biol 189 exam 3 review
pyrimidines
Cytosine and Thymine
gene expression in eukaryotes
DNA availability, transcription factor availability, mRNA processing, mRNA transport from nucleus, RNA degradation, protein processing and degradation
1. DNA availability
DNA can be tightly bound to histone proteins that can prevent gene expression. Chemical modifications of histones can open up (or close off) DNA for transcription
AFTER DUPLICATION
DNA doesn't condense into 2 visible sister chromatids until the first phase of mitosis (prophase)
X-linked recessive
Disorder = Hemophilia A - Males more likely affected (hemizygous) - Females often carriers but no display of phenotype
mutagens
a cause of mutations; any external agent that induces mutations such as radiation, chemicals, infectious agents
cancer
a class of diseases characterized by malignant cell growth in the body; can overwhelm normal function of organ systems and result in death
theory of evolution
a comprehensive explanation of some aspect of nature that is supported by a vast body of evidence
autosomal dominant
a disorder expressed with 1 or 2 more copies of disease-causing allele
ophioglossum reticulatum
a fern with ~1440 chromosomes
transcription
a gene's DNA sequence is rewritten into a mRNA molecule in the nucleus
lac operon
a group of genes that function to break down lactose sugar but are expressed only in the presence of lactose sugar
species
a group of organisms that can successfully interbreed and produce viable offspring
tumor
a mass of cells undergoing uncontrolled cell division
semi-conservative replication
every new DNA molecule is half old DNA and half new DNA; old strands are templates for DNA polymerase to build the complementary strand
model organism
garden pea plant to study patterns of heredity
evolution
genetic changes in population over many generations
incomplete dominance
heterozygote has intermediate phenotype - Ex: Rr phenotype is pink bc neither red nor white alleles are dominant, resulting in a blended phenotype
chromosomes
highly condensed (compacted) chromatin; found only during active cell division/mitosis
viral replication: synthesis
host cell is hijacked to produce millions of copies of the viral genome and viral proteins
viral replication: release
host cell releases the newly formed viral particles (some viruses kill host cell during release [lysis] others released by exocytosis [vesicles])
somatic cell cycle phases
interphase and mitosis
6. Protein processing and degradation
just like mRNA, proteins can be regulated at the level of production and degradation. Some proteins get degraded as they are transcribed while others can be maintained long after production.
malignant tumor
lack a capsule and can enter in circulatory systems and seed new regions of the body
viable offspring
offspring that are healthy and also capable of reproduction
splicing
process of removing introns and connecting exons from pre-RNA to form mature mRNA
Hardy-Weinberg Equation
p2 + 2pq + q2 = 1
sex chromosome
pair 23; determines biological sex of a person; XX = FEMALE, XY = MALE
autosomes
pairs 1-22; contain genetic instructions of general life processes
silent mutations
point mutations that do not change protein's amino acid sequence; tolerated in wobble position of a codon
sexual reproduction
requires the combination of genetic material from two individual organisms; when 2 gametes fuse to make new individual offspring and next generation of organism; need to find mate, 50% of each parent's genes, increases genetic diversity
introns
segments removed from pre-mRNA- trash RNA
true-breeding or pure-breeding plants
self-fertilization yields offspring with same seed color as parent plant; Mendel used these plants to produce monohybrids
termination in translation
stop codons mark protein ends; protein releases factors bind to stop codons and ribosomes release from mRNA
cytokinesis
the cytoplasm is split between new cells then separated with new cell membrane
sex-linked traits
traits dictated by genes on sex chromosomes; disproportionately affect one sex more than the other
benign tumor
uncontrolled cell division contained in a tough capsule (size limited and does not spread)
lysogenic phase of bacteriophage
viral genome incorporated into host genome aka prophage; stressful condition can cause translation into lytic phase
viral replication: assembly
viral particles assemble and genetic information moves inside
viral replication: attachment
virus binds to host cell surface receptors
viral replication: penetration
virus genome enters the host cell (phagocytosis, injection)
what is a gene?
a segment of DNA that contains instructions to make a specific protein or RNA molecule
autosomal dominant pedigree
affected individual appear in every generation - no specific sex
first key principle of evolution: common descent with modification
all life on earth began with the universal common ancestor = first living cell capable of reproduction
what multicellular eukaryotic organisms sexually reproduce?
all mammals, most birds, most reptiles, fish, flowering plants
what is a genome?
all of the DNA inside of a cell
interphase
bulk of a cell's life cycle will be spent in this phase; has 3 sub-phases (gap 1, synthesis [where DNA is replicated], gap 2)
frameshift mutation
cause the reading frame for the protein to be altered
polygenic trait
controlled by more than one gene (skin, eye, hair color depend on multiple genes for phenotype determination)
monohybrid crosses
crosses focused on only one trait in which Mendel crossed thousands of true-breeding plants
large-scale chromosome mutation examples
deletion, duplication, inversion, insertion, translocation
recessive allele
denoted by lowercase letters
dominant allele
denoted with capital letters
Hardy-Weinberg equilibrium
determines if evolution is occurring (change in allele and genotype frequencies)
allele
different forms of a gene
Mendel's Law of Independent Assortment
different genes separate independently/randomly during gamete formation in Metaphase I
Gregor Mendel (1822-1884)
discovered fundamental rules of heredity in diploid organisms (the mechanisms of passing traits or genes from parents to their offspring
Franklin, Gosling, Wilkins (1952)
discovered the helix shape, the size of a helix turn, how many base pairs per turn (10), and phosphate groups outside the helix through X-RAY CRYSTALLOGRAPHY
cystic fibrosis
disease caused by a genetic mutation in one transmembrane protein gene and often affects the lungs and mucous membranes; symptoms only apparent in those carrying 2 mutated alleles
cytokinesis in animal cells
- cleavage furrow, cells pinch off
diploid
2 sets of chromosomes; most sexually reproducing organisms
allele frequency
# specific allele / all alleles in gene pool
homozygous dominant
(YY) 2 copies of dominant allele
heterozygous
(Yy) 1 dominant 1 recessive
homozygous recessive
(yy) 2 copies of recessive allele
Lamarck (1800s)
- Animals inherit characters from their parents - Use or disuse of a structure or organ can cause it to enlarge or shrink in successive generations
Georges Cuvier (1769-1832)
- claimed extinction is a fact - periodic catastrophes led to organisms going away forever
X-linked traits
- Ex: red-green color blindness - proteins in cone cells of the eye are involved in color perception - males affected more b/c only one X copy
conclusion of Mendel's monohybrid crosses
- F1 generation always 100% one phenotype - F2 always had 3:1 phenotypic ratio - heritable factors came in pair and some traits were able to dominate others
cell theory
- all cells come form pre-existing cells - cells reproduce by dividing
transfer RNA
- carry specific amino acids to the ribosome - one end binds to specific amino acid - other end has anticodon that is complementary to codon
structure of DNA
- double helix - rails = sugar-phosphate backbone - rungs = paired nitrogenous bases with hydrogen bonds - complementary base pairing - anti-parallel
when a cell cycle goes wrong...
- if DNA mutations are not eliminated, it can lead to tumors then cancer
natural selection
- in nature, if breeding is unrestrained = struggle for survival
why is genetic diversity good?
- increased through sexual reproduction - high genetic diversity = evolution (ability to adapt to different/changing environments) - ability to adapt increases long-term survival - asexual organisms at greater risk of extinction due to reduced genetic diversity and changing environments
parts of Mendel's experimental design using the pea plant
- noticed patterns of specific traits from parent to offspring - performed controlled crosses by transferring pollen (sperm) from plants to flowers (eggs) of other plants
metaphase of mitosis
- nuclear membrane has completely disintegrated - microtubules attach to sister chromatids - form mitotic spindle (cage-like structure) - 46 chromosomes pushed and pulled to line up single file at metaphase plate (middle)
why are pea plants a great genetic model organism?
- sexually reproducing - self-pollinators - grow fast, easy to maintain, produce many offspring
telophase of mitosis
- spindle fiber microtubules begin to disintegrate - 2 nuclear membranes (one cell, 2 nuclei) - chromosomes decondense into chromatin - ANIMAL CELLS: 2 sets of protein form at midline
how to read a pedigree
- squares = males - circles = females - horizontal lines between 2 shapes = reproductive partnerships - vertical lines = offspring of specific partnership - filled shape = phenotype is seen - open shape = phenotype is not seen - half-filled shape = carrier but trait is not expressed - ? = phenotype unknown
cell cycle checkpoints
- the cell ensures it is ready to progress to the next phase (G1, S, G2, Mitosis) - failure of a check point results in apoptosis
X-chromosome inactivation
- to balance simultaneous gene expression, one X chromosome is turned off - Ex: orange/black fur in cats
James Hutton and Charles Lyell (geologists)
- uniformitarianism: forces that molded the planet today molded throughout history; slow continuous changes over long periods of time
cytokinesis in plant cells
- vesicles with cell wall sent to middle between nuclei, then fuse until cell wall is established
Thomas Robert Malthus (1798)
- wrote "An Essay on the Principle of Population as it effects The Future Improvement of Society" - human population theory - struggle for existence - humans produced more offspring than can survive
prophase of mitosis
-DNA condensed into chromosomes - centrosome copies move to the poles and synthesize microtubule spindle fibers -nuclear membrane disintegrates - spindle fibers extend and attach to centromeres of chromosomes
haploid
1 set of chromosomes; asexually reproducing organisms and gametes; binary fission (asexual) and meiosis (gamete formation)
how pre-mRNA is processed in eukaryotes:
1. add mRNA cap (modified nucleotide that serves as recognition signal for ribosome) 2. add poly-A tail (100-200 As protects mRNA from degradation in cytoplasm) 3. mRNA splicing
dihybrid cross
Mendel found new phenotypic rations in F2 = 9:3:3:1
what is Chargaff's rule?
Adenine always equals/pairs with Thymine; Cytosine always equals/pairs with Guanine
purines
Adenine and Guanine
chromatin
DNA is wrapped around histone proteins; loose configuration (allows for easy gene expression) and common configuration (when cell is not undergoing cell division)
naked DNA
DNA not associated with histones or histone-like proteins; found in active gene expression
binary fission
DNA replicates and attaches to the cell membrane of a parent cell that contains one chromosome, then membrane growth between the two points moves the DNA molecules away to form a new cell wall resulting in two daughter cells that are identical to the original
S phase of interphase
DNA replication - results in 2 identical sister chromatids attached by protein centromere
operator
DNA sequence between promoter and protein-coding genes; serves as regulatory region
what is the central dogma of biology?
DNA to RNA to proteins
what are the possible gametes from F1?
FOIL: first, outer, inner, last (R r Y y)
Darwin's ideas
On the Origin of Species (1859)
traits Mendel studied
Parental (P), 2 offspring generations (F1 and F2)
elongation in transcription
RNA polymerase reads the DNA template and adds complementary RNA nucleotides to the growing molecule as it moves down the gene (think nitrogenous base pairings!)
repressor proteins
WITH NO LACTOSE...bind to the operator and physically stops RNA polymerase and operon gene expression
macroevolution
accumulation of microevolutionary changes over millions of years resulting in reproductive isolation resulting in the formation of new species
how do prokaryotes divide?
binary fission
wobble position
change in 3rd base of the codon; allows mutations to occur without effects in the protein
definition of evolution
change in genetic makeup of a population of organisms over many generations
microevolution
changes in allele frequencies/traits in a population over short evolutionary time (a few generations)
homologous chromosomes
chromosome pairs that have the same genes in the same location
operon
clustered group of genes related to a specific function that can be turned on or off as needed; contains promoter, operator, operon genes
operon genes
code the required proteins
Alfred Russel Wallace
conducted field studies of species diversity in the Amazon then Indonesia; developed identical theory as Darwin, but Darwin received credit
5. RNA degradation
enzymes in cell actively degrade RNA. mRNA can be chemically modified which can change its "lifespan" and the likelihood that a transcript will be made into a protein or not.
phenotype
expressed traits (physical appearance); determined by the genotype
G2 of interphase
extra growth and preparation for mitosis
Darwin's concepts leading to theory of evolution
gradualism (new species result from ancestral species undergoing slow constant changes over long periods of time) and the galapagos finches (all different species came from a single ancestor species from S. America)
cell division
growth and development, wound repair, tissue regeneration, microbial fission/budding
what enzymes are involved in DNA replication
helicase (unwinds and unzips DNA), DNA polymerase (assembles and proofreads new DNA strands), and ligase
selective pressures
how strongly the environment selects for a particular trait; any component of the living and non-living environment that results in differences in survival and reproduction
4. mRNA transport from nucleus
if mRNA is not specifically transported from the nucleus, it will not become a protein
karyotype
image showing all of an individual organism's chromosomes; typical karyotype has 46 chromosomes (23 pairs)
why are codons 3 bases?
in order to provide proteins with a huge variety of molecular interactions (h-bonds, hydrophilic, hydrophobic, charged, uncharged); needs to specify at least 20 unique amino acids with only 4 bases
where do inactived x-chromosomes stay?
in the condensed chromosome form called the Barr body in the nucleus
where does translation occur?
in the cytoplasm! or associated with the rough endoplasmic reticulum (bound ribosomes)
polysome
increase protein synthesis efficiency with multiple ribosomes on a single mRNA
Mendel's Law of Segregation
individual alleles separate during gamete formation such that each gamete receives only 1 copy of each gene; through meiosis
3 main steps of transcription
initiation, elongation, termination
3 steps of translation (in cytoplasm!)
initiation, elongation, termination
initiation in translation
mRNA cap helps mRNA associate with ribosomes
translation
mRNA molecule leaves the nucleus and enters a RIBOSOME (free or bound) where the mRNA codes for the specific amino acids in a polypeptide chain
microtubules
made of tubulin proteins; dynamic movements of chromosomes and cellular components during mitosis is dependent on microtubules
anaphase of mitosis
microtubules begin to pull sister chromatids apart toward opposite poles of cell; cell membrane elongates
how do eukaryotes divide?
mitosis (occurs in body cells [somatic cells] in multicellular organisms
polyallelic trait
more than two alleles (human blood type)
eukaryotes
multiple linear chromosomes
polypoid
multiple sets of chromosomes
five agents of evolution
mutation, gene flow, genetic drift, sexual selection, natural selection
how do prokaryotes evolve if binary fission makes cells that are identical copies?
mutations and horizontal gene transfer
what can result in aneuploidy?
nondisjunction that violates Mendel's law of segregation
G1 of interphase
normal cell functions and growth
ploidy
number of sets of chromosomes in a cell or an organism
centrosomes
organelle that makes microtubules for mitosis
apoptosis
programmed cell death; regulated by a class of enzymes called caspases (exist in every cell awaiting an activation signal)
initiation in transcription
promoter region; where the gene starts and what strand to use as a template; transcription factors (proteins) guide RNA polymerase to template DNA strand at the correct location
4 phases of mitosis
prophase, metaphase, anaphase, telophase
prions
protein-based infectious particles aka zombie proteins; misfolded proteins; results in massive accumulation of misfolded proteins that turns into cell death. ex: mad cow disease from eating nervous tissue of previous infected cows
2. Transcription factor availability
proteins that bind to promoter regions of DNA and help direct RNA polymerase to gene
recombination/crossing over
random process during prophase I that results in 2 parental chromatids and 2 recombinant chromatids (may mix up linked parental traits); ALSO more likely to occur spaced far apart on the same chromosome
lytic phase of bacteriophage
rapid viral replication which causes infected cells to die; massive release of new viral particles into the organism/environment
horizontal gene transfer
receiving genes from something other than parental cells (mechanisms in prokaryotes: transformation, conjugation, transduction)
3. mRNA processing (alternative splicing)
removal of certain introns/ exons can have dramatic effects on downstream protein products (see earlier slide)
virus function
replication & propagation - make more of itself and infect new hosts; there are 5 stages...
asexual reproduction
reproduction without the involvement of another organism; no need to find mate, maintain good genes, and reduced genetic variety
elongation in transation
ribosome moves mRNA down one codon after Met, next codon is read, tRNA enters, ribosome makes covalent peptide bond between amino acids, tRNA exits, ribosome moves down one codon, etc.
exons
segments joined together to make mature mRNA
prokaryotes
single circular chromosome
promoter
site where RNA polymerase binds
plasmids
small circles of DNA that contains one or a few specialized genes; gets replicated with main bacterial chromosome during binary fission
mitosis
somatic cell division; cell actively divides into 2 cells
2nd key principle of evolution: natural selection
some individuals in a population will have specific combinations of alleles better suited for a particular environment at that particular time = increased chance of surviving and reproducing
origins of replication
specific DNA sequences that signal where to begin replication
start codon
specific codon that starts amino acid incorporation (in eukaryotes...start codon is AUG [methionine] so all polypeptide sequences start with Met as first amino acid)
termination in transcription
specific termination sequence indicates end of gene; RNA polymerase releases from the DNA when it recognizes the sequence, then mRNA molecule is released
gametes
sperm and egg
late prophase of mitosis
spindle fiber microtubules become attached to the sister chromatids of each chromosome
Thomas Hunt Morgan
studied fruit fly traits and his work led to our understanding of chromosomes as hereditary unites (each chromosome carries many genes); realized that specific crosses in flies produced higher proportions of recombinant offspring
what happens when the ribosome reads the mRNA codon?
tRNA enters ribosome, codon-anticodon base pairing, new amino acid is covalently bound to previously added amino acid
reproduction
the biological process by which individual organisms (offspring) are produced from parents; also called vertical gene transfer
what are nucleic acids?
the information-bearing molecules of all life on earth (genetic material); polymers made up of nucleotide monomers
IF genes are located on the same chromosome...
they are inherited together! therefore, they do not follow the Law of Independent Assortment which leads to unexpected phenotypic ratios
codon
three bases are read at a time by a ribosome; specifies a specific amino acid to be added to the polypeptide
vaccines
to combat viruses, you can train the immune system to recognize the pathogen before actual infection occurs. otherwise, supportive therapy/waiting for the immune system recognizes the virus to create a natural immune response
genetic linkage
two genes are closely associated on the same chromosome and do not assort independently
mutations
unintended changes in the cell's DNA sequence; can affect a single DNA base, few bases, or large chromosome proportions; can cause diseases; silent or harmful; mutations are rarely beneficial
Watson, Crick (1953)
used Chargaff's rule and X-ray crystallography to determine molecular structure of DNA; purine + pyrimidine pairs
test cross
used to determine if the dominant parent is homozygous or heterozygous dominant; dominant trait crossed with true breeding recessive trait
viruses
very small protein shells that contain genetic material made of either DNA or RNA
punnett squares
visual representation of crosses; demonstrate potential offspring genotypes and phenotypes; used to determine likelihood (%) of specific genotypes/phenotypes that could result from specific genetic crosses
codominance
when 2 different alleles can be expressed simultaneously in the phenotype - Ex: ABO blood typing
subspecies
when microevolutionary phenotypic changes do not result in reproductive isolation