BIMM 116 Final

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?

24

If a rhythm is circatidal, what periodicity does it have at the equator in a 12 h light:12 h dark cycle?

24.8 h

Which of the following is a good definition of a heat map?

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

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

Which of the following is the most likely explanation for the fact that aCCA1 null mutant of Arabidopsis is not arrhythmic?

CCA1 is part of a family, and other members have partially over lapping functions

What molecular event is responsible for the resetting of the phase of rhythms in Drosophila that is given a short light pulse?

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

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?

CikA

Biological clocks based on which of the following rhythms probably do not exist in nature?

Circasemifortnight (~7 days)

Which of the following is a reasonable explanation for how the cyanobacteria circadian oscillator controls rhythmic expression of genes?

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

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?

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

What is the role of the circadian clock in human sleep?

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

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?

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

What is meant by the phrase "hands of the clock"?

Any observable process controlled by the clock

In what environments are cyanobacteria found?

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

What effect does bifurcation have on re-entrainment to different time zones?

Bifurcation accelerates re-entrainment

In rodents, light at night can make clocks more flexible if the light is approximately as bright as

Dim moonlight

Which of the following measurements are routine components of polysomnography?

Eye movements, muscle tension, brain waves

Which of the following proteins directly absorbs light and contributes to the"external coincidence" regulation of flowering time in Arabidopsis?

FKF1

Which factors prevent night shift workers from shifting their biological clock to a reversed phase?

Family and social obligations, Activities on days of, Sun light

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?

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

For a ground squirrel, which of the following is NECESSARY to entrain its circannual rhythm?

Having a working pineal gland

Which of the following describes the position of the main circadian pacemaker of mammals?

In the hypothalamus, close to a ventricle, above the optic chiasm

As discussed by Dr. McCarthy what manipulation led to increased measures of depression in mice?

Injection of shRNA to knock-down Bmal1 in SCN

Which statement about melatonin's use as a phase marker in humans is most accurate?

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

Which of the following is NOT a feature of KaiB in the cyanobacterial circadian oscillator?

It is a kinase that phosphorylates KaiC

Which of the following is true of the homeostatic drive in the human sleep-wake cycle?

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?

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

Some people are more active in the morning than others. This characteristic is an example of:

Lark chronotype

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

Manic Episode

Which of the following blind individuals is most likely able to entrain normally to the day/night cycle?

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

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?

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 of the following led to the negative feedback loop model for percircadian cycling?

PER protein levels are high when per mRNA is low

What is/are considered negative element(s) of the Drosophila clock TTFL?

Per and Tim

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?

Per3

Which of the following features is similar between cyanobacterial and eukaryotic circadian mechanisms?

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

What properties of circadian function appear to depend on having a network of SCN cells?

Resilience against genetic mutations

Which of the following is NOT clearly classified as a circadian rhythm disorder in the DSM5 psychiatry manual?

Schizophrenia

What geophysical phenomenon is associated with the depressive syndrome called SAD?

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?

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

Which of the following types of variations in human genomes forms the basis of genome-wide association studies of human disease?

Single nucleotide polymorphisms

What was used to test whether bifurcated activity patterns were a result of masking?

Skeleton photoperiods

All of the following are a reasonable hypotheses regarding why animals sleep EXCEPT

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?

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

To observe circadian rhythms in cyanobacteria using a luciferase reporter gene

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

Dr. Panda is performing studies of human eating habits using a smart phone app. All of the following are true regarding the study EXCEPT

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

What do ZTL and FKF1 have in common in their roles in biological timing in Arabidopsis?

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

What happens to SCN cells after 5-6 days of TTX?

They lose synchrony with other cells

How do mammalian peripheral tissues like liver and heart become entrained by the external environment?

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

What is the purpose of conducting an action spectrum experiment on the circadian system?

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

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?

Vest to restrict food intake to the daytime historically active hours of the day

Plants store starch during the day and metabolize it at night. In LD 12:12they will use the starch up right about dawn. If the lights are turned off 4h 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 left over starch. What explains this difference in how plants deal with these two unusual 4 h changes in the light pattern?

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

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?

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

Which of the following is true regarding circadian regulation of gene expression in various tissues in a mammal?

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

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?

less than 24 h

What is the Zeitgeber that is directly sensed by components of the cyanobacterial circadian oscillator for entrainment in day-night cycles?

oxidation state of the quinone pool

If given FRP, T and a phase response curve, what would you be able to predict?

phase angle of entrainment

What procedure eliminates melatonin in the bloodstream of mammals?

pinealectomy

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?

post-mortem brain analysis

Someone with ASPS is most likely to suffer from _____________ impairments and someone with DSPS is most likely to suffer from_______________ impairments,

social occupational

When cyanobacteria are dividing more than once a day

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

LD16:8 and LD8:16 can be assumed to result in different

waveforms