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BIOL1020 > Core skills in science > Flashcards

Core skills in science Flashcards

1
Q

Whats the correct sentence?

  1. The genome sequence is specific to a person
  2. The genetic code is specific to a person
A

The correct sequence is 1

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2
Q

Read through lecture 2 to look at the correct language and common beginnings for certain words

A
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3
Q

What do the following mean;

  1. Homologous
  2. homogeneous
  3. Homogenous
  4. Homodimer
A
  1. Homologous: same origin/ share ancestor
  2. Homogeneous: same compositio, nature of kind; uniform appearance
  3. Homogenous: same genetic origin
  4. Homodimer: joined pair of two identical things
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4
Q

in basic, acidic and neutral solutions, write the relationship between hydroxide and hydrogen ions?

A

Basic: [OH-] > [H+]

Neutral: [H+] = [OH-]

Acidic: [H+] > [OH-]

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5
Q

What should a sample chosen represent?

A

The whole population

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6
Q

There can be sample bias. What are the forms of this?

A
  • sample chosen by researcher with bias
  • sample is self-selected
  • sample of one population applies to another
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7
Q

What does an average show?

A

The central tendancy

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8
Q

What are the uses of bioinformatics?

A
  1. sequence database and analytical tools
  2. genome assembly, gene finding, gene structure
  3. evolutionary relationships (gene and organisms)
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9
Q

Why are computers needed for bioinformatics?

A
  1. quantity
  2. complexity
  3. time
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10
Q

The shotgun approach was the first approach to gene assembly. what did they do for this?

A
  • they broke the DNA up into around 500 bp fragments
  • find sequence of each fragments on its own
  • put back together into right order
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11
Q

Whats the equation for genome?

A

Genome= genes (minority) + ‘junk’ DNA (majority)

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12
Q

What are the major areas in sequence analysis by computers that they are able to spot in the genome to help with gene finding?

A
  1. ORFs (open reading frames)
  2. identify repeats
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13
Q

What can gaps in the genome represent and what is it labelled and why?

A

Gaps can represent insertion/ deletion mutations (indels). however; one cant tell which mutation it is so the region is labelled ‘indel’

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14
Q

Bioinformatics sequence comparisons can detect what 3 things?

A
  1. changes to the coding sequence (different protein/ function)
  2. Gene duplication (new protein/ function)
  3. Changes to regulatory regions (more/less proteins)
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15
Q

What two components does a hypothesis contains and what are these?

A
  1. The test hypothesis H1: The proposition of biologically informative patterns
  2. A refutable null hypothesis H0: No pattern, against which to callibrate the test hypothesis
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16
Q

What are the uses of hypothesis testing?

A
  1. detecting associations
  2. predicting future events
  3. testing cause and effects

(these are all probabilities based on defined assumptions)

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17
Q

What does an experiment measure and what is it designed to test?

A

An experiment measues a response to a controlled manipulation with a treatment; the experiment is designed to test a refutable hypothesis

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18
Q

What is the ‘bell’ shape graph a characteristic of?

A

many natural attributes that are free to vary on an unbound continuous scale

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19
Q

When is something called a normal distribution?

A

when it can be descirbed by just two parameters: the mean and the variance

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20
Q

when is something determined to have a non-normal distribution?

A

a proportion is bounded between 0 and 1, and its frequency distribution therefore has truncated tails

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21
Q

Whats the formula for the mean?

A
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22
Q

Whats the formula for the variance and standard deviation?

A
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23
Q

Whats the formula for the standard error of the mean?

A

SE= SD/ root N

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24
Q

look up tests for testing non-zero means, t-tests, chi tetss, one and two sample tests

A
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25
Q

Validity of all stats depends on meeting what underlying assumptions?

A
  • sampling units are randomly selected from the population
  • obervations are independant (one observation per individual)
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26
Q

What are additional assumptions made when testing means?

A
  • normal distribution of residuals around the sample means
  • all samples have equal variance
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27
Q

What are addition assumptions made when testing trends?

A
  • variance does not increase with mean
  • the relationship is linear
28
Q

When testing for differences between means with an analysis of variance (ANOVA) what does the test assume?

A
  • random sampling
  • independant observations
  • normally distributed residuals
  • equal variation around means
29
Q

Whats does a linear regression analysis test assume?

A
  • random sampling
  • independant observations
  • normally distributed residuals
  • constant variation around line
  • linear trend
30
Q

What does the chi-squared test assume?

A
  • random sampling
  • independant observations
31
Q

What are the principles from medical ethics?

A
  • doing good
  • not doing harm
  • autonomy
  • justice
32
Q

Why would we need a hippocratic oath for scientists?

A
  • ease puplic distrust of the scientist
  • prevent conflicts of interest
  • protect scientists’ emplyment
33
Q

What might a scientists hippocratic oath contains?

A
  • being honest and open with colleagues and the public ‘
  • reducing experimentation on animals
  • safeguarding the environment
  • not plagarising or sabotaging other scientists’ work
34
Q

What is modafinil used to treat?

A

Narcolepsy and other sleep disorders

35
Q

What are the ten most important things to know about research ethics?

A
  1. be honest
  2. be fair
  3. do no harm
  4. do good research
  5. know and follow the rules
  6. bad rules should be changed, not broken
  7. be a good citizen
  8. when in doubt, ask questions
  9. listen to the still, small voice of your conscience, especially when it is threatened to be overwhelmed by the loud, insisten voice of stress
  10. if you suspect unethical behaviour, proceed cautiously
36
Q

What are some gene editing tools?

A

1. TALENs

Transcription activator-like effector nucleases

2. ZFNs

Zinc finger nucleases

3. CRISPR-Cas9

Clustered reguarly interspaced short palindromic repeats

37
Q

Why is human genome editing a problem?

A
  • unnecessary (not-therapeutic)
  • risk
  • no ethical approval
  • limited informed consent
38
Q

Whats the definition of enhancement?

A

‘improvement’ of human performance, appearance or behaviour through genetic science, medicine and technology

39
Q

is correlation causation?

A

no

40
Q

Draw the following:

  • positive correlation
  • inverse correlation
  • no correlation
  • non-linear correlation (curvilinear)
A
41
Q

Does a line of best fit show the relationship of the data?

A

no

42
Q

What can be used to draw a LOBF?

A

logs

43
Q

what does an R2 value show?

A

the correlation

R2 = 0 means NO correlation

R2 = 1 means PERFECT correlation

44
Q

Whats meant by extrapolation?

A

extending a line beyond the measured points to help predict outcomes

45
Q

what type of graphs are error bars found with?

A

bar charts

line graphs

46
Q

what do error bars represent?

A

the variability of the data

47
Q

What can you get error bars for?

A
  • standard error (SEM)
  • standard deviation (SD)
  • confidence interval
48
Q

When there is a poorly visible sample as it could be too opaque, too transparent or even too small, what can be done in order to interpret the image?

A
49
Q

Name some detection tools?

A
  • X-rays and CT scans
  • spectroscopy and MRI
  • Microscopy- optical, confocal, electron
50
Q

Name some visualising tools?

A
  1. dyes/stains
  2. fluorescence
  3. radioisotopes
51
Q

Tell me some main features of X-rays?

A
  • monochrome/ grey scale
  • density-based visualisation
  • not all tissues show up
52
Q

Tell me about CT scans

A
  • X-ray images taken at multiple angles
  • CT scans can be assembled to create a 3D computer model
  • fossils: background rock can be digitally removed
53
Q

Tell me some key facts about NMR spectroscopy?

A
  • based on protons rather than electrons
  • MRI scans are a type of NMR
    also greyscale only
54
Q

Tell me key facts about MRI?

A
  • can be used on living speciments in real time
  • MRI san slices can be assembled to create an animation or 3D computer model
55
Q

What does 3D construction require?

A

it combines MRI (soft tissue) and CT (hard tissues) scans give even more information

56
Q

name 2 histology stains

A

Haematoxylin and Eosin (H&E)

57
Q

Name a grams stain

A

crystal violet (retained by gram +ve bacteria)

pink counterstains required to see gram -ve bacteria

58
Q

What can be used to stain bone?

A

Alizarin red

59
Q

What can be used to stain cartilage?

A

Alician blue

60
Q

Tell me about fluorophores (fluorescent visualisation tools)?

A
  • absorb one wavelength and emit at a longer wavelength
  • different fluorophores emit different colours
  • multiple colours on one sample
61
Q

Give some example uses for fluorophores?

A
  • Flura-2
  • cell type- specific
  • live/dead cells
  • infected versus healthy cells
  • cytoskeleton structure visualisation
62
Q

Tell me about GFP?

A

GFP: green fluorescence proteins

  • made of 238 Amino acids
  • excitation: blue
  • emission: green
63
Q

Name 3 types of microscopy?

A
  1. optical
  2. confocal
  3. electron
64
Q

Tell me about confocal microscopy?

and the colouring

A
  • laser based light microscopy
  • fluorescence based
  • very thin sections–> sharp images
  • optical slices through 2 types of cell, both of which have been labelled with red and green fluorophobes
  • yellow and orange colouring comes form co-localisation of red and green at the same place in the cell
65
Q

Tell me about electron microscopy and the two types of electron microscopes?

A
  • higher magnification
  • greyscale images
  • two types
  1. Scanning EM
  2. Transmission EM
66
Q

What are the two problems encoutered when trying to work out the molecular structure?

A
  1. determining the shape of moelcules
  • electron microscopy
  • X-ray crysallography
  • NMR
  1. displaying the 3D molecules in 2D
67
Q

What can be used to determine protein structures?

A
  • An electron density map: shape of amino acids is known and the order of amino acids is known and this can be used to map electron density
  • X-ray crystallography
  • NMR: 2D NMR spectrum–> ‘family’ of structures

BIOL1020 (1 decks)

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