4. Circadian Rhythms

Question 1

what is the circadian clock

Answer 1

an endogenous molecular pacemaker that drives daily rhythms affecting physiology, biochemistry and behaviour

Question 2

what species were the first clock mutants isolated in?

Answer 2

drosophila

Question 3

what is the most conserved mechanism of the circadian clock

Answer 3

the negative feedback loop

Question 4

what is the main way to measure the circadian clocks in drosophila

Answer 4

locomotor activity

Question 5

what does free run mean

Answer 5

the biological rhythm exists without any external input or cues

Question 6

what does entrainment mean

Answer 6

the biological rhythm is synchronised to an external oscillations

Question 7

give an example of an external oscillation that entrains biological rhythms

Answer 7

the light/ dark cycle

Question 8

at what point in the day are flies the most active

Answer 8

at dawn - they anticipate the light
Flies are also active at dusk

Question 9

what was the first gene identified that could affect circadian rhythms

Answer 9

period

Question 10

what happens in Per0 mutants

Answer 10

produces arrhythmicity

Question 11

what happens in PerL mutants

Answer 11

produced long period rhythms of 28 hours

Question 12

what happens in PerS mutants

Answer 12

produced short period rhythms of 19 hours

Question 13

what 4 properties define circadian rhythms

Answer 13

1. oscillations free run under constant conditions, indicating the presence of a self-sustaining clock
2. the clock driven events recur approximately every 24 hours
3. rhythms are entrained by sun-driven changes in light or temperature
4. the period of the clock is remarkably stable over a wide temperature range.

Question 14

circadian systems are organised into 3 main parts, what are the three parts?

Answer 14

the core clock
the input pathways
the output pathwyas

Question 15

what is the function of the input pathways

Answer 15

synchronise the clock to its environment

Question 16

what is the function of output pathways

Answer 16

transmit information to temporally organise behaviour and physiology

Question 17

what is the function of the core clock

Answer 17

keeps the time

Question 18

what degrades period, how?

Answer 18

double-time

via phosphorylation

Question 19

period and timeless are under the control of a promotor, what is the name of the element of this promotor

Answer 19

E-box element

Question 20

what happens when clock and cycle bind to the E-box

Answer 20

drives the production of per and Tim mRNA

Question 21

name the 5 things that modify period and timeless proteins before it dimerises

Answer 21

doubletime
casein kinase 2
shaggy
phosphates: PP2A and PP1

Question 22

what happens when period and timeless dimerise

Answer 22

they can enter the nucleus where they are able to inhibit clock and cycle proteins from binding to the E-box = suppressing their own expression

= negative feedback loop

Question 23

describe the processes occurring in a clock cell: in the morning

Answer 23

• all timeless has been degraded
• period is no longer protected in the dimer so is also degraded by hyperphosphorylation by double-time

Question 24

describe the processes occurring in a clock cell: at mid-day

Answer 24

no inhibition of per/Tim transcription
Clk and Cyc bind to the E-box and mRNA content rises
NO PROTEIN

Question 25

why is no protein content of period or timeless produced at mid-day

Answer 25

timeless protein is degraded by light and no period as it is not protected by timeless

Question 26

describe the processes occurring in a clock cell: at dusk

Answer 26

timeless is no longer degraded by light mRNA = proteins these proteins dimerise after being modified by a host of factors.

Question 27

describe the processes occurring in a clock cell: at midnight

Answer 27

dimers enter the nucleus period associated with clock = double-time phosphorylates clock phosphorylation prevents clock from binding to the E-box = inhibits the transcription of per/Tim all remaining protein content is degraded = repression is released

Question 28

define exogenous Zeitgeber

Answer 28

external cues that help regulate the internal biological clock

Question 29

name 2 exogenous zeitgebers

Answer 29

light temperature

Question 30

how does light reach clock neurons

Answer 30

via photoreceptive organs containing rhodopsins

Question 31

what organs contain rhodopsin in flies

Answer 31

ocelli and HB-eyelets

Question 32

what is cryptochrome

Answer 32

a blue light photopigment that is activated by light

Question 33

what does activated cryptochrome degrade

Answer 33

timeless

Question 34

what happens to cyrptochrome after timeless has been degraded

Answer 34

Jet Lag binds to Cry = degradation

Question 35

how does cryptochrome degrade timeless

Answer 35

binds to timeless and recruits F box protein Jet Lag = targets Tim for ubiquitination and degradation

Question 36

what happens in flies with a mutation to jet lag

Answer 36

cant adapt to different light/ dark cycles

Question 37

which gene and protein is evolutionarily conserved across mice and flies

Answer 37

clock genes / proteins

Question 38

what do clock neurons regulate in a fly

Answer 38

locomotion

Question 39

how many neurons in the fly brain regulate locomotion

Answer 39

20-30

Question 40

what neurons promote morning activity

Answer 40

S-lateral neurons

Question 41

what neurons promote evening activity

Answer 41

LNds s-LNv

Question 42

what neuron peaks at dusk

Answer 42

LNd

Question 43

what neuron peaks at dawn

Answer 43

s-LNv

Question 44

what neurons promote both morning and evening activity

Answer 44

DN1s

Question 45

what happens to DN1 neurons in the evening when there is high light

Answer 45

they have low output - similarly when there is low light in the evening = they have strong output

Question 46

what does PDF stand for

Answer 46

pigment dispersing factor

Question 47

what is the role of PDF neurons

Answer 47

synchronise clock neurons in the absence of light

Question 48

what are PDF neurons termed

Answer 48

internal zeitgebers

Question 49

name three things that sleep is important for

Answer 49

cognition immune function physiological and neural homeostasis

Question 50

what human gene underpins 'night owls'

Answer 50

CRY1

Question 51

describe sleep in tribes

Answer 51

tribes exhibit natural variation in chronotype (genes which dictate sleeping patterns) - this is driven by selective forces so that the entire tribe does not sleep at the same time = variation in sleep schedules can be beneficial in preventing predation.

Question 52

name 3 tools used to measure sleep in drosophila

Answer 52

infrared detection (to measure locomotion) neurophysiology (using electrodes) beam crossings

Question 53

how do beam crossings work to monitor sleep in drosophila

Answer 53

an infrared beam is placed in a tube with a fly the number of times the fly crosses the beam is counted by the DAM (drosophila activity monitor) - able to distinguish periods of sleep from periods of activity

Question 54

what happens when light activates I-vLNs?

Answer 54

they release PDF onto other s-vLNs that then project to other clock neurons or brain regions to increase motor activity

Question 55

name one of these brain regions that s-vLNs project to?

Answer 55

ellipsoid bodies

Question 56

what is the role of ellipsoid bodies

Answer 56

motor control

Question 57

what happens to these neural pathways at sleep

Answer 57

GABAergic sleep-promoting neurons inhibit these pathways via GABA activity which reduce alertness and arousal

Question 58

what are the 3 neuronal sleep centres in flies

Answer 58

Kenyon cells (MB) fan-shaped bodies ellipsoid bodies (EB)

Question 59

name 2 neuromodulatory neurons that regulate sleep centres

Answer 59

DA neuorns dorsal paired medial neurons

Question 60

what is the response to sleep deprivation caused by caffeine

Answer 60

sleep rebound = an increase in sleep to make up for the lost sleep

Question 61

what is the response to sleep deprivation caused by failed copulation or starvation

Answer 61

no sleep rebound = overrides homeostatic mechanisms to feed and breed which are essential to survival - a likely evolutionary process

Question 62

what happens to the activity of starved flies? why?

Answer 62

increased locomotor activity - which is likely to enable them to discover new food sources.

Question 63

ER: what is evidence for the role of the SCN?

Answer 63

DeCoursey et al. 2000 destroyed the SCN connections in 30 chipmunks - they were returned to their natural habitat and observed for 80 days results: their sleep wake cycle disappeared and a significant proportion were killed by predators by the end of the study.

Question 64

in humans what is the endogenous pacemaker and where is it found

Answer 64

the suprachiasmatic nucleus of the hypothalamus

Question 65

how many groups of clock neurons in flies and what are they named after

Answer 65

7 major groups named after their anatomical position

Question 66

what also expresses clock proteins in fly brains

Answer 66

a few hundred glial cells.

Question 67

ER: temperature can entrain flies, a change of how many degrees is sufficient to adapt a flies circadian clock

Answer 67

3 deg c change is sufficient to change the circadian rhythm

Question 68

what is the mechanism of how temperature entrains the clock

Answer 68

nobody knows - it has not yet been discovered

Question 69

temperature can entrain the clock under constant light conditions, what does this mean?

Answer 69

suggests there is an override of light dependent degradation of timeless

Question 70

where is temperature perceived, what is the evidence

Answer 70

in the tissues and not in the CNS evidence: - isolated body parts are able to perceive temperature = temperature reception is tissue- autonomous -isolated brain are not able to synchronise to temperature cycles

Question 71

what gene is involved in circadian temperature reception

Answer 71

norpA gene

Question 72

what does norpA encode

Answer 72

phospholipase C

Question 73

how do we know norpA is involved in temperature reception

Answer 73

animals with mutated norpA are not able to synchronise to temperature cycles.

Question 74

describe Siffre (1962) case study

Answer 74

spent 6 months in a cave - with no exposure to light (an exogenous zeitgeber) = his circadian rhythm remained consistent at 24 hours and 30 minutes - supports the fact that circadian rhythms free run under constant conditions