cytoplasm and eventually degenerate

  • Female produces only 1 b/c female wants to conserve as much cytoplasm as possible for the surviving gemet, the ovum

Meiotic Errors

• Sometimes set of chromosomes have an extra/missing chrome because of nondisjunction: when chromosomes fail to separate properly during meiosis

  • Produces wrong number of chromes in a cell; usually results in a miscarriage or severe genetic defects

• Ex. individuals that have 3 copies (instead of 2) of the twenty first chromosome have down syndrome

• Chromosomal abnormalities can also occur if 1+ segments of a chromosome break and are lost/reattach to another chromosomes

  • Most common ex: translocation (segment of a chromosome moves to another chromosome)

Heredity 

Fundamental points of genetics

• Traits: expressed characteristics that are influenced by 1+ genes

  • Gene is a chunk of DNA that codes for a particular trait (different codes=different trait)

  • DNA is passed from generation to generation and this process the genes and the traits associated with those genes are inherited

  • Within a chromosome, there are many genes with each controlling the inheritance of particular traits

  • The position of a gene on a chromosomes is called a locus

• Diploid organisms usually have 2 copies of a gene, on on each homologous chromosomes

  • Homologous chromosomes are the 2 copy versions of a chromosome diploids have

  • Humans have 23 pairs of homologous chromosomes

• Copies may be different from each other> alleles, or alternate versions/flavors of the same gene

• When an organisms has 2 identical alleles for a given trait, the organism is homozygous; if an organisms has 2 different alleles for a given trait, the organism is heterozygous

• Physical appearance of an organisms is its phenotype and tells us what the organism looks like; when talking about genetic makeup, genotype is referred to tell what alleles the organism possess

• An allele can be dominant or recessive (dominant allele given capital letter, and recessive given lowercase of same letter)

Test taking Tips

• Crosses involve the meeting of hypothetical organisms w phenotypes/genotypes

  • Label each generation in the cross (the first generation is always the parent/P1 generation. The offspring of the P1 are called the filial/F1 generation. The next generation/grandchildren are called the F2 generation) 

  •  Always write down the symbols used for the alleles

Mendelian Genetics

• Mendel worked with true-breeder pea plants that were genetically pure and consistently produced the same traits

• Came up with 3 principles of genetics: the law of dominance, the law of segregation, and the law of independent assortment

The Law of Dominance

• One trait masks the effect of the other traits

• The dominant tall allele of the pea plants T, somehow masked the presence of the recessive short allele, t

Monohybrid cross

• Monohybrid cross: when 2 individuals that are heterozygous for two traits are crossed

  • To be sure that they are heterozygous, the first step is to cross true breeding plants of allele #1 with  true breeding plants of allele #2

    • Setting up a punnett square for mendel’s tall and short pea plants

    • One parent was pure, tall pea plant: TT

    • Other was pure, short pea plant: tt

    • TT x tt = Tt, Tt, Tt, Tt (F1 generation)

The Law of Segregation

• Tt x Tt= TT, Tt, Tt, tt (F2 generation)

• The alleles are separated and recombined, pricing a new combination for the offspring

• Although all of the F1 plants are tall, the alleles separate and recombine during the cross; each gamete only gets one of the two copies of a gene

•  that a diploid organism passes a randomly selected allele for a trait to its offspring, such that the offspring receives one allele from each parent.

The law of independent assortment

•  states that the alleles of two (or more) different genes get sorted into gametes independently of one another. In other words, the allele a gamete receives for one gene does not influence the allele received for another gene.

• The four alleles can combine to give four different games

• Each allele of the -- gene can be paired  with wither allele of the -- gene

• Alleles segregate independently because chromosomes seg independently

  • During meiosis 1, each pair of homologous chromosomes is split and which one aligned during metaphase is different for each pair

Dihybrid Cross

• When two heterozygotes for two genes are crossed

• TG Tg tG tg x TG Tg tG tg 

  • T= tall; t=short; G=green; g=yellow

  • Results: 9 tall green; 3 tall yellow; 3 short green; 1 short yellow

• Ratio: 9:3:3:1 for when two heterozygotes for two genes are crossed

Test Cross

• Want to know if tall plant is homozygous (TT) or heterozygous(Tt); cross it with a recessive short plant (tt)

  • TT x tt = Tt, Tt, Tt, Tt

  • Tt x tt = Tt, Tt, tt, tt

• Uses a recessive orgaisms to determin the genotype of an unknown genotype

Non-Mendelian forms of Inheritance

• Incomplete dominance (blending inheritance): in some cases, traits will blend; neither allele is dominant over the other

• Codominance: equal expression of both alleles (an individual with AB blood type with each allele equally expressed (IaIb)) The expression of one allele down not prevent the expression of the other

• Polygenic inheritance: traits result from the interaction of many genes

  • Each gene will have a small effect on particular trait ( height, skin color, weight are ex)

  • Epistasis: one gene can override the effects of another gene

• Multiple alleles: some traits are the product of many different alleles that occupy a specific gene locus (ABO blood group system in which 3 alleles: Ia, Ib, and i, determine blood type)

• Non-nuclear inheritance: there is also genetic material that is contained in the mitochondria

  • The mitochondria are always provided by the egg during sexual production so mitochondrial inheritance is always through the maternal line, not the male line

• Linked genes: sometime genes on the same chromosomes may stay together during assortment as move as a group

  • Group of genes is considered liked and tends to be inherited together

  • Since they are found on same chromosome, they cannot segregate independently and violates the law of independent assortment

  • If parent and offspring has same phenotypes then they are linked genes

• The percentage of recombination (or recombination frequency) can be determined by adding up recombinants and dividing by the total number of offspring

  • Can also measure of how far apart the genes are 

  • The distance on a chromosome is measured in map units/centimorgans

Sex-linked traits

• Humans contain 23 pairs of chromosomes

  • 22 of the pairs of chromosomes are autosomes that code for many traits

  • The other pair contains the sex chromomes and determines the sex of an infdividuals

• A female has 2 X chromosomes

• A male has one X and one Y (one from mother and one from father)

• Traits such as color blindness and hemophelia are carried on sex chromomes> sex-linked traots

  • Most sex-linked traits are found on the x chromosome and referred to as x-linked

• If male has a defective x chromosomes, hell express it even if its recessive because he does not have another x to mask the effect of the bad x

  • If the female only has one defective x chromosomes, she wont express a recessive sex-linked trait     (needs to inherit 2 defective x chromosomes)

  • Female with one defective x is called a carrier, she can still pass onto her children

Barr Bodies

• Cell nucleus of normal females will have a dark-staining body known as a barr body

  • An x chromosomes that is condensed and visible

  • In female cell, one x chromosome is activated= and the other x chromosome is deactivated during embryonic development

  • In every tissue in the adult female one x chromosome remains condensed and inactive but is still passed onto daughter cell

PEDIGREES

Evolutionary Biology

• evolution is defined in terms of populations but occurs in terms of individuals (natural selection acts on individuals; evolution acts on populations)

  • Heterozygotes ae more fit than either of the homozygotes 

Natural Selection

• Charles darwin: 19th century british naturalist

  • Developed theory of evolution based on natural selection after studying animals in the galapagos islands, etc

  • Observed there were similar animals on various islands but the beaks varied in length on finches and the necks varied in length on tortoises

  • Concluded that it was impossible for the finches and tortoises of the galapagos to simply “grow” longer beaks or necks as needed but the traits were inherited and passed on from generation to generation

• Each species produces more offspring than can survive

• These offspring compete with one another for the limited resources available to them

• Organisms in every population vary

• The fittest or those with favorable traits, are the most likely to survive and therefore produce a second generation 

Lamarck and the Long Necks

• Jean-baptsiste de lamarck proposed that acquired traits were inherited and passed onto offspring

  • Giraffes had long necks because they were constantly reaching for higher leaves while feeding

• WRONG!! Acquired changes or changes in the body cells cannot be passed on to germ cells

Evidence for Evolution

• Paleontology (study of fossils): revealed  barely of organisms and major lines of evolution

• Biogeography (study of the distribution of plants and animals in the environment): scientists found related species in widely separated regions of the word

  • Possible explanation for similarities is a common ancestor

• Embryology (study of the development of an organism): looking at early stages on vertebrates (fish, amphibians, birds, humans) show dislike features called gill slits

• Comparative anatomy (study of the anatomy of various animals): discovered that some animals have similar structures that service different functions

  • Human’s arm, a dog's leg, a birds wing are all the same appendages and have evolved to serve different functions: homologous structures

  • Animals that have features with same function but are structurally different: analogous structures (a bat's wing and insects wing both used to flu but have evolved independent of one another)

• Molecular biology: scientists can examine the nucleotide and amino acid sequences of different organisms (organisms that are closely related have a greater proportion of sequences in common than distantly related species)

Common Ancestry

• Phylogenetic trees or cladograms are used to study the relationship between organisms

  • Begin with a common ancestor and branch out

  • Any fork in the road is called a common ancestor node

  • Common ancestors likely do not exist anymore but they are the point at which evolution went in 2 directions

    • 1 direction eventually led to one species and the other eventually led to the other species

Genetic Variability

• No two individuals are identical and have identical sets of alleles; the differences in each person are known as genetic variability

• Survival of a species is dependent on this genetic variation that allows a species to survive in  changing environment

• Natural secon can only occur if some individuals have more evolutionary fitness and can be selected

  • More variations among a population, the more likely that a trait will exits and help continue pop with changing conditions

• Random mutations result in variation and new alleles

  • Can be from errors by the DNA polymerase, changes to the DNA caused by transposons, or other DNA damage

• The mixing of genes through sexual reproduction - genetic variation among a pp

  • Meiosis, crossing-over mixes alleles among homologous chromosomes; independent assortment when chromosomes are packages further adds genetic uniqueness

• In bacteria, process called conjugation increases genetic variation evene though they are asexual

  • Viruses can pass around chunks of genome during infection: transduction

• EVOLUTION IS THE CHANGE IN THE GENE POOL OF A POPULATION OVER TIME

Causes of evolution

• Natural selection, the evolutionary mechanism that selects which members of a pop are best suited to survive and which are not works internally through random mutations and externally through environmental pressures

• EX OF PEPPERED MOTHS

  • How did the dark moths become dark-colored: through random mutation, and if they survive long enough to reproduce, they pass on the color (initial variation BY CHANCE)

  • Advantage become apparent when there was an abundance of soot from industrial revolution; the dark color is an adaptation, a variation favored by natural selection

Types of Selection

• Moths are an example of directional selection; one of the phenotypes was favored at one of the extremes of the normal distribution

  • Can happen only if the appropriate allele is that favored under new circumstances is already present in the population

• Stabilizing selection: organisms in a pop with extreme traits are eliminated

  • Favors organisms with common traits

• Disruptive selection: favors both the extremes and selects against common traits 

Species

• Species: group of organisms that share a genetic heritage, able to interbreed and create offspring that are also fertile

• To become different species, organisms have to be reproductively isolated from each other

  • Would allow the two groups to undergo natural selection and evolve differently

  • Different variations and different environmental pressures, they can change in different ways and no longer be able to mate: divergent evolution

• Geographic barriers, new stresses, diseases, and limiting resources are factors in evolution

• Prezygotic barriers prevent fertilization (ex. temporal isolation when species reproduce at different times of the year, mechanical)

• Postzygotic barriers: related to the inability of the hybrid to produce offspring (horse + donkey can produce sterile mule)

• Convergent evolution: process by which 2 unrelated and dissimilar species come to have similar (analogous) traits because they have been exposed to similar selective pressures

• Allopatric speciation:  population becomes separated from the rest of the species by a geographic barrier so that the two populations cant interbreed

  • Like mountain that separated 2 populations of ants

• Sympatric speciation: new species form without any geographic barrier

  • Common in plants

Population Genetics

• Hardy weinberg law: states that even with all the shuffling of genes that goes on, the relative frequencies of genotypes in a population still prevail over time

  • Alleles don't get lost in the shuffle

  • The dominant gene does not become more prevalent and the recessive gene doesn't disappear

Hardy-Weinburg Equilibrium

• Says population will be in genetic equilibrium when it meets 5 conditions

  • A large population

  • No mutations

  • No immigration or emigration

  • No Random mating 

  • No natural selection

• When met, the gene pool in the pop is very stable and departure results in changes in allele frequencies in a pop

• Genetic drift- founder effect: if small group of pop moves to new location, the allele frequency may be altered= evolutionary changes

• Genetic drift occurs in new colonies withs SMALL pop

• Bottleneck events: if most of a species is killed by a crazy weather event, individuals that are left now make up the new gene pool even if not previously selected for

Hardy Weinberg Equations

• P + q =1

  • p= frequency of the dominant allele

  • q= frequency of the recessive allele in the population 

• p^2 + 2pq + q^2 = 1

  • p^2= homozygous dominant

  • q^2 = homozygous recessive

  • 2pq= heterozygotes

Animal Structure and Function

The structure and function of organisms

• To carry on life, higher organisms must contend with challenges of obtaining nutrients, distributing them throughout bodies, voiding wastes, responding to their environments, reproducing

  • Unicellular and multicultural meet challenges through organization and specialization

  • Organelles within a cell allow compartmentalization (each organelle does its own task to work together and keep cell alive)

Homeostasis

• All living organisms have a steady state that they try to maintain

  • Structures + processes are sensitive to thinks like temperature, pH, pressure, salinity, osmotic pressure

• Homeostasis: set range of conditions that living things can live in successfully

• A negative feedback loop (feedback inhibition) works by typing itself off using the end product of the pathways

  • The end-product inhibits the process again, shutting down the pathways

  • Common strategy to conserve energy

• Positive feedback pathway: further stimulates the end-product

  • Occurs during fruit ripening and labor and delivery which ramps up and up as it proceeds

Development

Embryonic development

• Single-celled egg develops into complex, multicellular organisms by dividing and changes shape and organization through the succession of strategies (morphogenesis)

• Fertilization: triggers the zygote to go through series of divisions which makes it increasingly specialized/differentiated

  • Certain genes will be expressed and other genes might be turned off

  • Cells called organizers release signals that let each cell know how they should develop

• The early genes that turn certain cells in the early embryo into future wtv are called homeotic genes 

  • Timing is essential for the induction of the genes; the embryo must be modified at exactly right time or the embryo may become defective

Body systems

• Groups of cells that perform same function = tissue> group of tissues form organs> organs form body systems

The immune system

• Body’s defense system

• Pathogens: disease-causing biological agents that can generally be divided into bacteria, viruses, fungi, and parasites

Bacteria

• Prokaryotes that can or not be harmful 

• Bacteria divide by fission but does not increase their genetic diversity

  • Can preform conjugation with other bacterial cells and swap DNA

  • Genetic variety among bacteria > increased antibiotic antibiotics

Viruses

• Non living agents capable of infecting cells

  • Requires a host cell machinery to replicate

  • Virus consists of two main components: a protein capsid and genetic material made of DNA or RNA

• Viruses are specific in which type of cells (host) they infect

• Have one goal: replicate + spread and to do makes more genome and more capside

• Bacteriophage: a virus that infects bacteria

  • Undergoes 2 different types of replication cycles, the lytic cycle and the lysogenic cycle

    • Lytic cycle: the virus immediately starts using the host cell’s machinery to replicate the genetic material and create more protein capids; these spontaneously assemble into mature viruses and cause the cell to lyse/break open releasing new viruses into the environment

    • Lysogenic cycle: the virus incorporates itself into the host genome and remains dormant until it is trigger to switch into the lytic cycle

• Retrovirus like HIV virus are RNA viruses that use an enzyme called reverse transcriptase to convert their RNA genomes into DNA so they can be inserted into a host genome

  • RNA viruses have extremely high rates of mutation b/s they lack proofreading mechanisms when they replicate their genomes of mutations> creates variety

Immune System

• Defense system against pathogens that enter the organisms. Bacteria and viruses are common pathogens. Bacteriophages are viruses that infect bacteria. Viruses require a host to replicate and sometimes lyse the host cell during infection. There are two dies to the immune system:

  • The innate immune system is the first response, the iital protection, and it includes the skin and mucous linings. Phagocytes and complement proteins also target this initial response to neutralize invaders

  • Acquired immunity can be cell mediated or antibody based. T-lymphocytes include cytotoxic killer T-cells and helper T-cells. B-cells include plasma and memory B-cells.

Nervous System

• Neurons are highly specialized, terminally differentiated cells. They are composed of dendrites, cell bodies, axons and synaptic terminals:

  • Neurons are classified into 3 groups: sensory neurons, motor neurons, and interneurons

  • Neuronal transmission is based on action potentials, which are temp disruptions of the ion concentrations set up by the resting membrane potential

  • The junction between neurons is synapse. The presynaptic axon releases neurotransmitters to the postsynaptic dendrite to perpetuate the transmission

  • Myelin speeds the transmission along axons

• The central nervous system is composed of the brain and spinal cord

• The peripheral nervous system senses and responds to stimuli

Endocrine

• Endocrine glands are tissues or organs that excrete hormones. Hormones mediate growth, reproduction, waste disposal, nutrient absorption, and behavior

• Target cells receive the specific hormone via receptors either on the surface of the cell or internally and react through signal transduction and response.

Behavior and Ecology 

Behavior

• Some animals behave in a programmed way to specific stimuli, while some others behave according to learning

• Instinct, imprinting, classical condition, operant condition, insight

Instinct 

• Instrict: inborn, unlearned behavior

• Sometimes the instinctive behavior is trigger by environmental signals called releasers

  • Usually a small part of the environment that is perceived

• There are other types of instinct that last for only a part of an animal’s life and are gradually replaced by “learned” behavior

• Instinct is inherited circuitry that guides and direct behavior

• A particular type of innate behavior is fixed action pattern that are not simple reflexes wbut are not conscious decisions

Learning

• Learning refers to a change in a behavior brought about by an experience

Imprinting

• Imprinting: ex. Gosling newly hatched, if the mother is absent they will accept the first moving object they see as their mother

• Animals undergo imprinting within a few days after birth to recognize members of their own species

  • They all occur during a critical period a window of time when the animal is sensitive to certain aspects of the environment

• Imprinting is a form of learning that occurs during a brief period of time, usually early in an organism's life

Classical Conditioning

• Aka associative learning

• Classical conditioning is a type of learning that happens unconsciously. When you learn through classical conditioning, an automatic conditioned response is paired with a specific stimulus. This creates a behavior.

Operant Conditioning

• Another type of associative learning and is also called trial and error learning

• An animal learns to perform an act in order to receive a reward

• If the behavior is not reinforced, the conditional response will be lost>extinction

  • In operant conditioning , the animal’s behavior determines whether it gets the reward for the punishment; Classical conditioning is just the learned association of 2 things

• Habituation: occurs when an organisms learns not to respond to a stimulus

Internal Clocks: The circadian Rhythm

• Internal clocks/cycles: circadian rhythm

How Animals Communicate

• Chemical signals are the most common forms of communication among animals. 

  • Pheromones are chemical signals between members of the same species that stimulate receptors and affect behavior

• Visual signals 

• Electrical channels used to communicate

Social Behavior

• Agonistic behavior: aggressive behavior that occurs as a result of comp for food or other resources

• Dominance hierarchies: occurs when members in a group has established which members are the most dominant

• Territoriality: common behavior when food and nesting sites are in short supply

• Altruistic behavior: behavior that benefits another organisms in the group at the individual’s expense because it advances the gens of the group (when ground squirrel gives warning call to alert other squirrels at expense of being caught by predator)

Symbiotic Relationships

• Mutualism: in which both organisms benefit (lichen)

• Commensalism: in which one organism lives off another with no harm to the host organism (remora and shark)

• Parasitism: the organism actually harms its host

Plant Behavior

• Photoperiodism: plants flower in response to change in the amount of daylight and darkness they receive

Tropisms

• Tropism: training in response to a stimulus

  • Phototropism: refers to how plants respond to sunlight

  • Gravitropism: refers to how plants respond to gravity

  • Thigmotropism: how plants respond to touch

Ecology

• Biosphere: the entire part of the earth where living things exist

  • Can be divided by biomes

• Ecosystem: the interaction of living and nonliving things

  • Biotic factors: living factors

  • Abiotic factors: water, humidity, temp, soil/atmosphere composition, light, radiation

• Community: a group of populations interacting in the same area

  • Each organism has a niche, position or function in a community

  • Food chain: describes the way different organism depend on one another for food

• Population: a group of individuals that belong to the same species and that are interbreeding

Producers (autotrophs)

• Autotrophs, have all of the raw building blocks to make their own food

• Primary productivity is the rate at which autotrophs convert light energy into chemical energy in an ecosystem

  • Primary productivity: the gross productivity just from photosynthesis cannot be measured because cell respiration is occurring at the same time

  • Net productivity only measure organic materials left over after photosynthetic organisms have taken care of their own cellular energy needs (calculated by measuring oxygen production in the lights when photosynthesis and cellular respiration are both occurring)

Consumers (heterotrophs)

• Forced to find their energy source in the outside world

• Primary consumers are organism that directly feed on producers (herbivores like cows)> secondary consumers> tertiary consumer

Decomposer

• Organisms that break down organic matter into simple products

Keystone species

• If a keystone species is removed from the ecosystem, the whole balance can be undone very quickly

The 10% rule

• Only 10% of the energy is transferred from one level to the next

• Other 90% is used fir things like respiration, digestion, running from predators , etc.(power organism )

  • The energy flow, biomass, and number of members within an ecosystem can be represented in an ecological pyramid