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random bits throughout Flashcards

1
Q

what stains darker heterochromatin or euchromatin and what are they made up of?

A

Heterochromatin is darker - contains solenoids (packs of beads on a string), here genes are not expressed

Euchromatin is lighter - consists of beads on a string, genes here are expressed

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2
Q

DNA is a nucleic acid, nucleic acids are polynucleotides, what makes up a nucleotide?

A

base, deoxyribose sugar and a phosphate

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3
Q

Nitrogenous bases consist of two purines and three pyrimidines; name each and briefly describe their structure

A

Pyrimidines - Uracil, Thymine and cytosine - small single ringed structures
Purines - Guanine and Adenine - larger, double ringed structures

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4
Q

What bonds link together nucleotides in a DNA molecule?

A

Phosphodiester bonds between the OH group of one and the phosphate of the next

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5
Q

what bonds form between the bases of the polynucleotide chains to form an antiparallel double stranded DNA molecule?

A

hydrogen bonds (note GC have three bonds can form the rest 2)

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6
Q

Three steps make up the DNA replication process in eukaryotes, these are initiation, elongation and termination. Briefly describe each

(end of L2)

A

Initiation - DNA unwinds and DNA polymerase binds downstream at 3’ end and synthesises DNA in a 5’ to 3’ direction

Elongation - THe DNA unzips a little more and DNA polymerase falls off and a new one binds and synthesises the next segment. On the lagging strand this is done in Okazaki fragments unlike the leading strand which is continuous

Termination - a stop codon is reached

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7
Q

(start of L3)

To which groove do DNA binding proteins bind to?

A

The major groove, the pentose sugar blocks binding at the minor groove

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8
Q

What makes up a nucleoside?

A

Sugar and a base, no phosphate group

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9
Q

Distinguish between an exonuclease and an endonuclease

A

Exonucleases degrade DNA from one end, endonucleases are enzymes which cut DNA iwthin hte strand

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10
Q

DNA polymerases main function is extending the DNA strand, what other function does it have?
(end of L3)

A

Proof reading

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11
Q

(start of L4)

What are telomeres?

A

Repeating DNA sequence (TTAGGG) at the end of chromosomes to maintain chromosoma integrity

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12
Q

Explain the phases of mitosis

A

Prophase - chromosomes condense and nucelar membrane breaks down
Prometaphase - Spindle fibres from kinetochores bind the chromosomes
Metaphase - Chromosomes line up along the metaphase plate in their homolgous pairs (not sure if this is homologuous pairs)
Anaphse - They are pulled as sister chromatids to opposing poles of the cell
Telophase - cell cleavage begins and the nuclear membrane develops

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13
Q

Cells made in meiosis are haploid, what does this mean?

A

They have one copy of each chromosome (23)

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14
Q

Give the stages in meiosis

end of L4

A

Meoisis I
Prophase I - Nuclear membrane disintegrates, chromosomes condense, homologous pairs find each other by DNA sequence matching and recombination (crossing over occurs)
Metaphase I - Chromosomes line up on metaphase plate
Anaphase I - The homologous pairs separate to opposite poles of cell
Telophase I - nuclear membrane reforms and cytokinesis

Meiosis II
Prophase II - nuclear membrane disintegrates again
Metaphase II - Chromosomes line up RANDOMLY on metaphase plate
Anaphase II - chromatids separate
Telophase II - nucelar membranes form again resulting in four non-identical cells

NOTE - so it goes Mitosis -> meiosis I -> meisosis 2 -

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15
Q

start of L5

Give two consequences of nondisjunction (faulty meiosis)

A

Miscarriage (1/3 of all miscarriages caused by it)
Infertility
Mental retardation

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16
Q

Mitotic nondisjunction leads to anueploidy, what is this?

A

Incorrect number of chromosomes in the cell

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17
Q

Depending on where nondisjunction occurs in meisois after fertilisation we may end up with monosomy, trisomy or normal. What disorder is caused by having trisomy of chromosome 21?

A

Down’s syndrome

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18
Q

What is G0 and why does it exist?

A

A stage outside of the cell cycle where non-dividing cells can go and await growth signals

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19
Q

How many chromosomes does every human somatic cell contain in G2, just before mitosis?

A

46, they DNA doubles but the chromosome number does not

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20
Q

You can see 23 unduplicated structures moving toward each pole, what phase is this?

A

Anaphase II
Can’t be meiosis I as this would be 23 duplicated structures
Mitosis - would be 46 unduplicated structures moving to each pole

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21
Q

What gene determines male sex development?

A

Sry gene

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22
Q

What is anaphase lag?

end of L5

A

When some of the chromosomes lag behind on the metaphase plate in the cytoplasm as the nuclear membranes reform during telophase, this DNA is degraded

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23
Q

(start of L6)

Give some examples of endogenous and exogenous sources of DNA damage

A

Exogenous - ionising radiation/mutagenic chemicals/alkylating agents/anti-cancer drugs

Endogenous - Free radicals from metabolism/replication errors

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24
Q

Replication errors cause ‘replication stress’ which is inefficient replication that leads to replication fork slowing and/or breakage. They include misincorporation of bases, replication fork progression hinderance and defects in response pathways (e.g. in exonuclease machinery). Give an example of replication fork hinderance

A

This is any DNA lesion, commonly looping of the DNA or repetitive DNA

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25
Q

Repetitive DNA hinderance can lead to fork slippage. Outline the two types of fork slippage

A

Backward slippage - Repeated DNA causes the newly synthesised strand to loop out causing an extra nucleotide to be added because replication is happening too slowly

Forward slippage - A reduction in the number of nucleotides, can occur across codons. Replication is happening too quick

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26
Q

What disease is caused by CAG codon repeats

A

Huntingtons disease - abnormal aggregates of huntingtin form which aggregates in neurons and causes their egeneration mainly in the basal ganglia

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27
Q

The four types of DNA repair are base excision repair, nucleotide excision repair, recombination repair and mismatch repair. Briefly explain each

A

Base excision repair - Corrects an incorrectly incorporated base
Nucelotide excision repair - Example is UV radiation causing dimerisation of pyrimidines, section removed and replaced.
Mismatch repair -Mismatched bases are detected, segment removed and replaced
Recombination pair reapirs double stranded breaks and is split into homologous directed repair and non-homologous end joining
Non-homologous end joining - a last resort. Is genotoxic because mutations are likely but better than leaving exposed DNA. A complex forms a ring around the damaged region and the ring and regions are removed and ends ligated
Homologous end joining - Affected regions are cut away at different points of each strand, the unaffected single strands use the homologous chromosome and invade it to use it as a template to build the correct, healthy form

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28
Q

amino acids with a positively charged R group are ____ amino acids whilst those with a negatively charge R group are _____ amino acids

A

basic

acidic

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29
Q

The pK (pKa) value of an acos reers to the point at which there is a tendency to dissociate a proton. Acids have low pK’s whilst bases have high pK’s. If the pH of the solution is lower than the pK of the amino acid, will the group be protonated or deprotonated?

A

It will be protonated (+ve charge) - acid is a proton donor

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30
Q

What bonds form between amino acids in a protein?

A

Peptide bonds (CONH) - water is lost

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31
Q

What decides the secondary structure of a protein?

A

The bond angles on either side of the peptide bond

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32
Q

What is the isoelectric point of a protein?

A

The pH at which there is no overally net charge on a protein. For acidic ones this is less than 7, for alkaline it is hgher than 7

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33
Q

Hydrogen bonds naturally form between hydrogen atoms and really electronegative atoms like N and O. T/F

A

T

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34
Q

the rate of reaction is measured by V0 which describes the initial rate of reaction

A

T

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35
Q

What is Vmax

A

The theoretical maximum speed of the reaction if all of the active sites of all of the enzymes are filled at all times

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36
Q

What three things does the speed of a reaction depend upon?

A

Temp/Conc/enzymes

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37
Q

Define ‘Km’

A

The substrate concentration which gives half maximal velocity

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38
Q

What does a low Km mean for the affinity of an enzyme for the substrate

A

Enzyme has high affinity for the substrate

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39
Q

1 unit of VMax/V0 values is the amount of enzyme that converts 1umol of product per minute.

A

T

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40
Q

The michealis-menten equation gives a hyperbolic curve, the _____-__ plot gives a linear arrangement of this

A

Lineweaver-Burk

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41
Q

Where would you find Vmax and Km on a lineweaver-burk plot?

A

y axis = 1/Vmax x axis = -1/Km

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42
Q

What do the following enzyme inhibitors affect

a) competitive inhibitors (bind to active site)
b) non-competitive inhibitors (bind at a site on the enzyme away from the active site)

A

competitive inhibitors - Affects Km

Non-competitive inhibitors - Affects Vmax

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43
Q

What is the purpose of catabolic metabolism?

A

To break down molecules ot release energy in the form of reducing power

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44
Q

List the essential amino acids. Remembered by ‘If Learn This Huge List May Prove Truly Valuable

A 
Isoleucine 
Lysine
Threonine
Histidine 
Leucine 
Methionine 
Phenylalanine
Tryptophan
Valine
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45
Q

What kinds of fat contain double bonds?

A

Unsaturated

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46
Q

What are the major functions of the essential amino acids?

A

Provide essential acids for anabolic processes and are required for the absorption of fat soluble vitamins

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47
Q

What three things does the daily energy expenditure depend upon?

A

Basal metabolic rate
Enery required to process food
Physical activity level

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48
Q

How do you calculate BMI and what are the units?

A

Weight (Kg)/Height (m)2

Units are Kg/m2

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49
Q

Explain how a low protein diet can lead to kwashiokor

A

Low plasma protein synthesis -> low oncotic plasma pressure -> fluid drawn out of capilllaries into tissue -> formation of oedema

50
Q

What mneomnic can be used to remember what happends to electrons and a hydrogen atom in redox reactions?

A

OILRIG

51
Q

When ATP concentration in the cell goes up, anabolic pathways are activated by high enery signals, give some

A

ATP, NADH, NADPH, FAD2H (using these reducing powers now for anabolic pathways

52
Q

Give some examples of low energy signals

A

ADP/AMP/NAD+/NADP+/FAD

53
Q

What reserve of ATP does skeletal muscle have so it can be used straight away for energy?

A

Creatine phosphate

54
Q

Where does glycolysis occur in the cell?

A

In the cytoplasm

55
Q

Where does the Kreb’s cycle occur?

A

In the mitochondrial matrix

56
Q

Where does oxidative phosphorylation occur in the cell?

A

In the inner membrane of the mitochondria

57
Q

Give three cells that have an absolute requirement for glucose

A

RBC’s/neutrophils/innermost cells of the kidney medulla/lens of the eye

58
Q

Why can’t we digest cellulose

A

We don’t have the enzymes to break down there beta-glycosidic bonds

59
Q

Distinguish between primary, secondary and congenital lactase deficiency

A

primary - absence of an allele that allows lactase expression in the adult -> insufficient amount made
secondary - due to a disruption in the small intestine lining where lactase enzyme is present - reversible
Congenital - ineffective lactase protein due to an autosomal recessive mutation - can’t even digest breast milk

60
Q

Give two reasons for the high numer of steps in glycolysis

A

-Higher efficiency in small stages/chemistry is easier in small steps/allows for lots of pathwat interconnections/allows for fine control of the pathway

61
Q

What are the three control enzymes in glycolysis and which is the key rate-controlling enzyme?

A

Hexokinase/Phosphofructokinase-1/pyruvate kinase

62
Q

Give the net products of glycolysis

A

2 pyruvates/2 ATP/ 2NADH

63
Q

Give two important intermediates of glycolysis and their function

A

2,3-BPG - produced in RBC’s, an important regulator of oxygen affinity -> REDUCES haemoglobins affinity for oxygen

Glycerol phosphate - necessary for lipid TAG synthesis

64
Q

Where does the NAD+ necessary for glycolysis come from in RBC’s which don’t have krebs or oxphos?

A

anaerobic metabolism - production of lactate

65
Q

What is the equation for this anaerobic metabolism and list some tissues it’s used in
What enzyme powers the reaction?

A

NADH + H+ + pyruvate NAD+ + lactate
RBC’s/skeleyal muscle
lactate dehydrogenase

66
Q

What are the two functions of the enzyme lactate dehydrogenase?

A

Generation of NAD+ in RBC’s and skeletal muscle via anaerobic metabolism/
Aerobically producing pyruvate in the kidney and liver using the backward reaction (gluconeogenesis)

67
Q

Both fructose and galactose can feed into glycolysis. Desribe the difference between essential fructosuria and fructose intolerance

A

essential fructosuria - fructokinase builds up and fructose is lost in urine, just inefficient metabolism
Fructose intolerance - aldolase is missing, toxic fructose-1P builds up which famages the liver

68
Q

Deificency of any of the enzymes galactokinase, uridyl transferase or UDP-galactose epimerase can lead to galactosemia, what ar the symptoms?

A

Excess galactose enters other pathways and depletes NADPH levels -> disulfide bridges form in the eye -> cataracts
If one of the other two than galactokinase is deficient its worse because galactose-1P is damaging to the liver as well

69
Q

The pentose phosphate pathway is fed into in times of excess energy, give three of the pathways functions

A

Provides NADPH which
-is reducing power for biosynthesis
-maintains glutathione levels which protects against lipid peroxidaiton a form of oxidative stress
-is important in detox reactions
also provides pentose sugards for nucleic acid generation

70
Q

What is the rate limiting enzyme of the pentose phosphate pathway and describe someone with this deficiency (an inborn error of metabolism)

A

Glucose 6 phosphate dehydrogenase

deficiency would cause Heinz bodies in the blood and/or cataracts

71
Q

Describe the term ‘allostery’

A

This refers to the activation or inhibition of a substance binding to the active site of an enzyme by binding to a regulatory site elsewhere on the enzyme

72
Q

Give an example of a metabolic and hormonal stimulator of phosphofructokinase and thus glycolysis

A

Stimulatory hormone - insulin -> phosphatase activation -> keeps phosphofructokinase in active state
NOTE - opposite happens with glucagon -> feedback inhibition via PKA -
Stimulatory metabolite - NAD+/ADP etc.

73
Q

What is the major function of the kreb’s cycle?

A

To produce reducing in the form of NADH

74
Q

What are the rate limiting enzymes in the krebs cycle?

A

isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase

75
Q

What are the total yields from one glucose molecule in all the steps of carbohydrate metabolism up until the end of kreb’s?

A

4 ATP
10 NADH
2 FADH2’s

76
Q

Describe what happens in the electron transport chain and oxidative phosphorylation (the use of free energy to drive ATP synthesis)

A

The inner mitochondrial membrane is highly impermable and contains proton translocating complexes which strip the H ions from the reducing powers and pass them across into the inttermembrane space. It also removes the electrons from the reducing powers and passes them down the transport chain, this creates a huge proton gradient. The protons now move back through the last PTC ATP synthatse which drives the production of ATP

77
Q

Why does NADH provide more ATP yield than FADH2?

A

Because FADH2 only feeds into the second PTC whereas NADH feeds into the first one

78
Q

How do electron uncouplers work?

A

They increase the permeaility of the mitochondrial inner membrane to protons so they move back down their gradient without driving ATP synthase.

79
Q

How does cyanide work?

A

it binfs the PTC which normally bins oxygen -> oxygen can’t accept the electrons -> no proton motive force -> no ATP production

80
Q

What do ‘essential fatty acids’ have that means they can’t be made in vivo?

A

unsaturated double bond

81
Q

Where does beta-oxidation (fatty acid metabolism) occur?

A

In the mitochondria

82
Q

What are the fates of the fatty acids and glycerol produced by the breakdown of dietary lipids?

A

Glycerol enters trigylceride synthesis or glycolysis

FA’s enter beta oxidation -> produces reducing power and acetyl CoA which enters krebs

83
Q

HMG derivatives made from acetyl CoA can either go onto make _____ or be converted into _____ _____.

A

Cholesterol/ketone bodies

84
Q

Name two ketone bodies

A

Acetoacetate/acetone/beta-hydrobutyrate

85
Q

Why do we produce ketone bodies during starvation/

A

We arten’t getting sufficient acetyl-CoA from glycolysis so fat metabolism begins, this metabolism produces a huge amount of reducing power which inhibits the krebs cycle and drives it down the ketone body synthesis pathway

86
Q

which enzyme does insulin inhibit (released in the fed state) to force the production of cholesterol rather than ketone bodies

A

lyase

87
Q

What is meant by hemizygous?

A

Only having one allele of a gene as opposed to the normal two; this occurs in males as they only have one X chromosomes

88
Q

Explain why X-linked recessive genes are more commonly seen in males

A

Cos men only have one x gene and thus the expressof one allele is sufficient to present the disease

89
Q

In an autosomal reessive inheritance pattern, what is the chance of two heterozygotes having an affected offspring?

A

1 in 4

90
Q

Autosomal recessive diseases an skip generations T/F?

A

T

91
Q

Chance of getting the disease with two heterozygotes in an autosomal dominant inheritance pattern?

A

1 in 2 (doesn’t skip generations)

92
Q

In what direction are proteins synthesised?

A

N to C

93
Q

Once mRNA is created by RNA polymerase, what are the three steps that are needed to be completed to convert that mRNA to mature mRNA?

A

5’ capping (prevents degradation)
Polyadenylation at 3’ end (adding lots of A bases) to prevent degradation
Splicing - removes introns

94
Q

What is meant when we say that the genetic code is ‘degenerate’

A

More than cone codon codes for an amino acid

95
Q

what has an anticodon on and what is one?

A

three bases on a tRNA which are cmoplementary to the codon on the mRNA

96
Q

Which codon on the mRNA does the tRNA recognise as the start codon?

A

AUG (methionine)

97
Q

There are two main forms of post-translational processing - proteolytic cleavage and chemical modifications

A

Proteolytic cleavage - breakage of peptide bonds to remove part of the protein at defined sites to convert itto its active form

98
Q

Explain how secretory proteins formed and correctly targeted/

A

Protein has an intrinsic signal sequence -> an signal recognition particle (SRP) binds to the the protein at the signal sequence and the transcribing ribosome -> upon binding translation is halted -> binds its receptor on the RER membrane -> SRP drops off -> enzyme cleaves signal sequence and protein continues growth into lumen of RER

99
Q

Where does N linked glycosylation occur and why?

A

in the RER -> aids correct protein folding/helps stabilise the protein/helps facilitate interaction of proteins with other molecules

100
Q

What are the three main properties of collagen?

A

Non-extensible/non-compressible/high tensile strenght

101
Q

Describe the life cycle of collagen

A

preprocollagen synthesised in RER lumen -> signal sequence cleaved to form procollagen -> procollagen modified and three chains align with disulfide bonds to form triple helical structure -> procollagen secreted and cleaved outside of cells to form tropocollagne -> tropocollagen fibres bind to form mature collagen fibrils

102
Q

Substitution mutations can be subcategorises as transitions and transversions, differentiate between them

A

Transitions - A point mutation changing a purine to a purine (A->G) or a pyrimidine to a pyrimidine (C->T)

A transversion changes a purine to a pyrimidine and vice versa

103
Q

Describe missense and silent mutations

A

missense - SNP results in the change of the resultant amino acid
Silent - SNP results in no change in amino acid

104
Q

What’s a Robertsonian translocation?

A

Occurs on accentric chromoomes, tiny p arms are lost on each homologous chromosome, results in a chromosome that acts as a single chromosome resulting in monosomy or trisomy at meiosis e.g. trisomy of chromosome 21 - Down’’s syndrome

105
Q

Between what chromosomes does reciprocal translocation occur to give the philidelphia chromosome?

A

9 and 22 -> results in bcr-abl fusion gene

106
Q

What is P50 on an oxygen binding curve?

A

The partial pressure of oxygen which gives 50% saturation of the carrier molecule (hyperbolic curve with myoglobin, sigmoidal with haemoglobin )

107
Q

The R state of haemoglobin is the _____ _____ state

A

High affinity (R for Ready)

108
Q

2,3-BPG lowers haemoglobins affinity for oxygen and thus stabilises the T state, what wat then does it shift the oxygen binding curve?

A

To the right (things that reduce affinity shift the curve to the right because a higher partial pressure of oxygen is needed to bind haemoglobin

109
Q

What effects do acidic pH e/g/ in exercise and CO have on the curve?

A

acidic pH shifts it to the right, CO halves the maximal height of the curve because it binds to haemoglobin

110
Q

HbA adult haemoglobin is made by beta and alpha globin gene expression, HbF foetal haemoglobin mis made by alpha and gamma subunit ezpression

A

T

111
Q

Digestive enzymes are synthesised in the pancreas as zymogens (their inactive precursors), they are activated by proteolyic cleavage. Name a zygmogen

A

chymotrypsinogen -> trypsin cleaves it to chymotrypsin/prolipase cleaed by trypsin to lipase

112
Q

Proteolytic cleavage is irreversible so how do we turn it off?

A

inhibitors e.g. alpha-1 antitrypsin/ digestion by proteases/ dilution via blood flow and eventual degradation

113
Q

In which direction does DNA move on electropheretic gel?

A

-ve to +ve because it’s negatively charged

114
Q

Briefly describe steps in gene cloning

A

Isolate gene of interest with restriction enzymes -> place in a plasmid -> place in bacteria -> culture

115
Q

Give two uses of gene cloning

A

To make useful proteins like insulin
To find out what genes do
genetic screening
gene therapy

116
Q

Briefly describe the steps in the polymerase chain reaction

A

Taq polymerase, free nucleotides and complementary forward and reverse ptimers added to a thermocycler -> heated to 95 degrees to denature the DNA into single strands -> then cooled to allow annealing of the primers and extension of the DNA molecule/

117
Q

Proteins move through electrophoresis in serum gel electrophoresis until they reach their isoelectric point, what is this?

A

the pH at which they have no overall net charge (there’s a pH gradient on the gel)

118
Q

What does SDS-PAGE do and explain it briefly

A

Looks at molecular weight of proteins
Reducing agent added to get rid of disulfide bonds
SDS is a detergent and breaks down secondary structureand coats molecule with a uniform negative charge
Place on normal electrophoresis

119
Q

Give som uses of DNA sequencing

A

Sequencing of animal genomes can helo us learn why they aren’t susceptible to things we are
Sequencing microorganisms for disease
Comparison of gneomes between people

120
Q

Give collagen synthesis lifecycle

A

1) Ribosomes on RER synthesis prreprocollagen
2) RER cleaves to prcollagen
3) Hydroxylation by vitamin C dependent enzyme
4) Modified by ER
5) Chain align and form disulfide ponds and procollagen is sent to golgi
6) Golgi modifies
7) Procollagen exocytosed, to become tropocollagen, fibrils form
8) Fibrils aggregate to collagen fibres

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