Com. Phy notes

Question 1

What induces the cellular stress response?

Answer 1

Unfolded proteins in the cell

Question 2

What are HSPs and when are they expressed?

Answer 2

Heat shock proteins (HSPs) are targeted for expression while other genes cease to be expressed

Question 3

How quickly can the cellular stress response occur?

Answer 3

From gene to protein in 5-10 minutes

Question 4

What effect does transgenic of Hsp70 have?

Answer 4

Improves heat tolerance

Question 5

How does genotype relate to phenotype in the context of heat stress?

Answer 5

More copies of Hsp70 lead to greater protein synthesis, which leads to greater survival under heat stress

Question 6

What characterizes an extra-copy strain in relation to Hsp70?

Answer 6

Has 2x the number of Hsp70 genes and higher heat tolerance

Question 7

True or False: Higher Hsp70 expression is associated with higher heat tolerance.

Answer 7

True

Question 8

What is required for HSP expression to evolve?

Answer 8

Heritable variation in the trait

Question 9

What happens to HSP expression after the stressor is removed?

Answer 9

HSPs continue to be expressed for hours or days until the unfolded protein problem is resolved

Question 10

What is the function of the negative feedback system in HSP expression?

Answer 10

Prevents HSF1 from initiating the transcription of more HSPs when stress is resolved

Question 11

What is the cost of higher Hsp70 expression under benign conditions?

Answer 11

Associated with lower embryonic survival

Question 12

What metabolic cost is associated with Hsp70 production during the heat stress response?

Answer 12

High ATP consumption for repairing damage

Question 13

How do hot-adapted species like C. funebralis and C. rugosa differ in their heat tolerance?

Answer 13

They produce Hsp70 at higher temperatures and occupy high intertidal zones

Question 14

What is the thermal adaptation mechanism in C. funebralis?

Answer 14

More thermally stable proteins in the system

Question 15

What temperature do species begin synthesizing HSPs?

Answer 15

21-24 degrees Celsius

Question 16

Fill in the blank: Hsp70 appears to be turned on constitutively in _______.

Answer 16

L. scabra

Question 17

What is the role of cold shock proteins like cspA in bacteria?

Answer 17

Bind to mRNA and prevent base pairing to avoid secondary structure

Question 18

What happens to the half-life of capA mRNA at lower temperatures?

Answer 18

Becomes more persistent due to the ‘switched’ configuration

Question 19

What is the effect of positively supercoiled DNA?

Answer 19

Tends to tighten the winding and is less accessible

Question 20

What is the significance of negatively supercoiled DNA?

Answer 20

Tends to loosen the winding and is more accessible

Question 21

How does temperature affect supercoiling and gene expression?

Answer 21

Temperature-dependent changes in supercoiling can modify gene expression

Question 22

What do HMG proteins do?

Answer 22

Bind to DNA and increase its flexibility

Question 23

What is the cellular thermostat model of HSR?

Answer 23

Temperature adaptation of chromatin structure regulates transcription by nucleosomes

Question 24

What functions do cell/organelle membranes serve?

Answer 24

Semipermeable barrier, maintaining concentration gradients, cell signaling, separation of functions, exocytosis, endocytosis

Question 25

What does a lack of double bonds in lipid tails imply?

Answer 25

More saturated, leading to higher melting points

Question 26

How is membrane fluidity measured?

Answer 26

Using a hydrophobic marker and measuring anisotropy

Question 27

What is homeoviscous adaptation?

Answer 27

Conservation of fluidity in membranes

Question 28

What happens to neurotransmitter release at high temperatures?

Answer 28

More uncontrolled release occurs

Question 29

What are the phases of bilayer membrane structure at different temperatures?

Answer 29

Gel phase at low temps, liquid crystalline phase at warmer temps

Question 30

What is the Arrhenius equation used for?

Answer 30

Quantifying the rate of a chemical reaction

Question 31

What is the pejus range?

Answer 31

Functioning but not optimally environmental conditions

Question 32

What determines the upper limit for thermal tolerance?

Answer 32

Temperature acclimation of mitochondrial membranes

Question 33

What unique adaptations do hyperthermophilic archaea have?

Answer 33

Unique phospholipids with ether linkages for stability

Question 34

What is the Maxwell-Boltzmann distribution?

Answer 34

Describes the distribution of particle speeds in a gas

Question 35

What is acclimatation?

Answer 35

Changes in individual organisms in response to changing environmental conditions ## Footnote Acclimatation refers to physiological adjustments made by individuals to adapt to new environmental conditions.

Question 36

What is adaptation?

Answer 36

Changes in populations over generations by natural selection ## Footnote Adaptation involves genetic changes in a population that enhance survival and reproduction in a specific environment.

Question 37

What does sexual reproduction generate?

Answer 37

New combinations of alleles ## Footnote This process increases genetic diversity within a population.

Question 38

What is gene flow?

Answer 38

Migration that introduces new genes into populations ## Footnote Gene flow can enhance genetic diversity and influence evolution.

Question 39

What are the three types of horizontal gene transfer?

Answer 39

* Transduction * Conjugation * Transformation ## Footnote These mechanisms allow for the transfer of genetic material between organisms, contributing to genetic diversity.

Question 40

What is the holobiont concept?

Answer 40

Views an organism and all of its symbionts as a biological unit ## Footnote This concept emphasizes the interconnectedness of host organisms and their microbial communities.

Question 41

What does thermal energy represent (heat)?

Answer 41

The amount of random kinetic energy of particles in a system ## Footnote Thermal energy is a measure of the energy associated with the temperature of a substance.

Question 42

Define temperature?

Answer 42

Temperature is the average random kinetic energy of particles in a system ## Footnote Unlike thermal energy, temperature does not scale with the size of the system.

Question 43

What does the Arrhenius equation quantify?

Answer 43

The rate of a chemical reaction ## Footnote This equation relates the rate constant to temperature and activation energy.

Question 44

What is the Q10 value?

Answer 44

The effect of a 10 degree C increase in temperature on reaction rate ## Footnote Q10 is a measure of temperature sensitivity in biochemical reactions.

Question 45

How do enzymes affect activation energy?

Answer 45

Enzymes lower the activation energy for a reaction, increasing the reaction rate ## Footnote This catalytic action is crucial for facilitating biochemical reactions in living organisms.

Question 46

Kcat/ catalytic rate constant

Answer 46

the amount of substrate converted to product/enzyme when fully staurated with substrate (enzyme effciency)

Question 47

What does Km stand for in enzyme kinetics?

Answer 47

Michaelis-Menten constant, the substrate concentration at which the reaction velocity is half the maximum velocity ## Footnote Km is an important parameter for understanding enzyme efficiency and substrate affinity.

Question 48

What does a low Km indicate?

Answer 48

A high affinity of the enzyme for its substrate ## Footnote This means that the enzyme can effectively bind and catalyze reactions at low substrate concentrations.

Question 49

What does the dominant conformational microstate of a protein depend on

Answer 49

Temperature (protein will change shape at different temps, optimal is different for every species.)

Question 50

Define conservation and innovation

Answer 50

there is an optimal range of temperatures that species need to live optimally

Question 51

What are the two kinds of homologous genes

Answer 51

Orthologs and paralogs

Question 52

How were orthologs creates

Answer 52

Speciation/ they are homologous due to being inherited in common from ancestral species. Same locus in the genome Orthologous genes cannot be found in the same species

Question 53

How were paralogs created

Answer 53

Paralogs are created by gene duplication = they are homologous due to having originally been a single gene that was duplicated and the two copies diverged from one another. They are found at different loci in the genome Paralogous genes can be found in a single species

Question 54

What does the rate of divergence due to natural selection depend on

Answer 54

the strength of selection

Question 55

If more recently two genes diverged from one another, greater chance that the differences reflect___

Answer 55

adaption by natural selection

Question 56

What is marginal stability in proteins?

Answer 56

The 'goldilocks' state where proteins are neither too rigid nor too fluid ## Footnote This state is essential for proper protein function, allowing for necessary conformational changes.

Question 57

What is the Gibbs-Helmholtz equation?

Answer 57

Delta G = Delta H – T Delta S ## Footnote This equation relates changes in free energy to enthalpy and entropy, important for understanding thermodynamics in biochemical reactions.

Question 58

What characterizes exothermic reactions?

Answer 58

Delta H is negative, heat is released ## Footnote These reactions are often spontaneous and contribute to energy release in biological processes.

Question 59

What are hydrophobic effects in protein folding?

Answer 59

Water molecules form a shell around nonpolar residues, pushing them together to minimize unfavorable interactions ## Footnote This process is crucial for stabilizing protein structures by promoting the burial of hydrophobic regions.

Question 60

What happens during the heat shock response?

Answer 60

Induced by unfolded proteins, leading to the expression of heat shock proteins (HSPs) ## Footnote This response is a critical cellular mechanism to manage stress and repair damaged proteins.

Question 61

What does feedback inhibition involve?

Answer 61

A product acts as an inhibitor to an enzyme earlier in the pathway ## Footnote This regulatory mechanism helps maintain homeostasis and control metabolic pathways.

Question 62

What are the consequences of protein aggregation?

Answer 62

* Loss of protein function * Cytotoxicity ## Footnote Aggregation can lead to serious cellular consequences, impacting overall health and function.

Question 63

What is co-translational folding?

Answer 63

Nascent proteins start to fold while they are still being translated ## Footnote This process ensures that proteins begin to adopt their functional structures even before synthesis is complete.

Question 64

What is the role of molecular chaperones?

Answer 64

They assist in the proper folding of proteins and help prevent misfolding ## Footnote Chaperones are essential for maintaining protein homeostasis within the cell.

Question 65

What does increased Hsp70 expression indicate?

Answer 65

Improved heat tolerance but at a metabolic cost ## Footnote Higher levels of Hsp70 can enhance the heat shock response but require significant energy resources.