7. Biology 1 Flashcards
organelles
nucleus, rough er, smooth er, golgi apparatus, mitochondria, centrioles/centrosomes, lysosomes, peroxisomes
nucleus
organelle where DNA is stored (regular DNA, only other place where DNA is found is in the mitochondria, but mitochondrial DNA circular)
nucleolus
site of rRNA transcription and ribosome assembly
Rough ER
covered with ribosomes, transports proteins into ER lumen for translation, almost all proteins are made in the ER, post-translational modifications to proteins and DNA start in RER and continues in golgi
Smooth ER
lipid synthesis/modification (no metabolism, lipid metabolism is done in the mitochondria)
golgi apparatus
post-office, organizes proteins, continues post-translational modification, excrete in vesicles bound for the plasma membrane, back to the ER or to organelles
mitochondria (see diagram)
know mitochondria shape, and function: outer membrane, intermembrane space, inner membrane matrix. contains mitochondrial DNA (from aerobic prokaryotes- endosymbiotic theory)
How do the pH values of the matrix and the intermembrane space compare?
intermembrane space is acidic (around 1.4pH) and matrix is relatively neutral (7.8) due to the proton gradient crossing the inner mitochondrial matrix for ATP production
centrioles/centrosomes
proteins and nucleating factors within which the centrioles are located, it organizes microtubules, flagella, and cilia, and is important to cell division (sets up framework for it)
lysosomes
pH of 5, digests cell pats, fuses with phagocytotic vesicles, participate in cell death, buds off from the golgi
peroxisomes
self-replicate, detoxify chemicals, participate in lipid metabolism
A lab worker must inject a segment of DNA into the nucleus of a living cell. To access the nuclear lumen, the microscopic needle must pierce a minimum of how many layers of lipid membrane?
To enter the nuclear lumen, the needle must pass through the cell membrane (2), plus the outer nuclear membrane (2), plus the inner nuclear membrane (2), for a total of six single layers of lipids.
cytoskeleton
microtubules, intermediate filaments, microfilaments
tubulin
smallest structural unit, forms microtubules, alpha and beta tublulin form a heterodimer called a protofilament, 13 protofilaments make up a hollow 9+2 arrangement that makes up one microtubule
mictotubules
makes up cytoskeleton, with intermediate filaments and mictrofilaments, comprised of protofilaments
protofilament
comprised of alpha and beta tubulin in a 9+2, 13 protofilaments make a microtubule
cytoskeleton summary
alpha and beta tublulin form a heterodimer that forms long chains called protofilaments, 13 protofilaments surround a hollow core make up 1 microtubule, 20 microtubules form a nine doublet design (9+2)
cytoskeleton
network of microfilaments, microtubules and intermediate filaments that provides structure and stricture for intracellular transport
spindel aparatus
microtubules that grow out from the polar centrioles during mitosis, it binds the chromosomes during metaphase to the centromere and aids with disjunction of the cell
actin
a protein monomer that polymerizes to form microfilaments, forms filament of the sarcomere (tracks for which filaments (myosin motor proteins) to move on)
intermediate filaments
general class of proteins that polymerize to form filaments that are intermediate in diameter ti microfilaments and microtubules
myosin
motor protein
flagella
whip like, used for movement
cilia
protrusuons, numerous in number used to for many things, like movement and moving debris in the respiratory tract (note important places: cerebrospinal cavity- moves CSF, fallopian tubes - move egg, respiratory tract- clear debris)
9+2 arrangement
found in microtubules, and EUK cilia and flagella, not in proks
flagella
eukaryotic - whipping motion, made of microtubules/tubulin. prokaryotic - spinning/rotating motion, made of simple helices of flagellin
phosphlipids
lipid molecules with non-polar tail and polar phosphate head, think phospholipid bilayer and amphipathic characteristics
integral proteins
proteins that have one or more segments (moieties) embeded in the phopholipid bilayer
transport proteins
cross phopholipid bilayer, transports ions, proteins, etc.. into hydrophobic core
membrane receptor
any protein on a membrane that binds a ligand (signaling molecule)
cholesterol
amphipathic, steroid region, polar region, between phosphlipids in bilayer, add rigidity
fluid mosaic model
bilayer model, with polar heads facing outward, and non-polar tails facing inward
exocytosis
vesicles inside the plasma membrane dumps contents into outside as it fuses with membrane
endocytosis
cell uptake via invagination forming a endosome vesicle
phagocytosis
invagination of large particles, bacteria, etc.
pinocytosis
invagination of extracellular fluid and small particles, non-specific (phagocytosis is specific and is receptor mediated)
passive (simple) diffusion
no atp needed, materials cross with no aid, usually small molecules (water diffusion
facilitated diffusion
no atp needed, a type of passive diffusion, normally just a conformational ion channel that allows for the movement (sodium potassium gradient)
active transport
requires atp, travels against concentration gradient or electrical potential
secondary active transport
no direct coupling of atp required
tight junctions
waterproof barriers, found on skin, and linings of the bladder blood-brain barrier, and tubules of the kidneys
gap junctions
tunnels between cells, ex. between cardiac cells smooth muscle cells and neurons like in the eye
adherens junctions
strong mechanical attatchments, in epithelium and between cardiac cells
desmosomes
strong cellular junction, weld cells together to protect against stress, found in tissues that receive considerable amounts of stress such as the skin
tissues
epithelial, nervous, connective, and muscle
note: blood, fat, and dermis are connective tissue, the epidermis is epithelial
endocrine system
hormone signaling, secreted by cells of endocrine gland, travel through bloodstream,
second messenger systems
g-protein systems,
g protein system
a hormone or molecule binds to a g-protein coupled receptor, causes conformational change, activates alpha subunit (normally off when GDP is bound), alpha subunit separates fro the beta and gamma subunits and activates adenylyl cyclase where it hydrolyzes GTP to GDP and rebinds to the beta and gamma subunits, adenylyl cyclase helps convert ATP to cAMP, cAMP activates protein kinase A which then leads to phosphorylation and a cascade effect
intracellular receptors
lipid-soluble (steroids), do not require membrane surface receptor.They dissolve through the membrane and bind targets in the cytosol. In most cases, their activated target then acts inside the nucleus on the promoter region of a gene to regulate transcription up or down.
paracrine
signal molecules secreted by one cell bind to receptors on local cells, ex. neurotransmitters communicating in the synaptic gap
autocrine
signal molecules secreted by ta cell bind to receptors of the same cell
intracrine
signal molecules (usually steroids) bind to receptors inside the same cell that pruduced them without ever being secreted (like autocrine but without leaving the cell)
juxtacrine
direct cell signaling via contact
cell cycle pi chart
2 rings, outer ring mitosis and interphase only, inner ring: mitosis, G1, S, G2, mitosis
G0
gully differentiated neurons and cardiac muscle cells are frozen in G0 and do not divide, multicucleanted skeletal muscle cells can also be considered to be in G0 phase (AKA quiescent)
For human beings, how many chromosomes are there?: a) before replication, b) after replication, c) during interphase, d) before S-phase, e) after S-phase, f) in a diploid cell, g) in a haploid cell. Describe how the mass of DNA differs for each of the above scenarios.
a) 46; b) 46; c) 46; d) 46; e) 46; f) 46; g) 23; Before replication we have 46 diads (i.e., NO sister chromatids) or 46 unreplicated chromosomes. Let’s define that as a mass of m. After replication we have 46 tetrads, or duplicated chromosomes, so the mass would be 2m. During interphase the mass would change. Prior to S phase the mass would be m, then during S phase it would increase to 2m and remain so until mitosis. Before S-phase, as already stated, the mass would be m. After S-phase the mass is 2m. In a diploid cell the chromosome number will be 2n (46 for humans) and the mass could be m or 2m depending on whether or not S-phase has occurred. A

haploid cell would have a mass of 1/2m. The take home point is that the chromosome number does NOT change when DNA is replicated–you just end up with twice as much DNA per chromosome. The only time the chromosome number changes is during meiosis, and after fusion of gametes in the production of a zygote!
apoptosis
programmed cell death, autolysis of cell contents by lysosomes
histones
proteins that wrap DNA into compact chromosomes (predominantly his+ AA giving + charge to attract to - DNA backbone)
nucleosomes
a set of 8 histones in a cube shape with DNA coiled around it like thread
chromatin
general term for DNA and protein
diploid
2n chromosomes (46 in humans)
haploid
n chromosomes (23 in humans)
homologues
two related but non-identical chromosomes - one from each parent
sister chromatids
two strands of DNA in a duplicated chromosome attached by a centromere
centromere
region of the chromosome that joins the two sister chromatids
kinetochore
The term kinetochore is often used synonymously with centromere, but they are not identical. The centromere is a region on the chromosome and the kinetochore is a specialized group of proteins to which the spindle fibers attach directly during mitosis/meiosis.
cell division
prophase, metaphase, anaphase, telophase, interphase
prophase
nuclear membrane dissolves and chromosomes condense
metaphase
chromosomes lining up at metaphase plate and formation of spindle apparatus
telophase
nuclear membranes beginning to reform and chromosomes unwinding,
interphase
since cell with well defined nuclear edges and uncoiled chromosomes
know mitosis and meiosis phases (see diagrams)
see diagrams
nondiscuntion
when chromosomes fail to separate properly during anaphase, meiosis 1 &2 or mitosis- results in uneven number of chromosomes (ex. common one - trisomy - 21 chromosomes - downs syndrome)
cross-overs
crossovers occur during prophase of meiosis 1, sister chromatids switch segments or whole parts of their chromosomes with eachother
meiosis centromeres
centromeres do not split in meiosis 1 but split in meiosis 2
A karyotype is somewhat like a photographic list of all of the chromosomes found in a cell. If homologous pairs are present, they appear next to one another on the exposed film. All of the chromosomes for the entire cell are presented on the same slide, making differences in the relative length, size and orientation of the chromosomes readily apparent. If a karyotype were produced for a human cell that had just undergone Telophase I of Meiosis, the entire karyotype slide should contain (assume that the chromosome are still condensed and have not reverted back to chromatin):
Meiosis I takes a cell with 23 pairs of homologous chromosomes, or 46 total chromosomes, and creates two cells, each with 23 non-paired, non-homologous chromosomes. You should also know that chromosomes generally decrease in size, with chromosome One being by far the largest. Thus answer D is the best answer.
nucleotides
triphosphate, sugar, and base
common nucleotides
DNA, RNA, cAMP, NADH, FADH2, FMN, CoA, ATP, GTP, UTP, etc..
DNA bases
Adenine,thymine, cytosine, guanine
adenine
A, pairs with T in DNA and U in RNA, forms 2 hydrogen bonds
thymine
T, analogous with U in RNA, in DNA, forms 2 hydrogen bonds
uracil
U, analogous with T in DNA, in RNA, forms 2 hydrogen bonds
cytosine
C, forms 3 hydrogen bonds with guanine
guanine
G, forms 3 hydrogen bonds with cytosine
Draw a short DNA helix. Include the bases, sugar-phosphate backbone, and exact connectivity (i.e., Which element bonds to which, via which type of bond?).
Below is a diagram of a section of DNA helix. Be sure students can visualize and easily draw all connections—especially the phosphate connection between the 3’ hydroxyl group and the 5’ carbon. A common mistake students make when drawing these structures is to have too many bonds to the phosphate, too few, the incorrect charge, etc. Also make sure they have drawn the ribose WITHOUT a 2’ hydroxyl group. It is NOT required knowledge to be able to draw each base (A,T,C,G,U) from memory, but drawing a helix a few times will solidify the concept of how hydrogen bonds form between strands.
Which of the four DNA bases are purines and which ones are pyrimidines?
Adenine and Guanine are purines, Cytosine and Thymine are pyrimidines. Later in this lesson we will discuss Uracil, which is also a pyrmidine.
purines
A and G
prymadine
C and T, and U
origin of replication
location on the chromosome where replication begins, human chromosomes have multiple origins
bidirectional
refers to the fact that replication in both directions simultaneously from the origin
semi-conservative
refers tot he fact that each newly formed daughter helices are made up of one old strand and one new strand
semi-conservatie
refers to the fact that one strand is senthesized continuously and the other strand is synthesized in okazaki fragments
DNA replication
DNA replication begins at an origin of replication. Helicase unzips the double-helix. Immediately, single strand binding proteins coat the individual strands and prevent them from re-annealing. Simultaneously both strands are fed through a replication complex that contains all of the proteins necessary for replication. Because DNA polymerase can only add to an existing 3’ OH group, primase (an RNA polymerase) first constructs short RNA primers on both strands. Two DNA polymerase molecules then begin building new complementary DNA strands. In doing so, they must “read” (i.e., move along the strand) in the 3’ to 5’ direction and are therefore building the new strands in the 5’ to 3’ direction. The sliding clamp is a protein that helps keep the DNA polymerase tightly associated with the strand. Because both enzymes must move along the strand in the 3’ to 5’ direction, they will be moving in opposite directions. If this continued indefinitely the two enzymes would move farther and farther apart. Instead, all enzymes and proteins remain closely associated with the replication fork in what is often called the “replication complex.” As a result, the enzyme working on the lagging strand must copy short segments downstream, release from the strand, move upstream, and copy another short segment downstream—and then repeat. This also means that while the leading strand requires only a single primer, the lagging strand requires multiple primers—one for each these short segments called Okasaki fragments. After this initial replication step, the enzyme RNase H removes all RNA primers. DNA polymerase then fills in the gaps. However, remember that DNA polymerase can only add nucleotides to existing 3’ OH functional groups. Therefore, although it can add a nucleotide to fill the last missing base pair in a gap, it cannot connect that last nucleotide to its downstream neighbor. This functionality is performed by DNA ligase. DNA ligase creates the last necessary phosphodiester bond, completing the strand.
What causes the daughter strand to be shorter after replication?
The DNA polymerases require an existing 3’ hydroxyl group to which they can add their first nucleotide—they cannot set down a nucleotide with a free 5’ end. For this reason, an RNA primer must be placed at the 5’ end of any DNA strand. Later in the process all primers are removed and the gaps are filled in by DNA polymerase and DNA ligase. At the 5’ end, however, there will still be no existing 3’ hydroxyl group and so DNA polymerase cannot replace that section of primer. As a result, every time a chromosome is replicated the new daughter strands will be slightly shorter than the parent strands—by an amount exactly equal to the RNA primers that were in place on both ends of the chromosome.
telomeres
long sections of repetitive DNA nucleotides found at both ends of each chromosome that they provide a buffer region of non-coding DNA so that these repetitive losses in length do not impact a gene sequence, approximately 50 replication cycles will consume the entire theorem region and any subsequent replications will result in the loss of gene sequences
telomerase
an enzyme that adds length to the telomeres,
Telomerase is active in somatic cells early in development, but is turned off in somatic cells thereafter. Why would a mature somatic cell with telomerase activity be potentially harmful?
Because telomeres are shortened by each round of cell division, they provide somewhat of a “time clock” for cells. After the telomeres are gone, subsequent division will quickly damage important coding sections of the DNA and presumably the cell could not survive very many additional divisions without being directed into apoptosis. This would act to prevent the uncontrolled cell division found in tumors. However, if the enzyme telomerase were present, the cell could replace the telomere as it was being used up—essentially removing the “clock function” of the telomeres and theoretically allowing for unlimited cell division.
DNA Damage and Repair
spontaneous hydrolysis of DNA, damage by external chemicals or radiation, mismatch base repairs
spontaneous hydrolysis
spontaneous hydrolysis of DNA
damage by external chemicals or radiation
neighboring prymadines react with each other to form a covalent dimer, various chemicals cause alkylation of functional groups on DNA bases, carcinogens are often large polycyclic compounds that bind to the DNA and create bulky side groups
mismatched base pairs
results from errors during replication, or methylation of guanine (paired accidentally with thymine instead of cytosine)
mechanisms of DNA repair
proofreading, mismatch repair system, base excision, nucleotide excision
proofreading
DNA polymerase proofreads most mismatched base pairs on the spot
mismatch repait system
enzymes scan newly copied DNA and locate, excise, and replace mismatched base pairs missed by the proofreading of DNA polymerase
base excision
the base portion is excised by DNA glycoylase, other enzymes then remove the sugarphosohate backbone then DNA polymerase and ligase replace the nucleotide
nucleotide excision
excision of an oligonucleotide that includes several bases on either side of the error, DNA polymerase and ligase replace the missing segment
restriction endonuclease
enzymes that cut DNA at specific sequences, (leaves sticky ends for recombination in cloning)
recognition sequence
specific base sequences recognized by the endonuclease
sticky ends
staggered cut ends of DNA
hybridization
joining together of two fragments
vector
a segment of DNA used to transfer desired DNA sequence into another cell (often a plasmid or phage)
phage
short for bacteriophage ( a virus that can infect bacteria) ex. think of various hijacking a cell.
plasmid
small circular DNA
gel electrophoresis
lab technique used to separate molecules by size, pulled through agarose gel, charged field, smallest molecules travel furthest down,
PCR
To answer the second question first, to perform PCR one must know ahead of time a specific sequence on the DNA that will be used. Primers are then synthesized that that will anneal with the DNA on either side of the target sequence. Two primers are required, one that is complimentary to the 3’ end of the sense strand and one complimentary to the 3’ end of the antisense strand. The DNA is heated to a temperature sufficiently high to denature the helix (around 95°C). The primers are added along with special DNA polymerases harvested from thermophilic bacteria that live in hot springs (usually Taq Polymerase). The mixture is then cooled to a much lower temperature to allow the primers to anneal (50-65°C). The temperature is then raised again to the optimum temperature range for the thermophilic enzyme (around 72° for Taq Polymerase). The polymerase then copies the DNA, creating two new DNA helices. The temperature is raised again high enough to denature both helices and the entire process is repeated. The number of copies doubles for each cycle.
southern blot
used to verify the presence/absence of a specific DNA sequence, also used to indicate relative size of restriction fragments
northern blot
just like southern blot with with RNA instead of DNA
western blot
same as northern and southern blot, but used on proteins, probes are radio labeled antibodies rather than nucleotide sequences
eastern blot
same as western blot, but used to verify post translational modification, probes are used to bind to lipids, carbs, and phosphates i.e. common post translational modifications
RNA
has a 2prime hydroxy group (DNA only has 5’ and 3’), single stranded, uracil base instead of thumbing, can exit the nucleus
rRNA
makes up ribosomes (ribosomes are assembled in the nucleolus) ribosomes have enzymic activity while a chunk of rRNA alone does not
tRNA
transfer rna is the molecule that bridges between mRNA and the assembled protein, each tRNA has an anticodon on one end and on the other end is covalently bonded to the amino acid associated with the anti codon (codon is complementary to anti codon)
mRNA
messenger RNA, complementary RNA strand copied from the DNA template strand, , pre modified pre-mRNA contains non-coding introns, lacks, poly-A tail, and 5’ cap, when processed it becomes mature mRNA
transcription
RNA polymerase binds to the promoter region with he aid of transcription factors, helices unwinds the DNA forming the transcription bubble, RNA pol reads the template strand 3’ to 5’ creating pre-mRNA transcript with U instead of T, termination factors cause release of the mRNA transcript. post translational processing, large non-coding sequences called introns are sliced out, leaving only eons (the part that actually codes for amino acids), a poly adenosine tail is added to the 3 end along with a 5’ cap for added stability and protection agains degradation until it can be translated in the ribosome
exons
coding sequences that remain in mature mRNA
introns
non-coding spliced sequences
alternative splicing
eons can be assembled in different orders, giving much more variation with much less genes
Lac Operon
Lac operon, an upstream operon that controls the expression of lactase, normally a repressor is bound, needs repressor to get off and cAMP to activate.
when glucose is present and no lactose = repressor is bound, when there is no glucose but lactose = end is transcribed, no glucose and no lactose = no transcription since repressor is bound, glucose and lactose = still no to little transcription occurs as there no repressor, but cAMP activator is low when there is glucose
gene regulation
rate of transcription, activators and repressors, permanent or semi-permanent suppression
rate of transcription
RNA has a short half life so the gene products will only continue to be expressed if DNA is continually transcribed
activators and repressors
regulatory molecules that can upregulate DNA transcription (Lac operon), or down regulate DNA transcription (glucose in Lac operon), these molecules are often hormones, byproducts can build up of gene product is low
permanent/semi-permanent suppression
methylation or other covalent modification that prevents or dramatically decreases transcription
start codon
AUG
stop codons
RNA: UAG, UAA, UGA,
DNA: TAG, TAA, TGA
human genetic code, degenerative and unambiguous
degenerative because specific AA cannot be determined which codon coded for that AA, unambiguous because given a codon there is no ambiguity about which AA it will code for
translation
Translation begins when the small subunit attaches to the mRNA strand at the 5’ end under the influence of various initiation factors. The small subunit scans the mRNA until it reaches the start codon, AUG. The first tRNA, which will always carry methionine and will have the anticodon 3’ UAC 5’ (to complement the start codon 5’ AUG 3’), binds to the start codon along with the large ribosomal subunit (both ribosomal subunits are made up of rRNA plus some protein). The process up to this point is considered initiation. The complete ribosome then begins moving along the mRNA strand from 5’ to 3’. There are aminoacyl (A), peptidyl (P) and exit (E) sites on the ribosome. New tRNA molecules carrying their associated amino acid enter at the A site driven by hydrogen bonding between the anticodon of the tRNA and the codon on the mRNA strand. A peptide bond then forms between the amino acid on the new tRNA and the amino acid on the previous tRNA which sits in the adjacent P site. The new tRNA then shifts over into the P site and the previous tRNA enters the E site, dissociates from the protein and exits the ribosome. Another new tRNA enters the A site and the process repeats. This entire process is called elongation. Finally, at some point the ribosome reaches a codon on the mRNA such as UAG, which is a stop codon. There are no tRNAs that recognize and bind the stop codons. Instead a protein called a release factor binds to the stop codon and causes dissociation of the ribosome complex. This is referred to as termination.
post translational modifications
occur in the endoplasmic reticulum and the golgi, done on polysacchs, lipids and phosphates
translation
occurs in the cytoplasm on free floating ribosomes and on the RER.
mutations
point mutations, missense , neutral, silent, frameshift, and nonsense mutations
point mutations
single basepair substitution
missense mutation
changes codon so a different AA is added
silent mutation
any mutation that does not alter AA sequence, ex. mutations in introns, or mutations that give the same AA as if it was not mutated, etc.
neutral mutation
mutation that does not negatively impact the organism
frameshift mutation
mutation that changes the reading frame either from a deletion or addition,
nonsense mutation
changes a normal codon into a premature stop codon
germ cells
only cells passed on to offspring, gametes, heritable defective DNA
somatic cells
self cells, not passed onto offspring
chromosomal mutations
Duplications(non-disjunction)
Deletions (non-disjunction)
Translocations
Inversions
cancer
uncontrolled cell division due to failure of the cell;s normal regulatory mechanisms
post translational modifications
occur in the endoplasmic reticulum and the golgi, done on polysacchs, lipids and phosphates
translation
occurs in the cytoplasm on free floating ribosomes and on the RER.
mutations
point mutations, missense , neutral, silent, frameshift, and nonsense mutations
point mutations
single basepair substitution
missense mutation
changes codon so a different AA is added
silent mutation
any mutation that does not alter AA sequence, ex. mutations in introns, or mutations that give the same AA as if it was not mutated, etc.
neutral mutation
mutation that does not negatively impact the organism
frameshift mutation
mutation that changes the reading frame either from a deletion or addition,
nonsense mutation
changes a normal codon into a premature stop codon
germ cells
only cells passed on to offspring, gametes, heritable defective DNA
somatic cells
self cells, not passed onto offspring
chromosomal mutations
Duplications(non-disjunction)
Deletions (non-disjunction)
Translocations
Inversions
cancer
uncontrolled cell division due to failure of the cell;s normal regulatory mechanisms
punnett square
always draw it out
benign
tutors that are slowly growing, have not invaded other tissues, could be cancerous later on
metastasis
spreading of cancer from tissue to tissue
proto-oncogenes
good or normal genes, regulate cell division, cell cycle, growth, apoptosis, etc
oncogenes
mutated proto-oncogenes, gain of function gene (dominant, only needs one to become cancerous)
tumor suppressor genes
genes that help protect against uncontrolled growth, loss of function gene (recessive, needs two copies to work)
carcinogens
mutagenic chemicals that can cause or promote cancer
P1
first parental generation
F1
first generation, from P1
F2
second generation, from F1
test cross
crosses double recessive with a dominant or double dominant
law of segregation
Mendel’s law, alleles segregate independently of one another when forming gametes
law of independent assortment
Mendel’s law, genes located on different chromosomes assort independently
punnett square
always draw it out
epigenetic
refers to any heritable phenotype resulting from any process other than a change in the DNA sequence itself. You could think of this as any genetic influence that is “outside” of the DNA sequence itself just as Epi-dermis is on the “outside” of the body (The prefix epi- translates in Greek to mean above, beyond, outside, or near).
Probabilities
BOTH (AND): If both events must occur simultaneously, multiply the probabilities of each event occurring individually.
EITHER (OR): If either event occurring fulfills the requirement, add the probabilities of each event occurring individually.
Important Convention: Homozygous dominant is assumed for an individual with the dominant phenotype. If an individual is a carrier for a recessive allele (heterozygote), or is affected (homozygous recessive), that fact will always be clearly stated. Some questions may ask you to predict the genotype of offspring when you are only given information on one of the parents. By convention, you assume the other parent is NOT affected and is NOT a carrier.
wildtype
normal or typical phenotype
sex linked inheritance
genes on the sex X or Y chromosomes, use punnet square
hemophilia
hemophilia is carried on an X chromosome, it is worse in males as they only have 1 X chromosome, while in females, generally have a good X chromosome to help make up for the bad X
cross hemophilic dad and partially hemophilic mom,
half of sons will have, half do not, both daughters will have, but one is worse than the other
incomplete dominance
is the case in which the phenotypes of the dominant and recessive alleles appear to be mixed or blended in the phenotype of a heterozygote. For example, RR may give red flowers, rr white flowers, but Rr gives pink flowers (rather than the normal dominant- recessive pattern wherein Rr would still produce red flowers).
co- dominance
is the case in which both phenotypes are fully-expressed at the same time in a heterozygote. In the flower example this could mean that RR gives red flowers, rr gives white flowers, and Rr gives red-and- white striped flowers. Blood antigens are a good human-body example. A person with the genotype AB does not have a blend of the A and B antigens, they have BOTH A and B antigens. Incomplete Penetrance is where various individuals all have identical genotypes and yet some get the disease phenotype and others do not.
limited expressivity
is the case in which various
individuals all have the same genotype AND all of them have the disease phenotype (i.e., 100% penetrance), but individuals are impacted in varying degrees.
polygenic
is a case where many genes contribute toward one phenotypic trait.
pleiotropy
is the case where one single gene contributes to multiple phenotypic traits
mosaicism
is the case in which different cells within the same individual contain non-identical genotypes (NOT different alleles for the same gene, but different genotypes. Normally, all cells have the same genotype: Tt, Rr, etc. In this case one cell line may be TT and the other Tt).
genetic imprinting
(a.k.a. Genomic Imprinting) is a case in which one specific gene is expressed differently depending on which parent it originated from.
epigenetic
refers to any heritable phenotype resulting from any process other than a change in the DNA sequence itself. You could think of this as any genetic influence that is “outside” of the DNA sequence itself just as Epi-dermis is on the “outside” of the body (The prefix epi- translates in Greek to mean above, beyond, outside, or near).
linkage
When we say that two genes are linked we mean that they are not assorted independently. In other words, inheriting one gene changes the probability of inheriting the other. When you look at chromosomes and consider that they contain many, many genes, and yet are inherited as a single, whole chromosome, we would expect that all of the genes on a chromosome would be linked. This is not the case due to crossing over. Crossing over between chromosomes during Prophase I of Meiosis happens to such a large extent that it is as if all of the genes were not riding together on chromosomes, but were individual little segments assorted independently and each having an equal and independent probability of landing in one cell or the other. Linkage does occur, however, when two genes are very, very close to each other on the same chromosome because at certain proximity it become unlikely that a crossing over event will occur exactly between them. (ex. any non 9:3:3:1 or 3:1 dihybrid or monohybrid crosses)
gene pool
is the complete set of genes and/or alleles in a population.
evolution
is defined as any change in the gene pool across generations.
polymorphisms
are random variations in genetic sequence among individuals that create variable forms. Polymorphisms are random, usually due to mutation, and may or may not be increasingly represented in future generations depending on whether or not that particular variation in form provides an evolutionary fitness advantage
niche
is the very specific status or role an organism plays in its ecosystem. It can also refer to a specific habitat occupied by one organism with its ecological community.
survival of the fittest
is a term meaning that the individual best suited to its environment will be most likely to survive and pass on its genetic information to future generations.
natural selection
the process by which individuals with genetic traits that provide them with an advantage in terms of interacting with their environment differentially produce more offspring and therefore those traits become more prevalent in subsequent generations
speciation
simply means the formation of new species from existing ones
adaptive radiation
s the rapid formation of a variety of species from one ancestral species—usually characterized by a strong environment-species connection. In other words, if one species of turtle immigrated to five different environments and rapidly formed five different species based on natural selection driven by the unique characteristics of each environment.
evolutionary bottleneck
is a
sudden decrease in the number of individuals in a population.
genetic drift
is a change in the allele frequency within a population due to random, non-genetic, non-selective factors. A bottleneck would be an example of genetic drift because there is no “fitness advantage” or other factor responsible for the change in allele frequency. For example, if a meteorite struck the earth the question of who survived and who did not would not be a question of fitness, it would be a random result of who happened to be in the meteors path. note different from microbiology genetic drift and genetic shift
carrying capacity
is the maximum number of individuals an ecosystem or environment can sustain.
natural selection
one must have a polymorphism that provides an evolutionary fitness advantage, advantage must result in the individual favored polymorphism differentially producing more offspring
divergent evolution
is the process by which species develop different forms and form new species all radiating from a common ancestor. Adaptive radiation is an example of rapid divergent evolution. (basically two different lineages coming from a common ancestor)
convergent evolution
Convergent evolution is when two individuals happen to have the same or similar form, but have arrived at that form from very different evolutionary pathways. The last common ancestor between bats and birds did not have wings, so wings are not part of their shared evolutionary connection. Therefore, it must be convergent evolution. (basically two different lineages developing the same trait without being related, coincidence)
Hardy-Weinberg equilibrium
assume: 1) Large population
2) No mutation
3) No immigration or emigration
4) Random mating
5) No natural selection
H-W formulas
p2 +2pq+q2 =1
p+q=1,
p and q refer to the percentage of each allele present as a fraction of all of the alleles in the population. The term p2 represents the fraction of individuals who have the homozygous dominant genotype (TT). The term q2 represents the fraction of individuals with the homozygous recessive genotype (tt). The term 2pq represents the fraction of individuals with the heterozygous genotype (Tt)
If 90 out of every 1,000 individuals in a population have a recessive phenotype, which of the above terms are known or can be calculated?
All of the variables can be calculated simply by knowing that 90/1,000 individuals have a recessive phenotype. The fraction 90/1,000—by definition—is the term q2. Simplifying 90/1,000 we get 0.09. The square root of this is 0.3 and therefore q = 0.3. Because p + q = 1, p must equal 0.7. We can then calculate 2pg as: (2)(.7)(.3) = 0.42. To find p2 we simply square p: (.7)2 = 0.49. Therefore, 49% of the population have the genotype TT, 42% are Tt, and 9% are tt. From p and q we now that 70% of all alleles are p and 30% of all alleles are q.
taxonomy
kingdom, phylum, class, order, family, genus, species
Provide the name of the group to which humans belong for each of the classification levels listed above. For each classification level note one or two distinguishing features of the members of that group.
Kingdom: Animalia; Phylum: Chordata; Class: Mammalia; Order: Primates; Family: Hominidae; Genus: Homo; Species: Homo sapiens.
how to: taxonomy
Embryology: Often two organisms have similarities that are only present during
embryological development (e.g., human embryos have tails and gill slits).
Phylogeny: A shared evolutionary history can reveal similarities.
Anatomy: Shared anatomy is a reason to classify two organisms more closely.
DNA Sequencing: Comparison of DNA sequences can reveal otherwise hidden connections or help add legitimacy to current classification models.
Fossils: Fossil records often reveal traits that were once shared but have since been lost.
species distinction
Organisms classified as different species should not be able to mate with one another and produce viable, fertile offspring.
fungi
mushrooms, yeasts, molds, heterotrophs, most are saprophytic (live off of dead, decaying matter), but a few are parasitic (live off of live host, often killing it), or mutualistic (symbiotic relationship with living host, as in mycorrhizae—a symbiosis between fungi and plant roots).
chemotrophs
oxidize organic or inorganic compounds to harvest energy.
phototrophs
can capture their own energy directly from the sun via photosynthesis
autotrophs
are capable of

fixing CO2 and can therefore use CO2 as their carbon source for synthesizing organic molecules.
heterotrophs
by contrast cannot fix CO2 and therefore must ingest organic molecules such as carbohydrates as their carbon source.
fungi cell walls
made of chitin
gungal reporoduction
spend most of their life as haploid, Fungi grow via long, intertwining branches called hyphae. Hyphae are haploid and a mass of
hyphae is called a mycelium, yeasts reproduce by budding, fungi can reproduce both sexually and asexually, sexual
symbiosis
mutualism, commensalism, parasitism
spirilla
spiral shaped bac
commensalism
only one benefits, the other is neutral
parasitism
only one benefits, the other is harmed
lichens
materialism between fungi and algae
mycorrhizae
lichen in plant roots
viruses
not a living thing, but hijacks living things, only works when inside another cell, inactive outside of a cell
viral components
some form of nucleic acid (DNA or RNA, but never both) plus proteins. Bacteriophages (viruses that infect bacteria) have a more specific structure, with a capsid head, a tail, tail fibers, etc. (see below). Enveloped viruses such as the cold virus, HIV, etc. are small circular membranes surrounding a protein capsid and the nucleic acid (see below). If the virus is known to be a retrovirus then we know that it must contain a specific enzyme called reverse transcriptase that can translate its RNA nucleotide sequence into DNA (because RNA could not be incorporated into the host’s genome).
lytic cycle
The lytic cycle of a virus is the period during which viral genes are actively being transcribed and new viruses are being assembled. During this phase infected cells eventually burst to release large numbers of new viruses. Examples would be an active cold sore (herpes virus) or AIDS
lysogenic cycle
lysogenic cycle is the dormant cycle of the virus during which time viral DNA is incorporated into the host’s genome but new viruses are not being assembled. This would be equivalent to HIV infection without AIDS symptoms, or to the presence of the herpes virus in the DNA of the host without any present cold sores or other symptoms.
vaccines
A vaccine is an inactivate virus or portion of a virus delivered to a person so that their immune system can develop antibodies against the virus without actually being infected. Upon exposure to the viral proteins, the immune system will create memory B-cells with antibodies that match the viral proteins. If this host is later infected with that virus these B-cells will differentiate into plasma cells that rapidly produce and release antibodies for the virus. Vaccines tend to lose effectiveness over time because viruses mutate at a rate that is faster than any known living thing.
bacteria structure
prokaryote, Capsule, peptidoglycan cell wall, plasma membrane, no complex membrane-bound
organelles, single circular DNA chromosome, tiny circular DNA molecules called plasmids.
bacilli
rod shaped bac
cocci
spherical shaped bac
spirilla
spiral shaped bac
bacteria repoduction
binary fission, no mitosis or meiosis, distribution of extrachromosomal DNA (plasmids) is random and daughter cells may or may not receive a copy, (causes decrease in diversity)
bac diversity
conjugation, transformation, conduction
conjugation
One bacteria must have an F plasmid (F+); the F plasmid is a plasmid containing the gene for a sex pilus. The recipient can be (F-). (note, F+ + F- = 2 F+, Hfr + F- = Hfr + F-
transformation
bacteria pick up DNA from the enviroment
transduction
viruses incorporate host genetic material into their nucleic acids
mitosis
is a complex process coordinated and heavily regulated by a large number of genes and involving intricate interactions between centrioles, spindle fibers (microtubules), centromeres, chromosomes, etc. Absent any errors, mitosis delivers an exact and equal amount of DNA to each new daughter cell.
binary fission
Binary fission is the method employed by prokaryotes and involves none of the items listed above, except for DNA. In binary fission the circular DNA is copied and attached to the membrane. The cell splits, pulling the two copies apart and each daughter cell gets one copy of the chromosome. An important caveat, however, is that prokaryotes contain extrachromosomal DNA (usually circular plasmids). There is no system for segregating this DNA, so each daughter cell may or may not get certain plasmids based solely on random chance.
prokaryotes
Prokaryotes have no nucleus, no complex, membrane-bound organelles, circular DNA, no histones or chromosome structure, and 70S (50S & 30S) ribosomes.
eukaryotes
Eukaryotes have a true nucleus, complex, membrane-bound organelles, linear DNA with histones and chromosome structure, and 80S (60S & 40S) ribosomes. Explain to students that the ribosome measures do not add up (i.e., 50S + 30S ≠ 70S) because they are not directly related to mass or volume, but are sedimentation coefficients derived from the result of centrifuging the ribosomes.
bacterial growth
Bacterial colonies grow exponentially, doubling each generation. However, there is a limit to colony size as food and resources decrease and waste accumulates.
gram positive bac
Stain purple
Very thick cell wall
Form endospores
Single cell membrane
gram negative bac
Stain pink
Relatively thin cell wall and LPS layer
Do NOT form endospores
Contain two (2) cell membranes: one inside the cell wall and one outside the cell wall.
