BIMM 166: let's go f**king ham

Which of the following is true of the homeostatic drive in the human sleep-wake cycle? A) It starts building up a pressure to sleep from the time you wake up until the next time you sleep B) It has a different circadian period than the circadian sleep-wake cycle C) It cycles in activity every day whether you sleep or not D) It is the drive to stay awake even when your body prefers to sleep

A) It starts building up a pressure to sleep from the time you wake up until the next time you sleep

What is the prediction regarding wheel-running behavior of a mouse that is Opn4-/- and Rd/Rd? A) It will exhibit a free-running circadian rhythm in a light/dark cycle B) It will be arrhythmic under all conditions C) It will have a shorter than normal circadian period in constant darkness D) It will entrain normally to a light/dark cycle

A) It will exhibit a free-running circadian rhythm in a light/dark cycle

Which of the following is the current prediction for healthy human eating habits based on the human feedograms and mouse studies from the Panda lab? A) Best to restrict food intake to the daytime historically active hours of the day B) Best to restrict food intake to the nighttime hours of the 24-h cycle C) Best to eat small meals every few hours throughout a 24-h cycle D) Best to skip breakfast and eat a high-calorie snack late at night

A) Best to restrict food intake to the daytime historically active hours of the day

Which of the following proteins directly absorbs light and contributes to the "external coincidence" regulation of flowering time in Arabidopsis? A) FKF1 B) CO C) FT D) TOC1

A) FKF1

Which of the following blind individuals is most likely able to entrain normally to the day/night cycle? A) Someone who has lost rods and cones and cannot make visual images but still has an intact inner retinal ganglion layer B) Someone who has had their eyes removed, but is bald and does not wear a hat outdoors C) Someone whose optic nerve has been severed, but the parts of the retina are still intact D) Someone whose retina is entirely inactive

A) Someone who has lost rods and cones and cannot make visual images but still has an intact inner retinal ganglion layer

What geophysical phenomenon is associated with the depressive syndrome called SAD? A) Decreased average temperature in winter months B) Shortened photoperiod in winter months C) Altered period of the daily cycle in winter months D) Altered tidal cycles during winter months

B) Shortened photoperiod in winter months

Based on Dr. Panda's smartphone app study, which of the following phrases best describes typical human feeding behavior in our current culture? A) Similar to a Time-restricted protocol in mice, concentrated in the active period B) Similar to an ad-libitum protocol in mice, fairly arrhythmic C) Similar to a Time-restricted protocol in mice, concentrated in the inactive period D) Similar to an ad-libitum protocol in mice, with a strong peak at noon

B) Similar to an ad-libitum protocol in mice, fairly arrhythmic

What is the role of the circadian clock in human sleep? A) The circadian clock counts down how long it has been since you woke up B) The circadian clock provides an alerting signal to keep you awake as sleep pressure rises during the daytime C) The circadian clock pushes you to sleep when it is nighttime D) The circadian clock removes the specific metabolites that cause sleep pressure

B) The circadian clock provides an alerting signal to keep you awake as sleep pressure rises during the daytime

When cyanobacteria are dividing more than once a day... A) Temperature compensation is lost B) The daughters and grand daughters of the original cells faithfully complete the 24 h cycle C) The PRC is dramatically altered D) Circadian rhythms are lost

B) The daughters and grand daughters of the original cells faithfully complete the 24 h cycle

Which of the following is the most likely explanation for the fact that a CCA1 null mutant of Arabidopsis is not arrhythmic? A) CCA1 is only a hand of the clock, not part of the oscillator B) CCA1 affects only flowering, not circadian rhythms C) CCA1 is part of a family, and other members have partially overlapping functions D) CCA1 is a photoreceptor

C) CCA1 is part of a family, and other members have partially overlapping functions

What molecular event is responsible for the resetting of the phase of rhythms in Drosophila that is given a short light pulse? A) Rods and cones in the fly eyes absorb light and send a resetting message to the brain B) CRY, only in the SCN of the brain, absorbs light and causes TIM to degrade C) CRY, in essentially any tissue, absorbs light and causes TIM to degrade D) Melanopsin in the fly eyes absorbs light and sends a resetting message to the brain

C) CRY, in essentially any tissue, absorbs light and causes TIM to degrade

Which of the following measurements are routine components of polysomnography? A) Brain waves, eye movements, melatonin levels B) Eye movements, melatonin levels, core body temperature C) Eye movements, muscle tension, brain waves D) All of the above

C) Eye movements, muscle tension, brain waves

Which of the following is NOT a feature of KaiB in the cyanobacterial circadian oscillator? A) It undergoes a structural change between the form that binds KaiC and the form that is unbound B) When bound to KaiC it captures KaiA in an inactive form C) It is a kinase that phosphorylates KaiC D) When it binds to KaiC, it knocks SasA off of KaiC

C) It is a kinase that phosphorylates KaiC

You are interested in identifying genes involved in the mating dance of West African dung flies. These genes have not been discovered previously, so you are not sure what genes you are looking for. What would be a genetic approach to find the relevant genes? A) Sequence the West African dung fly genome and find its period gene to compare with the Drosophila period gene. B) Mate a fly that does the mating dance with one that doesn't and look at the ratio of offspring that perform the mating dance to determine whether the gene is recessive or dominant. C) Mutagenize flies, find mutants that do not perform the mating dance or perform it incorrectly, and add back wild-type genes to find the gene that restores the mating dance. D) Use wild-type flies to map genes responsible for the mating dance, then mutate these genes and look for the absence of the mating dance.

C) Mutagenize flies, find mutants that do not perform the mating dance or perform it incorrectly, and add back wild-type genes to find the gene that restores the mating dance.

Which clock gene tends to have slightly different alleles (Variable number tandem repeat ) in people living close to the equator compared to people living closer to the poles? A) Cry2 B) Bmal1 C) Per3 D) Clock4

C) Per3

Which of the following features is similar between cyanobacterial and eukaryotic circadian mechanisms? A) A transcription-translation feedback loop as the primary timekeeping mechanism B) The ability to reconstitute circadian oscillations in a test tube C) Phosphorylation of one or more proteins is an important step in timekeeping D) The involvement of cryptochrome

C) Phosphorylation of one or more proteins is an important step in timekeeping

Which of the following is NOT clearly classified as a circadian rhythm disorder in the DSM5 psychiatry manual? A) Advanced Sleep Phase Syndrome B) Non-24 sleep wake syndrome C) Schizophrenia D) Delayed Sleep Phase Syndrome

C) Schizophrenia

Which of the following types of variations in human genomes forms the basis of genome-wide association studies of human disease? A) Presence or absence of a single defective allele that causes a genetic disease B) Differences in which specific genes are present C) Single nucleotide polymorphisms D) Differences in which specific chromosomes are present

C) Single nucleotide polymorphisms

All of the following are a reasonable hypotheses regarding why animals sleep EXCEPT... A) Sleep is a period of memory consolidation B) Sleep is a period of toxin removal from the brain C) Sleep is a period in which animals are more susceptible to predators because they are not alert D) Sleep is a period of synaptic rebalancing after the stimulation of wakefulness

C) Sleep is a period in which animals are more susceptible to predators because they are not alert

Which of the following is true regarding circadian gene expression in mammalian liver? A) The highest proportion of genes expressed rhythmically in mouse liver is seen under ad-libitum feeding conditions. B) Essentially all genes are expressed rhythmically in mouse liver, regardless of the feeding schedule. C) The highest proportion of genes expressed rhythmically in mouse liver is seen under time-restricted feeding conditions. D) More genes are expressed rhythmically in the liver if a mouse is not given food than if it is allowed to feed.

C) The highest proportion of genes expressed rhythmically in mouse liver is seen under time-restricted feeding conditions.

Refer to the figure below showing the drinking rhythm of a squirrel monkey. Each dot is the peak drinking time and the shaded area represents times of exposure to a possible zeitgeber. What statement is most accurate? A) The rhythm was free-running throughout the entire period of measurement. B) The rhythm was masked by the zeitgeber because there was never drinking in one phase C) The rhythm was entrained because its final free-run phase is predicted by the phase in the presence of the zeitgeber. D) The rhythm was masked by the zeitgeber because it free-runs in the last third of the actogram

C) The rhythm was entrained because its final free-run phase is predicted by the phase in the presence of the zeitgeber.

How do mammalian peripheral tissues like liver and heart become entrained by the external environment? A) Through melanopsin in the peripheral tissue that directly senses green light B) Through humoral and neuronal signals that transmit information that was processed in the brain based on light perceived directly by extraoccular photoreceptors in the pineal gland C) Through humoral and neuronal signals that transmit information that was processed in the brain based on light perceived by the eyes D) Through humoral and neuronal signals that transmit information from the brain after melanopsin-containing cells in the SCN directly sense light

C) Through humoral and neuronal signals that transmit information that was processed in the brain based on light perceived by the eyes

What is meant by the phrase "hands of the clock"? A) a stimulus that resets the clock B) the endogenous free-running period C) any observable process controlled by the clock D) the mechanism that makes the clock keep time

C) any observable process controlled by the clock

In rodents, light at night can make clocks more flexible if the light is approximately as bright as A) mid-dawn B) a cloudy day C) dim moonlight D) bright sunlight

C) dim moonlight

If given FRP, T and a phase response curve, what would you be able to predict? A) the duration of the rest phase B) the duration of the activity phase C) phase angle of entrainment D) all of the above

C) phase angle of entrainment

Someone with ASPS is most likely to suffer from _____________ impairments and someone with DSPS is most likely to suffer from _______________ impairments. A) occupational social B) social social C) social occupational D) occupational occupational

C) social occupational

If a rhythm is circatidal, what periodicity does it have at the equator in a 12 h light:12 h dark cycle? A) 12 h B) 24 h C) 28 days D) 24.8 h

D) 24.8 h

which of the following is a good definition of a heat map? A) The color-based representation of the temperature under which an experiment was conducted B) A representation of a tissue in which different temperatures are represented by different colors C) A representation of a tissue in which the presence of a particular protein is represented by a color D) A representation of the expression levels of many genes at once in which colors are used to indicate quantity of RNA so that patterns are easy to distinguish

D) A representation of the expression levels of many genes at once in which colors are used to indicate quantity of RNA so that patterns are easy to distinguish

Which factors prevent night shift workers from shifting their biological clock to a reversed phase? A) Family and social obligations B) Activities on days off C) Sun light D) All of the above

D) All of the above

Absence of which of the following cyanobacterial circadian clock proteins causes gene expression to still be rhythmic, but with almost no ability to reset the phase of the rhythm with a dark pulse? A) KaiC B) KaiA C) RpaA D) CikA

D) CikA

Which of the following is an appropriate interpretation of the results shown above? A) Waveform of activity is stable under any light/dark conditions. B) Waveform of activity can be adjusted according to seasonal changes in photoperiod. C) Dim green light during the dark phase interferes with entrainment to T15/T30 cycles. D) Dim green light during the dark phase enables mice to entrain to an extreme T cycle.

D) Dim green light during the dark phase enables mice to entrain to an extreme T cycle.

Why were the components of the cyanobacterial circadian oscillator found in Synechococcus elongatus rather than in the cyanobacteria in which rhythms of biological processes were first discovered? A) S. elongatus is the only cyanobacterium that has a circadian clock B) S. elongatus doesn't fix nitrogen C) S. elongatus is the only cyanobacterium that naturally glows in the dark D) Genetics is easy in S. elongatus, so it's a good model system

D) Genetics is easy in S. elongatus, so it's a good model system

Some people are more active in the morning than others. This characteristic is an example of: A) Owl chronotype B) Delayed sleep phase syndrome C) Shift work sleep disorder D) Lark chronotype

D) Lark chronotype

The figures below show behavior of mice housed in light/dark cycles without (A-B) or with (C-D) dim green light during dark phase. In which part of the graphs are animals entrained to a T15 or T30 cycle? A) A and C B) B and D C) Only C D) Only D

D) Only D

Which of the following led to the negative feedback loop model for per circadian cycling? A) PER has a PAS domain B) PER protein levels are high when tim mRNA is high C) PER protein levels are affected by the action of kinases D) PER protein levels are high when per mRNA is low

D) PER protein levels are high when per mRNA is low

What was used to test whether bifurcated activity patterns were a result of masking? A) Constant LL conditions B) Asymmetric LDLD cycles C) Measurement of sleep D) Skeleton photoperiods

D) Skeleton photoperiods

What effect does bifurcation have on re-entrainment to different time zones? A) Bifurcation prevents re-entrainment B) Bifurcation slows re-entrainment down C) Bifurcation accelerates re-entrainment D) Bifurcation speeds up advances and slows down delays

C) Bifurcation accelerates re-entrainment

Two sets of identical mice are fed a high-fat diet; one set (ad lib) has access to the food all of the time, and the other has access to the food only during their normally active time (TRF). What is the predicted outcome? A) The ad lib mice will become fatter than the TRF mice, even though both sets consume the same number of calories B) The ad lib mice will be fatter, but the TRF mice will have fattier livers C) The ad lib mice will become fatter than the TRF mice, because the TRF mice will consume fewer calories during the restricted time D) The two sets of mice will weigh the same, because the TRF mice will eat more than the ad lib mice to make up for the short period of time they can eat

A) The ad lib mice will become fatter than the TRF mice, even though both sets consume the same number of calories

To observe circadian rhythms in cyanobacteria using a luciferase reporter gene A) The luciferase gene can be fused to essentially any promoter in the genome B) The luciferase gene must be fused to the kaiC promoter C) The luciferase gene must be fused to the kaiB promoter D) The luciferase gene must be fused to the kaiA promoter

A) The luciferase gene can be fused to essentially any promoter in the genome

Dr. Panda is performing studies of human eating habits using a smartphone app. All of the following are true regarding the study EXCEPT... A) The majority of people naturally restrict their eating to a duration of 12h or less per day. B) The majority of people eat breakfast later on the weekend than on weekdays (metabolic jet lag). C) In a very preliminary study, people on a time-restricted feeding schedule have lost weight without being told to make any other changes in what they eat. D) Participants are instructed to take a photo of everything they eat

A) The majority of people naturally restrict their eating to a duration of 12h or less per day.

If you give Drosophila a short pulse of light you can reset the phase of its circadian rhythms. What determines whether you get a phase advance or a phase delay? A) Whether TIM levels are rising or falling at the time of the pulse B) Whether the light is absorbed by CRY or TIM C) Whether PER is a PERshort or PERlong version D) Whether Doubletime is present

A) Whether TIM levels are rising or falling at the time of the pulse

what is the zeitgeber that is directly sensed by components of the cyanobacterial circadian oscillator for entrainment in day-night cycles? A) oxidation state of the quinone pool B) red light C) temperature D) blue light

A) oxidation state of the quinone pool "Conclusion: They concluded that quinone is the signal for cyanobacteria to perceive the time of the day. "

What procedure eliminates melatonin in the bloodstream of mammals? A) pinealectomy B) exposure to constant darkness C) ovariectomy D) blinding

A) pinealectomy

The light given off by luciferase is easy to measure, but for technical reasons it's hard tell exactly where the light souce is. Green Fluorescent Protein (GFP) doesn't give off light unless you shine blue light on it, so it requires a little more work, but you can tell where the light is coming from. Given that information, what kind of reporter fusion would be the best if you need to know not only whether a gene is being expressed, but where inside the cell your protein of interest is localized? A) A transcriptional fusion between the luciferase gene and the promoter of your gene of interest B) A translational fusion (protein fusion) between GFP and your protein of interest C) A translational fusion (protein fusion) between luciferase and your protein of interest D) A transcriptional fusion between the GFP gene and the promoter of your gene of interest

B) A translational fusion (protein fusion) between GFP and your protein of interest

Biological clocks based on which of the following rhythms probably do not exist in nature? A) Circalunar (~28 days) B) Circasemifortnight (~7 days) C) Circatidal (~12.4 or ~24.8 hours) D) Circannual (~365 days)

B) Circasemifortnight (~7 days)

Below is a heat map that shows the expression of 1300 rhythmic genes in the liver over the course of a 24 h period. What correctly completes this sentence. From this we should conclude that... A) The interval between each sample was 6 h B) Genes in the liver peak at different phases C) Genes in the liver have different free-running periods D) Genes in the liver are free-running with a period > 24 h

B) Genes in the liver peak at different phases

As discussed by Dr. McCarthy what manipulation led to increased measures of depression in mice? A) Knocking in extra copies of Cry1 B) Injection of shRNA to knock-down Bmal1 in SCN C) Lesion of the SCN D) Injection of luciferin into ventricles

B) Injection of shRNA to knock-down Bmal1 in SCN

Which statement about melatonin's use as a phase marker in humans is most accurate? A) It is a poor phase marker because it fluctuates markedly from day to day B) It is a good phase marker because it is not masked by sleep, feeding and exercise C) It is a good phase marker because it is not affected by any environmental factor D) It is a good phase marker because it reflects the homeostatic need for sleep

B) It is a good phase marker because it is not masked by sleep, feeding and exercise

What is/are considered negative element(s) of the Drosophila clock TTFL? A) E-boxes B) Per and Tim C) phosphorylation D) CYC and CLOCK

B) Per and Tim

How could we determine whether the 2 hamsters from the following figure are truly differently entrained and the differences we are seeing are not an acute response to the different photoperiods? A) The fur coat will look different and testis will have different sizes in the two conditions B) The relative lengths of subjective night will endure after release in DD C) Their melatonin profiles will look different. D) All the above statements are true, but NONE of them distinguishes between entrainment differences and acute effects.

B) The relative lengths of subjective night will endure after release in DD

Which of the following is true regarding circadian regulation of gene expression in various tissues in a mammal? A) If a gene is expressed rhythmically in one tissue, it is expressed rhythmically in other tissues as well, and with the same phase of expression. B) Whether a given gene is expressed rhythmically, and if it is, the phase of rhythmic expression, is specific to a particular tissue. C) Whether or not a gene is expressed rhythmically depends on the gene itself: there are fundamentally rhythmic and non-rhythmic genes, regardless of tissue. D) Essentially all genes are expressed rhythmically in all tissues of a mammal, and only the phase is different from tissue to tissue.

B) Whether a given gene is expressed rhythmically, and if it is, the phase of rhythmic expression, is specific to a particular tissue.

For a ground squirrel, which of the following is NECESSARY to entrain its circannual rhythm? A) experiencing annual fluctuations in temperature B) having a working pineal gland C) experiencing a completely natural cycle of daylengths D) exposure to a daylength pattern that is 365 days long

B) having a working pineal gland

An organism shows stable entrainment to a daily light pulse. The light pulse always falls 1 h into the subjective night. What is tau in DD? A) greater than 24 h B) less than 24 h C) exactly 24 h D) impossible to determine

B) less than 24 h

The following symptoms all relate to which DSM-5 diagnosis? 1. persistently elevated or irritable mood 2. grandiosity (may be of delusional quality) 3. decreased need for sleep 4. pressured speech 5. racing thoughts A) insomnia B) manic episode C) major depressive disorder D) minor depressive disorder

B) manic episode

What evidence was collected to establish that clock gene rhythms are damped in specific parts of the brain of people with a history of depression? . A) sleep/wake behaviors B) post-mortem brain analysis C) PET scans D) neural imaging

B) post-mortem brain analysis

What properties of circadian function appear to depend on having a network of SCN cells? A) sensitivity to neurotransmitters B) resilience against genetic mutations C) having a period that is long enough to work for a circadian system D) Choices A, B and C

B) resilience against genetic mutations

A completely blind person is free-running with a period of 24.5 h. Today, her clock is in perfect phase with her normal (and permanent) 9 a.m.-5 p.m. work schedule. In approximately how many days will her sleep/wake rhythm be 12 h out of phase with her work schedule? A) 12 B) impossible to know because FRP is too unstable for such calculations C) 24 D) 48

C) 24

Nitrogen fixation in the unicellular cyanobacterium Cyanothece is under circadian control, and it peaks in the night in an LD cycle. However, nitrogen fixation in the filamentous cyanobacterium Anabaena, which makes heterocysts, is not restricted to the night time. What difference between the organisms explains this difference in timing? A) Anabaena nitrogenase is not sensitive to oxygen B) Photosynthesis in Anabaena does not produce oxygen C) Anabaena confines oxygen-producing photosynthesis and oxygen-sensitive nitrogen fixation to two different cell types D) The PRC of Anabaena for photosynthesis is very different from that in Cyanothece

C) Anabaena confines oxygen-producing photosynthesis and oxygen-sensitive nitrogen fixation to two different cell types

In what environments are cyanobacteria found? A) Only on the human body B) Only in enviroments where light and dark oscillate noticeably year-round C) Aquatic and terrestrial environments from the north to south poles and in between D) Only in environments where there is abundant water

C) Aquatic and terrestrial environments from the north to south poles and in between

Which of the following is a reasonable explanation for how the cyanobacterial circadian oscillator controls rhythmic expression of genes? A) KaiC binds to RNA polymerase rhythmically B) KaiC binds to promoters rhythmically C) The KaiABC complex itself acts as a kinase to phosphorylate a transcription factor rhythmically D) The KaiABC oscillator interacts directly with the kinase SasA and the phosphatase CikA, which results in rhythmic phosphorylation of the transcription factor RpaA

D) The KaiABC oscillator interacts directly with the kinase SasA and the phosphatase CikA, which results in rhythmic phosphorylation of the transcription factor RpaA

Refer to the figure below depicting wheel-running under free-running conditions... Which statement is FALSE? A) The actogram is double-plotted B) The FRP > 24 h C) The record includes a phase advance D) The recording must come from a nocturnal animal

D) The recording must come from a nocturnal animal

What do ZTL and FKF1 have in common in their roles in biological timing in Arabidopsis? A) They both absorb red light B) They are both transcription factors C) They are both components of the basic, simplified, TTFL D) They both absorb blue light and affect the stability of other proteins

D) They both absorb blue light and affect the stability of other proteins

What happens to SCN cells after 5-6 days of TTX? A) They increase expression of per1 B) They lose the ability to oscillate C) They die D) They lose synchrony with other cells

D) They lose synchrony with other cells

What is the purpose of conducting an action spectrum experiment on the circadian system? A) To provide a summary of the various possible effects of light on circadian rhythms B) To determine which organs are sensitive to zeitgebers C) To assess phase-resetting effects of drugs on the SCN in vitro D) To compare effects of different wavelengths of light on a specific circadian response

D) To compare effects of different wavelengths of light on a specific circadian response

Plants store starch during the day and metabolize it at night. In LD 12:12 they will use the starch up right about dawn. If the lights are turned off 4 h early one evening, the plants will use the starch more slowly and still use it up about dawn. However, if the lights are turned on 4 h early one morning (when the plants are usually still in the dark), the plants will have leftover starch. What explains this difference in how plants deal with these two unusual 4h changes in the light pattern? A) The starch degradation genes are acutely affected by light B) This phenomenon has nothing to do with circadian rhythms C) The PRC is different at dawn and dusk D) When the lights come on 4 h early, the clock cannot anticipate this change

D) When the lights come on 4 h early, the clock cannot anticipate this change

Which of the following describes the position of the main circadian pacemaker of mammals? A) in the hypothalamus B) close to a ventricle C) above the optic chiasm D) all of the above

D) all of the above

LD16:8 and LD8:16 can be assumed to result in different... A) zeitgeber strength B) coupling C) periods D) waveforms

D) waveforms