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SEM2 > BIOL1080 midterm 1 (1-6) > Flashcards

BIOL1080 midterm 1 (1-6) Flashcards

1
Q

What is Systems Biology?

A

“The systematic study of complex interactions in biological systems”

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2
Q

What is a reductionist vs Integrative approach?

A

Reductionist approach- “taking the pieces apart”- we don’t know how/why they work together
Integrative approach- “putting the pieces together”- figure out how and why

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3
Q

What are emergent properties?

A
  • Properties of an entire system (or organism) that are not necessarily evident from examining individual components i.e. “the whole is greater than the sum of the parts”
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4
Q

What is an example of emergent properties?

A

our personalities- consciousness is made up of many emotions which cannot be understood by looking at single neurons

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5
Q

What are the 3 components of “Omics” (in order of smallest to largest)?

A

genomics < proteomics < metabolomics

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6
Q

What are genomics?

A

study of an organism’s complete set of DNA

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7
Q

What are proteomics?

A

study of the set of all proteins produced within a biological unit (can be an organ, organ system, or entire organism)

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8
Q

What are metabolomics?

A

study of metabolites within a given unit e.g. cell, tissue, organ, organism

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9
Q

Compare labs of reduction vs integration approaches

A

Isolated:
- very specific, variables controlled exquistely over experimental conditions
Integrated:
- more real world, with less control over variables, less mechanistic

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10
Q

Give an example of how integration showed better results in a lab than a reductionist approach

A

Leptin for weight loss-
- data in lab shows it is good at burning fat
BUT
- leptin has numerous other effects in other tissues
- overweight individuals become leptin resistant
- hormones could antagonize/amplify its effects
**Clinical trials with leptin not successful!

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11
Q

What is a clinical example of diagnosis with reductionist approach?

A

Type 2 Diabetes & Blood Glucose Regulation

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12
Q

Give a nutritional example of reductionist/integrative approach

A

Whether or not you should take antioxidants

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13
Q

What are some reasons why you should take antioxidants?

A
  • Reactive oxygen species (ROS) can induce oxidative damage (DNA, proteins, lipids), promoting aging & disease
  • Antioxidants protect the cell from these damaging effects
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14
Q

What are some reasons why you should not take antioxidants?

A
  • A certain amount of ROS is protective e.g. leads to apoptosis of damaged cells
  • ROS are a natural signal involved in adaptation e.g. adaptation to exercise training (Some studies show that Vitamin C/E supplementation block mitochondrial adaptations to exercise training)
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15
Q

When is a systems biology research approach best?

A

When studying chronic, complex conditions such as diabetes, where multiple complex systems are at play

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16
Q

What is reductionism?

A

examines specific responses in isolated, controlled
situations

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17
Q

What is integration?

A

examines more wide-spread responses in less controlled, more realistic situations

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18
Q

What is an emergent property?

A

a property which a collection or complex system has, but which the individual members do not have

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19
Q

What makes us unique from other humans and from other species?

A
  • our emergent properties (even a 0.01% difference could mean thousands of base pair changes)
  • they produce incredible variation among human individuals (despite 99.9% genetic homology)
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20
Q

Give an example of an emergent property

A

ants building an ant colony:
- 1 ant alone cannot build an ant hill, but their collective behavior can
- Their emergent property is building the hill together

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21
Q

What are the 7 characteristics of life?

A
  1. Responsiveness to the environment
  2. Growth & change
  3. Ability to reproduce
  4. Have a metabolism & breathe
  5. Maintain homeostasis
  6. Being made of cells
  7. Passing traits onto offspring
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22
Q

Why is homeostasis important?

A

If blood potassium levels are regulated in fairly narrow range, going out (particularly above) can lead to death

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23
Q

Who is Dr. Robert Sapolsky?

A
  • Neurologist & primatologist (Stanford)
  • Explores long-term health impacts of stress (e.g. long-term stress exposure contributes to mental health risk)
  • Investigates how culture/society influence our moral compass
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24
Q

What are the components of the control and communication network (CCN)? (all interconnected)

A
  • central nervous system (brain + spinal cord)
  • peripheral nervous system (Somatic (voluntary) nervous system & autonomic (involuntary) nervous system)
  • endocrine system (endocrine tissues + exocrine glands, hormones)
  • support and defence system (our immune system- specific and non-specific)
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25
Q

What does the CCN do?

A

in the adult human biological system; coordinate our functions

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26
Q

What are properties of the CCN

A
  • Controls & coordinates the function of all physiological systems & individual organs, including itself
  • It is always “on”
  • It is distributed throughout the entire body
  • Each component of the network has multiple functions; the network has redundancy
  • Information flow within the network via chemical-based, cell-cell communication
  • mind is not separate from body; emotions/thoughts are biochemically based
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27
Q

How does the CCN affect health in the adult human?

A
  • integrator of inputs to health, disease, & aging – genetics, environment, & lifestyle
  • integrator of output to the seven dimensions of health
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28
Q

Which of the 7 dimensions of health are shared across species?

A

not sure

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29
Q

What are all 7 dimensions of health?

A

spiritual, emotional, cognitive and intellectual, environmental, professional and vocational, physical, social

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30
Q

What are the 3 inputs to health, disease, and aging?

A

genetics, environment, lifestyle

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31
Q

Which of the 3 inputs to health, disease, & aging are typically shared in human species?

A

environment and genetics

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32
Q

Which processes represent compromised function/structure of the CCN?

A

aging and disease

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33
Q

What is P4 medicine?

A
  1. Personalized
  2. Predictive
  3. Preventive
  4. Participatory
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34
Q

Which of the 4 P’s of 4P medicine is the most challenging?

A

participatory
- if the patient isn’t willing to implement changes, the P4 medicine is nearly useless

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35
Q

Outline the CCN

A
  • Information flow is chemical based
  • This network is a focal point & integrator of our health
  • Deterioration of this network occurs in disease & aging
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36
Q

What is the McClintock effect?

A

the occurence of period synching when women live together in close quarters

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37
Q

Is period synching actually tested true?

A
  • Studies show that period synching is pretty unlikely, and just due to mathematical coincidence
  • hard to test; some studies support, others do not
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38
Q

What is evidence in support for period synching/the mcclintock effect?

A
  • Menstrual pain seemed to be stronger when women lived together (perpetual pain)
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39
Q

What are 4 Experimental Models for Human Medical & Health Research?

A

In silico
In Vitro + Ex Vivo
Animal
Human participants

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40
Q

What does in silico mean?

A

performed on a computer ; simulations with mathematical models/computer

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41
Q

What does in vitro and ex vivo models mean?

A

“in glass” (in petri dish or other labware) and “out of the living” (studying something that has been removed from the body)

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42
Q

How are in vitro and ex vivo models made?

A

In vitro: Cell system in cell structure lab
Ex vivo (more complex): Not created artificially, taken from natural organisms with minimal changes

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43
Q

Give examples of in vitro

A
  • Culturing cells
  • Growing skin (epidermis)
  • Transformed (cancer) cells
44
Q

Give examples of ex vivo

A
  • Isolated perfused (and beating) heart
  • Isolating rat gastrocnemius muscle for incubation
45
Q

What are the main purposes of In Vitro & Ex Vivo research?

A
  • Allows for more controlled experimental conditions
  • Understanding fundamental mechanisms
46
Q

Explain the use of nematodes as an animal model

A

C. Elegans-
40% genetic homology to human * Easy & cheap to study
* Short life cycle (~3 days)
* Self-fertilizes
* Can be frozen, thawed, & remains viable
* Transparent – facilitates the study of cell differentiation

47
Q

Why are animal models used?

A

to study genetics

48
Q

Explain the use of laboratory mice as an animal model

A
  • Very social & intelligent
  • Often used to study lifestyle effects on metabolism (diets, exercise, drugs)
  • Tend to take a “more severe approach” than with humans * E.g.50%fatdiets,10hours/weekofveryintenseexercise
  • Not a very good model for human infant nutrition & metabolism
  • Some genetically modified rats (not as common as mice)
  • E.g. Zucker rats lack leptin receptors & are used to study obesity & diabetes
49
Q

Explain the use of fruit flies as an animal model

A

Drosophila Melanogaster- 65% genetic homology to human * Life cycle & development are very sensitive to environmental changes

50
Q

Explain the use of laboratory mice as an animal model

A

Mice (many different strains):
* Popular due to ease of applying recombinant DNA technology (knockout a
gene, over-express a gene, etc.)
* Can test importance of a single protein
* Compensatory mechanisms
* Ob/ob mouse fails to secrete functional leptin
* Used to study lifestyle effects on metabolism; results may differ from rats (i.e. cannot assume one rodent model is equal to another)

51
Q

Explain the use of primates as an animal model

A
  • The closest model you will likely get to represent humans * Ethics? Cost?
  • Very little primate research in Canada; more in the USA
  • What type of research?
    (Human pathologies, (AIDS, etc.), Transplantation, Drug abuse, toxicology)
52
Q

Explain the use of swine as an animal model

A
  • Piglets are best non-primate model for human infant development & metabolism
  • Used to study organ transplants (xenografts- tissue/organ derived from a species that is different from the recipient of the specimen; tissue from one species, into another species)
  • Cloned miniature pigs can be purchased from companies so that the animals are genetically identical
53
Q

Outline non-clinical studies

A

Non-intervention
* No medicinal/lifestyle treatment given
* Cannot predict or prove “cause & effect” of a medicinal substance * Only predicts associations/correlations
* Epidemiological studies are the most common
- Conflicting results in non-clinical studies: there are many confounding factors (nutrition, age, different populations (Americans vs Japanese), etc)

54
Q

Outline clinical studies

A

Intervention
* A medicinal/lifestyle treatment &/or a control substance/placebo is given i.e. an intervention
* Can be used to predict cause and effect
* Double-blind, placebo- controlled clinical trials are the gold standard for medical & healthcare research

55
Q

Do non-intervention studies have no benefit?

A
  • No, Still gives valuable information
  • Can be used to guide clinical previews
56
Q

How are human clinical trials ensured to be safe?

A
  • All human research must go through rigorous review by institutional ethics review boards
  • Human clinical trials are always volunteers * Tests performed to test a new drug’s safety
57
Q

What are the 3 steps (explain each briefly) of human clinical trials

A
  1. Preclinical (<100 people)
    * Animal studies before testing on humans
  2. Phase I clinical trial
    * Is the drug safe for humans? * Small group of people
  3. Phase II clinical trial
    * Does the drug work for its intended purpose (effectiveness)? * Larger group of people (100s)
    * Still check safety
    * Figure out dose
  4. Phase III clinical trial
    * How does the drug compare with other available treatments? * Even larger group of people (1000s)
  5. After approval
    * Ongoing assessment of long-term use, benefits, & risks

lasts about 10 years

58
Q

What are cochrane reviews?

A

a database of systematic reviews & meta-analyses which summarize & interpret the results of medical research

59
Q

How is the optimal decision made for evidence-based medical outcome?

A

considers evidence, clinical expertise, patient preferences

60
Q

What are the 4 types of medicine in New Dimensions in Medical & Healthcare Practice

A

A. Evolutionary Medicine
B. Integrative Medicine
C. Collective Medicine – Eco Health Medicine & One Health/One World/One Medicine
D. Enhancement Medicine

61
Q

Outline evolutionary (Darwinian) medicine

A

“The application of modern evolutionary theory to understanding health & disease”
“Knowledge about evolution provides physicians with an integrative framework that links otherwise disparate bits of knowledge”
I.e. our bodies have been shaped by evolutionary process – can we use that knowledge
- Often receives criticism from those in favour of evidence-based medicine

62
Q

Outline integrative
medicine

A
  • Treats the whole person, not just disease symptoms
  • Arizona Center for Integrative medicine: IM is healing-oriented medicine that take account of the whole person, including all aspects of lifestyle. It emphasizes the therapeutic relationship between practitioner & patient, is informed by evidence, & makes use of all appropriate therapies
  • not evidence-based, has received scrutiny
63
Q

Outline Collective Medicine

A

One health: an approach calling for “the collaborative efforts of multiple disciplines working locally, nationally, and globally, to attain optimal health for people, animals and our environment

64
Q

Outline Enhancement Medicine

A

Non-prescribed
* Botox, Viagra, Anabolic steroids, etc

65
Q

What is trajectory (biological systems- dimension of time)?

A

growth, development, and aging (years, decades)

66
Q

What is rhythms (biological systems- dimension of time)?

A

maintenance/repair, other processes (days, weeks, months

67
Q

What is homeostasis/balance (biological systems- dimension of time)?

A

maintenance of steady state (seconds, minutes, hours)

68
Q

What is energy and information flow (biological systems- dimension of time)?

A

action potentials, enzymatic reactions (Milliseconds, microseconds)

69
Q

Compare lifespan and healthspan?

A

How long do I have to live? vs How long will I be living a healthy, independent lifestyle?

70
Q

Define lifespan

A
  • 81 years of age in Canada
  • Paleolithic man lived to ~35-40 years
    (lengthen lifespan by approx. 2x since paleolithic man)
71
Q

Define healthspan

A
  • 72 years of age in Canada
72
Q

“Is healthspan more important than lifespan?”

A
  • more studies towards living healthy, independent life
  • first world countries has longer healthspan than 3rd world
  • Japan highest, followed by Canada; Sierra Leone is low (approx. 29)
73
Q

How can you maximize healthspan?

A
  • A goal in most individuals & societies
74
Q

How can you maximize lifespan?

A
  • Various attitudes & practices around the world
  • Moral, ethical, religious implications
75
Q

Are online lifespan calculators accurate?

A

No- it bases it on many different factors

76
Q

How do we track aging & disease processes?

A
  • If we can’t find “things” to measure objectively, then we can track the aging/disease process
  • biomarkers (indicators of the biological state of the organism)
77
Q

Give an example of a biomarker and what it assesses

A
  • Dramatic changes in height
  • Growth tables are important tools in assessing health early in life
  • Slow growth – infectious disease, malnutrition, hormonal problems
  • Fast growth – hormonal problems (excess growth hormone), over-nutrition would affect body weight but not likely height
78
Q

What is kyphosis?

A

Kyphosis= shortening in height due to osteoporosis (shortened distance between discs)

79
Q

What is sarcopenia?

A
  • Age-related loss of muscle mass
  • Up to 1% loss per year after age 40
  • Males: associated with decrease in testosterone, IGF-1, inactivity * Females: associated with inactivity & likely estrogen
  • Best strategy to prevent/reverse:
  • Resistance training 2-3x per week for each major muscle group
  • Dietary considerations: protein can stimulate protein synthesis if you are also doing resistance training (elderly may require more protein)
80
Q

What are biomarker requirements?

A
  • Reflect “normal” (i.e. healthy)
  • Function (e.g. high HDL-cholesterol)
  • Disease processes (e.g. high blood PSA)
  • Or predict the risk of future development of disease (e.g. high LDL- cholesterol)
  • Have a predictable range across an identifiable category of individuals, or must be routinely monitored over time within each individual (e.g. height)
  • Have methods available for accurate & precise measurement
81
Q

Compare high LDL vs low LDL

A

the lower the number the better

82
Q

Can biomarkers change during the lifespan?

A

Must be interpreted in relationship to age, sex, & physiological state of the individual
Most markers have normal ranges & diagnostic value if they are too high or too low

83
Q

Describe the graph for reference ranges for blood biomarkers

A
  • When values taper off over a greater range, there is a tapered end to the box
  • When there is a disagreement between research sources, there is a faded end to the box
  • Note different ranges of some parameters with age (TG) & sex (HDL)
  • When you are outside the reference range for a biomarker, it may indicate risk for development of a disease (e.g. high LDL), or the presence of a disease condition (e.g. high fasting glucose)
84
Q

What is chronobiology

A
  • the study of timescales and cycles in biology
  • branch of biology concerned with natural physiological rhythms
85
Q

What are the three biological rhythms?

A

ultradian < circadian < infradian

86
Q

Describe the ultradian rhythm

A

<24 hours; appetite e.g. ghrelin (meals), cortisol (pulse)

87
Q

Describe the circadian rhythm

A

24 hours, cortisol (lowest at midnight i.e. sleep, peak at 8am i.e. after awakening)

88
Q

Describe the infradian rhythm

A

> 24 hours (every 24-30 days); menstrual cycle

89
Q

What is diurnal variation?

A
  • Biological rhythms based on a 24-hour cycle
  • Involved in essentially all physiological processes
  • Controlled by peripheral “clocks” that are governed by a “master or central clock”
  • Controls gene expression, regulation of enzymatic activities, neural function, hormone secretion, etc.
90
Q

Describe circadian rhythms

A
  • Circadian rhythms coordinate sleep, nutrient supply, & activity patterns with metabolic patterns required at different stages of the day
91
Q

What does disruption of circadian rhythms in experimental animals lead to>

A

wide spectrum of health problems & premature aging
* Elevated inflammatory cytokines
* Gastrointestinal function (ulcer, irritable bowel) * Obesity
* Metabolic syndrome (best in morning, worst at night)

92
Q

Circadian rhythms day vs night

A

The master or central “clock” is a brain region called the “suprachiasmatic nucleus”, which keeps time based on light signals from the retina

Nearly every cell in the body has a subsidiary (peripheral) clock that coordinates its metabolism with the rest of the body

93
Q

What controls the molecular clock?

A

Not very well understood
* Entrained by light/dark cycles
* Still intact in most blind individuals (retina still detects light)
* Chemical signals involved are not clear – likely involves melatonin * Melatonin is a hormone produced by pineal gland of the brain
* Blue spectrum light (screens/monitors) inhibit melatonin release

94
Q

How does checking your phone affect your melatonin?

A

Checking phone (blue light) inhibits melatonin, making it harder to sleep
Melatonin should not be used for a long period, because your body would get used to it and you would be unable to sleep without it

95
Q

How do shift workers have health implications from disruption of circadian rhythms?

A

experience greater incidence of
* Heart attacks
* Obesity, diabetes, cardiovascular complications
* Cancer
* Alzheimer’s Disease

96
Q

Late vs early chronotypes

A

Late- night owls (* More likely to suffer from mental stress * More likely to smoke: Correlation vs causation !! (no intervention, cannot say that being a night owl causes mental stress))

97
Q

Give a health-related example of circadian rhythms disruption?

A

Risk of sudden heart attack is greatest mid-morning
* No clear answer yet
* May be due to a protein called Kruppel-like factor 15 (Klf15), which affects K+ efflux in the heart
* Combination of factors: caffeine, stress, high fat diet, etc.

98
Q

How could you use height as a biomarker?

A
  • Measuring height at the same time everyday
  • Anything potentially linked to “master clock” will change at different times, so must measure it at the same time daily
99
Q

What is DEXA?

A
  • Dual energy X-ray absorptiometry to determine bone mineral density: More definitive, Generally safe
  • Mineral structure of bone composed of hydroxyapatite which is an insoluble deposit of calcium & phosphate within an extracellular protein (collagen) matrix
  • DEXA estimates the amount of hydroxyapatite (dense & able to absorb the x-rays)
100
Q

Compare osteoblast and osteoclast

A

Bone: Osteoblast (build-up), osteoclast (break down)

101
Q

How does bone and plasma calcium homeostasis?

A

Bone serves as functional calcium store in the body * Acts as a “buffer” for plasma calcium levels
Plasma calcium must be maintained over a very narrow range (e.g. limited variation between fed & fasted states)
* Needed for normal cell signaling & generation of action potentials
* Parathyroid hormone (PTH) prevent a decreased in plasma calcium
* Calcitonin prevents an increase in plasma calcium

102
Q

What is a high amount of calcium called?

A

hypercalcemia

103
Q

Explain the pathway of PTH to increase calcium levels in the blood

A

PTH: parathyroid hormone; released and goes into the blood stream
When UV hits the skin, turns cholesterol derivative to D3; goes to liver, which transforms it into calcidiol, and leaves liver to go to the kidney: turns into into calcitriol (vitamin D); together they do things to increase blood calcium
1. Increase activity of osteoclasts (break down bone, releasing calcium in blood)
2. Decrease calcium excretion in urine
3. Increase calcium absorption in intestines (to put in blood plasma)
When calcium in blood reaches good level, sends signal to parathyroid gland to stop the hormone from being released

104
Q

Why do pregnant women need to have more calcium?

A

In pregnancy, if you do not have enough calcium, fetus will take calcium from the bones

105
Q

How can you maximize bone density at age 20-30?

A

(90%+ of maximal bone density is achieved by age 20 in the average individual)
1. Consume sufficient calcium (food, supplementation) in adolescence & early adulthood
2. Get adequate vitamin D (sun exposure, diet, supplements)
3. Participate in weight-bearing physical activity/exercise most days of the week
4. Maintain stable body mass
5. Get plenty of sleep

106
Q

What factors hinder maximal bone density?

A
  • Smoking, alcohol, caffeine
  • High phosphate
  • Drugs e.g. corticosteroids

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