19 - Biological Complexity

Question 1

Levels of biological organization

Answer 1

1. Biosphere
2. Biome
3. Ecosystem
4. Community
5. Population
6. Organism
7. Organs
8. Tissues
9. Cells
10. Organelles
11. Proteins
12. Genes

Question 2

Two ways of going about biological organization

Answer 2

1. Reductionism: explains biological complexity by reducing systems to simpler components
2. System biology: explains biological complexity in terms of increasing complexity within hierarchical levels

Question 3

When is reductionism used vs systems biology? Analogy for each:

Answer 3

Reductionism: primary approach to research and teaching in Medicine and Public Health. Analogy = quantum physics (understand the small)

SB: one health approach. Analogy = gravitational physics

Question 4

Complexity increases with…

Answer 4

Each increasing level of biological organization

Question 5

What are emergent properties?

Answer 5

Complexity that is greater than the sum of the parts, representing the new/unpredictable interactions among the players

Question 6

What is genomics? Two types

Answer 6

Study of genome structures

• metagenomics: study of composite collection of genomes represented within an ecological niche or sample
• transcriptomics: study of composite collection of mRNA transcripts produced by the genome under certain condition

Question 7

What is proteomics

Answer 7

Study of the complete repertoire of proteins in a cell, tissue, organ, system or organism

Question 8

What is metabolomics

Answer 8

Study of metabolites produced by a tissue, organ, system or organism

Question 9

What is the genetic code?

Answer 9

• discovery of DNA molecule associated with genetic inheritance
• code is universal and therefore complexity is encoded in simplicity

Question 10

What are the information coding molecules? other possibilities?

Answer 10

Nucleic acids

Other possibilities are proteins? Carbohydrates?

Question 11

Describe the human genome

Answer 11

3.2 billion base pairs of DNA, encoding an estimated 20,500 genes, on 46 chromosomes

Question 12

Mouse genome? Fruit fly? Largest genome?

Answer 12

Mouse = 2.5 billion bp, 30,000 proteins, 40 chr

Fruit fly = 0.18 billion bp, 13,600 proteins, 8 chr

Largest genome = Amoeba dubia (600 billion bp)

Question 13

What % of nucleotides are exactly the same in all people

Answer 13

99.9%

1.4 million locations where single-base DNA differences (SNPs) occur in humans

Question 14

Similarity of human and chimp genome? How much of genome is composed of transposable elements? Derived from viruses? Junk DNA?

Answer 14

96% similarity

Nearly half genome is jumping DNA

8% derived from viruses

50% considered junk DNA

Question 15

What is the human genome project? Cost?

Answer 15

Sequencing the human genome. Took 15 years to complete
95% of genome published in 2001, complete by 2005

Cost ~$3 billion

Question 16

How fast can the human genome be sequenced now?

Answer 16

A few days

Question 17

Slides 15-17

Answer 17

DNA microarrays

Question 18

How many human cells on a person? Microbes?

Answer 18

10^3 human cells
10^4 microbes
“second genome”

Question 19

What benefits do the gut microbiome provide the host (5)

Answer 19

• nutrition and colonization sites
• digest food (nutrients normally indigestible for humans)
• produce important compounds (Vit K)
• stimulate immune system
• barrier to defend pathogen infection

Question 20

What human/animal diseases may be a result of an altered microbiome

Answer 20

• obesity
• diabetes
• cancer, autoimmunity
• enteric infections (antibiotic treatment clears microbiome = C difficile recolonizes)
• autism

Question 21

Distinct nodes of control between proteins

Answer 21

• Negative (inhibitory)
• Positive (stimulatory)
• Variations

Question 22

What is biological degeneracy

Answer 22

Ability of elements that are structurally different to perform the same function or yield the same output

Prominent property of many biological systems

Question 23

What is biological redundancy?

Answer 23

When the same function is performed by identical elements

Question 24

Biological degeneracy and redundancy are both necessary for…

Answer 24

natural selection (evolution)

(and an outcome of)

Question 25

Examples of degeneracy at different levels of biological organization

Answer 25

- genetic code (many nucleotide sequences encode a polypeptide) - genes (functionally equivalent alleles) - protein functions - interanimal communication (transmit same message) - body movements (muscle contractions yield equivalent outcomes)

Question 26

Why is biological degeneracy and redundancy important in one health context (4)

Answer 26

1. Disease is a major driver of them 2. buffer against environmental stresses/changes 3. biochemical/metabolic plasticity, ensures that no one biochemical pathway can be exploited (e.g. induction of cancer growth requires 7-10 mutation events) 4. allows for high degree of fine tuning of individual physiological responses (e.g. immune responses)

Question 27

Biological complexity and the insurance hypothesis

Answer 27

- healthy ecosystems have high lvl complexity (and red/deg) - biodiversity can buffer ecosystem from env pressures/fluctuations - biodiv can have enhancing effect on ecosystem productivity - greater species richness can support maintenance of ecosystem, some spp persist while others fail - biodiv insures ecosystem sustainability