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biochemistry > semester 1 > Flashcards

semester 1 Flashcards

1
Q

define population

A

all the individual items that can be studied

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2
Q

define sample

A

a selection from a population

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3
Q

define individuals

A

in a sample are sample units, subjects or cases

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4
Q

define the variable type: continuous

A

have an infinite number of values eg. length, weight, height

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5
Q

define the variable type: discrete (discontinuous)

A

have limited number of values + can be subdivided

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6
Q

define the variable distribution type: parametric

A

these can be plotted to follow a distribution model these can be discrete (poisson, binomial, neg binom, hypergeometric) or continuous (rectangular, uniform, chi^2, exponential, normal)

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7
Q

define the variable distribution type: non-parametric

A

can’t be assigned to any distribution + so can be less ‘powerful’

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8
Q

define the variable distribution variation: modality

A

a distribution can be uni or multi-modal

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9
Q

define the variable distribution variation: skewness

A

a distribution have symmetry, positive or negative skew

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10
Q

define the variable distribution variation: kurtosis

A

a distribution can be neutral, platy or lepto-kurtic

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11
Q

what’s the basic 3 of central tendency?

A

mean- sum all + divide by number of individuals
median-put in order + find one in middle
mode-most common one

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12
Q

what’s the basic 3 of variation?

A
  • variance= s^2
  • standard deviation= S
  • standard error of mean
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13
Q

variance, SD + SEM step by step

A

-calculate mean
-write table that subtracts the mean from each observed value
-square each of differences
-sum all
-divide by n-1 where n is number of individuals. this is s^2
-square route to get S
-to get SEM divide S by square root of n
-

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14
Q

define variation

A

how far individuals are spread out in relation to each other

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15
Q

define standard deviation

A

how far observations are comparatively from a mean

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16
Q

what is required when using T test?

A

paired or unpaired data

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17
Q

what is a t-test?

A

tests whether there’s significant difference in means of 2 data sets. value obtained is compared to a critical value which helps determine how likely results were due to chance

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18
Q

what is the p value in a t-test?

A

gives the probability of any observed difference in measurement between the 2 groups having happened by chance

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19
Q

when is the null hypothesis rejected?

A

if there’s a difference between 2 groups (p<0.05)

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20
Q

what needs to be reported when doing a t-test?

A
  • 1 vs 2 tailed test?
  • p value + significance + level
  • degrees of freedom
  • t-value
  • test of variance
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21
Q

what is linear regression?

A
  • used to quantify how one set of variables relates to another
  • used if relationship is linear between the variables
  • 2 variables: dependent (response) y-axis vs independent (explanatory) x-axis
  • dependent variable value dependent on independent value
  • y=mx+c
  • R^2 (goodness of fit)
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22
Q

how do you calculate C1?

A

C1=(C2V2)/V1

  • C1, initial concentration
  • V1, initial volume
  • C2, diluted concentration
  • V2, diluted volume
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23
Q

what are the beer-lambert equations?

A

A= ε x C x l

  • A, absorbance (unitless)
  • ε, absorption coefficient
  • c, concentration of solution
  • l, pathlength, ie width of curvette
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24
Q

when do you round using decimal places?

A

when using addition or subtraction

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25
Q

when do you round using significant figures?

A

when using multiplication or division

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26
Q

The subatomic particles found in atoms consist of which fundamental particles?

A

quarks and leptons

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27
Q

what is the atomic number equal to?

A

number of protons

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28
Q

what is the mass number equal to?

A

sum of protons and neutrons

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29
Q

what are isotopes?

A

2 of the same element differ in number of neutrons but have the same number of protons

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30
Q

what are electrons?

A

sub-atomic particles having almost negligible mass. electrons move around nucleus of atom with speeds close to that of speed of light

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31
Q

what are atomic orbitals?

A

regions in space where there’s high probability of finding electrons

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32
Q

define the 1s orbital

A

a spherical region of space close to and surrounding the nucleus where there’s high probability of finding electron

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33
Q

why is water important?

A
  • most abundant substance in living systems, 75% human brain is water, 75% of tree is water
  • normal metabolic cellular activity can only occur when cells are at least 65% water
  • water + its ionisation products are critical determinants biomolecule structure and function, proteins, lipids, carbohydrates
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34
Q

what are some properties of water?

A
  • melting point 0°C
  • boiling point 100°C
  • heat of vaporization 2,260J/g
  • water in aqueous form still has high number of hydrogen bonds however, lifetime of each bond is very brief + then it’ll form a bond with different or same water molecule. known as flickering clusters
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35
Q

why is waters melting point high?

A

due to hydrogen bonding that can occur between these molecules. when water is in its ice structure + forming a crystal lattice it means each water molecule is making 4 hydrogen bonds

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36
Q

are hydrogen bonds unique to water?

A

no

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37
Q

describe hydrogen bonds

A
  • special dipole, dipole bond between an electronegative atom + a hydrogen atom bonded to another electronegative atom
  • relatively weak bonds, bond dissociation energy ~23KJ/mol
  • always involves hydrogen atom
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38
Q

what are biologically important hydrogen bonds?

A
  • between hydroxyl group of an alcohol + water
  • between carbonyl group of a ketone + water
  • between peptide groups in polypeptides
  • between complimentary bases of DNA
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39
Q

what are amphipathic compounds?

A
  • contain regions that are polar + regions that aren’t
  • non-polar parts interact leaving polar parts on outside
  • when mixed with water, hydrophilic regions interact with water + dissolve, whilst hydrophobic regions cluster together to form von der waals
  • able to minimise hydrophobic interaction with water but maximise hydrophilic interaction with water to form stable micspelles
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40
Q

what are examples of amphipathic compounds in biology?

A
  • phospholipid bilayer of cell membrane
  • proteins + their 3D folding
  • proteins interaction with phospholipid bilayer of cell membrane
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41
Q

what’s hydrolysis?

A

chemical reaction/ process in which chemical compound is broken down by reaction with water

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42
Q

what’s condensation?

A

reaction in which 2 molecular fragments are joined + a water molecule is produced

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43
Q

describe the dissociation of water

A

hydrogen atom of hydrogen bond may find itself closer to the oxygen atom of a neighbouring water molecule than to the oxygen atom of its own molecule. the covalent O-H bond in H2O molecule stretches + hydrogen bond between molecules shortens. eventually covalent O-H bond stretches so far it breaks + new O-H bond forms with neighbouring molecule. process creates 2 new species each of which has full electric charge

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44
Q

how many water molecules dissociate in pure water at room temperature?

A

1 in a billion

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45
Q

define acid

A

substance that donates hydrogen ions (H+, protons) by dissociation

46
Q

what happens to strong acids in water?

A

completely dissociates

47
Q

what happens to weak acids in water?

A

partially dissociates

48
Q

what’s a base?

A

substance which can extract a proton from water forming a hydroxide ion and can directly produce a hydroxide ion by dissociation

49
Q

what happens to strong bases in water?

A

completely dissociates

50
Q

what happens to weak bases in water?

A

partially dissociate; they extract a H+ from water and leave OH- , an equilibrium is formed

51
Q

how is pH measured?

A

by molar concentration of hydroxonium ions

-pH= -log10[H+]

52
Q

what’s the physiological pH?

A

7.4

53
Q

what are the units of [H] in pH=-log[H+]

A

M

54
Q

how is physiological pH maintained?

A

by buffer systems:

  • dihydrogen phosphate system
  • carbonic acid system
55
Q

what is a buffer?

A

a solution that can resist changes in pH after the addition hydroxonium or hydroxide ions and consist of almost equal concentrations of conjugate acid and base

56
Q

at what point does [conjugate base] = [conjugate acid]?

A

pKa

57
Q

What is the pKa when the buffering region is 4.5 to 6.5?

A

5.5

58
Q

what’s the pH of lysosomes?

A

4.5

59
Q

what’s the pH of stomach?

A

1.5-3.5

60
Q

what’s the buffer region?

A

pKa +/- 1 pH unit

61
Q

what is Henderson-Hasselbalch equation?

A

pH=pKa + log(base/acid)

pH= pKa + log(proton acceptor/ proton donor)

62
Q

what’s the isoelectric point?

A

pH at which net charge for a molecule is 0

63
Q

Carbon is an element in group 4, how many electrons in its outer bonding orbital?

A

2

64
Q

how does carbon form 4 covalent bonds?

A

by creating a hybrid sp3 orbital

65
Q

A single carbon-carbon bond consist of how many electrons and is known as what?

A

2 electrons + a sigma bond

66
Q

what’s a pi bond?

A

part of a double carbon-carbon bond

67
Q

what is an alkane?

A

molecule of carbon and hydrogen only with all single bonds

68
Q

what’s the formula of an alkane?

A

CnH2n+2

69
Q

what is an alkane molecule with a single carbon referred to as?

A

methane

70
Q

what is an alkane molecule with 2 carbons referred to as?

A

ethane

71
Q

what is an alkane molecule with 3 carbons referred to as?

A

propane

72
Q

what is an alkane molecule with 4 carbons referred to as?

A

butane

73
Q

what are some of the properties of alkanes?

A
  • non-polar, so few intermolecular bonds
  • small hydrocarbons have very low melting + boiling points so tend to be gasses at rt
  • as chain length increases carbon chains wrap around each other increasing boiling points
  • hexane, heptane, octane tend to be liquid at rt
74
Q

what’s the formula for an alkene?

A

CnH2n

75
Q

describe alkenes

A
  • all unsaturated so have at least 1 pi bonded carbon
  • more reactive than alkanes and less flexible
  • low melting + boiling points
76
Q

what are the naming rules for alkenes?

A
  • named for longest chain of carbon atoms
  • number indicates location of double-bond
  • use lowest number possible
  • suffix =ene
77
Q

what are aromatic compounds?

A

all contain benzene, pi bonding, delocalised electrons provide stability to the molecule. benzene + its derivatives are all carcinogenic

78
Q

what does an increase in chain length of alcohols lead to

A

increase in organic nature

79
Q

how do you oxidise a primary alcohol into a carboxylic acid?

A

Reflux with acidified Potassium Dichromate

80
Q

why can’t a tertiary alcohol be oxidised?

A

Carbon can only make 4 bonds

81
Q

describe naming alcohols?

A
  • named for longest chain
  • number represents location of alcohol group
  • suffix= ol
82
Q

describe aldehydes

A
  • when you oxidise alcohol you react it or heat it with a catalyst (acidified potassium dichromate)
  • named for longest carbon chain
  • number represents location of functional group
  • suffix= al
83
Q

describe ketones

A
  • comes from oxidising a secondary alcohol with acidified potassium dichromate
  • formed often from breakdown product of fatty acids + lipids + proteins
  • named for longest carbon chain
  • number represents location of functional group
  • suffix= anone
84
Q

describe carboxylic acids

A
  • terminal oxidation product of a primary alcohol
  • in order to achieve carboxylic acid status, you must reflux with acidified potassium dichromate
  • named for longest carbon chain
  • number represents location of the functional group
  • suffix= anoic acid
  • can be found in amino acids + fatty acids
85
Q

how are carboxylic acids made?

A
  • once ethanol is in body it’s metabolised by 2 different enzymes. first is alcohol dehydrogenase which converts ethanol into acetaldehyde (ethanal). aldehyde dehydrogenase is a molecule which will create or generate acetic acid from the ethanal + that acetic acid is converted safely in liver to acetyl-scoA
  • NADH + acetyl-scoA produce ATP which diminish reliance on cells of liver on glucose + fat so less energy obtained from glucose + fats and so mechanism of detoxification is one of sources of weight gain through alcohol consumption
86
Q

describe esters

A
  • often involved in hormone formation
  • combination of alcohol and a carboxylic acid
  • suffix= anoate
87
Q

describe amines

A
  • organic amines can be fairly toxic in terms of carcinogenicity
  • group represented by NH2
  • primary amine is one where you have a single organic chain attached to the nitrogen element
  • in secondary amine you have 2 organic chains attached to central nitrogen
  • primary amine named for carbon chain
  • secondary + tertiary amines begin with N and N denotes that the nitrogen is at the centre
  • chins named for length of chain
88
Q

what does a chiral carbon have

A

4 different functional groups

89
Q

what are amine bonds?

A

have an organic acid bonding with an organic amine, which is what happens when amino acids linked together to form protein chains

90
Q

describe phosphates

A
  • represented by the PO4- group
  • nucleotide involves having a base molecule of ribose or deoxyribose
  • triphosphate is one where all phosphate molecules are attached to each other
91
Q

describe sulfhydryl’s

A

-in construction, every gene in genome, methionine is very first amino acid. it’s often edited out of final protein. however, it’s first amino acid because sulfhydryl’s group ive protein level of stability

92
Q

what are the 2 stereoisomers for most amino acids?

A

L-isomer + D-isomer

93
Q

amino acid classification of polar, uncharged R group

A
  • don’t have an explicit, positive or negative charge in chain
  • serine, threonine =hydroxyl amino acids
  • cysteine= can form disulphide bonds/bridges
  • asparagine, glutamine = a c double bond o
94
Q

describe the formation of disulphide bonds/bridges/cross-links

A
  • 2 cysteine’s can form oxidised product cystine + this is formation of disulphide bridge
  • important because used + important in forming 3D structure of proteins, linking different parts of protein or even components of protein. secondly conversion to cystine important in terms of disease because this component here is found at high levels in tissues that are under oxidative stress
95
Q

amino acid classification of aromatic R group

A
  • characterised by inclusion of benzene ring structure
  • phenylalanine, tyrosine, tryptophan
  • amino acids characterised by being highly hydrophobic due to benzene ring structure + often referred to as bulky amino acids because of large size of side chain
  • only 3 protein based amino acids that absorb UV light
96
Q

amino acid classification of positively charged R group

A
  • lysine, arginine, histidine
  • also known as basic amino acid
  • amino acid has explicit positive charge on side chain. charge can be important in forming charge charge interactions ie electrostatic interactions, interactions can occur between positively + negatively charged amino acids in protein structures or can take place between positively charged amino acid and a negatively charged metal or micronutrient
97
Q

amino acid classification of negatively charged R group

A
  • also known as acidic amino acids
  • aspartate + glutamate
  • have explicit negative charge so can form electrostatic interactions with positively charged basic amino acids or with other compounds
98
Q

how is the isoelectric point calculated?

A

P1= (pKa1 + pKa2) / 2
-pKa1 is carboxyl group
pKa2 is protonated amine group

99
Q

what is the effect of a low pH on amino acids?

A

carboxylate will be in carboxylic acid form, it’s fully protonated

100
Q

what is the effect of a increased pH on amino acids?

A

1 of carboxylates in amino acid will lose its proton, so this forms coo-

101
Q

What are the dietary sources of Acetyl CoA?

A

carbohydrates + proteins

102
Q

what processes is Acetyl-Co-A important?

A
  • Fatty acid biosynthesis
  • B-oxidation of fatty acids
  • Krebs cycle
  • Transport of fatty acids into the mitochondria
103
Q

what process is NADH produced by?

A
  • Krebs cycle
  • Glycolysis
  • oxidation of isoleucine
104
Q

NADP+ is an electron acceptor, where is it usually found in high quantities?

A
  • eye
  • liver
  • adipose tissue
105
Q

what is a property of a signalling cascade?

A

amplification of the message from the membrane to nucleus

106
Q

what does metabolism of purines leads to the production of?

A
  • inorganic phosphate
  • ribose
  • uric acid
107
Q

NADPH is used in metabolism of what?

A

thymine + valine

108
Q

The phosphodiester bond in DNA and RNA links which features of the nucleotides?

A

3’ carbon with 5’carbon through a phosphoryl group

109
Q

What is the difference between a nucleoside and a nucleotide?

A

Nucleosides can be acted on by kinases to create nucleotides

110
Q

What are the properties of a pyrimidine base?

A

It contains a single 6 member ring

111
Q

What is the difference between DNA and RNA?

A

RNA has an extra OH group to DNA on the cyclic sugar

112
Q

What is considered the most reactive part of an ATP molecule?

A

phosphate groups

biochemistry (1 decks)

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