2013 FHB WEEK 1 Task-oriented Learning Objectives.

FHB-2 Human Evolution (Varki)

LO 2-1. Describe the evolutionary relationships of primates, great apes, hominids, and
hominins.
a. Primates include all of the sub groups mentioned in the question, a subset of primates
are hominids, hominids= hominins + great apes, hominins refer to human beings (perhaps
closely related human species would also be considered hominins). All four groups had a
common ancestor at some point early in history.
b. Primates diverged around 98mya from non-primate mammals.
Examples of primates include prosimians (~67 mya),
new world monkeys (~54 mya),
old world monkeys (~35 mya), and
gibbons (~19 mya).
Hominids (~15 mya) is a classification including orangutans, gorillas, chimpanzees, bonobos,
and humans. To make ourselves feel special, humans call themselves hominins and the other
hominids Great Apes (Apes = lacking a tail).
c. We (hominins) share a common ancestor with the common ancestor of the chimpanzee and
the bonobo (~6-7 mya).

** Another comment:
Humans/ hominins/hominids/great apes/primates = mammals from metazoans in eukaryota
Humans/hominins/hominids/great apes = Old World primates
Humans/great apes = hominids
Humans/hominins = subgroup called great apes among apes within Old World monkeys
subset within Old World primates.
o Great apes = chimps, bonobos, gorillas, orangutans, humans.
o We share LCA with chimp and bonobo.
o Hominins = fossil species that appear after LCA with chimps, includes Ardi. Hominins are
bipedal, which separates them from other hominids.
o Humans = only hominin species left
o Homo = genus that first exhibited brain size increases
o Modern Humans = Homo sapiens

LO 2-2. Contrast the likely time of emergence of a striding bipedal gait (upright walking as some
running) versus sustained running ability in hominins, and list three common examples of
negative medical consequences of bipedalism.
a. 6mya = striding bipedal gait after divergence from chimps /// 2mya = sustained running
ability
i. Low back pains
ii. Spine deformities
iii. Varicose veins
iv. Hernias
v. hemorrhoids
vi. osteoarthritis of knee

b. Striding bipedal gait soon after divergence of chimp and human lineages, i.e., > 6 mya.
Sustained running ability ~2mya. Negative consequences of bipedalism: low back
pains/straights/injuries, spine deformity problems, herniated inter-vertebral discs, varicose veins,
hernias, hemorrhoids, knee join osteoarthritis, obstetric difficulties (narrow pelvis)

LO 2-3. Explain the term cephalo-pelvic disproportion and its medical consequence in Homo
sapiens; briefly explain the major source of the disproportion present in hominins 3 mya that
began this difficulty, and the second disproportion that has increased the difficulty significantly in
modern humans.
a. Refers to the difference between the skull size of infants and the pelvis of the mother
significantly larger brains, As for the medical significance in humans, the disproportion between
the head and the pelvis causes serious problems for mothers and newborns and can cause
death. 3 mya, newborns were able to easily pass through.
b. Babys head is too large for mothers pelvis. More difficult parturition: multiple hours, high
pain, unpredictable delivery time (also: increased variation in gestation period). First change 3
mya was narrowed mothers pelvis, second change was larger baby brain.

LO 2-4. Correlate the most likely time of emergence of large brain size, hunting and meat eating
and use of stone tools with either emergence of bipedal posture or sustained running ability.
a. 300,000 years ago, based off the remains of humans in Ethiopia; 3.4 million years ago
use of tools for meat consumption; stone tools 1.8 million years ago
b. 6 mya: bipedal posture, 5.5 mya: large brain size, 2 mya: sustained running ability, 1.9 mya:
hunting, meat eating, stone tools
c. The most dramatic difference (of the earliest hominins) from the other hominids (Great
Apes) is the emergence of bipedalism (standing upright and walking on two feet) from ~5-7
mya. They could still use their arms to climb and swing through trees as chimpanzees and
bonobos currently do.
Beginning ~ 2-2.5 mya, fossil evidence of Homo, some increase in brain size and beginnings of
the use of stone tools. Approximately 2 mya, there is an emergence of sustained running ability.
Along with this change comes gradual increase in brain size and some increased sophistication in
the complexity of stone tools used - either for hunting or scavenging.

LO 2-5. Name two hominin species that co-existed with modern Homo sapiens.
a. Homo neanderthalensis, and homo floresiensis
b. Neanderthals, Denisovans

LO 2-6. Briefly contrast the usefulness of the US Federal definition of race vs percentage
geographic ancestry in reflecting genetic heredity, and appreciate how this definition of race
might affect disease statistics.
A. African Ancestry ranges from 20-100% African ancestry, white/Caucasians with 30%
estimated to have less than 10% European ancestry
B. The US Federal definition of race is strongly rooted in cultural identification and is much
less reflective of genetic heredity than % geographic ancestry.
c. Official US federal definitions of race are largely subjective and based on cultural self-
identification. Percentage of geographic ancestry has wide variation (20-100% African ancestry
among self-identified Black; estimated 30% of White/Caucasian to have <10% European
ancestry). Thus labels of race are of limited value for their highly imprecise application, which
will skew disease statistics. <= Though the US federal definition of race is unscientific, it can
still (somewhat) help us understand cultural/behavioral influences in disease differences between
races.

LO 2-7. Explain the basis of natural selection, describe the source of most of the common
human diseases and list two reasons the slowness of natural selection contributes to disease.
a. Disease selects for favorable variations as well, natural selection is the driving force that
argues that species with alleles that are successfully passed on will remain in the gene pool,
genes that maximize reproductive fitness will be naturally selected
b. Natural selection is the process by which traits become more or less common because of
conferred reproductive advantage. Most human disease is traits accumulated through natural
selection that have left humans vulnerable . Natural selections slowness because of mismatch
(bodies in novel environments that differs from the one it was selected for) and humans replicate
slowly (pathogens evolve faster).

LO 2-8. List and correct common fallacies concerning the effects of biological evolution on: i)
selection optimizing a species, ii) pathogen evolution, iii) health and longevity, and iv) aging.
a. Natural selection favors reproduction, not optimization of strength etc (only useful if it
helps increase reproductive fitness), pathogens evolve as well to go around immunities, health
and longevity wont be favored for unless they help increase fertility, wont get longer life or
prevent aging unless this helps fertility

1. selection optimizing a species
a. natural selection operates according to survival of the fittest selection only favors
those with high reproductive fitness species evolved through generations in a way such that
those with more reproductive fitness will be the most likely to pass on their genes to the next
generation.
b. selection shapes traits to benefit the speicies natural doesnt have a plan to benefit
or hurt any species.
c. natural selection leads to optimal design natural selection works by adjusting what
is available. once something is lost, you cant get it back
d. imperfections cannot be eliminated b/c natural selection is too weak natural
selection is never over so they always have a chance of being eliminated.
2. pathogen evolution
a. pathogens evolve primarily to co-exist with hosts pathogens evolve to maximize
their reproductive fitness only
3. health and longevity
a. natural selection shapes health and longevity natural selection only shapes
reproductive fitness so health and longevity are only relevant if they contribute to the
reproductive fitness
4. aging
a. aging results only because body parts wear out selection only operates on
reproductive success, not aging.
b. natural selection cannot influence anything after re-production ends this is
generally true, but kin and cultural selection impact humans.
i. There is no plan for optimization. Natural selection is based upon current environment and
cannot be optimized for the future.
ii. Pathogens evolve to increase their replication, not to co-exist with hosts.
iii. Natural selection selects for reproductive success. Any effect on health or longevity is
accidental, unless health/longevity increase reproductive success.
iv. There is no selection for or against aging.
QUESTION: ^ Is this true? I feel like if someone has a longevity trait, they can take
better care of their kids (human babies are pretty hopeless by themselves). The kid, who inherits
the longevity gene, then has a better chance of growing up well and has increased reproductive
fitness. What do you guys think? <-you dont need to be 120 to take care of a baby though, the
idea is that longevity is present - enough longevity. If you are interested in this question, there
are some theories that say there is a tradeoff between cell resources dedicated to haploid vs
diploid cells producing people that are fertile and die younger vs people that live longer and are
less fertile. There are other arguments for death and aging saying that it allows a population to
replenish itself and better meet the environmental needs of the time by having newer generations
exist that replace the old.
Thank you!! what a detailed response! :)


LO 2-9. Briefly explain the genetic basis of human variation in skin color, lactose tolerance and
alcohol intolerance.
a. Mate selection, perhaps survival
1. skin color--> melanin pigmentation cause differences in skin color. these differences are
caused by multiple independent events related to latitudes of where humans lived on earth.
some methods include the fact that sunlight generates vitamin D and sexual selection by mate
choice contributed to skin color variation.
2. lactose tolerance--> based on a combination of cultural factors (mostly found in regions that
drink milk as there was a survival advantage to drinking milk) and multiple independent
mutations that were favorable.
3. alcohol intolerance--> found mostly in the far east. a mutation in alcohol dehydrogenase
was passed down and was possibly favorable to give protection against liver parasites?
Skin color: Genes affecting melanocytes affected by UV, which allows for creation of vitamin D
that destroys folate. Cultural preferences also can have an effect.
Lactase persistence: Conferred advantage among adult milk drinkers in regions with cattle
domestication.
Alcohol intolerance: Genes affecting alcohol dehydrogenase. Unknown mechanism (possibly
protective against liver parasites, drunk folk couldnt make babies haha).

LO 2-10. Briefly describe the hygiene hypothesis and identify one disease correlated
with it.
a. Prior to modern vaccinations, humans were frequently exposed to viral, bacterial, and
parasitic pathogens cleanliness may cause greater prevalence of allergies
b. Increased cleanliness has left microbiomes and immune systems in unnatural state. Allergies,
autoimmune disease, and other processes go awry in absence of pathogens.
Hygiene hypothesis = humans used to always be exposed to pathogens, and recent trend
towards cleanliness increased rates in asthma and allergies because the human immune
system is not fighting as it was supposed to, evidenced by increased incidence of allergies
in more developed societies. Inflammatory bowel diseases risk rises with the number of
antibiotic courses taken (antibiotics keep killing the good bacteria)


LO 2-11. Define the time period of the environment of evolutionary adaptation (EEA)
of humans and contrast human diet during the EEA with modern Western diet.
a. 10,000 (according to slide 58 no citation given in presentation)
b. Environment of evolutionary adaptation (EEA) of humans is the 100,000 year period prior to
Holocene, which is the most recent 10,000 years characterized by stabilized warmer temperature.
Increased spread, agricultural products, and population boom. Diet during EEA consisted of that
which humans could hunt and gather. After the EEA, agricultural products increased (decreased
fruits, nuts, fiber; increased rice, wheat, red meat, milk)
c. The EEA is the period of time prior to 10,000 years ago, when there was no evidence for
agriculture or the establishment of major civilizations. During this time, most humans lived in
small scattered groups or tribes of hunter gathers. The Holocene is the most recent 10,000 year
period that we are currently in and is characterized by an usually stable and warm environment,
which has allowed for agricultural advancements, an increase in meat in our diets, and a decrease
in fruit/nut consumption.

LO 2-12. Identify four diseases correlated with the thrifty gene hypothesis and
briefly explain the evolutionary rationale for this hypothesis.
a. For humans that evolved around (Prior to?) agrarian cycles healthy to crave nutrients,
useful to eat a lot when food was available, we still crave salt, sugar, saturated fat, but these
nutrients are now superabundant in our environment
b. Genetic alleles that encouraged craving/eating fatty foods were adaptive for
increasing reproductive fitness when food supplies were unpredictable. Food is
abundant in modern societies, resulting in high incidence of metabolic syndromes (e.g.,
diabetes), chronic inflammation, and polycystic ovarian disease..
c. Diseases: insulin resistance, diabetes, obesity, heart disease

FHB-3 Cancer Etiology (Millard)
LO 3-1. Use destruction (or not) of normal tissue to distinguish between localized tumor growth by
benign tumors versus tissue invasion by malignant tumors; distinguish tissue invasion from metastasis;
compare and contrast the features of benign tumors, malignant tumors and normal cell growth.
Normal tissues engage in controlled and regulated cell division, a benign tumor grows
unregulated but remains localized and does not spread to other sites; a malignant tumor on the other hand
has the capacity to invade and destroy adjacent structures, this will metastasize - and invade into other
regions of the body, normal cells grow, and die - (like us) (cell cycle - g1, s, g2, m)
Localized tumor growth by benign tumors remains localized. Tissue invasion by malignant
tumors invades and destroys adjacent structures. Metastasis is the discontinuous spread of
cancer from one organ to another non-adjacent organ. Benign tumors, malignant tumors, and
normal cells all undergo the cell cycle; benign and malignant tumors have mutations that cause
their growth to be unchecked (e.g., mutated tumor-suppressor , oncogenes)

Benign Malignant
- stays localized; doesnt infiltrate surrounding
tissues
- invade/destroy other structures
- can be surgically removed - may metastasize
- patient will most likely survive - may lead to death


LO 3-2. Correlate carcinomas, sarcomas, lymphomas and leukemias with the cell type of origin for
each.
carcinomas - malignancy of epithelial cells : cells of the gut, squamous (skin), lung, bladder,
breast
sarcoma: malignancy of mesenchymal cells ; soft tissue, connective tissue, bone
lymphomas and leukemias are malignancies of the cells of the immune system and bone marrow -
lymphoma is of mature WBCs and leukemia is of immature WBCs

LO 3-3. For sporadic cancers (no known inherited predisposition) and cancers with inherited
predisposition:s
inherited cancers refers to inheriting a single mutant gene, autosomal dominant, sporadic cancers
on the other hand - come from external factors such as chemicals, radiation, viruses and bacteria
a. Contrast the frequencies of sporadic cancer versus cancers with inherited predisposition.
according to slide 22, inherited cancers are uncommon (5-10%)
the point i think is: sporadic cancers are far more frequent and inherited only makes up about 5-10% of
cases
Most cancers are sporadic. Inherited predispositions account for 5-10% of cancer. I agree with
black. Inherited forms of cancer make up 5-10% and sporadic 90-95%.

b. Correlate inheritance being single gene versus polygenic for i) inherited cancer syndromes, ii)
syndromes of defective DNA repair, and iii) familial cancers

1. inherited cancer syndromes: inheritance of a single mutant gene, autosomal dominant, rare
2.Syndromes of defective DNA repair: syndromes may be dominant or recessive; best known -
xeroderma pigmentosum -altered nucleotide excision repair; also Hereditary non-polyposis colon cancer
(HNPCC) - altered DNA mismatch repair, chromosomal, DNA instability
3. familial cancers: no specific known gene, complex inheritance, typically early age, tumors in
closely related family members, multiple/bilateral tumors
c. Contrast the features typical of familial cancers versus sporadic cancers
Most cancers are sporadic, inherited forms - 5-10% I thought that familial cancers were largely a
product of faulty repair mechanisms and the sporadic cancers result from DNA/chromosomal damage that
even normal repair mechanisms failed to correct (Familial: early age, tumors in closely related family
members, multiple/bilateral tumors, vs. Sporadic: random)

LO 3-4. Identify the general process(es) common to many pre-neoplastic conditions, and correlate a
specific pre-neoplastic condition with i) endometrial carcinoma, ii) colon carcinoma, iii) liver cancer, and
iv) skin cancer; briefly explain whether or not pre-neoplastic conditions always cause cancer.
1. fatty foods, geography, age, smoking, sex [HPV], sunlight cirrhosis for liver cancer,
endometrial hyperplasia for endometrial carcinoma, chronic ulcerative colitis for colon cancer, and
chronic non-healing skin wounds and skin cancer - these cause increased risk but these cancers can come
even without these preneoplastic conditions
b. Processes associated with excessive cellular division. Increased risk does not mean
inevitability.
i. endometrial carcinoma from endometrial hyperplasia
ii. colon carcinoma from chronic ulcerative colitis
iii. liver cancer from cirrhosis
iv. skin cancer from chronic non-healing skin wounds

LO 3-5. For chemical carcinogenesis:
a. Distinguish between direct acting and indirect acting agents and give an example of each.
direct acting agents - no metabolic conversion : ex chemotherapy drugs.
Indirect acting agents require metabolic conversion to carcinogen - example compounds in
cigarette smoke and burned animal fats
b. Define mutagen and describe the relationship between carcinogens and mutagens.
a mutagen binds to DNA, RNA, and proteins, and changes , chemical carcinogens act as
electrophiles , examples of important mutated genes: p53 guardian of the genome, RAS: signal
transduction protein; DNA damage isnt necessarily random, some carcinogens cause characteristic
mutations - aflatoxin B1 causes specific mutations of p53 (carcinogens have a molecular fingerprint)

Mutagen: agent that changes genetic material & thus increases mutation frequency can be neutral,
beneficial, or harmful
Carcinogen: causes a mutation that leads to cancer, type of mutagen

Mutagens bind to DNA and mutate genes. Most chemical carcinogens are mutagens. --
c. Distinguish between the mechanism of initiators and promoters and their roles in carcinogenesis.
an initiator: causes DNA damage, ex: a carcinogen
a promoter: ex a mitogen - promotes cell division
BOTH ARE REQUIRED FOR CARCINOGENESIS
d. List promoters for head and neck squamous cancers, endometrial cancers and colorectal cancer,
and note which is also considered a pre-neoplastic condition.
head and neck squamous cancers: alcohol (esp w/smoking); endometrial cancers: estrogen; colon
cancer: (high fat diet->lots of bile acids->high risk of colorectal cancer)
e. Name the category (type) of enzymes that most commonly convert indirect acting agents.
polymorphic enzymes ; example on slide 41 - cytochrome p450
LO 3-6. For radiation carcinogenesis: (this LO integrates with FHB Lecture 11 Mutagenesis and
DNA Repair)
a. Describe the mechanism of (damage caused by) ionizing radiation that makes it a mutagen, and
identify the two tissues most sensitive to this mutagenesis and carcinogenesis.
ionizing causes a loss of electrons (energy of the radiation causes electrons to be lost (any physics
people know whats up? H20 -> Hydroxyl radical) , this in turn leads to chromosome breakages,
translocations, and point mutations
lymphoid tissues (leukemia) and thyroid (thyoid cancers, only in young) are most sensitive
according to wikipedia: DNA double-strand breaks (DSBs) are generally accepted to be the most
biologically significant lesion by which ionizing radiation causes cancer.
[4]
In vitro experiments show that
ionizing radiation cause DSBs at a rate of 35 DSBs per cell per Gray,
[5]
and removes a portion of the
epigenetic markers of the DNA,
[6]
which regulate the gene expression
b. Describe the mechanism of (damage caused by) UV radiation damage that makes it a mutagen,
and identify two types of skin cancer associated with UV exposure.
UV causes sun burns (acute damage) and wrinkles (solar elastosis UVB - higher frequency than
UVA, causes a reactive oxygen species, leads to acute skin damage and mutates pyrimidine dimers;
squamous cell carcinoma/basal cell carcinoma and melanoma are two types of skin cancer caused by UV
exposure
UVB causes pyrimidine bases to dimerize. Associated cancers include squamous cell carcinoma,
basal cell carcinoma, and melanoma.
c. Identify the DNA repair system that repairs UV damage, and name the disease cause by an
inherited deficiency of this repair.
Repair takes place through the nucleotide excision repair system - this can detect P53 mutations
after UVB exposure BEFORE tumors (I dont think NER can detect P53 mutations I think P53
mutations are usually a result of pyrimidine dimers..which is caused by UVB damage and NER can
recognize and fix pyrimidine dimers), xeroderma pigmentosum is an example of a disease caused by the
deficiency of this repair system (NER is defective)
LO 3-7. For microbial carcinogenesis:
a. Name a type of benign tumor and a type of cancer associated with certain strains of human
papilloma virus (HPV), describe the mechanism by which high risk HPV causes cancer, and briefly
explain why a Pap smear is the most successful cancer screening test.
warts - low risk version of HPV, cervical cancers- high risk version of HPV; HPV causes cancer
through integrating into the genome in the HIGH RISK type version, high risk HPV integrates through
proteins E6 and E7 (I think it integrates into the genome and then transcribes E6 and E7. I am not sure if
E6 and E7 proteins exist before they integrate into host genome), induces transformation which speeds up
cell proliferation and removes cell cycle checkpoint. The viral DNA initially remains within the nucleus,
but extra-chomosomally. E6 prevents p53 from keeping the cell cycle in check (preventing apoptosis) and
activates telomerase (thus immortalizing the cell). E7 prevents the tumor suppressor Rb from doing its job
of blocking E2F from allowing transcription of DNA replication genes. Both high and low risk HPVs
produce E6 and E7 proteins, but the high risk forms are substantially more effective (have higher
molecular affinities) at doing the damage just mentioned. Pap smears are effective because they detect
characteristic changes in cervical cells BEFORE they become cancerous, this allows for early detection
and intervention
b. Briefly explain the mechanism by which Epstein Barr virus (EBV) promotes B-cell lymphoma.
EBV drives B-cell proliferation, infected cells are transformed; for unlucky individuals, the
infected cells mutate MYC (a regulatory gene) which drives cellular proliferation
c. Name two viruses responsible for over 2/3 of liver cancer.
HBV and HCV
d. Name the bacteria that is the main cause of peptic ulcers and is a carcinogen for gastric carcinoma
H/ Pylori causes inflammation and increased cell turn over in the stomach lining, this in turn
causes an increased risk for lymphoma and gastric carcinoma
LO 3-8. Describe conceptually how the accumulation of mutations in a cell can lead to cancer and how
this correlates with the statement that non-lethal genetic damage lies at the heart of carcinogenesis.
The accumulation of mutations within a cell may eventually interfere with regulatory mechanisms
and control cell division. All you need is a carcinogen (initiator) to cause DNA damage and a mitogen
(promoter) to trigger cell division and you have a cancer. Small damage that by itself is not harmful, over
time as mutations accumulate causes cancer.
Carcinogens must cause enough damage to a cell to alter DNA, but not so much damage that it kills the
cell.

FHB-4 Cell Structure and Function (Novick)
LO 4-1. Identify the plasma membrane, the cytosol and each of the following membrane-bound
organelles on an unlabeled cell diagram and on a unlabeled transmission electron micrograph of a
mammalian cell:
a) endoplasmic reticulum b) Golgi complex c) lysosomes d) mitochondria
e) nucleus f) peroxisomes





For electron transmission - see slide 10, powerpoint 4



LO 4-2. For the membrane bound organelles:
a) List three molecular processes that occur in the nucleus and the route by which proteins and
RNAs move into and out of the nucleus.
Three molecular processes that occur in the nucleus include DNA replication, RNA transcription
and RNA processing (modification after transcription and before being sent out to the cytosol). Proteins
and RNA flux occur through the use of nuclear pores. It is active transport using GTP.
1) DNA replication, 2) RNA transcription and processing, and 3) assembly of ribosomal subunits.
Proteins + RNA leave nucleus by active transport via pores in the nuclear envelope.
b) Name three groups of proteins synthesized on the rough endoplasmic reticulum and briefly
describe the role the Golgi apparatus plays for these proteins.
a. Proteins that are destined to be enzymes in the lysosome, proteins that stay in the plasma
membrane (like receptor structures), and those that are secreted from the cell; the role of the Golgi
apparatus includes modifying, packaging and shipping the proteins.
c) Briefly describe the function of lysosomes and of endosomes.
Lysosomes break down proteins or entire organelles that arent functioning properly and need to
be degraded. Endosomes are membrane bound compartments that often bring what theyre holding to
lysosomes for degradation. Endosomes also sort out endocytosed material that enters the cell.
d) Label two compartments and membranes in a mitochondrion and identify location of the electron
transport chain and the ATP synthase.
The two compartments are the matrix and the intermembrane space. The two membranes are the
outer and inner membranes. The ETC and ATP synthase are found on the inner membrane (large surface
area)
Matrix: site of enzymes involved in basic biochemical pathways (e.g., oxidation of pyruvate,
synthesis of amino acids)
Inner membrane: exaggerated membrane here that is where most ATP is synthesized. Done with
gradients to drive phosphorylation of ADP to ATP. Location of ETC and ATP synthase.
Outer membrane: fairly large pores to allow passage of materials (e.g., ATP)
Intermembrane space: between membranes, enzymes, use ATP to drive other reactions
e) List a function of peroxisomes.
a. Contains peroxidase for the breakdown and production of hydrogen peroxide. Peroxisome also
contains oxygen necessary for the oxidation of toxic molecules
catalyze the production and breakdown of hydrogen peroxide, and are
responsible for the oxidation of long-chain fatty acids

LO 4-3. For the following specialized cell types: i) pancreatic acinar cell, ii) adrenal gland steroid
secreting cell, iii) endothelial cell, iv) skeletal muscle fiber, v) endocytic cells, vi) intestinal epithelial cell,
vii) sperm, viii) red blood cell, be able to:
a) correlate its function with specific specialized structural features, e.g., abundance of specific
organelles, lipid droplets or granules, plasma membrane specializations, cytoskeletal
specializations
b) recognize each cell from a diagram or transmission electron migrograph and label the
specialized features that correlate with its function.
c) identify the specialized cell and its function from a description of the cell features.

i) pancreatic acinar cell- HUGE rough ER and lots of granules containing enzymes to make a
bunch of secretory proteins; recognize the extensive amount of rough ER and the granules
secreting out of the cell; function: secretes a lot of digestive enzymes. The granules congregate
around the duct lumen (site of secretion). Has a kind of funnel shape, and distinct Golgi
complexes on the side of the nucleus facing the excretory site.
ii) adrenal gland steroid secreting cell- lots of smooth ER and lipid droplets; the lipid droplets
look like theyre spread out throughout the cell (unlike the granules in secretory cells which
tend to congregate on the excretory end). More mitochondria than the pancreatic acinar cell,
more square shape (probably due to lack of a designated excretory site).
iii) endothelial cell - stretched out with a squished nucleus, also has a space in the middle;
recognize the big space in the middle; transcytosis occurs (when materials are taken up and
carried across the epithelial layer; so basically endocytosis + exocytosis)
iv) muscle cells - lots of MITOCHONDRIA and lipid droplets, which provide ATP for
continuous contractile motions. Very organized spindles, looks sort of like a woven table
setting you put plates and stuff on. :) love this comment
v) endocytic structures - clathrin coated pits, lots of lysosomes and endosomes
vi) intestinal epithelial cell - look for the microvilli, which maximizes surface area and absorption
vii) sperm - lots of mitochondria that line the midpiece; long flagella specialized for motility
viii) red blood cell - no internal organelles; look like donuts (im hungry); carries oxygen;
basically a sack of hemoglobin


LO 4-4. For intestinal wall tissue and tracheal wall tissue:
a. Identify epithelial cells, endothelial cells, and muscle within a diagram or microscopic image
epithelial cells line cavities/structures; form glands. Epithelial cells are simple columnar, non-
ciliated <- they can be ciliated, right? ex: trachea
endothelial cells: lines the interior of blood vessels.
muscle cells: highly striated; organized. Smooth muscle cells = circular fibers + longitudinal
fibers.
b. Describe the contribution of each cell type to intestinal or tracheal function
Intestine: epithelium promotes absorption
Trachea: ciliated to help clear particles, goblet cells to secrete mucous

c. Identify and correlate cilia and microvilli with the appropriate cell types in each tissue.
cillia are small structures, for example in the cells of the tracheal that help brush off mucous and
dirt out of the lungs, microvilli increases surface area of the membrane of the cell, allowing for greater
ability to absorb material


LO 4-5. Identify the organelle whose dysfunction in neurons results in in Tay Sachs disease, name the
specific enzyme deficiency and the enzyme substrate whose accumulation results in brain damage.

lysosomal storage causes all the problems! due to mutations in a single lysosomal enzyme that leads to
the accumulation of substrate in lysosomes (its not digestiHJLon quickly enough); more specifically this
is a mutation in hexosaminidase (abbreviated hexA) - which breaks down GM2 gangliosides - which are
abundant in the brain ; cells unable to break down gangliosides accumulate and no longer function
correctly

FHB-5 Chromosomes and DNA (Holm)
LO 5-1. Identify the feature that distinguishes purine from pyrimidine nucleotides and identify the purine
and pyrimidine nucleotides in the diagrams at right; for any one nucleotide: i) label the sugar and its ring
oxygen, ii) label each sugar carbon by number, iii) identify the carbon and chemical group that would
distinguish deoxynucleotides from ribonucleotides, iv) label the phosphate group, and v) label the 3 and
5 ends of the nucleotide.

Purine: so pure that it has TWO purity rings; pyrimidine - a pyramid only has ONE ring base




so the first two are pyrimidines, the second two are purines; the presence of oxygen on carbon 2
determines whether or not this is DNA (no oxygen) or RNA (with oxygen); the 5 refers to the carbon
number,
5 is the phosphate end on the 5th carbon, 3 is the OH on the 3rd carbon

LO 5-2. List a base pair with three hydrogen bonds in DNA and in RNA; list a base pair with two
hydrogen bonds in DNA and in RNA. 3 H-bonds -> C and G, 2 H-bonds -> A and T
LO 5-3. List a difference between DNA and RNA in their polymeric structure, in their sugars and in their
bases. RNA is single-stranded and folds back on itself, has ribose, and uses A, U, G, and C. DNA is
double-stranded and is neatly wound, has deoxyribose, and uses A, T, G, and C.
LO 5-4. Describe the chemical groups on each of two deoxynucleotide triphosphates involved in the
formation of a phosphodiester bond (to form a dinucleotide). phosphodiester bond forms between 5-
phosphate and 3-OH
LO 5-5. Describe the role of antiparallel strands and base complementarity in a double-stranded DNA
helix and in the local helical regions of single-stranded RNA that form when the RNA folds back on
itself.
DNA can undergo reversible strand separation; complementary bases allow each nucleotide to
have a particular match - this keeps the two strands highly organized and thermodynamically stable with
one another ; this could allow organized packing of DNA/RNA material
from Wiki: RNAs often contain self-complementary sequences that allow them to fold back on
themselves and form helices
A helix keeps the hydrophilic sugar phosphate backbone in contact with water where they can H-bond,
and the hydrophobic bases sequestered to inside, hydrophobically bonded to each other.
- A nucleic acid helix is formed when 2 antiparallel and complementary nucleic acid strands
form hydrogen bonds (H-bonds) between their nucleotide bases.
- Complementary is determined by the chemical structures of the bases.
- In order to create a double helix, the two strands must be antiparallel.
LO 5-6. On an unlabeled outline diagram of DNA that uses the same nucleotide structures as in LO 5-1:
a) label a bond: i) formed by a polymerase, ii) broken by a helicase, and iii) broken by a
glycosidase.
- Polymerase forms phosphodiester bonds
- Helicase breaks H-bonds
- Glycosidase breaks N-glycosidic linkages (causing an apurinic/apyrimidic state) N-glycosidic linkage:
the bond between carbon 1 of the sugar and the N of the nucleotide base
b) label the 5 and 3 end of each strand and explain the feature that identifies each, the carbon
number identifies the 5 and 3 of each strand, on the 5 carbon, bound to phosphate groups
while the 3 is bound to a hydroxyl.
c) identify the DNA sequence of each strand based on base size and hydrogen bonds between base
pairs (remember three H bonds - GC, two H bonds, AT); two rings - purine, one ring - pyrimidine
LO 5-7. List Chargaffs four rules of DNA base composition and briefly explain the rationale for each;
apply these rules in the analysis of experimental base composition data.
Chargaffs Rules
1. Base composition varies between species; 2 .DNA from different tissues of same species has
the same composition; 3. Base composition does not change as a function of age, nutrition, environment
(unless mutations occur right?); 4. regardless of species, A=T, G=C, purines = pyrimidines. (P A G -
purple and green are PURE colors (though they arent), AG - Purines; ) (Pyrimids are CT, remember -
pyrimids are in Cairo and are Towers) - these pneumonics may help, if they confuse, sorry
Or purines = Pure As Gold
LO 5-8. Briefly explain the cause of DNA supercoiling and describe the basic function of topoisomerases;
list a clinical use for inhibitors of i) eukaryotic topoisomerases, and ii) prokaryotic topoisomerases
(gyrase), and provide a brief rationale for each clinical use.
DNA supercoiling is caused by a protein latching on the DNA strand, causes coils that hinder
opening of DNA in positive supercoiling and facilitate helix opening in negative supercoiling both
take place when the protein molecule interacts with the DNA, this allows long DNA to be packaged and
organized
topoisomerases are enzymes that undo supercoils,
i) eukaryotic topoisomerase: clinical intuition is that it stops DNA from being coiled, this in turn
interferes with the cell cycle (chemotherapeutics)

ii) prokaryotic topoisomerase: bacterial DNA gyrase - topoisomerase inhibited by Ciproflaxin
LO 5-9. Recognize the centromere and telomeres on a simple chromosome diagram, and describe the
basic functions of centromeres and telomeres.
Telos - Greek word for end, (if any of you have studied Artistotle, may we reach the proper telos
of human life -to be virtuous beings!)(thanks for that awesome reference); telomeres are on the ends of
the DNA strands, centromeres are in the center - more importantly they are the attachment point for the
mitotic spindle
telomeres deter the degradation of genes near the ends of chromosomes by allowing chromosome ends to
shorten (without telomeres, genomes would progressively shorten and lose information after cell
division)

LO 5-10. Describe the components and structural features of a nucleosome; define chromatin; describe
euchromatin and heterochromatin and the potential for transcription of genes within each form.
nucleosome: structural unit of chromosome in Eukaryotes, DNA wound around 8 histone protein
cores; two tetramers of histones. Chromatin is a complex of DNA, histones, and proteins; Euchromatin
(30 nm) - region of chromosome that is less compact and more likely to be transcriptionally active,
heterochromatin (300 nm) - region of chromosome that remains in the form of extremely condensed
chromatin - usually transcriptionally inactive
fun fact: chromatin structure is usually inherited when cell divides (epigenetics!) -> only after mitosis,
but not after meiosis! (germ cells do not usually show epigenetic modifications)

LO 5-11. Of 2 nm, 11 nm, 30 nm, 300 nm and 700 nm, indicate the size category that best
corresponds to/is the most common or prominent size category for: a) beads on a
string chromatin, b) chromatin during mitosis, c) chromatin containing loops in an
extended form, d) chromatin with nucleosomes but no other protein, e) DNA with no
protein, and f) unperturbed euchromatin.
short region of DNA double helix: 2nm, beads on a string chromatin: roughly 11nm; chromatin
fiber of backed nucleosomes - 30nm (during mitosis?), section of chromatin in extended form -
300nm, condensed section of chromosome - 700nm, entire mitotic chromosome:1400nm

a. beads on a string chromatin
- 11 nm
b. chromatin during mitosis
- 1400 nm ?? - I dont think this is the one. Not one of the options in the question.
700 nm - present only during mitosis or meiosis
c. chromatin containing loops in an extended form
- 300 nm
d. chromatin with nucleosomes but no other protein
- 11 nm (30 nm fiber requires Histone H1) but arent histones part of nucleosomes!? Yes,
but different histones. Histones H2A, H2B, H3, and H4 are the four histones that form the
two tetramers used in constructing nucleosomes. H1 is a fifth kind of histone that
specializes in forming the 30nm fibers of condensed nucleosomes.
Reason: When chromatin is treated to remove all proteins except the nucleosomes, a
characteristic beads on a string morphology is observed (11 nm) - (source: one of the last
slides that Dr. Holm did not cover) - Histone H1 is NOT a part of the nucleosome complex

e. DNA with no protein
- 2 nm
f. unperturbed euchromatin
- 700 nm?? - i dont think this is the one
from a slide: In the unperturbed state, non-histone and histone proteins in the
chromatin pack together in a coil, forming a 30nm fiber
im pretty sure 700 in the figure is just showing half of a mitotic chromosome.
700x2=1400nm (pg 187 of cell bio book)


LO 5-12. Contrast the features of epigenetic and genetic heritability, and describe: i) an
epigenetic modification of DNA and ii) epigenetic modifications of nucleosome proteins.
epigenetic: hertiable traits that are controlled by chromatin structure or composition; these are commonly
passed through mitosis BUT not through meiosis (epigenetics works in SOMATIC cell division, but not
GERM cell division); note epigenetic changes do not alter the DNA sequence
i) epigenetic modification of DNA: not changing DNA sequence, but adding methyl to C or A locks
genes in off position
ii) epigenetic modification of nucleosome proteins (histones):
a) acetylation of histone lysine: association with euchromatin (loosened chromatin increased
access to DNA) b/c it weakens the charge attraction between histone protein and DNA, enabling it to
decondense and increase transcription
b) methylation of histone: can be repressive OR (less commonly) activating

FHB-6 Control of Transcription (Glass)
LO 6-1. Review LO 5-10 and 5-11, name the complexes that decondense (reposition)
nucleosomes in 11 nm chromatin, list their energy source, and predict their effect on gene
transcription.
Chromatin remodeling complexes reposition the nucleosomes using ATP as an energy
source. These proteins would increase gene transcription by loosening up chromatin structure,
allowing transcription factors, RNA pol II, etc. to bind DNA and begin transcription.
DNA wraps around 4 pairs of nucelosomes organized into a octamer this repositions the DNA
into the 11nm form (beads on a string); packages and organizes DNA for mitotic replication,
energy source:ATP

LO 6-2. Correlate histone acetylation and deacetylation with gene expression level
(increased/decreased); name the histone modification associated with gene silencing and
heterochromatin formation; briefly explain the role of reader and effector proteins in these
types of regulation of gene expression.
Histone acetylation = increased gene expression
Histone deacetylation = decreased gene expression
methylation: triggers gene silencing
methylation AND acetylation: triggers gene expression
phosphorylation AND acetylation: triggers gene expression
Histone is modified, reader and effector proteins carry out biological effect: silencing,
expression etc

reader and effector proteins: the code reader complex binds to specific histone modifications
on nucleosome - this triggers a covalent modification on the histone tail; this in turn attracts
other components: the effector protein then binds and allows for additional catalytic activites
and binding sites - the net result: this interactions lead to gene expression/gene silencing/ or
other biological functions

LO 6-3. Review LO 5-3 and correlate the eukaryotic RNA Polymerases I, II and III with
synthesis of their appropriate RNA products (tRNAs, rRNAs, mRNAs and miRNAs).
RNA polymerase I: transcribes most rRNA genes (what the hell is rRNA you ask? they
form the core of the ribosome and catalyze protein synthesis)
RNA polymerase II: transcribe mRNA, miRNA genes, plus genes for some small RNAs
(ex - those in spliceosomes); (miRNA regulate gene expression)
RNA polymerase III: transcribe tRNA genes, 5S rRNA gene, genes for many other small
RNAs (tRNA serve as adaptors between mRNA and amino acids during protein synthesis); (the
other small RNA are used in splicing, telomere maintenance, and many other processes)

LO 6-4. For Pol II transcription of mRNA, name the:
a. category of transcription factors that form the initiation complex with Pol II and the DNA sequence
on which the initiation complex forms
Binding of the core transcription factor, TFIID, to the TATAAA core promoter sequence is rate-
limiting for complex formation in many Pol II-transcribed genes.
(core/general transcription factors?)acet
b. category of transcription factors required for regulation of mRNA transcription and the category of
DNA sequences to which they bind
The rate of gene transcription in differentiated cells is regulated by transcriptional activator and
transcriptional repressor proteins that act on genes within 30 nm euchromatin
<- where was this found?
regulatory elements LECT6.24-25 shows some regulatory elements
There are also regions upstream of promoter sites where transcriptional factors can modify
histones and binding ability. These sites can be 1000s of bp away, but are different and not
necessarily in every kind of cell.
(sequence-specific/regulatory transcription factors?)
c. type of transcription factor that binds to an enhancer and its effect mRNA initiation,
-Each enhancer sequence contains a combination of binding sites specific for certain
transcriptional activators. The effect of an enhancer can have a very different function in two
different types of cells. It may enhance gene transcription in the liver, but not necessarily in the lung. Also
enhancers tend to affect transcription in a position and distance independent manner. Insulators act to
restrict area of influence of enhancers
.
d. type of transcription factor that binds to a silencer and its effect on mRNA initiation.
- Each silencer sequence contains a combination of transcriptional repressor binding sites.
LO 6-4. In the formation of the initiation complex for mRNA transcription, briefly explain potential roles
for:
core transcription factors: allow initiation complex formation which causes Pol II to begin
transcription at +13
enhancers: allow transcriptional activators to recruit co-activators to loosen chromatin
structure or recruit/stabilize the initiation complex
histone acetylating complexes: loosens the nucleosome packaging to help unfold 30 nm to 10
nm chromatin and increase access of other transcriptional activators and core transcription factors
to their binding sites
nucleosome remodeling complexes: slide nucleosomes within chromatin: nucleosome
remodeling co-repressors hydrolyze ATP to tighten nucleosomes and increase
nucleosome frequency in reg sequences -> dec TA and TF access
Pol II: core TFs bind to the DNA and to Pol II to allow complex formation

sequence-specific transcriptional activators: recruits co-activators to loosen chromatin
structure or recruit/stabilize the initiation complex
promoter: sequence on which the initiation complex assembles


LO 6-5. Using histone acetylating complexes and nucleosome remodeling complexees and
the description of the glucocorticoid receptor, describe a specific sequence by which cortisol (a
glucocorticoid) could increase expression of a liver cell enzyme.
a. Introns are typically significantly longer than exons,
b. Steroid hormones, glucocorticoids all act on ligand activated transcriptional activators, the binding of
the ligand of the hormone to the repressor changes its conformation it binds to a specific sequence (gene
specific)
Steroid hormones, e.g., estrogen, testosterone (slide 4) and glucocorticoids (slide 33), bind to nuclear
receptors (slide 31). Hormone binding activates the receptaror to act as sequence-specific transcription
factor by binding to specific enhancer sequences (slide 24) within certain genes and increasing
transcription of the gene (slide 33). Two important mechanisms by which transcription initiation can be
increased are by recruiting nucleosome remodeling complexes to reposition (decondense) nucleosomes
within the chromatin (slide 9) or by recruiting proteins to modify histones to increase gene expression,
e.g., histone acetylating enzymes (slide 11). So the cortisol-receptor complex is likely to recruit one or
both of these types of complexes to increase gene expression. (Aprils answer to Dr. Glasss question at
the end of lecture that fits perfectly for this question)


LO 6-6. Define cell differentiation; integrating with LO 5-13, briefly explain why
differentiation of specialized cell types during development must be mediated by combinations
of transcription factors exerting epigenetic regulation, and cannot be mediated by changes in
DNA sequences.
Epigenetic regulation of transcription initiation provides the mechanisms by which
certain genes can be silenced even through changing conditions or mitosis, and so
provides the mechanism for differentiation.

All cells in an individual share the same genes, so the mechanism of cell differentiation must
determine which genes are expressed in a given cell without changing the DNA sequence, and be
reproduced after DNA replication so kidney cells divide to generate kidney cells, etc

Cell differentiation is the process by which a cell becomes specialized into a particular cell type.
Differentiation must be mediated by combinations of TFs exerting epigenetic regulation (and not
changes in DNA sequences) because all cells of an individual contain the same DNA sequence.
The different cell types arise from differential transcription of the same genome. Thus,
epigenetic modifications that increase/decrease different gene products will determine the cell
type.

LO 6-7. Name the specific nucleotide modification meant by DNA methylation, and:
Methylation of DNA nucleotides in the gene promoter specifically methylating Cs of
CpG dinucleotides prevents gene transcription and promotes folding into heterochromatin
Cytosine 5-methylcytosine
a. diagram the double-stranded DNA helix containing the sequence: 5 ACGTACCTCGT3 and label
the nucleotides in each strand potentially be targeted by DNA methylases for epigenetic regulation
5 - CG - 3=methylation target
5 ACGTACCTCGT 3
3 TGCATGGAGCA 5
Cs that are on the 5 side of Gs get methylated
b. propose how sequence-specific transcriptional activators and de novo DNA methylases could result
in decreased transcription of a specific gene
-TAs and TRs can recruit co-activators and co-repressors that express the complex
activities that regulate initiation of transcription.
-de novo DNA N-methyl transferases (DNMTs) methylates DNA nucleotides, DNA
methylation is an important means of supressing a gene
The binding of gene regulatory proteins and sequence-specific transcriptional activators
near an active promoter may prevent DNA methylation by excluding de novo
methylases. The loss of these gene regulatory proteins would turn the gene off but
leaky (decrease transcription) loss would also enable de novo DNA methylation
enables other proteins to bind these shut down the gene completely by further
altering chromatin structure (greater decrease in transcription).
c. briefly explain how maintenance methyltransferases (DNA methylases) allow this epigenetic
modification to be maintained after cell division.
-DNA methylation enables other proteins to bind, and these shut down the gene
completely by further altering chromatin structure.
DNA methylation patterns can be faithfully inherited. An enzyme called a maintenance
methyltransferase guarantees that once a pattern of DNA methylation has been
established, it is inherited by progeny DNA. Immediately after replication, each daughter
helix will contain one methylated DNA strand, inherited from the parent helix, and one
unmethylated, newly synthesized strand. The maintenance methyltransferase interacts
with these hybrid helices, where it methylates only those CG sequences that are base-
paired with a CG seq that is already methylated.
d. briefly explain how DNA methylation can lead to gene silencing
-Methylation of DNA nucleotides in the gene promoter specifically methylating Cs of CpG
dinucleotides prevents gene transcription and promotes folding into heterochromatin.
-Dimethylation and trimethylation of histones in the nucleosomes in the regulatory sequences of
a gene prevents gene transcription and promotes folding into heterochromatin.

Integrative application LOs:
LO 6-8.
On the diagram of a typical eukaryotic protein-coding gene below, the arrow indicates the start and
direction of mRNA transcription and the darkest grey boxes are exons:
a. label 5 and 3 ends of each DNA strand, label the template DNA strand read by Pol II,
and label the coding DNA strand (complementary to the template strand),
b. label the location of the promoter and the stop transcription sequence
c. number the exons (E1, E2, etc.) and introns (I1, I2, etc.)
d. indicate two different likely locations for an enhancer and for a silencer.
1
Each gene contains a combination of enhancer and silencer sequences near its core promoter.
Exons are gray, introns are white.

LO 6-9. For a mutation deleting a) an enhancer, b) a promoter and c) a silencer, predict the effect of the
mutation (increase, decrease, no change) on: i) the amount of gene-specific mRNA, ii) the length
of the gene-specific mRNA, iii) the amount of the protein product, and iv) the amino acid
sequence of the protein product.


-Deletion or inactivation of the core promoter prevents mRNA transcription
-Mutations in enhancers or silencers change mRNA levels (and therefore protein levels) with
no change in mRNA sequence, and so no change in protein sequence.



LO 6-10.Provide a possible mechanism by which i) DNA methylation can silence gene transcription and
ii) accidental DNA methylation of a tumor suppressor gene (e.g., the protein needed for
p53-mediated apoptosis) could occur and contribute to cancer development.

DNA methylation prevents gene transcription and promotes folding into
heterochromatin thereby silencing gene transcription. Accidental methylation could
silence cancer repressor gene.
Propagation of DNA methylation extends the range of silenced DNA (an unmethylated DNA region can
become methylated due to neighboring DNA methylation) and the new DNA methylation state is
inherited if the region was a tumor suppressor gene, it is now silenced can lead to cancer (see slide
40).

FHB-7 Histology Lab 1 for MS1s (Calcutt) these will be posted in a separate file later in
Week 1.

FHB 8 - mRNA processing and miRNAs (Spector) Post Translation Modification
LO 8-1. List three major processes that modify the transcribed mRNA into its mature form and
briefly describe how each affects the structure of the mature mRNA.


1) 5 Cap- allows binding of cap proteins in initiation of translation, facilitates transport and
protects mRNA from degradation in cytosol
5 end of GTP is attached to the 5 end of the mRNA transcript by guanyltransferase
first few nucleotides (including GTP at N7) are methylated by guanine methyltransferase.
2) Poly A tail (Polyadenylation)- protects mRNA from degradation in cytosol, facilitates
transport, and aids in translation initiation
Poly A Polymerase (PAP) adds 40-250 adenosine nucleotides onto the transcribed
mRNA and Poly A Binding Proteins (PBPs) bind the poly-A-tail.
3) Splicing- removes introns and joins exons which forms mRNA, template for translation

LO 8-2. For the polyadenylation (pA or polyA) sequence, the polyA tail and the 5 cap:
a) identify each as a DNA sequence in the gene that is also transcribed into the
mRNA versus being present only in mature mRNA

pA has the sequence AATAAA in DNA and this sequence is also present in mRNA.
However, polyA sequence (AAAAA.) is only present in mRNA because
polyadenylation enzyme recognizes AAUAAA from the RNA and polymerizes the RNA.
5 cap DNA sequence is that of exon 1 and is present in both.

- polyadenylation sequence (AAUAAA and U/GU-rich sequence) DNA sequence
in gene that is also transcribed into the mRNA
- polyA tail only present in mature mRNA
- 5 cap only present in mature mRNA

b) briefly describe the role of each (if any) in transcription termination and initiation of
mRNA translation

Both 5 cap and polyA tail are critical for initiation of translation. pA sequence signals
termination of transcription. (is this supposed to say termination of translation? No,
stop codon = termination of translation)-pA sequence is made during initial
transcription of mRNA and is at the 3 end, or termination of transcription. The polyA
tail helps stabilize and facilitate transport of the mature mRNA and facilitates the
initiation of translation.

c) briefly explain why loss of the only pA sequence in a gene is likely to result in less
protein being made and why loss of the 5 cap would have a similar effect.
If there is a loss of the poly A tail, it will be degraded losing the 5 cap would
also cause the mRNA to be degraded quickly

Losing the pA sequence would result in the loss of the polyA tail and thus much of the
mRNA would be not be translated. The same would be true for the loss of the 5 cap.



LO 8-3. Define intron and exon, explain why the number of exons in a genes coding sequence
(transcription start site to last pA sequence) always equals the (number of introns + 1); name the complex
that mediates mRNA splicing and the two types of macromolecules that make up each of its subunits
(snRNPs).

Intron = intervening sequence
Exon = expressed sequence
The first and last sequences of an mRNA are exons and the space between them is filled with introns, so
#exons=#introns+1. The complex that mediates splicing is the spliceosome and is made up of snRNAs
(snRNPs?) and (SR?) proteins.


LO 8-4.
The diagram at right depicts two exons (grey boxes) and a single intron within a gene.
a) Label the location of the two invariant nucleotides of the 5 splice site (5SS) and the 3
splice site (3SS) in the gene and briefly explain why none of the invariant splice site s say
nucleotides are present in mature mRNA. They just want you to know that the splice sites are
located in the intron. 5 GU---A---AG 3 of intron allows for recognition by spliceosome
(what are they asking here?)
b) Briefly explain how the snRNPs identify each splice site. the GU signal at the 5 end after
the first exon and the AG site at the 3 end before the next exon indicates splicing sites.
LO 8-5. Briefly explain how phosphorylation of the CTD tail of Pol II ensures that unregulated splicing
occurs sequentially from the first intron to the last intron of the mRNA.

Phosphorylation of CTD tail of Pol II allows processing proteins to bind and affect the growing mRNA
transcript as it is transcribed. This ensures that introns are removed in the correct order.

LO 8-6. Briefly explain why detecting two different lengths of mRNA that each contain sequences
complementary to a particular gene indicates alternative processing of that gene, and how alternative
processing increases the diversity of proteins produced from the genome.
multiple combos of splice acceptors and donors, increase coding potential because one primary mRNA
can give rise to many different mRNAs

LO 8-7. Note which of the following characterize miRNAs, siRNAs, both or neither: i) code for very
short proteins- neither ii) decrease expression of certain genes-both, iii) increase expression of certain
genes-neither (not certain, but didnt see anything in lectures about increasing expression from miRNAs
or siRNAs), iv) are processed from a single-stranded precursor transcribed by RNA Pol II- miRNA v) are
processed into an RNA duplex 20 nt long,-both vi) exert activity as a single stranded RNA in a protein
complex- both?, vii) exert activity as a double-stranded RNA duplex none, viii) target mRNAs through
hybridization both.
ii) describes miRNAs and siRNAs. The main difference being that miRNAs inhibit translation of proteins
by binding to mRNAs and making them inaccessible to translational machinery, and siRNAs bring in
proteins that modify the chromatin, making transcription less likely. I do not believe that is accurate. My
understanding is that miRNA and siRNAs function in the same way (sterically blocking translation or
marking RNA for degradation). The difference lies in the way they are manufactured.
Si RNA is seen more in plants.LOLLL

LO 8-8. Name two mechanisms by which miRNAs are known to inhibit gene expression.
i thought the two mechanisms were either degradation due to perfect miRNA binding to mRNA or
blocking of poly A tail associating with the ribosomal subunit so no translation could occur. theyre
already transcribed so i dont remember there being any change any chromatin structure.

miRNA
Mech1 mRNA with proteins form RISC Block
translation of mRNA
Mech2 Change chromatin structure


I believe the answers here are: 1 - high homology mRNA degradation or 2 - partial homology mRNA
translation inhibition (see slide 33)

I believe my friend in blue is correct. If I remember correctly, both miRNAs and siRNAs form RISC
complexes, which can block or degrade mRNAs, but only siRNAs are capable of forming RITS
complexes, which modify chromatin structure to decrease gene expression

Integrative application LOs:
LO 8-9. Label on the typical eukaryotic gene diagrammed below: the promoter, an enhancer, a silencer,
the polyadenylation signal sequence (pA), the number of each exon and intron (E-1, I-1, E-2, etc.), each
5 splice site (5SS), and each 3 splice site (3SS). Using the same scale:
a) diagram the pre-mRNA below the gene as if it were transcribed fully prior to splicing; use
arrows or lines to indicate the sequences that will be spliced out.
b) diagram the mature mRNA below the pre-mRNA
c) label all sequences remaining in the mRNA and any added during transcription.


LO 8-10. Using the gene diagrammed below, predict the specific exon and/or intron sequences
that will be present in the mature mRNA under each of the following conditions:


a) Normal splicing pattern in a cell with polyA factors that dont recognize the 1st pA.
you will get a mature mRNA with e1,e2,e3,e4
b) Normal splicing pattern in a cell with polyA factors that do recognize the 1
st
pA.
you will get a mature mRNA with e1,e2,e3
c) Mutant gene lacking the 5SS at the beginning of intron 2 in a cell with polyA factors that
recognize the 1st pA; does this mutation lengthen or shorten the mRNA?
it will lengthen the mature mRNA. you will get e1,e2,i2,e3
d) Mutant gene lacking the 3SS at the end of intron 1 in a cell with polyA factors that dont
recognize the 1st pA; does this mutation lengthen or shorten the mRNA?
it will shorten the mature mRNA. you will get two strands (?). first strand will be e1. then you
will get i1,e2,e3,e4. I thought it would just treat I1E2I2 as one intron then because it will still
recognize the I2 3splice site which is stop sequence? (I dont know that splicing will occur at
all at the I1 3SS because it seems to need both the 5SS and the 3SS for any splicing to
occur?)
E1-I1-E2-E3-E4 (Since it lacks the 3SS in I1, I1 will be included in the mRNA transcript. Also,
since pA1 is not recognized, transcription will not stop until pA2 is recognized no?)
Lengthens.So whats the concensus here? I think it might actually be E1-E3-E4 because the
spliceosome at the 5 splice site of I1 would just find the 3 splice site at the end of I2 and cut
out I1, E2, and I2. Just to add my two cents, its definitely the last, underlined option. The 5SS
will be recognized by the splicesosome and then it will find the next working 3SS (which will be
in I2) and cut out everything inbetween. You have just E1, E3, E4 so it shortens the mRNA
(which is the opposite effect of a mutation in the 5SS which would lengthen the mRNA like in
part c). yep its the last.
e) Briefly explain why a mutant of this gene that lacks pA1 would likely express a protein
product, while little or no gene product would be expected from a mutant gene that lacks any
pA sequence (see slide 12 on alpha-thalassemia).
When pA1 is lacking the pA2 could be recognized and the larger protein could be translated
from the mRNA transcript. If NO pA sites were recognized there would be no defined end for
the mRNA to have a polyAtail and the pre-mRNA transcript would likely be degraded
LO 8-11. Alternative mRNA processing is mediated by splice regulatory proteins that bind to
sequences in the mRNA and either prevent recognition of the nearby splice site (splice
silencers) or promote recognition of a nearby weak splice site (splice enhancers). For a gene
that contains 5 exons and is usually expressed as an mRNA with those 5 exons, explain whether
the optional mRNA described is due to: i) silencing a 5 SS, ii) silencing a 3SS, iii)
enhancing a 5 SS, or enhancing a 3 SS.
a) In one cell type, this gene is expressed as an optional mRNA with only exons 1, 2, 4
and 5 (not 3).
Silencing a 3SS at the end of intron 2
Silencing a 5SS at the beginning of intron 3 (Im not 100% sure but this is what I think) No,
silencing a 5SS would just keep intron 3 in the mRNA; it wouldnt affect exon 3 because its
already past that point. Its only a splice silencer that silences the 3SS end of intron 2.
b) In one cell type, this gene is expressed as an optional mRNA that includes what is
normally intron 3.
Silencing a 5SS at the beginning of intron 3 or
Silencing a 3SS at the end of intron 3 or both (Im not 100% sure but this is what I think) -> If
you silence 3SS of intron 3 wouldnt the sequence just be E1 E2 E3 E5? I dont think so,
silencing the 3SS at the end of intron 3 would simply prevent any splicing recognition to occur
there. It would theoretically be E1 E2 E3 (silenced 5SS) I3 (silenced 3 SS) E4 E5. However, I
have a feeling that the silencing of 3SS is not even necessary based off of the mechanism of
action of intron removal (slide 16). The lariat is only removed after the OH group attacks the 3
SS, which would never happen if the 5 SS is not available. Any thoughts?
I think the correct answer is silencing the 5SS at the beginning of intron 3, for that prevents the
intron from being spliced out. Silencing a 3SS at the end of intron 3 would lead exon 4 to not
be a part of the sequence.
LO 8-12. Using their basic characteristics and mechanisms, predict generally how an miRNA:
i) Could help prevent inappropriate cell proliferation (act as a tumor suppressor),
ii) Could suppress p53 activity (act as an oncogene by increasing risk of cancer),
iii) Could be theoretically be used therapeutically in a disease caused by expression of an
abnormal form of a particular enzyme or protein (e.g., SOD with familial amyotrophic lateral
sclerosis, ALS)
i. miRNA can hybridize with mRNA and increase degradation. It can also bind to the DNA and
promote heterochromatin formation. Either mechanism would result in reduced protein product,
potentially acting as a tumor suppressor.
ii. miRNA can hybridize with p53 mRNA, resulting in reduced p53 protein products. Because
p53 increases cell death, a lack of p53 will increase cell lineages. This increases the risk of
cancer.
iii. miRNA could be used therapeutically to degrade the mRNA or to prevent the transcription of
an abnormal protein.


FHB-9 Genetic Code and Protein Synthesis (Spector)
LO 9-1. Name three types of RNA needed for protein synthesis and briefly describe the
role of each; name two types of macromolecules found in each ribosome subunit.

mRNA - messenger RNA, that is the product of transcription, and it goes from the nucleus of
the cell to the cytoplasm, carrying the code for a specific protein to be synthesized.

tRNA, transfer RNA, this is a RNA with a unique structure that allows it to hold an amino acid,
as well as an anti-codon region that is complementary to a codon on the mRNA. In the
ribosome complex, the matching tRNA will bring an amino acid to be bonded to the growing
peptide, and then exit the ribosomal complex when that is complete.

rRNA, ribosomal RNA, segments of RNA that make up the core of the ribosomal subunits,
catalyzing the peptidyl transferase reaction and more

Ribosomes are constructed of a core of rRNA and encased in proteins

miRNA, or micro RNA is a small segment of RNA that has the ability to regulate protein
translation by inhibition. Specifically, if the miRNA sequence is complementary to the mRNA
(it does not have to be a complete match), it can bind to the mRNA, and prevent the
translational machinery from gaining access to the mRNA. Because the matching does not have
to be exact, a single miRNA can regulate multiple mRNAs.

LO 9-2. Based on codon structure and the number of nucleotides, predict the number of
codons; list the number of termination codons and the number of codons that code for amino
acids.
4 nucleotides (AGUC); 1 codon = 3 nucleotides
4^3 = 64 codons total --> 61 amino acids codons, 3 stop codons
61 codons for amino acids, but only 20 amino acids (genetic code is degenerate - multiple
codons encode 1 amino acid)

LO 9-3. Define open reading frame (ORF) and briefly explain why the start codon
determines the ORF; name the type of mutation caused by addition or deletion of a number of
nucleotides not divisible by three into the translated exons of a gene, and explain its effect on
protein structure and function. ORF: reading frame beginning at start codon and ending
at a stop codon; codes for the correct protein. Start codon determines ORF because tRNA
anticodons bind to triplets of nucleotides (codons) beginning immediately after start
codon (so, if the start codon is one nucleotide further downstream, the entire reading
frame will be one nucleotide downstream). Frameshift mutation occurs when addition or
deletion of a number of nucleotides not divisible by 3 occurs; it is often catastrophic as it
changes the length of the reading frame while leading to completely different amino acids
being added to the protein after the insertion/deletion point.

LO 9-4. Interpret a genetic code table to determine which codons code for which amino
acids.
LO 9-5. Diagram a tRNA bound to an mRNA codon, indicating the 5 and 3 ends of
mRNA and tRNA, the amino acid attached to the tRNA and the anticodon of the tRNA;
name the enzyme that charges a tRNA with an amino acid .aminoacyl tRNA?
synthetase
Amino acid on 3 end of tRNA
LO 9-6. Describe the basic non-standard base-pairings that allow wobble and use them
to: As long as the first Nucleic Acid on the anti-codon is the same type (pyrimadine,
pyramidine), as the appropriate nucleic acid, then there should still be matching and the
placing of the appropriate amino acid via peptidyltransferase.
a) Predict an example of two different codons that are recognized by one tRNA
b) Predict an example of two different codons that code for the same amino acid but must be
recognized by two different tRNAs
c) Briefly explain why a transition substitution in the third codon position is less likely to
cause a missense or nonsense mutation than the same substitution in the first codon position.
Because of Wobble

LO 9-7. For initiation of eukaryotic translation: i) on a line representing the first exon of
an mRNA, label the 5 cap and the start codon and name the sequence between the two; ii)
diagram the sequence of interactions between these mRNA sites, the two key initiation factors
(eIF-2, eIF-4), charged initiator tRNA, and small and large ribosomal subunits that result in
initiation.

LO 9-8. For elongation of eukaryotic translation: i) draw a ribosome covering two codons
in an mRNA, and label the tRNAs in the P and A sites before the peptide bond formation as
either tRNA-peptide or tRNA-aa; ii) name the type of macromolecule that catalyzes peptide
bond formation, iii) draw the ribosome and tRNAs after peptide bond formation, labeling
tRNA-peptide and tRNA-OH (no amino acid attached), and iv) draw the ribosome after
translocation, labeling tRNA-peptide and tRNA-aa.

LO 9-9. Briefly explain how: i) the lack of tRNAs specific for stop codons contributes to
termination of translation, ii) the polyA tail increases the efficiency of initiation of translation.
i) Stop codon on mRNA corresponds to a tRNA with no AA attached. This causes
release factors eRF1 and eRF3 to bind to A site of ribosome, with GTP attached. GTP
hydrolysis promotes peptidyl-tRNA cleavage, in which the AA sequence dissociates from
tRNA, and the whole structure falls apart.
ii) PolyA tail allows for circularization of mRNA increases efficiency
LO 9-10. Given the description of an antibiotic drug or toxin activity, determine if it inhibits
initiation or elongation, and whether activities of the small or large ribosomal subunits are most
likely affected.
Aminoglycosides: bind 30S ribosomal subunit, preventing tRNA from binding ribosome.
Inhibits initiation
Tetracyclines: blocks prokaryotic A site, so AA-tRNA cannot bind. Inhibits elongation
Streptomycin: code misreading. inhibits initiation
Diphtheria toxin: inactivates eEF2, responsible for translocation. Inhibits elongation
Ricin: depurinates 28S rRNA, inactivating 60S subunit. Inhibits elongation
LO 9-11. Briefly describe why: i) viral destruction of eIF-4 proteins inhibits host mRNA
translation but not translation of viral mRNAs that include an IRES (internal ribosome entry
sequence), and ii) activation of an eIF-2 kinase that inhibits eIF-2 activity will inhibit both host
and all viral mRNA translation. eIF-2 kinase phosphorylates eIF-2, inactivating it.
Phosphorylated eIF-2 cant be recycled; met-charged initiator tRNA cannot be brought to
start site, so translation will not begin (for host or viral mRNA). However, destruction of
eIF-4 (cap binding complex) simply means that the host cant bring the ribosome to bind
with the 5 cap. If the virus has an IRES that mimics the 5 cap and eIF-4 complex, the
ribosome can still bind to viral mRNA only. (Devious!)

LO 9-12. Briefly describe how changing protein degradation can change protein levels with no
change in protein synthesis, and briefly describe the mechanism for turnover of:
a) proteins in the cytosol, including the roles of general ubiquitin ligases that recognize
old or misfolded proteins, protein-specific ubiquitin ligases, and the proteasome (dont worry
about other enzymes).
b) proteins endocytosed from the plasma membrane, naming the organelle in which it
occurs (see Lec 4).
LO 9-13. Briefly explain how the following specific ubiquitin ligase deficiencies could cause
the listed disease:
a) ubiquitin ligase specific for a neural structural protein could result in neurological disease
b) ubiquitin ligase specific for a transcriptional activator important in cell growth and
growth of blood vessels could be associated with increased tumors
Integrative LO for transcription, mRNA processing and protein translation:
LO 9-14. Label on the typical eukaryotic gene diagrammed below: the promoter, an
enhancer, a silencer, the polyadenylation signal sequence (pA), the exons and introns, each 5
SS, each 3SS, a start codon within E1, and a stop codon within E3. Using the same scale:
a) diagram the mature mRNA below the gene and label the start and stop codon in the
mRNA
b) label the 5UTR and the 3UTR in both the gene and the mRNA
c) diagram the protein below the mRNA and label the N-terminus and the C-terminus






Integrative LOs for molecular biology application questions that involve MUTATIONS:
LO MUT1 Briefly describe how a point (single bp) substitution within a coding exon could have
the effect of:
i) not changing the amino acid sequence
if it changes a pyrimidine to another pyrimidine (or purine to another purine), the codon could
still code for the same amino acid and there would be no change in the sequence (wobble)
ii) changing the amino acid but not change the protein activity name this type of mutation
missense mutation: changes the amino acid in the sequence
iii) terminating translation early name this type of mutation.
Nonsense mutation (changes an amino acid codon to a stop codon)

LO MUT2 Diagram a likely location in the gene diagram below for each of the eleven (11)
mutations in the chart (there are multiple possibilities for many of the mutations)




LO MUT3 Fill in the relative effect (increased, decreased, no change) of each listed mutation or
other effect on the factors in the following chart. Note that the amount of mRNA or protein can
result from a change in the initiation rate or the rate of degradation. (The usefulness of this
exercise is finding the patterns of change in the different columns, so look for groups of
mutations that cause similar changes and ask yourself what characteristic is responsible that
will reinforces the basics that are important.)
Mutation or
other effect
Amount of
specific mRNA
Length
of
mRNA
Amount of
protein (what
stimulates
protein
degradation?)
Amount
of
protein
activity
Predict any changes in
protein length and
amino acid sequence
(even if protein would
be degraded very
rapidly)
Delete a
promoter or
enhancer
amount
initiation rate
degradation
rate
amount
initiation rate
degradation
rate

Delete a
silencer
amount
initiation rate
degradation
rate
amount
initiation rate
degradation
rate

Delete a
5SS
amount
initiation rate
degradation
rate
amount
initiation rate
degradation
rate

Delete a
3SS
amount
initiation rate
degradation
rate
amount
initiation rate
degradation
rate

Delete the
only pA in a
gene
amount
initiation rate
degradation
rate
amount
initiation rate
degradation
rate

Delete the
first of two
pAs in a
genes
3UTR
amount
initiation rate
degradation
rate
amount
initiation rate
degradation
rate

Missense
mutation
amount
initiation rate
degradation
rate
amount
initiation rate
degradation
rate

Nonsense
mutation
amount
initiation rate
degradation
rate
amount
initiation rate
degradation
rate

Frameshift
mutation
amount
initiation rate
degradation
rate
amount
initiation rate
degradation
rate

Delete a
start codon
amount
initiation rate
degradation
rate
amount
initiation rate
degradation
rate

Delete a
stop codon
amount
initiation rate
degradation
rate
amount
initiation rate
degradation
rate

eIF-2
deficiency
amount
initiation rate
degradation
rate
amount
initiation rate
degradation
rate

Non-
functional
ubiquitin
ligase for
that specific
protein
amount
initiation rate
degradation
rate
amount
initiation rate
degradation
rate

miRNA
binding with
partial
homology to
a specific
mRNA
amount
initiation rate
degradation
rate
amount
initiation rate
degradation
rate


LO MUT 4 From a combination of data including some combination of the categories in LO3,
predict what mutation is most probably responsible for the findings.
LO MUT 5 From data provided on a patients condition combined with appropriate molecular
information (as listed above), predict what mutation is most probably responsible for the
patients disease.