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FAU / Process Biology / PCB 3063 / What is a bacteria found in mammals such as humans?

What is a bacteria found in mammals such as humans?

What is a bacteria found in mammals such as humans?

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School: Florida Atlantic University
Department: Process Biology
Course: Genetics
Professor: David binninger
Term: Fall 2018
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Cost: 50
Name: Genetics
Description: This study guide contains detailed notes covering chapters 1-23 which will be covered for your cumulative final exam
Uploaded: 12/09/2018
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Genetics Final Exam Study Guide 


What is a bacteria found in mammals such as humans?



Chapter 1: Introduction to Genetics 

Central Dogma of Biology: 

-DNA is transcribed into RNA

-RNA is translated into a protein

Model Organisms: 

-Organisms with characteristics that are useful for research so they are studied  extensively.

-The maintenance of such organisms is easy and inexpensive. They adapt easily to  the environment of the labs, have a significant number of offspring, a short  generation time, and have genomes that are fully sequenced.

Important Model Organisms to know: 

1. Escherichia coli: Bacteria found in mammals such as humans. 2. Saccharomyces Cerevisiae:  


It is also known by the common name “fruit fly”. what is it?



-“Budding yeast”,

- Fungus that is single celled  

- Eukaryotic

3. Caenorhabditis Elegans:  

-found in soil

-Nematode (worm)

-used for studies of development as well as differentiation of cells 4. Drosophila Melanogaster

- Also known by the common name “fruit fly”

- Has been a useful genetic study for more than 100 years

5. Apis Mellifera

- Also known by the common name “Honey Bee”

- Useful for studies such as communication, behavior, neurology, ecology, and  evolution.

6. Mus Musculus

- Also known by the common name “house mouse”

- model organism: mammalian


When does crossing over take place?



7. Danio Rerio: Don't forget about the age old question of How does the speaker of the house work?

- Zebra Fish

- useful for studies of development over time

*Science helps better understand human condition

Chapter 2: Chromosomes and Cellular  

Reproduction 

Prokaryote:

-unicellular organism

-simple cell structure

-no nuclear membrane We also discuss several other topics like Enumerate the emergent properties.

-no membrane bound organelles

-prokaryotic cell is a single circular chromosome that uses binary fission to replicate Eukaryote:

-have cells that are compartmentalized by intracellular membranes -separates material from cytoplasm

-multiple linear chromosomes

- either unicellular or multicellular

Virus:

Not living organisms because in order to be living you must have both RNA and DNA

Histone: Protein, important for chromatin organization. In eukaryotic cells, not  found in prokaryotes.  

Origins of Replication:

- Chromosome has to duplicate prior to cell division

- Each chromatid has a single DNA molecule

- After the replication of DNA there are two identical copies that are held together at what  is known as the centromere.

Diploid Cells: (homologous, somatic) have two chromosomes that are closely  identical

Haploid Cells: Has a single set of chromosomes which is half of the usual  number of chromosomes. (Consequence of Meiosis)

Somatic Cell: Diploid, cells not destined to be gametes have two sets of  chromosomes. Any cell other than the reproductive cells. If you want to learn more check out What is the definition of humanistic psychology?

Germline Cell: Diploid at first but end as haploid once it undergoes meiosis.  Reproductive cell, destined to be gametes and have one member of each  homologous pair.

Mitosis:  

-One nuclear Division

-produces two cells with the same amount of chromosomes

-takes a cell and creates two identical daughter cells

-Phases Include:

-Prophase, Prometaphase, metaphase, anaphase, telophase, and cytokinesis

Meiosis:

-Two nuclear divisions (cell division occurs twice)

-produces four cells with half the amount of the normal chromosome number.  - Phases include:

Meiosis I- prophase, metaphase, anaphase, and telophase

Meiosis II- Fancy identical form of mitosis

When does crossing over take place? Prophase

Metaphase: Where chromosomes align in the center of the cell Interphase: Phase where cell grows, develops, and prepares for cell division This phase includes: G1, S, and G2 If you want to learn more check out What is the difference between conflict and integration?

Anaphase: In Mitosis, when chromatids separate and move toward opposite  spindle poles

Telophase: Final part of cell division where chromosomes reach the spindle poles  and two nuclei are formed. Cytoplasm Divides (Cytokinesis)

Nondisjunction: When sister chromatids or homologous chromosomes fail to  separate in both either meiosis or mitosis.

M-phase: Mitotic, period of active cell division

S-phase: Synthesis, phase where DNA replicates

G1: Cell growth phase, the checkpoint right before replication We also discuss several other topics like Are things valuable because god said so?

G2: Continue growing and preparing for mitosis. It is the checkpoint before the M phase but if it does not fulfill and pass the checkpoint it then goes to Go.

Chapter 3: Basic Principles of Heredity 

Phenotype: Characteristics that can be observed and measured. Affected  by gene products and the environment

Genotype: A potential phenotype

Allele: Different kinds of genes

Wildtype: dominant, most common found allele. Indicated with a +  superscript

Locus: “location” (where gene is located on the chromosome) Homozygous: AA (dominant), aa (recessive)

Heterozygous: Aa(dominant) If you want to learn more check out How do witnesses decide whether to report or not report a crime?

*Be sure to practice and be aware of your probability rules Read carefully and look for key words such as: either, or, and, and implied Nonsense Mutation: protein with no function

Monohybrid: cross plants that are different in one trait

-F1 and F2 generation

Mendel’s Laws:

1­ Principle of Segregation

2­ Independent Assortment

Chapter 4: Sex Determination and Sex-Linked  Characteristics 

Sex Determination: Sex is based on phenotype

All must have at least one X chromosome to be a living.

XY- male

The Y chromosome is much smaller than the X chromosome but both are  required in Meiosis to form male cells. Both chromosomes although not the  same in size, have an identical region called pseudo autosomal.

XX zygote- female

XO zygote- male (egg was fertilized by a sperm lacking a sex chromosome) O= the absence of a sex chromosome.

Dioecious: Most organisms are dioecious meaning they have distinct male  and female members of species

Hermaphroditism: have both male and female reproductive structures also known as monoecious. An example being C. elegans (soil nematodes)

ZZ: Male, homogametic

ZW: Female, heterogametic

~Be familiar with the Drosophila sex determination

Expressivity: the degree to which a trait is expressed

Dosage Compensation: balances gene expression in both males and  females

Chapter 5: Extensions and Modifications of Basic  Principles 

Mendel Dihybrid: 9:3:3:1

Epistasis: Gene masks the effect of another gene

Recessive Epistasis: 9:3:4 presence of homologous recessive genotype at  one locus fully masks the alleles at another locus

Ex: Coat color in Labradors

Sex Limitation: sex influenced, genes are autosomal, expressed differently on sex of organism ex: Bearded goat

Cytoplasmic Inheritance: Mitochondria and Chloroplasts have their own  genomes. These organelles come from only one gamete (the egg, mom)

Dextral vs. Sinistral: Know the difference in the shell coil of the snails

Pleiotropy: Single gene affects multiple phenotypes

Codominance: interaction between alleles where the heterozygote expresses  the phenotype of both homozygotes.  

Ex: MN blood types

Dominance: heterozygote has a phenotype that is indistinguishable from the  homozygous dominant

Incomplete Dominance: the heterozygote has a phenotype that is  intermediate compared to that of the two homozygous phenotypes.

Penetrance: Percentage of individuals that have a particular genotype that  expresses the phenotype.

Incomplete Penetrance: Just because genotype is present does not mean  the phenotype will be present as well. If present then the allele is dominant.

Genetic Complementation: determining whether mutations are at the  same locus or different loci. This has occurred if there is appearance of wildtype  characteristic in an organism.  

Chapter 6 and 7: Linkage, Recombination, and Eukaryotic  Gene Mapping 

Autosomal Dominant Trait:

-Do not skip generations  

-Not sex linked

-Affects both males and females with similar frequencies

-if affected, one of the parents have the dominant allele

Autosomal Recessive Trait:

-Skip generations

-Not sex linked

-Affects both males and females with similar frequencies

-Both parents are heterozygotes

- 25% affected and 50% carriers

X-Linked Recessive Trait:

-Skips generations  

-tends to affect males more but is possible to occur in females as well -never transmitted from father to son  

-all sons affected

-daughters of father who is affected will be a carrier

X-Linked Dominant Tait:

- Do not skip generations

- Appear in both male and female

-female are usually more affected then male

-trait goes from mother to both son and daughter but trait can only go from father  to daughter, none of the sons will get the allele from father.

Y- Linked Trait:

-Does not skip generations

-only in males

- trait transferred from father to son

Twins and Concordance:

-the traits are genetically linked

-Dizygotic twins vs. Monozygotic twins

-There is a greater concordance with monozygotic twins  

-Discordance is environmental

(Chapter seven) 

Recombination Frequency Formula= (# recombinant progeny)/ (total  # of progeny)

-50% is the maximum that it can be and that tells you that the two genes are  not linked

-The frequency for recombination decreases with less distance between the  genes.

Cis=wild types are found on the same side (coupling)

Trans= wild types are found on the opposite sides (repulsion)

1%=1cM so 25cM=25%  

(When we calculate frequency the double crossover causes us to underestimate)  

3 point test cross steps:

1. Identify the sets of progeny (highest numbers are the non-recombinants also known as the parental/ dominant and the least are the double cross overs,  everything else is single)

2. Find the middle gene  

3. Write your gene order  

4.** If the gene order found differs than the listed then reorder the genes in the data to match data

5. Identify all single crossover  

6. Calculate the recombination frequencies  

7. Plug it into the given formula and convert it to cM which is equal to the  percentage.

Interference Formula: I=1-Coc

(Coc= # of observed double crossovers / # of expected double crossovers) COC stands for Coefficient of Coincidence.

Chapter 8: Chromosome Variation 

Chromosomal rearrangements: when the chromosomes structure has a physical change

- There are four of these rearrangements that include: Duplication, Deletion, Inversion, and  Translocation

Duplications- portion of chromosome gets copied  

-Reverse duplication

Deletions- segment of chromosome gets deleted  

can lead to:  

- pseudodominance

- Haploinsufficiency

Inversion- reversing the order

You are given two kinds of inversion which include:

∙ Paracentric­ centromere is untouched

Can be non-viable because they could have no copies of a certain gene

∙ Pericentric­ the centromere is moved 

Can cause non-viable gametes if the centromere is removed

Translocation- When there is an exchange of genetic material between  nonhomologous chromosomes (1 could lose and the other gains or vice versa)

*Heritable form of down syndrome is known as the Robertsonian translocation.

Aneuploidy: the gain or loss of one or more single chromosomes   2n-2 nullisomy

Lost of 1 copy is known as monosome

When gaining an extra chromosome it is referred to as copytrisomy Gain of 2 chromosomes is known as tetrasomy 2N+2

(not supported in humans)

Polyploidy 2N+N

-Gains a whole new set of chromosomes.

Chapter 9 

U-Tube Experiment:

-Bernard Davis

-In this experiment two strains that were auxotrophic were separated using a filter  that helped mix the medium without mixing the bacteria. It resulted in a minimal  medium with no growth and no prototrophic bacteria was produced.

F factors:

- F+ is the donor cell (episome) that requires a plasmid

- Produces a pilus that connects to an F- cell.

-F- is a recipient cell that lacks the fertility factor  

Competent:

Cells that can take DNA from an extracellular environment.

Electroporation:

Uses a brief high voltage pulse

Bacteriophages:  

Also called just phages.

Lytic: infectious phage where progeny is made and host cell is killed. The new phage infects the other cells. Phages that go through lytic cycles are called virulent.

RNA Viruses:

- Positive­strand RNA virus

- Negative­strand RNA virus

- Retroviruses

Reverse transcriptase:

Novel DNA polymerase

Chapter 10: DNA: The Chemical Nature of the Gene 

DNA has four nitrogenous bases that include: Adenine,  Cytosine, Guanine, and Thymine

Chargaff’s Rules state that :

A=T,and G=C but it only works in double stranded molecules.

The molar amount of G and C summed together varies and depends on the source  of DNA

Structure of DNA:

Viewed in three levels that is primary, secondary, and tertiary.

The primary focuses on the nucleotide sequence, the secondary is the helical  structure, and the tertiary is the chromatin organization. Tertiary is not needed in  this exam because it is not spoken about in depth until Chapter 11.

Nucleotides three components:

1. Nitrogen­containing base

2. Pentose Sugar

3. Phosphate

Sugars:

-5 Carbon Atoms

*Phosphates overall charge is negative.

RNA differentiates from DNA because it contains Uracil instead of  thymine.  

3 Major forms of DNA:

1. B­DNA

2. A­DNA

3. Z­DNA

“Loop”- hairpin structure, most common in RNA, and begin to  form when an mRNA strand folds and forms a base pair but with  another section of the same strand.

 “Stem”- Is formed when the correct sequence is followed on  both strands such as A paired with T and C paired with G.

*DNA methylation slows down transcription.

Chapter 11: Chromosome Structure and Organelle DNA 

∙ Supercoiling takes place when DNA is over or under-wound o Positive supercoiling: over rotated

o Negative supercoiling: under rotated

o Topoisomerases: add or remove rotations from a DNA helix ∙ Euchromatin: In the cell cycle this goes through condensation as well as  decondensation. It has most of the transcribed DNA which is used for  synthesis of RNA

∙ Heterochromatin: located in the centromeres and telomeres of every  chromosome.  

∙ Histone proteins: some of the most highly conserved proteins ∙ H1,H2A, H2B, H3, and H4: these are the five major histones ∙ three types eukaryotic DNA sequences:

o Unique sequences

o Moderately repetitive sequences

o Highly repetitive sequences

Chapter 13: Transcription 

∙ major classes of RNA :

o mRNA: carries genetic informaiton

o rRNA: site of polypeptide

o tRNA:brings along the correct amino acid

o snRNA:forms small nuclear ribonucleoproteins

o snoRNA: processes the rRNA in the nucleolus

o siRNA and miRNA: intereference with translating mRNA or initiating degradation ∙ Transcription: 3 major components

o ssDNA template:

o rNTPs

o RNA polymerase

∙ Transcription unit

o Promoter

 Consensus sequences

o RNA-coding region

o Terminator

∙ Bacterial RNA polymerase:

o Core enzyme

o Sigma factor

∙ the three main eukaryotic RNA polymerases:

o RNA polymerase I

o RNA polymerase II

o RNA polymerase III

∙ Bacterial transcription

o Initiation

o Elongation

o Termination: there are two kinds

 Rho-dependent termination

 Rho-independent termination

Chapter 15: The Genetic Code and Translation 

∙ Amino acids

o Alanine- ala-A

o Arginine- arg-R

o Asparagine-asn-N

o Aspartic acid- asp- D

o Cysteine- cys- C

o Glutamine- gln-Q

o Glutamic acid- glu-E

o Glycine- gly- G

o Histidine- his-H

o Isoleucine- ile-I

o Leucine-leu- L

o Lysine- lys- K

o Methionine- met- M

o Phenylalanine- phe- F

o Proline- pro- P

o Serine- ser- S

o Threonine- thr- T

o Tryptophan- trp- W

o Tyrosine- tyr- Y

o Valine- val- V

∙ levels of polypeptide organization:

o Primary Structure: sequence of amino acids

o Secondary Structure: beta and alpha

o Tertiary Structure: overall three dimensional shape

o Quaternary Structure: two or more polypeptides interact to yield final protein ∙ genetic code:

o Codons: group of 3 nucleotides that specify either an amino acid or a translation  stop signal

o Universality: genetic code is known to almost be universal amongst eukaryotes  and prokaryotes

o Degeneracy: an amino acid can be coded for by two or more codons o Wobble: synonymous codons are known to differ in the third position o Reading frame: three potential ones are found in any RNA sequence ∙ Translation

o tRNA Charging

 amino acid is connected to the correct tRNA

 Aminoacyl-tRNA synthetase

o Initiation: assembles the mRNA and its necessary factors to the ribosome  50S and 30S subunits

 Initiation factors

 Start codon

∙ fMet-tRNAfMet 

o Elongation: with the addition of amino acids it synthesizes the polypeptide  E, P, and A sites

o Termination: synthesis stops and the ribosome as well as the polypeptide are  released.

 Stop codon

Chapter 16: Control of Gene Expression in Prokaryotes 

∙ Helix­turn­helix, Leucine Zippers, and zinc fingers are structural motifs commonly  associated with DNA binding proteins

∙ Operon: genes with related functions are clustered together and often  transcribed into a single mRNA.

o Operator

o Regulator

o Structural genes

∙ Four kinds of gene expression:

o Negative inducible

o Negative repressible

o Positive inducible

o Positive Repressible

∙ lacZ : lactose must be broken into glucose and galactose o ß-galactosidase

∙ lacY : lactose must be transported across the cell membrane o Permease

∙ lacA: thiogalctoside transacetylase

Chapter 18: Gene Mutations and DNA Repair

Mutation: inherited change in genetic information

Missense: base substitution that changes the codon from one amino acid to  another

Nonsense: base substitution that changes a codon coding for an amino acid  to a nonsense codon (codes for polypeptide termination)

Silent: A mutation that changes the nucleotide sequence of a codon, but  does not change the amino acid specified by the altered codon

Null: complete loss of function

Deletion: unequal crossing over, occurs more frequently than base  substitutions

LOF: Recessive mutations in genes controlling development, also called a null mutation

GOF: usually dominant, creates an entire new trait or causes the trait to  appear in the wrong tissue or at the wrong time in development

∙ mutation rate: how often a specific gene undergoes mutations ∙ mutation frequency: incidence of a specific type of mutation in a group  of individual organisms

∙ deamination: loss of an amino group

∙ depurination: loss of a purine from a nucleotide

∙ Base analog:

o 5-bromouracil

∙ The effects of mutagens on DNA:

o Alkylating agent:

 Ex: Ethyl methanesulfonate

o Deaminating agent:

 Ex: Nitrous acid

o Intercalating agent:

 Ex: Acridine orange

Depurinating DNA.

∙ Loss of a purine from a nucleotide 

∙ Results from cleavage of the glycolytic bond joining the base to the sugar at the 1’ ­carbon  ∙ Produces an apurinic site (AP site) 

Alkylating DNA.

∙ Alkylation alters the base pairing during replication

1. Mismatch Repair : After DNA synthesis is complete, improperly paired bases can be removed and  replaced with the proper base pair by this DNA repair process.

 MutSHL

2. Base Excision Repair

a. Glycosylase

b. AP endonuclease: is one of the enzymes needed to remove uracil bases in  DNA that often results from deamination of cytosine.

3. Nucleotide Excision Repair

a. Direct Repair

i. Photoreactivation: uses light energy to break covalent bonds

1. Photolyase: enzyme in eukaryotes

Chapter 19: Molecular Genetic Analysis and Biotechnology 

4. Recombinant DNA: manipulation of DNA, DNA from different sources is combined  together to create a novel DNA molecule.  

5. DNA termini that does not have a single stranded overhanging ends following  treatment with a restriction enzyme: Blunt Ends

6. Polymerase Chain Reaction: a simple test tube reaction that allows a DNA  fragment to be amplified more than one billion-fold in just a few hours a. required to run PCR:

i. ssDNA template

ii. DNA primers

iii. dNTPs

iv. Taq polymerase

7. “Fluorescence in situ hybridization”

8. DNA fingerprinting:

a. Microsatellites also known as short tandem repeats

b. RFLPs

9. transgenic animal: germline transformation

Chapter 20: Genomics and Proteomics 

10. Metagenomics: genecentric..does not focus on specific species  but rather genes in a community.

11. Paralogs: class of genes, resulting of an ancient gene  duplication.

12. Orthologs: homologous genes in different species that arose  from a common ancestor

13. Bioinformatics: Data mining of the human genome database 14. SNPs: Single Nucleotide polymorphisms

15. Microarrays: Based of technology for the making of computer  chips

Chapter 21: Epigenetics 

16.Epigenetics is defined as phenotypes that are passed on to future  generations without a change of DNA sequence.

17.DNA methylation

a. CpG Islands

b. Methyltransferases: type of enzyme that most likely associates with  decreased gene expression.

c. Hemimethylation

d. Dnmt3

e. Histone modification

f. RNA molecules

i. Xist RNA

ii. Paramutation: interacts between two different alleles leading  to inheritable change in the expression of one allele.

Chapter 22: Developmental Genetics and Immunogenetics 

18. Egg polarity genes “Maternal Effect Genes” i. Dorsal protein: distributes along cytoplasm in the egg  

before fertilization takes place.  

ii. Bicoid protein: found in the egg

iii. Nanos protein: found in the posterior part of the egg

19. Segmentation genes

a. Gap genes: functions to form the pattern of sementation b. Pair-rule genes: functions to form pairs of segments

c. Segment-polarity genes: functions to form segments individually 20. Homeobox: another name being homeodomain, it is an 180  nucleotide sequence that codes for a 60 amino acid DNA binding motif. 21. Apoptosis= Cell Death

22. Somatic recombination:

a. V-variable

b. J-Joining

c. C-Constant

Chapter 23: Cancer Genetics 

23. “Oncogenes” stimulate cell division but are dominant mutations 24. “Proto-oncogenes” normal cellular counterparts 25. “Tumor suppressor genes” are mutations that are recessive  

and cause an inactivation of genes that bring about cell division.  a. Example: Rb-1

26. Note: Mutations in homeotic genes in Drosophila result in  transformation of one body segment into another.

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