Biology Flashcards
Metabolism
The sum of all chemical reactions that occur in the body. Can be divided into CATABOLIC REACTIONS and ANABOLIC REACTIONS
Catabolic Reactions
which break down large chemicals and release energy
Anabolic Reactions
Which build up large chemicals and require energy
Ingestion
The acquisition and consumption of food and other raw materials
Digestion
The process of converting food into a usable soluble form so it can pass through membranes in the digestive tract enter the body
Absorption
The passage of nutrient molecules through the lining of the digestive tract into the body proper. Absorbed molecules pass through cells lining the digestive tract by diffusion or active transport
Transport
The circulation of essential compounds required to nourish the tissues and the removal of waste products from the tissues
Assimilation
The building up of new tissues from digested food materials
Respiration
The consumption of oxygen by the body. Cells use oxygen to convert glucose into ATP, a ready source of energy for cellular activities
Excretion
The removal of waste products (such as carbon dioxide, water, and urea) produced during metabolic processes like respiration and assimilation
Synthesis
The creation of couple molecules from simple ones (anabolism)
Regulation
The control of physiological activities. The body’s metabolism functions to maintain its internal environment in a changing external environment.
Homeostasis
The steady state of the internal environment
-includes regulation by hormones and the nervous system
Irritability
the ability to respond to a stimulus and is part of regulation
Growth
An increase in size caused by cell division and synthesis of new materials
Reproduction
The generation of additional individuals of a species
External Respiration
refers to the entrance of air into the lungs and the gas exchange between the alveoli and the blood
Internal Respiration
Includes the exchange of gas between the blood and the cells and the intracellular processes of respiration.
What are the favored FUEL molecules in cells?
Carbohydrates and Fats
Dehydrogenation
oxidation reaction
-high-energy hydrogen atoms are removed from organic molecules
Glycolysis
1st stage of glucose catabolism
-is a series of reactions that leads to the oxidative breakdown of glucose into two molecules of pyrvuate, the production of ATP, and the reduction of NAD+ and NADH
Where does glycolysis occur?
cytoplasm
Substrate Level phosphorylation
ATP synthesis is directly coupled with the degradation of glucose without the participation of an intermediate molecule such as NAD+.
How many ATP’s are produced per glucose molecule in glycolysis
2 ATP per glucose molecule
How many NADH is produced per PGAL during glycolysis
One NADH is produced per PGAL.
- Since two PGAL are produced per glucose molecule there is a net production of two NADH
Under anaerobic conditions what happens to pyruvate after glycolysis?
pyruvate is reduced during the process of Fermentation
Under aerobic conditions what happens to pyruvate after glycolysis?
Pyruvate is oxidized during cellular respiration in the mitochonidria
Fermentation
-NAD+ must be regenerated for glycolysis to continue in the absence of oxygen. Accomplished by reducing pyruvate into ethanol or lactic acid.
What does fermentation produced?
Produced only 2 ATP per glucose Molecule
Alcohol Fermentation
- occurs in yeast and some bacteria.
- the glycolysis is converted to ethanol
- NAD+ is regenerated and glycolysis continues
Lactic Acid Fermentation
- occurs in certain fungi and bacteria and in human muscle cells during strenuous activity.
- When the oxygen supply to muscle cells lags behind the rate of glucose catabolism, the pyruvate is generated is reduced to lactic acid
- Also, like alcohol fermentation the NAD+ is regenerated when pyruvated is reduced so glycolysis can continue
Cellular Respiration
- most efficient catabolic pathway used by organisms to harvest the energy stored in glucose.
- Aerobic Process
What is the net production of ATP in cellular respiration?
can yield 36-38 ATP
What is the final accepter of electrons during the final stage of glucose oxidation in cellular respiration?
Oxygen acts as the final acceptor of electrons that are passed from carrier to carrier
Where do the metabolic reactions of cell respiration occur?
Eukaryotic Mitochondrion and are catalyzed by reaction-specific enzymes
What are the stages of cellular Respiration?
1) Pyruvate Decarboxylation
2) Citric Acid Cycle
3) Electron Transport Chain
Pyruvate Decarboxylation
The pyruvate formed during glycolysis is transported from the cytoplasm into the mitochondrial matrix where it is decarboxylated(LOSES a CO2)
- The acetyl group that remains is transferred to coenzyme A to form acetyl-CoA
- NAD+ is reduced to NADH
Citric Acid Cycle/ Krebs Cycle
The cycle begins when the acetyl group (2 C’s) from the acetyl-CoA combines with oxaloacetate (4 C’s) to for the 6-carbon CITRATE.
-Through the reactions, 2 CO2 are released, and oxaloacetate is regenerated for use in another turn of the cycle.
How much ATP is produced for each turn of the citric acid cycle?
One ATP is produced by substrate level phosphorlation via GTP intermediate
What is the net production of the citric acid Cycle?
6 NADH
2 FADH2
2 ATP
Electron Transport Chain
-complex carrier mechanism located on the inside of the INNER MITOCHONDRIAL MEMBRANE.
-ATP is produced when high-energy potential electrons are transferred from NADH and FADH2 to oxygen by a series of carrier molecules located in the inner mitochondrial membrane.
As the electrons are passed from carrier to carrier-free energy is released- which is used to form ATP
-Most molecules are CYTOCHROMES
-redox reactions continue to occur as the electrons are transferred from one carrier to the next
-The last carrier of the ETC passes its electrons to the final electron accepter O2.
What is the function of O2 in the Electron transport chain?
is the final electron acceptor. also picks up a pair of hydrogen ions from the surrounding medium, forming water
Net production of substrate phosphorylation?
degradation of one glucose molecule yields a net of two ATP from glycolysis and one ATP for each turn of the Citric Acid Cycle.
–A total of 4 ATP are produced!!
Oxidative Phosphorylation
- process that produces more than 90 percent of the ATP used by the cells in our body
- major steps occur within the ETC or respiratory chain of the mitochondria
Steps at the end of the ETC chain
Steps at the end of ETC chain, where ATP are generated:
- The respiratory enzymes continually pum hyrdogen ions from the matrix of the mitochondria to the inter membrane space, which creates a large concentration gradient
- Hydrogen ions pass thorough channels in the respiratory enzymes along the concentration gradient at the end of the ETC.
- As the hydrogen ions pass through these enzymes, the energy released is used to convert ADP to ATP.
Oxidative Phosphorylation Yields
>
What is the tool amount of ATP produced during Eukaryotic Glucose Catabolism?
4 via substrate-level phosphorylation
32 via oxidative phosphorlation
36 TOTAL ATp
What is the tool amount of ATP produced for Prokaryotes
38 ATP because the two NADH of glycolysis doesn’t have any mitochondrial membranes to cross and therefore don’t lose energy
What is the preferential order of alternate energy sources when glucose is running low?
1) other carbohydrates
2) Fats
3) proteins
Alternate Energy sources
-are first converted to either glucose or glucose intermediates, which can then be degraded in they glycolytic pathway and the citric acid cycle
Cytochromes
electron carriers that resemble hemoglobin in the structure of their active site.
- the functional unit contains a central iron atom that is capable of undergoing a reversible redox reaction
- MOST MOLECULES OF THE ETC ARE CYTOCHROMES
Carbohydrates as an alternative energy source
Disaccharides are hydrolyzed into monosaccharides, which can be converted into glucose or glycolytic intermediated
-Glycogen stored in the liver can be converted, when needed, into a glycolytic intermediate
Fat as an alternative energy source
Fat molecules are stored in adipose tissue in the form of triglycerides.
-They are hydrolyzed by LIPASES to FATTY ACIDS and GLYCEROL and are carried by the blood to other tissues for oxidation when needed.
Glycerol (FAT) as a alternative energy source
can be converted to PGAL, a glycolytic intermediate
Fatty Acid (FAT)
- Fatty Acid-must first be “activated” in the cytoplasm; this process requires TWO ATP. Once activated the fatty acid is transported into the mitochondrion and taken through a series of Beta-oxidation cycles that convert it into 2-carbon fragments, which are converted into Acetyl-CoA. Acetyl-CoA then enters the Citric Acid cycle.
- With each round of B-oxidation of a saturated fatty acid, one NADH and one FADH2 are generated
What compound in cellular respiration yields the greatest number of ATP per gram?
FATS, which makes them extremely efficient energy storage molecules.
Proteins as a alternative energy source
- most amino acids undergo a TRANSMINATION REACTION-in which they lose an amino group to form an alpha-keto acid
- The carbon atoms of most amino acids are converted into Acetyl-CoA, pyruvate, or one of the intermediates of the citric acid cycle.
- These intermediates enter their respectable metabolic pathway allowing cells to produce fatty acids, glucose, or energy in the form of ATP
Oxidative Deamination
Removes an ammonia molecule directly from the amino acid
Ammonia
is a toxic substance in vertebrates
- fish can excrete ammonia
- insects and birds convert it to uric acid
- mammals convert it to urea for excretion
Catalyst
are any substance that affects the rate of a chemical reaction without itself being changed
Enzymes
- are crucial to all living things because all living systems must have continuously controlled chemical activity.
- They regulate metabolism by speeding up certain chemical reactions
- They affect the reaction rate by decreasing the activation energy
- they are proteins thus thousands of different enzymes can be formed
- many are conjugated proteins and thus have a nonprotein coenzyme (both must be present for the enzyme to function)
- selective
- DO NOT alter equilibrium constants
- Are NOT consumed in the reaction. They will appear in both the reactants and the products
- PH and temperature dependent, with optimal activity at specific pH and temp ranges
- most enzyme catalyzed reactions are reversible
- the produce synthesized by an enzyme can be decomposed by the same enzyme
- an enzyme that synthesizes maltose from glucose can also hydrolyze maltose back to glucose
substrate
the molecule that the enzyme acts upon
active site
area on each enzyme to which the substrate binds
Lock and Key Theory
The spatial structure on an enzymes active site is exactly complementary to the spatial structure of its substrate.
-the two fit together like a lock and key
OR
-Receptors are large proteins that contain a recognition site (lock) that is directly linked to transduction systems. When a drug or endogenous substance (key) binds to the receptor, a sequence of events is started
Induced Fit Theory
More accepted
- the active site is flexible when it comes to its shape
- when the appropriate substrate comes in contact with the active site, the conformation of the active site changes to fit the substrate
Temperatures effect on enzymes
- As temperature increases the rate of the enzyme action increases until an optimal temp is reached (usually around 40 C)
- beyond optimal T, heat alters the shape of the active site of the enzyme molecule and deactivated it, leading to a rapid drop in the rate of active site
pH affect on enzymes
-for each enzyme there is an optimal pH, above an below that pH enzymatic activity declines.
What is the maximal pH of most human enzymes?
7.2 since this is the pH of most body fluids.
-exception is PEPSIN, which works best in highly acidic conditions of the stomach (pH=2)
-pancreatic enzymes work optimally in the alkaline conditions of the small intestine (pH=8.5)
-
How does the concentration of the enzyme and substrate affect the reaction rate
When the concentration of both enzyme and substrate are low, many of the active sites on the enzyme are unoccupied, and the reaction rate is low
increasing the substrate concentration will increase the reaction rate until all of the active sites are occupied. After this point in substrate concentration will not increase the reaction rate, and the reaction is said to have read the maximum velocity, Vmax
Competitive Inhibition
If a similar molecule that is similar to the substrate is present it may be able to bind to the active site of the enzyme. If the substrate and the similar molecule are equal in concentration then they will compete with each other for binding sites on the enzyme and interfere with the enzyme activity.
- known as competitive inhibition because the enzyme is inhibited by the inactive substrate.
- If sufficient quantities of the substrate are introduced then the substrate can over compete the competitor molecule
Non-competitive inhibition
- noncompetitive inhibitor is a substance that forms strong covalent bonds with an enzyme making it unable to bind with its substrate. Thus the noncompetitive inhibitor cannot be replaced
- Addition of excess substrate will not affect the rate of the reaction and the reaction site will never reach Vmax.
- the noncompetitive inhibitor may be bound at , near, or far from the active site.
Allosteric inhibition
when the inhibitation takes place at a site other then the active site.
-the interaction changes the structure of the enzyme so that the active site is also changed
Hydrolysis reactions
function to digest large molecules into smaller components.
Lactase
hydrolyzes lactose to the monosaccharide glucose and galactose
Proteases
degrade proteins to amino acids
Lipases
breakdown lipids to fatty acids and glycerol
Synthesis reactions
can be catalyzed by the same enzymes as hydrolysis sections but the directions of the reactions are reversed
protein synthesis
occurs in the ribosomes and involved dehydration reactions between amino acids
Cofactors
enzymes require the incorporation of these cofactors which is a nonprotein molecule-this is how they become active
-can be metal cations such as Zn2+ and Fe2+ or small organic groups called coenzymes
Prosthetic groups
cofactors that bind to the enzyme by strong covalent bonds
Genes
-are composed of DNA(Deoxyribose bonded to a phosphate group and one of the four nitrogenous bases) and are located on chromosomes
alleles
when a gene exists in more than one form
genotype
the genetic makeup of an individual
Phenotype
the physical manifestations of the genetic makeup
Mendel’s four principles of inheritance
- genes exist in alternative forms (alleles). A gene controls a specific trait in an organism
- An organism has two alleles for each inherited trait, one inherited from each parent
- the two alleles segregate during meiosis, resulting in gametes that carry only one allele for any given inherited trait.
- If two alleles in an individual are different, only one will be fully expressed, and the other will be silent. The expressed allele is said to be dominant while the silent allele is said to be recessive.
Mendel’s Law of Dominance
The dominant allele is expressed in the phenotype
Monohybrid cross
when only one trait is being studied in a cross of two parents
Parental or Pgeneration
the individuals being crossed in a punnet square
F generations or filial
are the progeny generations and are labeled F1,F2, F3, etc.
What are the genotypic and phenotypic ratios produced during a monohybrid cross?
Genotype: 1:2:1
Phenotype: 3:1
Testcross
is a diagnostic tool used to determine the genotype of an organism.
- Only with a recessive phenotype can genotype be predicted with 100 percent accuracy.
- the appearance of the recessive phenotype in the progeny indicates that the phenotypically dominant parent is genotypical heterozygous
Mendels Law of Independent Assortment
-postulated that the inheritance of one such trait is completely independent of any other as long as the genes are on separate chromosomes and assort independently of any other.
Non medelian genetics argument against law of independent assortment
genes on the same chromosome will not follow this rule and instead will stay together unless CROSSING OVER occurs.
Crossing Over
exchanges information between chromosomes and may break the linkage of certain patterns.
-Generally the closer the genes are on the chromosome the more likely they are to be inherited together
What is the typical ratio of inheritance for a cross between two heterozygotes
9:3:3:1 with independently assorting traits
Drosophila Melanogaster and its advantages with genetic research
Fruit Fly
-helped to provide explanations for mendelian genetic patterns.
- it reproduces often (short life cycle)
- it reproduces in large numbers (large sample size)
- its chromosomes (especially in salivary glands) are large and easily recognizable in size and shape
- Its chromosomes are few (4 pairs, 2N=8)
- Mutations occur relatively frequently
-through the research scientists have found a pattern of embryological development, discovered how genes expressed in development can affect the adult organism
Incomplete dominance
NonMendelian Inheritance Patterns
-some progeny phenotypes are apparently BLENDS of the parental phenotypes (heterozygotes)
Ex: red and white flower crossed and produces some pink flowers
-an allele is incomplete dominant if the phenotype of the heterozygote is an intermediate of the phenotypes of the homozygotes
Codominance
occurs when MULTIPLE alleles exist for a given gene and more than one of them is DOMINANT.
-when two dominant alleles are present, the phenotype is the result of the expression of both dominant alleles simultaneously
-condominance differs from incomplete dominance because in incomplete dominance the phenotype is expressed is a blend of both genotypes. While in codominance both alleles int he genotypes are expressed at the same time NO BLENDING
ABO blood groups
CODOMINANCE
- Bood type is determined by three different alleles I^A, I^B, and i.
- only two alleles are present in any single individual, but the population contains all three alleles
- I^A and I^B are both dominant to i.
What are the different genotypes that result in blood type A
I^A homozygous
I^Ai heterozgyous
What are the different genotypes that result in blood type B
I^B homozygous
I^Bi Heterozygous
What genotypes result in blood type O
ii
What genotypes result in blood type AB
I^AI^B
How many autosomes do all humans have?
22
Sex Chromosomes
-the sex chromosomes pair during meiosis and segregate during the first meiotic division.
Sex Linkage
Recessive genes carried on the X chromosome will produce the recessive phenotypes whenever they occur in men because no dominant allele is present to mask them.
- Femals have 2 X chromosomes while men only have one
- The recessive phenotype will be made much more frequently in men
What are some examples of sex-linked recessives in humans
hemophilia
color blindness
Nondisjunction
is the failure of the homologous chromosomes to separate properly during meiosis I or the failure of sister chromatids to separate properly during meiosis II
- the resulting zygote might have three copies of the chromosome called a TRISOMY or a single copy of that chromosome called MONOSOMY
- most monosomies and trisomies are lethal, causing the embryo to spontaneously abort early in the pregnancy
What is an example of a trisomy?
the birth defect Down Syndrome, which is caused by trisomy of chromosome 21
Mutations
are changes in the genetic information coded in the DNA of a cell.
- most mutations occur in regions of DNA that do not code for proteins and are silent (not expressed in the phenotype)
- Mutations that do change the sequence of amino acids in proteins are most often recessive and deleterious
What do mutations in somatic cells result in?
lead to tumors in individuals
What do mutations in sex cells (gametes) result in?
the mutations will be passed down to the offspring
Mutagenic agents
- induce mutations
- include cosmic rays, X-rays, ultraviolet rays, and radioactivity as well as chemical compounds such as colchicine or mustard gas
-they can also be carcinogenic
What does colchicine result in?
inhibits spindle formation
What does mustard gas result in?
alkylates guanine in DNA
Point Mutation
a nucleic acid is replaced by another nucleic acid.
-The number of nucleic acids substituted may vary, but generally point mutations involve between one and three nucleotides
Codon
the sequence of three nucleotides that determines the identity of the amino acids
Silent mutation
the new codon may code for the same amino acid and no change in the resulting protein is seen
Missense Mutation
the new codon may code for a different amino acid
-this may or may not lead to a problem with the resulting protein, depending on the role of that amino acid in determining the protein structure
Nonsense Mutation
the new codon may be a stop codon
-are often lethal or severely inhabit the functioning of the protein, which can lead to many different problems depending on the role of that protein in organism function
Frameshift Mutation
nucleic acids are deleted or inserted into the genome sequence.
- this frequently is lethal
- the insertion or deletion of nucleic acids throws off the entire sequence of codons from that point on because the genome is “read” in routs of three nucleic acids
- the length of the genome changes
Phenylketonuria (PKU)
molecular disease caused by the inability to produce the proper enzyme for the metabolism of phenylalanine
- a degradative produce (phenylpyruvic acid) accumulates as a result
- administration of any product that contains phenylalanine (such as aspartame) to an individual with this condition could be detrimental to their health.
- these individuals are thus unable to consume products containing aspartame
- PKU may result from an impaired conversion of phenylalanine to tyrosine.
- **characterized by an increased concentration of phenyalanine in blood, increased concentration of phenylalanine and its by-products in urine, and mental retardation
**PKU is caused by deficiency of phenyalanine hydrolase
Sickle Cell Anemia
a disease in which red blood cells become crescent shaped because they contain defective hemoglobin.
- The sickle Cell Hemoglobin carries less oxygen
- the disease is caused by a substitution of valine for gluatmic acid because of a single base pair substitution in the gene coding for hemoglobin
-These individuals do have less severe symptoms of malaria if they are infected, indicating a possible evolutionary advantage in regions where malaria infection is common
Bacterial Genome
consists of a singular chromosome located in the nucleoid region of the cell.
-many bacteria also contain smaller circular rings of DNA called PLASMIDS which contain accessory genes
What do Plasmids contain
accessory genes
Episomes
are plasmids that are capable of integration into the bacterial chromosome
Replication in a bacterial chromosome
UNIQUE origin of replication and proceeds in both directions simultaneously.
-DNA is synthesized in the 5’ to 3’ direction
What three mechanisms do bacteria utilize to increase their genetic variance
Transformation
Conjugation
Transduction
Transformation
is the process by which a foreign chromosome fragment(PLASMID) is incorporated into the bacterial chromosome via recombination, creating new inheritable genetic combinations
Conjugation
can be described as SEXUAL MATING in bacteria
- it is the transfer of genetic material between two bacteria that are temporarily joined
- a cytoplasmic conjugation bridge is formed between the two cells and the genetic material is transferred from the donor male (+) type to the recipient female (-) type.
- only bacteria containing plasmids called sex factors are capable of conjugating
Conjugation in E. Coli
F Factor in E. Coli, bacteria that possess this are called F+ cells and replicate its F factor and donates the copy to the recipient-> which converts it to a F+ cell.
Hfr cells
during conjugation, the entire bacterial chromosome replicates and begins to move from the donor cell into the recipient cell. The conjugation bride usually breaks before the entire chromosome is transferred, but the bacterial genes that enter the recipient cell can easily recombine with the genes already present to form NOVEL genetic combinations
HFR means high frequency of recombination
Transduction
occurs when fragments of the bacterial chromosome become packaged into the viral progeny produced during a viral infection by a bacteriophage.
- These visions may infect other bacteria and introduce new genetic arrangements through recombination with the new host cell’s DNA
- the closer the two genes are to one another on a chromosome, the more likely they will be to transduce together
Recombination
occurs when linked genes are separated.
-it occurs by breakage and rearrangement of adjacent regions of DNA when organisms carrying different genes or alleles for the same traits are crossed.
Prokaryotic regulation of transcription
- enables prokaryotes to regulate their metabolism
- based on the ability of RNA polymerase to gain access to the genes being transcribed and is directed by an operon
What does the operon consist of?
consists of structural genes, an operator region, and a promoter region on the DNA before the protein coding genes
What do structural genes contain
sequences of DNA that code for proteins
Operator
is the sequence of non transcribable DNA that is the REPRESSOR binding site
Promoter
is the noncoding sequence of DNA that services as the initial binding site for RNA polymerase
Regulator Region
codes for the synthesis of a repressor molecule and binds to the operator and blocks RNA polymerase from transcribing the structural genes
RNA polymerase function
must be able to move past the operator to transcribe the structural genes
Inducible Systems
require the presence of a substance called the INDUCER for transcription to occur
–the repressor binds to the operator, forming a barrier that prevents RNA polymerase from transcribing the structural genes
Repressible Systems
are in a constant state of transcription unless a COREPRESSOR is present to inhibit transcription
- the repressor is inactive until it combines with the corepressor
- Corepressors are often the end products of the biosynthetic pathways they control
Process of inducible systems to transcribe
For transcription to occur, the inducer must bind to the repressor, forming an INDUCER-REPRESSOR COMPLEX.
- this complex cannot bind to the operator thus removing it as a barrier and permitting transcription
- enzymes are only transcribed when they are actually needed
RNA
is a ribose sugar bonded to a phosphate group and one of the four nitrogenous bases: A, G, C, U
How many hydrogen bonds are between adenine and Thymine?
2 Hydrogen Bonds
How many hydrogen bonds are between Guanine and Cytosine?
3 hydrogen bonds
DNA replication steps and characteristics
-is SEMICONSERVATIVE, because half of the original DNA molecule is incorporated into each daughter strand
Steps:
- DNA helix is unwound by helicase which breaks the hydrogen bonds between the bases
- DNA polymerase synthesizes new strands complimentary to the original parental strands in the 5’ to 3’ direction beginning at the origin of replication
- A replication fork is formed
- The leading strand is synthesized continuously using one RNA primer
- The lagging strand is synthesized discontinuously using an RNA primer for every Okazaki fragment
What is Transcription?
is the prices by which information stored in the bases of DNA is copied into RNA
Steps of Transcription
1) RNA polymerase binds to the TATA box in the promoter region of the DNA template strand (only one strand of the DNA is used for a give gene)
2) Nucleotides are added in a 5’ to 3’ direction
3) heterogeneous nuclear RNA (hRNA) is formed
4) the introns are cleaved out and the eons spliced together to form the mRNA
5) the 5’ end of the mRNA is capped
6) the 3’ PolyA tail is added to the mRNA
What is Translation?
is the synthesis of an amino acid using mRNA as a template
Steps of Translation
1) mRNA binds to a ribosome- translation begins when the ribosome encounters a start codon
2) tRNA delivers amino acids to the ribosome
3) the tRNA/amino acid complex temporarily bonds to the mRNA codon
4) Peptidyl-transferase (a enzyme) forges a peptide bond between adjacent amino acids
5) Protein synthesis stops when a stop codon is reached
6) Post-translations modifications occur to the protein
What are some post translational modifications?
- 3D folding
- Addition of a carbohydrate, lipid, or phosphate group
- cleavage of signal sequences
Where does translation occur?
occurs in the cytoplasm and requires energy (GTP)
Base Substitution
one base pair is substituted for another
Transition
a form of base substitution
-substitution for a pyrimidine(T or C) by another pyrimidine or of a purine (A or G) by another purine
Transversion
a form of base substitution
-substitution of a pyrimidine by a purine or of a purine by a pyrimidine
pyridmidine
Thymine or Cytosine
Purine
Guanine or Adenine
Deletions
a form of base substitution
-one or more nucleotides are lost from a sequences
Insertions
a form of base substitutions
- one or more nucleotides are added to a sequences
- this can lead to a transposition
Transposition
a sequence is inserted at an incorrect location in the DNA
What can result in DNA damage?
- Mismatches during DNA replication
- Spontaneous Deamination (cytosine loses its amino group to form uracil)
- alkylation of bases (the addition of a methyl group to a base
- UV light causing the formation of Thymine Dimers
- Ionizing radiation producing double strand breaks
- Chemicals causing the formation of bulk adducts
Direct Repair Mechanism
reverse DNA damage with out cutting the deoxyribose phosphate backbone
EX: removing a methyl group in order to restore the original base
Base Excision Repair
Is used when incorrect bases are present in DNA
Ex: Uracil is incorporated into DNA
-the damaged base is recognized by a glycosylase and is hydrolytic ally removed from the deoxyribose phosphate backbone. This leaves an apurinic or apyrimidic site where a purine or pyrimidine was removed. The correct base is then inserted and the break is sealed by DNA ligase
MisMatch Repair Mechanism
use a method similar to Base Excision Repair to remedy incorrect pairings of the normal bases
EX: A parked with Cor G will be repaired so that A pairs with T and C pairs with G
Nucleotide Excision Repair
Removes Thymine dimers and bulky adducts. The area of DNA surrounding and including the damaged portion is unwound and an endonuclease makes cuts on both the 5’ and the 3’ sides of the damage. The bases are removing by an exonuclease and DNA is resynthesized, using the sister strand as a template to fill the gap. DNA ligase seals the new section into the backbone
Post Replication Repair
is used to repair double stranded breaks. This involves a type of recombination repair in which a single strand of DNA from a homologous chromosome is used to resynthesize the missing position. Broke ends can also be rejoined directly and ligated together
-the original sequence is not always maintained and mutations such as translocations can often occur as a result of this.
Nucleosome
the most basic unit.
- consists of 8 histone proteins
- DNA is wound almost 2 times around this protein core to produce a “bead-like” structure
30 nm chromatin fiber
nucleosomes are jointed together by linker DNA and coiled into a 30 nm fiber which is organized into loops. This structure is maintained by the histone H1 protein which is attached to the linker DNA
Loop-scaffold complex
provides the compact structure of the chromosome seen during metaphase
Euchromatin
region of the chromosome that is light.
- single copy,
- active DNA
Heterochromatin
region of the chromosome which is dark
- repetitive sequences
- genetically inactive
Centromeres
essential for proper chromosome segregation and site of kinetochore formation
Telomeres
cap the ends of chromosomes
- maintain structural integrity
- ensure complete replication and positioning of the chromosome
During Meiosis, what happens crossing over occurs between two homologous chromosomes?
results in genetic recombination.
-produces combinations of alleles that are not present in either parent
What are the guidelines of crossing over
- it occurs randomly along the entire chromosome
- two genes close together on a chromosome have a low chance of cross over (the genes are said to be linked)
- the further a part two genes are on a chromosome, the greater the shane of these genes crossing over
Holliday Model
-provides an explanation for the events that occurring during recombination
1) Homologous pairs link up
2) an endonuclease nicks a single strand of DNA at each homolog at the same place
3) The homologs exchange strands and are ligated togeth forming the holliday Structure
4) Branch migration can occur, incorporating a portion of the opposite strand into each molecule
5) cleavage occurs: if the same strands are cleaved the original chromosome are reformed. If opposite strands are cleaved then recombinant chromosomes are the result
Constitutional Chromosomal Abnormality
the abnormality is found in all of the body
Somatic Chromosomal Abnormality
the abnormality is found in only certain cells or tissues
What are the two kinds of chromosomal abnormalities and what pertains to each
Numerical-the gain or loss of complete chromosomes
Structural-the formation of abnormal chromosomes through the disrepair of chromosome breaks or a malfunction during recombination
Aneuploidy
- a type of numerical abnormality
- one or more chromosomes are poising or are present in more than the normal number
- usually results from nondisjunction
Monosomy
A type of aneuploidy
- the loss of a single chromosome
- autosomal monosomy is always lethal
- monosomy of sex chromosomes X results in Turner Syndrome (45,X)
Trisomy
A type of aneuploidy
-the gain of an extra chromosome
EX: down syndrome (trisomy 21)
Tetrasomy
a type of aneuploidy
-the gain of an extra pair of homologous chromosomes
EX: Tetrasomy 9p, tetrasomy 18p
Euploidy
a type of numerical abnormality
-an extra, complete set of chromosomes is present or missing
Polyploidy
a type of Euploidy
-more than two sets of chromosomes is present or missing -Triploid, tetraploid, pentaploid etc
Monoploidy
a complete chromosome set is missing
-LETHAL
Mixoploidy
a type of numerical abnormality
Mosaicism
a type of mixoploidy
-two or more genetically different cell lines within a single individual derived from a single zygote
Chimerism
A type of mixoploidy
-Two or more genetically different cell lines within a single individual derived from different zygotes
Structural Abnormalities
-occur when part of a chromosome is duplicated, deleted, or has been switched to another part of the chromosome. Therefore the chromosome # is normal but there is either excess or deficiency in the genetic material present in the cell
What are the way structural abnormalities can arise? what can these malfunctions result in?
1) Recombination Malfunction
2) Misrepair of chromosome breaks
Result in:
- Inversions
- Duplication
- Deletions
- Translocations
Inversions
the chromosome segments is rejoined opposite of its normal configuration without loss of genetic information
Duplications
a segment of the chromosome is repeated
Deletion
a segment of the chromosome is lost
Translocation
chromosomal material is exchanged between non-homologous chromosomes
- Reciprocal Translocation- there is not loss of genetic information although gene arrangement is altered (CONSIDERED BALANCE TRANSLOCATION)
- Robertsonian Translocation- the short arm of two chromosomes breaks off and the long arms are fused together; this can result in a blanked translocation or a unbalanced transaction i which genetic material is gained or lost
Negative Transcriptional control in eukaryotes
(Repression)
-a protein binds to DNA in order interfere with the binding of the RNA polymerase to the promoter region. This prevents transcription
Postive Transcripitonal control in eukaryotes
(activation)
-a protein binds to DNA in order to facilitate the binding of RNA polyermase to the promoter region. This initiates transcriptions
What are some other ways in which an active protein product can also be modified or controlled at various points along the transcription control pathway?
mRNA processing and Modification -Alternate splicing can form different gene products -Capping an dPolyA tails RNA transport out of the nucleus Transcript stablity
Transcriptional control in Prokaryotes
- the predominate site of control for gene expression is at the level of transcriptial imitation
- prokaryotic genes are clustered into operons
Operons
are gouts of genes that perform a related or coordinated function
What do operons consist of?
- a promoter region where RNA polymerase binds to initiate transcripiton
- operator-where a repressor protein can attach to prevent transcription, and the gene cluster
- The genes are transcribed together to from polycistornic RNA which codes for multiple protein products
PCR
Polymerase Chain Reaction
- is used to selectively amplify target DNA
- The DNA to be amplified, primers, DNA polymerase, and dNTPs are added to a reaction mixture
What are the steps of PCR
1) Heating the original DNA strand in order to DENATURE (94C) the DNA; this produces two complimentary single strands of DNA
2) ANNEALING (54C) primers to the single stranded DNA; the specific single stranded primers that are used to attach to the complementary portion of single stranded DNA
3) DNA polymerase attaches to the primer/DNA complex and moves down the DNA chain reading the template strand and adding the appropriate complimentary base (dNTP); this EXTENSION (72C) produces a new double stranded DNA molecule from each strand of the original DNA causing an exponential increase in the number of copies of a particular gene
DNA sequencing
is the same as PCr for replicating targeted DNA.
- it utilizes template DNA, free nucleotide (dNTPs), primers, and a polymerase to undergo denaturation, annealing, and replication.
- HOWEVER in DNA sequencing the reactions are run in the presence of a small amount of dideoxynucleotides (ddNTPs), which lack a hydroxyl group at the 3’ position, as well as dNTPs therefore the addition of one of the ddNTPs to the growing chain will terminate chain elongation since no further nucleotides can be added without the 3’ hydroxyl group
- the reaction is ran with all four ddNTPs which are labeled with Fluoresence. The resulting fragments are subjected to polyacrylamide gel and electrophoresis and therefore are separated on size alone
Human genome
it is estimated that the human nuclear genome contains 30,000 to 40,000 genes with about 3,000 genes per chromosome.
-the human genome contains over 3 billion DNA base pairs however, only about 3% of the genome contains coding sequences with the remainder being non-coding regions
Mitochondrial Genome
- Consists of a double stranded, and a very short portion of triple stranded circular DNA. It contains 37 genes, 24 of which code for a type of DNA and 13 which code for polypeptides which are used in the respiratory complexes that produce ATP
- Mitochondrial DNA is maternally inherited. Mitochondria from sperm are destroyed by the egg after fertilization leaving only MATERNAL mtDNA originally foun din unfertilized egg
Loss of function mutation
the gene product this can be RNA or protein product ahas reduced (leaky mutation) or no (null mutation) function
- typically these are recessive phenotypes- if one allele is mutated and loss function, the normal allele can usually produce enough gene products to prevent the disease phenotype and the disease results when both alleles are mutated
- point mutations, frameshifts, and splicing mutations can all lead to the loss of function of a gene product
- the same phenotype can result from many different mutations
- Epigenetic modifications can result in the loss of function without altering the DNA sequence
Gain of Function Mutations
results from over-expression of a gene product, a new function for a gene product, or expression in the incorrect location of a gene product
-typically are dominant phenotypes- the presence of one normal allele cannot mask or prevent the over production or abnormal behavior of the mutated allele
-often involves a product signaling inappropriately or falling to terminate a normal process
-mutations that cause gain of function are muc more specific then those that cause lost of function
A) the same phenotype typically only results from from one or two specific mutations (mutational homogenecy)
B) results in the “FOUNDER EFFECT” where a disease is typically seen only within a certain population reflecting a mutation found only in the founder of the new population
-
Cystic Fybrosis
- caused by the loss of function mutations in the CFTR gene
- most common lethal genetic disease in the US
- the normal gene codes for a membrane protein that transports chloride ions in and out of cells.
- This has the greatest effect on the epithial cell lining organs and evident in the lining of the lungs
- when one of the chloride channels is defective or absent, chloride ions are not removed from the cell and consequently water does not flow out of the cells into the mucus of the linings. This disrupts normal balance of salt and water and results in buildup of airway secretions
Huntington’s DIsease
- results from a gain of function mutation that produces an autosomal dominant disorder characterized by neurodegeneration
- other phenotypic manifestations are uncontrollable movements, personality alterations, and memory loss
- Typical onset of HD is not until 35-40 years of age
- HD is caused by the expansion of a triplet repeat, which is a set of 3 nucleotides (CAG) that code for glutamine
- the mutation causes more glutamine to be inserted in the protein produce which appear to cause the product to form new function which ultimately leads to cell death, particularly in the nervous system.
Cell Theory
- all living things are composed of cells
- the cell is the basic functional unit of life
- the chemical reactions of life take place inside the cell
- cells arise only from pre-existing cells
- cells carry genetic information in the form of DNA. This genetic information is passed from parent cell to daughter cell
Organelles
components of a cell
-include: nucleus, ribosomes, endoplasmic reticulum, golgi apparatus, vesicles, vacuoles, lysosomes, mitochondria, chloroplasts, and centrioles
what are the six kingdoms?
Bacteria, Archaea, Protista, Fungi, Plantae, Animilia
Cell membrane
- encloses the cell and exhibits selective permeability
- consists of a phopholipid bilayer with proteins embedded throughout
- lipids and many of the proteins can move free throughout
- permeable to both small, non polar, hydrophobic molecules, such as oxygen.
- Permeable to small polar molecules such as water
- small charged particles are usually able to cross the membrane through protein channels
- Charge ions and larger charged molecules cross the membrane with assistance of carrier proteins
Phospholipid structure of the cell membrane
- forms spontaneously
- the long, non polar, hydrophobic “fatty chains of carbon and hydrogen face each other (inside)–face each other in the water free region
- the phosphorus containing, polar, hydrophilic heads faces outward–faces the water regions outside of the cell
Nucleus
- controls the activities of the cells, including cell division
- surrounded by a nuclear membrane
- the nucleus contains DNA
Nucleolus
a dense structure in the nucleus where RIBOSOMAL RNA synthesis occurs (necessary for protein synthesis at the ribosome)
Ribosome
are the sites of protein production and are synthesized by the nucleolus
- free ribosomes are found in the cytoplasm
- Bound ribosomes line the outer membrane of the endoplasmic reticulum
Endoplasmic Reticulum
- is a network of membrane-enclosed spaces throughout the cytoplasm involved in the transport of material throughout the cell, especially those materials DESTINED TO BE SECRETED by the cell
- provides a direct continuous passageway from the plasma membrane to the nuclear membrane
Smooth Endoplasmic Reticulum
-does not contain ribosomes so is not involved with protein synthesis but INSTEAD is involved with metabolism and the production of lipids
Rough Endoplasmic Reticulum
-contains ribosomes and plays an important role int he production of proteins
Golgi apparatus
- receives vesicles and their contents from the smooth ER and then modifies them by processes such as glycosylation,
- repackages them into vesicles
- and distributed them to the cell surface for exocytosis
Mitochondria
- are the sites of aerobic respiration within the cell and hence the suppliers of energy(ATP)
- each mitochondria is composed of an outer and inner phospholipid bilayer
Cytoplasm
- most of the cells metabolic activity occurs in the cytoplasm
- includes the CYTOSOL and all the organelles of the cell
- transport within the cytoplasm occurs by CYCLOSIS
Vacuoles/Vesicles
- are membrane bound sacs involved in the transport and storage of materials that are ingested, secreted, processed, or digested by the cell.
- Vacuoles are larger than vesicles and are more likely to be found in plants than in animal cells
Centrioles
- are composed of microtubules and are involved in spindle organization during cell division
- not bound by a membrane
- Animal cells usually have a pair of centrioles oriented at right angles to each other that lie in a region called the centrosome
- Plant CELLS DO NOT CONTAIN
Centrosome
organizes microtubules and helps regulate the progression of the cell cycle
Lysosomes
are membrane bound vesicles that contain HYDROLYTIC ENZYMES involved in intracellular digestion
-break down material ingested by the cell
autolysis
an injured or dying cell may self-destruct by rupturing the lysosome membrane and releasing its hydrolytic enzymes
Cytoskeleton
- supports the cell, maintains its shape, and aids in cell motility
- composed of microtubules, microfilaments, and intermediate filaments
Microtubules
- are hollow rods made up of polymerized TUBULIN that radiate throughout the cell and provide it with support
- provide a framework for organelle movement within the cell
- Centrioles are composed of microtubules
- CILIA AND FLAGELLA are specialized arrangements of microtubules that extend from certain cells and are involved in cell motility and cytoplasmic movement
Microfilaments
are solid rods of ACTIN, which are important in cell movement as well as support
-move materials across the plasma membrane
Simple Diffusion
the net movement of dissolved particles down their concentration gradients from a regions of higher concentration to lower concentration
-passive process that requires no external source of energy
Osmosis
the simple diffusion of water from a region of lower solute concentration to a region of higher solute concentration
Hypertonic
- when the cytoplasm of a cell has a lower solute concentration than the extracellular medium
- the water will flow out of the cell into the surrounding medium which will cause the cell to SHRIVEL
when a cell shrivels what is this process called?
plasmolysis
Hypotonic
when the extracellular environment has a lower solute concentration than the cytoplasm of the cell
-the water will flow into the cell, causing it to swell and lYSE
Isotonic
when the extracellular environment has the same concentration of solutes as the cell cytoplasm
-the water will move back and forth in equal amounts across the cell membrane
Facilitated Diffusion
- -passive transport (DOES NOT REQUIRE ENERGY)
- is the net movement of dissolved particles down their concentration gradient through special channels or carrier proteins in the cell membrane
Active transport
- is the net movement of dissolved particles against their concentration gradients with the help of transport proteins
- REQUIRES ENERGY
- carrier molecules or transport proteins aid in the regulation of the cell’s internal content of ions and large molecules
Symporters
- carrier molecule
- move two or more ions or molecules in the same direction across the membrane
Antiporters
- carrier molecule
- exchange one or more ions (or molecules) for another ion or molecule across the cell membrane
Pumps
- carrier molecule
- energy dependent carrier (REQUIRE ATP)
ex: sodium potassium pump
Endocytosis
is a process in which the cell membrane invaginates, forming a vesicle that contains extracellular medium
- allows the cell to bring large volumes of extracellular material inside the cell
- particles may bind to receptors on the cell membrane before being engulfed
Pinocytosis
the ingestion of fluids or small particles
Phagocytosis
the engulfing of large particles
Exocytosis
is when a vesicle within the cell fuses with the cell membrane and releases a large volume of contents to the outside
-fusion of the vesicle with the cell membrane can play an important role in cell growth and intercellular signaling
Brownian Movement
- a way materials move about within a cell
- kinetic energy spreads small suspended particles throughout the cytoplasm of the cell
Cyclosis or streaming
- a way materials move about within a cell
- the circular motion of cytoplasm around the cell transports molecules
Cell division
is the process by which a cell doubles its organelles and cytoplasm, replicates its DNA, and then divides in two
-can follow in two different course, mitosis or meiosis, but each is preceded by interphase
cell division in unicellular organisms
is a means of reproduction
Cell division in multicelluar organisms
is a method of growth, development, and replacement of worn-out cells
Interphase
- a period of growth and chromosome replication
- cell normally spends 90% of its life in interphase
- the cell continues to perform its normal cellular functions and each chromosome is replicated so that during division a complete copy of the genome can be distributed to both daughter cells
- after replication- the chromosomes consists of two identical SISTER CHROMATIDS ahead togeth at a central region called the centromere
- the individual chromosomes are not visible
- the DNA is uncoiled and is called chromatin
G1 phase of interphase
initiates interphase
- described as the active growth phase and can vary in length
- cell increases in size and synthesizes proteins
- the length of the G1 phase determines the length of the entire cycle
S phase of interphase
is the period of DNA synthesis
G2 phase of interphase
the cell prepares to divide
-it grows and synthesizes proteins
Mitosis
- is the division and distribution of the cell’s DNA to its two daughter cells such that each cell receives a complete copy of the original genome
- takes place in somatic cells
- Karyokinesis (nuclear division) is followed by cytokinesis (cell division)
Mitosis: Prophase
- chromosome condenses
- centriole pairs separate and move toward the opposite poles of the cell
- spindle apparatus forms between centriole pairs
- nuclear membrane dissolves allowing the spindle fibers to interact with the chromosomes
Mitosis: Metaphase
- centriole pairs are now at opposite poles of the cell
- the fibers of the spindle apparatus attach to each chromatid at its corresponding KINETOCHORE (a protein location on the centromere)
- the spindle fibers align the chromosomes at the center of the cell (equator) forming the METAPHASE PLATE
Mitosis: Anaphase
- centromeres split so that each chromatid has its own distinct centromere- thus allowing sister chromatids to separate
- sister chromatids are pulled toward the opposite pose of the cell by the shortening of the spindle fibers
What are spindle fibers composed of?
microtubules
Mitosis: Telophase
- spindle apparatus disappears
- nuclear membrane forms around each set of newly formed chromosomes- thus each nucleus contains the same number of chromosomes as the original or parent nucleus
- the chromsomses uncoil, resuming their interphase form
Mitosis: Cytokinesis
- near the end of telphase the cytoplasm divide into two daughter cells each with a complete nucleus and its own set of organelles
- In animal cells a CLEAVAGE FURROW forms and the cell membrane indents along the equator of the cell, eventually pinching through the cell and separating the two nuclei
- In plant cells a plate forms between the two nuclei, effectively splitting the plant cell in half and allowing the cell to divide
Meiosis
is the process by which sex cells are produced.
- similarto mitosis in that a cell duplicates its chromosomes before undergoing the process
- Meiosis produces haploid cells (halving the number of chromosomes) where mitosis keeps the diploid number
The first meiotic division of Meiosis
produces two intermediate daughter cells with N chromosomes and sister chromatids
Meiosis Prophase I
- the chromatin condenses into chromosomes
- spindle apparatus forms
- nucleoli and nuclear membrane disappear
- homologous chromosome come together and intertwine in a process call SYNAPSIS.
Meiosis Metaphase I
Homologous pairs (tetrads) align at the equatorial plane and each pair attaches to a separate spindle fiber at the kinetochore
Meiosis Anaphase I
the homologous pairs separate and are pulled to opposite poles of the cell- process is DISJUNCTION and accounts for a fundamental mendelian law
-the distribution of homologous chromosomes to the two intermediate daughter cells is random with respect to parental origin.
Meiosis Telophase I
A nuclear membrane forms around each new nucleus
-at this point each chromosome consists of sister chromatids joined at the centromere
Second Meiotic Division of Meiosis
- very similar to mitosis
- except it is not precede by chromosomal replication in interphase
- the chromosome align at the equator
- seperate and move to opposite poles
- are surrounded by a reformed nuclear membrane
- new cells have a haploid number of chromosomes
evolution
the change in the genetic makeup of a population
Lamarckian Evolution
- new organs or changes in existing ones arose because of the needs of the organism
- the amount of change was thought to be based on the use or disuse of the organ
- any useful characteristic in one generation was thought to be passed on to the next generation (such as the long necks in giraffes)
Darwins Theory of Natural Selection
- pressures in the environment select for the organism most FIT to survive and reproduce
- Darwin concluded that a member of a particular species that is equipped with beneficial traits, allow it to cope effectively with the immediate environment, will produce more offspring than individuals with less favorable genetic traits
Fitness
the ability to survive and reproduce
Evolution of a new species
over many generations of natural selection, the favorable changes (adaptations) are perpetuated in the species. The accumulation of these favorable changes eventually results in such significant changes in the gene pool that we can say a new species has evolves
-theses physical changes in the gene pool were selected by environmental conditions
Speciation
is the evolution of new species
What are some factors that can lead to speciation?
- new environment
- natural selection
- genetic drift
- isolation
Species
are groups of individuals that can interbreed freely with each other but not with members of other species
-gene flow is impossible between different species
Demes
form within a species before speciation occurs
- they are small, local populations within the species
- members of a deme resemble one another more closely than they resemble members of other demes. They are closely related genetically since mating between members of the same deme occurs more frequently
- they are also subject to similar environmental factors and therefore are subject to the same selection processes
-if demes become isolated then SPECIATION may occur
isolation among groups
when groups are isolated from each other, there is no gene flow among them.
- any difference arising from mutation or new combinations of genes will be maintained in the isolated population
- overtime these genetic differences may become significant enough to make mating impossible
Phylogeny
evolutionary relationships among species alive today.
HISTORY
Convergent evolution
when two species from different ancestors develop similar traits
parallel evolution
is similar to convergent evolution but occurs when a more recent ancestor can be identified
Divergent evolution
occurs when spices with a shared ancestor develop differing traits due to dissimilarities between their enviroments
Adaptive radiation
- the emergence of a number of lineages from a single ancestral species
- a single species may diverge into an umber of distinct species; the differences between them are those adaptive to a distinct lifestyle or NICHE
Population
include all members of a particular species inhabiting a given location
gene pool
the sum of all alleles for any given trait in the population
Gene frequency
-is the decimal fraction representing the presence of an allele for all members of a population that have this particular gene
p
frequency of the dominant allele
q
frequency of the recessive allele
The Hardy Weinburg Principle conditions
- the population is very large
- no mutations affect the gene pool
- mating between individuals in the population is random
- there is no net migration of individuals into or out of the population
- the genes in the population are all equally successful at reproducing
Hardy weinburg equation
p^2 + 2pq + q^2 =1
Frequency of the dominant homozygote for hardy weinburg
p^2
Frequency of the heterozygotes
2pq
Frequency of the recessive homozygotes
q^2
Agents of microevolutionary change
- natural selection
- mutation
- assortive mating
- genetic drift
- gene flow
** all deviations from the five conditions of a hardy-weinburg population
Assortive mating
if mates are not randomly chosen but rather selected according to criteria such as phenotype and proximity (sexual selection)
Genetic Drift
refers to change in the composition of the gene pool due to chance
-tends to be more profound in small populations rather than large where it is called FOUNDER EFFECT
Gene flow
migration of individuals between populations will result in a loss or gain of genes, thus changing the composition of a population’s gene pool
Fossils
direct evidence of evolutionary change
- represent the preserved remains of an organism
- generally found in sedimentary rock
Petrification
-the process by which minerals replace the cells of an organism
Imprints
are impressions left by an organism
Homologous structures
- *SIMILAR IN ORIGIN BUT NO NOT NECESARRILY IN FUNCTION
- have the same basic anatomical features and evolutionary origins
- they demonstrate similar evolutionary patterns with late divergence of form due to differences in exposure to evolutionary forces
- their functions may not be the same though
Analogous structures
have similar functions but may have different evolutionary origins and entirely different patterns of development
-represent a superficial resemblance that cannot be used as a basis for classification
What stages in an organisms evolutionary history resembles the human embryos stages of development?
- the human embryo passes through stages that demonstrate common ancestry with other organisms
- the two layer GASTRULA is similar to structure of the hydra, a cnidarian
- the three layer gastrula is similar in structure to the flatworm
- Gill slits in the embryo indicate a common ancestry with fish
- posses a tail, like most other mammals
Vestigial Structures
have no known current function but had some ancestral function
what is an example of a vestigial structure in humans
the appendix is small and useless while in herbivores it assists in the digesting of cellulose
-the tail is reduced to a few useless bones (coccyx) at the base of the spine
Geographic Barriers: Marsupials
- a lineage of pushed mammals (marsupials) paralleling the development of placental mammals developed on the australian side of a large water barrier
- the geographic barrier protected the pouched mammals from competition and hybridization with modern placental mammals
- this barrier results in the development of uniquely australian marsupials, such as kangaroos and wolves
Geographic Barriers: Darwin’s Finches
- over a short period of time a single species of Galapagos finch underwent adaptive radiation to form 13 different species of finches
- slight variations in the beak
- such adaptations minimized the competition among the birds, enabling each spies to become firmly involved in its environmental niche
Heterotroph Hypothesis
- the first forms of life lacked the ability to synthesize their own nutrients; they required preformed molecules. These organisms were heterotrophs, which depended upon outside sources for food
- the primitive seas contained simple inorganic and organic compounds such as salts, methane, ammonia, hydrogen, and water
- Energy was present in the form of heat, electricity, solar radiation, cosmic rays, and radioactivity
- The presence of these building blocks and energy may have led to the synthesis of simple organic molecules such as sugars, amino acids, purines, and pyridmidines. These molecules dissolved in the PRIMORDIAL SOUP and after many years the simply monomeric molecules combined to form a supply of macromolecules
Evidence of Organic Synthesis: Stanley L Miller
- set out to demonstrate that the application of ultraviolet radiation, heat, or a combination of these to a mixture of methane, hydrogen, ammonia, and water could result in the formation of complex organic compounds
- he set up an apparatus in which four gases were continuously circulated past electrical discharges from tungsten electrodes
-after circulating the gases for a week, he analyzed the liquid in the apparatus and found that an amazing variety of organic compounds, including urea, hydrogen cyanide, acetic acid, and lactic acid had been synthesized
Formation of Primitive cells
- Colloidal protein molecules tend to clump together to form coacervate droplets
- these droplets tend to absorb and incorporate substance from the surrounding environment.
- the droplets also tend to possess a definite internal structure
- although these droplets were not living, they possess some properties normally associated with living organisms
- most of these systems were unstable but a few systems were stable enough to survive. a small percentage of these cells may have had favorable characteristics and they eventually enveloped the first primitive cells
- these cells probably possessed nucleic acid polymers and become capable of reproduction
Development of autotrophs
- the first heterotrophs slowly evolved complex biochemical pathways, enabling them to use a wider variety of nutrients
- they evolved anaerobic respiratory process to convert nutrients into energy. BUT these organisms required nutrients at a faster rate than they were being made
- life would have ceased to exist if autotrophic nutrition had not developed
- Autotrophs are able to produce organic compounds from substances in their surroundings
-the pioneer autotrophs developed primate photosynthetic pathways, capturing solar energy and using it to synthesize carbohydrates from carbon dioxide and water
Development of aerobic respiration
- the first autotrophs fixed carbon dioxide during the synthesis of carbohydrates and released molecular oxygen as a waste product
- the addition of molecular oxygen to the atmosphere converted the atmosphere from a REDUCING to an OXIDIZING ONE.
- in this way living organisms destroyed the conditions that made their development possible
- Once molecular oxygen became a major component of the Earth’s atmosphere, both heterotrophs and autotrophs evolved biochemical pathways of aerobic respiration
Autotrophic anaerobes organism examples
chemosynthetic bacteria
Autotrophic aerobes organism examples
green plants and photo plankton
Heterotrophic anaerobes organism examples
yeast
Heterotrophic aerobes organism examples
amoebas, earthworms and humans
Reflexes
are automatic responses to simple stimuli and are recognized as reliable behavioral responses following a given environmental stimulus
simple reflex
controlled at the spinal cord, connecting a two neuron pathway from the RECEPTOR (afferent neuron) to the MOTOR (efferent neuron)
efferent nerve
supplies the effect (ex: muscle or gland)
Reflex behavior
-is more important in the behavioral response of lower animals versus in the behavior in higher forms of life such as vertebrates
Complex Reflexes
-involve neural integration at higher level of the BRAINSTEM or even the CEREBRUM
Startle response
- complex reflex
- alerts an animal to a significant stimulus
- it can occur in response to potential danger or to hearing one’s name called
- involves the integration of many neurons in a system termed the RETICULAR ACTIVATING SYSTEM
Reticular Activating system
-responsible for sleep-wake transition and behavioral motivation
Releaser
the stimulus that elicits the behavior
Fixed-action patterns
- are complex, coordinated, INNATE behavioral responses to specific patterns of stimulation in the environment
- relatively unlikely to be modified by learning
- the particular stimuli that triggers a fixed action pattern are easily modified
Circadian Rhythms
daily cycles of behavior
-animals with such behavior cycles lose their exact 24 hour periodicity if they are isolated from the natural phases of light and dark.
habituation
- is one of the simplest learning patterns involving the suppression of the normal start response to stimuli
- repeated stimulation results in decreased responsiveness to that stimulus
- stimulus is suprressed
Spontaneous recovery
if the stimulus is no longer applied, the response tends to recover over time
-can also occur with modification of the stimulus
-the recovery of the conditioned response after extinction
Classical Conditioning
- also called Pavlovian conditioning
- involves the association of a normally autonomic or visceral response with an environmental stimulus
- the normal innate stimulus for a reflex is replaced by one chose by the experimentor
Conditioned relfex
the response learned through classical conditioning
unconditioned stimulus
the innate reflex
unconditioned response
the response that is naturally elicited
Neutral stimulus
is a stimulus that will not by itself elicit the response (prior to conditioning)
Conditioning
the establishment of a new reflex by the addition of a new, previously neutral stimulus to the set of stimuli that are already capable of triggering the response
Pseudoconditioning
- is determining whether the conditioning process is actually necessary for the production of a response by a previously “neutral stimulus”
- many cases the “neutral stimulus” is able to elicit the response even before conditioning thus is not actually a neutral stimulus
Operant conditioning
or instrumental conditioning
- involves the conditioning response to stimuli with the use of reward or reinforcement
- when the organism exhibits a specific behavioral pattern that the experimenter would like to see repeated, the animal is rewarded
Positive Reinforcement
or reward
- includes providing food, light, or electrical stimulation of the animal’s brain “pleasure centers”
- following positive reinforcement the animal is much more likely to repeat the desired behavior
Negative reinforcement
involves stimulating the brain’s pleasure centers
-links the lack of certain behavior with a reward
Punishment
- involves conditioning an organism so that it will stop exhibiting a given behavior
- may involve painfully shocking the organism each time the chosen behavior appears
- after punishment the organism is less likely to repeat the behavioral response
Habit family Hiearchy
- a stimulus is usually associated with several possible responses, with each response having a different probability of occurrence
- reward strengthens a specific behavioral response and raises its order in the hierarchy
Extinction
the gradual elimination of conditioned responses in the absence of reinforcement
extinction with classical conditioning
occurs when the unconditioned is removed row as never sufficiently paired with the conditioned stimulus
Stimulus generalization
the ability of a conditioned organism to respond to stimuli that are similar but not identical, to the original conditioned stimulus
-the less similar the stimulus is to the original conditioned stimulus, the less the response will be
Stimulus discrimination
involves the ability of the learning organism to respond differentially to slightly different stimuli
Stimulus Generalization gradient
is established after the organism has ben conditioned, where stimuli further and further away from the original conditioned stimulus elicit responses with decreasing magnitude
Imprinting
-is a process in which environmental patterns or objects presented to a developing organism during a brief CRITICAL PERIOD in early life become accepted permanently as an element of its behavioral environment
Critical periods
are specific time periods during an animals early development when it is physiologically able to develop specific behavioral patterns
-if the proper environmental pattern is not present during the critical period, the behavioral pattern will not develop properly
Intraspecific interactions
communication between members of a species
Display
an innate behavior that has evolved as a signal for communication between member of the same species
Ex: a song call, or intentional change in an animal’s physical characteristics
Reproductive displays
- are specific behaviors found in all animals, including humans
- evolved a variety of complex actions that functions as signals in preparation for mating
Agonistic displays
- nice behavior example: dog wagging tail
- mean behavior: dog arching body
Pecking order
social hierarchy of a species
Pheromones
animals secrete this substance which influence the behavior of other members of the same species
Releaser pheromones
-trigger a reversible behavorial change in the recipient
can be sex attractant pheromones or alarm or toxic defense substance
Primer pheromones
produce a long term behavioral and physiological alterations in receiving animals
-are important in social insects such as ants, bees, and terminates where they regulate role determination and reproductive capacities
