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MDENT210 > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

What is a pseudogene?

A

a section of a chromosome that is an imperfect copy of a functional gene

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2
Q

What are some of the functions of junk DNA?

A

at least 80 % of DNA serves some kind of purpose apparently

  • places for proteinsto attach to that infuence gene activity
  • strands of RNA with various roles, influencing gene action - non coding
  • Places where chemical modification (backbone/methylation/phospharylation) silence stretches of chromosome
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3
Q

Which base is different in RNA?

A

Uracil instead of thymine

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4
Q

What sugars are in the backbone of DNA and RNA?

A

DNA - deoxyribos

RNA - ribox

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5
Q

What is the coding strand and the template strand?

A

Genetic info carried on the coding strand and not the template strand - template strand used for replication of DNA

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6
Q

Where does RNA polymerase attach?

A

Binds to one or more short sequences upstread of the start of each gene i.e. slightly closer to the 5 prime end (these are the promoter sequences of DNA)

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7
Q

What are the 3 types of RNA polymerase? -

A

Polymerase I - nucleolar region of nucleus, transcribes
large ribosomal RNA

Polymerase II - mRNA precursors (mostly producing the mRNA)

Polymerase III - small RNAs (tRNA), 5S ribosomal RNA
and other small DNA sequences

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8
Q

What is RNA polymerase composed of?

A

Several subunits and requires several accessory proteins (transcription factors).
All added to the complex in a defined order to initiate and carry out transcription.

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9
Q

What are basal promoters?

A

basal promoter contains TATA box and found in all protein-coding genes

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10
Q

What are enhancers?

A

DNA sequences which can control efficiency
and rate of transcription. Regulate expression of genes in
specific cell type and control timing of gene expression.
Effects can be powerful

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11
Q

Why are promotors and enhancers cis acting elements?

A

they are on the same molecule of DNA as the gene they regulate

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12
Q

What can changes in promoter strength, deleterious effects on a cell result in?

A

disease e.g tumours

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13
Q

Where can enhancers be placed?

A

can be 5’ or 3’ of transcription start site, in introns or even on non-coding strand

Can be thousands of nucleotides away from promoters with which they interact, brought into close proximity by looping of DNA (due to interactions between proteins bound to enhancer and those bound to promoter)

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14
Q

What are activators and repressors?

A

Protein facilitating looping are called activators and those that inhibit are repressors

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15
Q

How do enhancers affect Transcription factors?

A 
Enhancers contain binding 
site sequences for 
transcription factors (TF) 
and enhance/upregulate
transcription.

Active enhancers are bound by activating TF and brought into proximity of target promoters by looping

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16
Q

What are transcription factors?

A

Transcription factors bind to promoter and enhancer sequences
and recruit RNA polymerase

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17
Q

Why are TF trans acting factors?

A

they are encoded by a different gene to that being regulated

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18
Q

What does the polymerase enzyme do to the DNA?

A

it unwinds the double
helix over a short length and splits them apart – “bubble” of
about 10 bases

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19
Q

How can RNA become functional?

A

base-pair interactions between complementary sequences found elsewhere on same molecule allow an RNA molecule to fold into a three-dimensional structure that isdetermined by its sequence of nucleotides - similar to protein folding, this allows it to have structural and catalytic functions

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20
Q

How is polymerase 1 terminated?

A

hair pin loop which causes RNA pol to pause and release transcript.

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21
Q

How is polymerase 2 terminated?

A

Transcription of pol II genes can continue for hundreds or thousands of nucleotides beyond the end of a coding sequence.

Mature pol II mRNAs are polyadenylated at the 3’ end
= poly(A) tail (AAAAAAAAAAA).

  • signifies end of RNA sequence
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22
Q

What does the CAP on the 5 prime end do?

A

stabilize the mRNA,
essential for transport of RNA out of nucleus

PROTECTS RNA FROM DEGRADATION

Serves as assembly point for proteins needed to recruit
small subunit of ribosome to begin translation

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23
Q

What is altenative splicing?

A

Different parts (introns and exons) of the same sequence can be removed to make different sequences i.e. one exon may be removed in one sequence but kept in in another so different proteins produced from the same gene by alternative splicing

  • gives us diversity
    alternative selection of splice sites within a pre-mRNA
  • leads to production of different mRNA isoforms of a gene
  • alters composition and function of encoded protein
  • plasticity allows for disease development –cancer
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24
Q

What is a spliceosome?

A

The enzyme that does the splicing

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25
Q

What are the 2 types of spliceosome?

A

Major – removes 99.5% of introns

Minor – removes remaining 0.5%

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26
Q

What are the 2 main functions of a spliceosome?

A
  1. Recognition of intron/exon boundaries

2. Catalysis of cut and paste reactions which remove non-coding introns and stitch flanking exons back together

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27
Q

How can spliceosomes cause disease?

A

Mutations altering splice site or spliceosome proteins
Mis-splicing = rapid degeneration of mRNA
Mis-regulation of splicing factor levels = cancer

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28
Q

What are the types of RNA?

A

mRNA

rRNA

  1. tRNA
  2. Non-coding RNA (ncRNA)
  3. Small nuclear RNA (snRNA)
  4. small nucleolar RNA (snoRNA)
  5. micro RNA (miRNA)
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29
Q

What does rRNA do?

A

Build ribosomes, the machinery for synthesizing proteins by translating mRNA

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30
Q

What are the 4 types of ribosomes?

A

18S - one of these along with other proteins
make the small subunit of the ribosome.

28S, 5.8S and 5S - one each of these, along with 45 other
proteins used to make the large subunit of the ribosome

(how dense)

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31
Q

How many different kinds of tRNA are there?

A

32 kinds

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32
Q

What can non coding RNA do?

A

ncRNA can modify protein levels by mechanisms independent of
transcription.

ncRNA play major roles in cellular physiology, development,
metabolism and are implicated in disease process.

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33
Q

What type of RNA are part of spliceosome?

A

Small nuclear RNA

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34
Q

What do snoRNA do?

A

Participate in making ribosomes by helping to cut large
precursor of 28S, 18S and 5.8S.

Modify many nucleotides in rRNA, tRNA and snRNA e.g. can
add methyl groups to ribose

Implicated in alternative splicing of pre-mRNA

Template for synthesis of telomeres

In vertebrates snoRNAs made from introns removed during
RNA processing.

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35
Q

What does micro RNA do?

A

Tiny RNA molecules regulate gene function post-transcriptionally - estimated more than one third of protein-coding genes are under control of microRNAs

very small - 18-25 nucleotides

Binds to mRNA and causes degradation - inhibits protein synthesis

Regulation of developmentally timed events.

Exhibit tissue-specific and/or developmental-
stage-specific expression.

Cancer development

microRNA’s apparently play a critical role in tooth development

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36
Q

What are the essential amino acids from diet?

A 
Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Threonine
Typtophan
Valine
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37
Q

What are non-essential amino acids?

A 
Alanine
Aspargine
Aspartate
Glutamate
Serine
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38
Q

Which amino acids are conditionally essential? (more needed in certain cirumstances)

A 
Arginine
  Cysteine
  Glutamine
  Glycine
  Proline
  Tyrosine
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39
Q

How can non-essential amino acids be made?

A

9 non-essential amino acids are made from glucose + N source (amino acid or ammonia)

Non essential amino acids can also be made from essential amino acids:

  • Methionine donates S for cysteine
  • Phenylalanine forms tyrosine
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40
Q

Why do amino acids have to be degraded?

A

excess can neither be stored or excreted

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41
Q

Sources of excess amino acid?

A

diet exceeds need

some amino acids no longer needed during normal synthesis and degra

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42
Q

What can happen during fasting?

A

Proteins in the muscle can act as an energy source and be broken down into amino acids

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43
Q

What are glucogenic amino acids converted to?

A

their carbons are converted to glucose

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44
Q

What are ketogenic amino acids converted to?

A

acetyl CoA or acetoacetate (ketone bodies)

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45
Q

Where are amino acids broken down?

A

Liver

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46
Q

What is the nitrogen of amino acids used to form?

A

formation of ammonia then fed into urea cycle

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47
Q

What is transamination

A

Removal of nitrogen from amino acids

Amino group from one amino acid transferred to another

α ketoglutarate and glutamate usually one pair

Cofactor involved - pyridoxyl phosphate (derived from vit. B6 )
Reaction reversible- involved in synthesis & degradation

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48
Q

What can glutamate do?

A

Glutamate can collect nitrogen from other amino acids

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49
Q

What converts the nitrogen to ammonia for it to then enter the urea cycle?

A

glutamate dehydrogenase

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50
Q

What does ubiquitin?

A

Small proteins that targets protein for degradation

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51
Q

What is a proteasome?

A

protease complex where protein is unfolded & degraded (ATP)

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52
Q

What is the useable form of nitrogen?

A

ammonia Nh3

ammonium nh4+ toxic

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53
Q

What do we use to get rid of nitrogren?

A

Urea (urea cycle)

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54
Q

What is nitrogen balance?

A

nitrogen ingested (dietary proteins) = nitrogen excreted

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55
Q

Where do the urea cycle steps occur?

A

1st two in mitochondrion, other 3 in cytosol

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56
Q

What forms can nitrogen enter as?

A

amino acids - ammonia (transamination)

or as aspartic acid

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57
Q

Which amino acid is initiating and regenerating

A

Ornithine

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58
Q

What type of regulation is in the urea cycle?

A

feed forward - higher the rate of ammonium production, higher the rate of urea

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59
Q

What sort of activation of enzymes in the urea cycle?

A

Allosteric activation

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60
Q

What induces urea cycle enzymes

A

High protein diet or fasting (protein in muscles being broken down into amino acids which need to get rid of) induces urea cycle enzymes

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61
Q

Where is alanine formed?

A

From pyruvate in the muscles

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62
Q

What are alanine and glutamine used for?

A

These are broken down to glucose and ketone bodies in the liver & used for energy

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63
Q

What are ketone bodies?

A

Combo of Acetoacetate, beta hydroxybutyrate

Reconverted to acetyl CoA and enters TCA cycle for energy when glucose low

Acetoacetate spontaneously breaks down to acetone

‘Fruity’ smell of breath in ketotic states

Ketone bodies are acidic- ketoacidosis

64
Q

What is phenylketonuria?

A

mutation in phenylalanine hydroxylase, mental retardation

65
Q

What can urea cycle disorders lead to?

A

accumulation of ammonia, toxic to the nervous system

66
Q

What are variable number of tandem repeats?

A

repeating nucleotide sequences - number of repeats and loci are inherited from parents.

Large variation of number of these regions between individuals.

  • run according to size in the gel
67
Q

How can you produce variable number of tandem repeats?

A

PCR - measuring transcription of gene

mRNA reverse transcribed to DNA then use PCR to detect lots of copies of the DNA

68
Q

What do you need for PCR?

A

template dna
A, C, G, T
primers
magnesium and Taq polymerase

69
Q

How does PCR work?

A

step 1 denaturation - heat to break hydrogen bonds between chains to open them up
step 2 annealing
primers sticking to specific base sequences of the template DNA at the beginning and end - 55 ish degrees
- enzyme added at 72 egrees
Step 3 - extension
base pairs join onto the template strand in the middle to complete copy of strand

70
Q

Problems with PCR?

A 
Poor precision
Lower sensitiity
Short dynamic range
low resolution
non-automated
size based discrimination only
results not expressed as numbers
staining is not quantitive
71
Q

What does real time PCR allow?

A

Gives you kinetics of reaction - quantifies it

72
Q

What is the exponential phase?

A

The optimal point for analyzing data

73
Q

How can DNA in PCR be identified?

A

Tags attached to the DNA ives of fluorescent dye picked up by machine to tell you new DNA piece been made

74
Q

What does SYBR green bind to?

A

Any double stranded DNA

75
Q

What are the advantages of real time PCR?

A
  • Traditional measure at end point and real time collects data in exponential phase
  • increase in reporter fluorescence directly proportional to number of amplicons generated
  • increased dynamic range of detection
  • no post PCR processing
  • Detection down to 2 fold change
76
Q

What is in situ hybridisation?

A

localisation technique for the detection of a gene product (RNA) in tissues - staining method using RNA as a probe

77
Q

What is transcriptomics?

A

Genome- wide RNA transcript expression levels

78
Q

What is proteomics?

A

large scale study of proteins partciularly their structures and functions, includes post translational modifications

79
Q

What is metabolomics?

A

Comprehensive characterization of small molecule metabolites in biological systems.

80
Q

What is a single nucleotide polymorphism?

A

DNA sequence variations when single nucleotide in genome sequence is altered

81
Q

What are the 3 types of cell communication?

A

Remote signalling by secreted molecules

Contact signalling by membrane bound molecules

Contact signalling via gap junctions

82
Q

What are the types of chemical signalling?

A
  • Endocrine - hormone produced, enters bloodstream and is carried to target cell.
  • Paracrine - local chemical mediator released, acts on cells in immediate environment (eg cytokine)
  • Autocrine – on itself
  • Synaptic - neurotransmitters released at synapses, diffuse to post synaptice target cell
83
Q

What is the pathway to convert a signal to a response?

A

Signal - reception - transduction - response

84
Q

What types of extracellular signals exist?

A 
Growth factors
 Hormones
 Extra-cellular matrix
 Chemicals
 Proteins
 Sugars
 Synaptic
85
Q

What type of cell responses exist?

A 
Growth, cell division
Differentiation
Metabolism
Apoptosis
Gene transcription
Secretion
Contract / relax
Membrane charge
Migration
86
Q

How can intracellular receptors cross plasma membrane?

A

Hydrophobic

87
Q

How does phosphorylation affect cell responses?

A

Phosphate from ATP added

big charge changed - used as on/off signal

88
Q

What type of membrane receptors exist?

A

G-protein linked
Tyrosine kinases
Enzyme linked
Ion channels

89
Q

What do G-protein coupled receptors do?

A

Integral trans-membrane proteins

Receptor occupation promotes interaction with G-protein

Promotes exchange of bound GDP for GTP

activates G protein (α subunit) which leaves receptor

initiates signalling through secondary
messengers

90
Q

What do receptor tyrosine kinases do?

A

Dimerise upon ligand binding

Have intrinsic enzymatic activity

Phosphate from ATP to tyrosine on itself (autophsophorylation)

Bind src homology-2 (SH-2) proteins

Initiate series of phosphorylation reactions

91
Q

What do cytokine receptors do?

A

No intrinsic activity but associates with enzymes - JAKs

92
Q

What do ion channels do?

A

Receptor is an ion channel

Ligand (eg neurotransmitter) binds to & opens channel (some are voltage gated)

Response: influx of Na+, change in membrane potential, action potential

93
Q

What are secondary messengers?

A

Small molecules that bind and activate other molecules

cAMP
IP3
Ca2+
Diacylglycerol

94
Q

How do FGFR’s stimulate fibroblasts and neuronal cells differently?

A

Fibroblasts - proliferation

Neuronal cells - differentiation

95
Q

Which 3 amino acids can be phosphorylated?

A

Serine, threonine, tyrosine

96
Q

How does phosphorylation of proteins allow it to react?

A

Charge change - change of shape so can react

97
Q

What happens with Ras becomes insensitive to GTPase due to a genetic defect of the monomeric protein?

A

Uncontrolled growth - tumour/cancer

98
Q

What do tyrosine kinases do?

A

Adds phosphate molecule to itself from ATP

99
Q

What purpose do cascade systems serve?

A

Amplify the reaction and lots of opportunities to control the processes

100
Q

What do cytokines receptors associate with?

A

Enzymes (JAKs)

101
Q

What is cross talk?

A

2 different signals at cell
1 pathway can activate or inhibit the other pathway
E.g. integrin receptors and growth factor receptors

102
Q

What is a scaffold protein?

A

Bring things closer together to make the reaction more likely or protect molecules from a reaction so it is less likely to occur

103
Q

What does the cell cycle lead to the production of?

A

Two identical daughter cells - DNA duplicated exactly and divided equally

104
Q

What happens in the S phase of the cell cycle?

A

Replication of DNA

105
Q

What happens in the G1 and G2 of the cell cycle?

A

G1 - cell grows

g2 - cell prepares to divide

106
Q

What did the Rao and Johnson experiment show?

A

Mitotic nuclei release mitosis stimulating factor for cells in all phases

107
Q

What do cyclin dependent kinases do?

A

Phosphorylase proteins that control cell cycle, levels remain fairly constant, must bind to appropriate cyclin

108
Q

What is the G0 phase

A

Cells that have permanently or temporarily left the cell cycle e.g. terminal differentiation -neurones

109
Q

What does dysregulated cell growth lead to?

A

Cancer

110
Q

What type of gene is p53?

A

Tumour suppressor gene

P53 blocks cell cycle if DNA damaged but if mutated allows cell cycle to continue with damaged DNA

111
Q

What happens in reduced levels of p27?

A

Poor outcome in breast cancer

112
Q

What does a greater number of cells in active mitosis indicate?

A

Healing/ growth/ repair

113
Q

What does suprabasal mitosis suggest?

A

Pathology

114
Q

What may apoptosis destroy?

A

Destroys cells that may be a threat - virus infected, immune, dna damage

115
Q

What can signal a cell to begin apoptosis?

A

Withdraw of positive signals e.g. growth factors, hormones

Receipt of negative signals e.g. UV, death activators, hypoxia

116
Q

What happens to apoptotic bodies?

A

Phagocytosed by other cells in the surrounding area

117
Q

What does the intrinsic system depend on?

A

Integrity of mitochondrial membrane
If compromised, cytochrome C released - leads to cascade of caspase activation and eventually apoptosis

Onca gene - bel 2 binds to apaf 1 and prevents cytochrome C from forming so inhibits apoptosis

118
Q

What are caspases?

A

Proteolytic enzymes - effectors of apoptosis

Present as inactive proenzymes (zymogen)

Activation cascade

119
Q

What does HPV inactivate?

A

P53

120
Q

What does EBV protein cause?

A

NasopharyngeAl cancer

121
Q

What do apoptotic bodies appear as under H&E stains?

A

Very eosinophilic areas in the images

122
Q

What is biological ageing?

A

Complex biological process in which changes at the molecular, cellular and organ levels results in a progressive inevitable and inescapable decrease in the body’s ability to respond appropriately to internal and/or external stressors

123
Q

What are the characteristics of ageing?

A

Increased mortality
Increased susceptibility & vulnerability to disease

Changes in biochemical composition of tissues

Decrease in physiological capacity

Reduced ability to respond to environmental stimuli

124
Q

What are some theories of ageing?

A

Galen (AD129- 199)
Changes in body humours beginning in early life
Slow increase in dryness & coldness of the body

Roger Bacon (1220-1292)
Wear & tear theory
Result of abuses & insults to the body
Good hygiene may slow process

Charles Darwin (1809-1892)
Loss of irritability in nervous & muscular tissue
125
Q

What are programmed theories of ageing?

A

Biological clocks

Purposeful programme driven by genes

126
Q

What are non programmed theories of ageing?

A

Progressive random, accidental damage

Loss of molecular fidelity

127
Q

Is the evolutionary theory of ageing programmed or non programmed?

A

Programmed - ageing genes

128
Q

Is moleculer/cellular theory of ageing programmed or non-programmed?

A

Non programmed - free radical damage to molecules

increased frequency of senescence

129
Q

Is the system theory of ageing programmed or non-programmed?

A

Non - programmed

Neuroendocrine alterations result in age related physiological changes

Immunologic function declines- decreased resistance to infection, cancer & increased recognition of self

130
Q

What is hutchinson-guilford progeria?

A

Rare genetic disorder

Mutation in LMNA encoding nuclear envelope protein: lamin A

Affects RNA transcription & chromatin organisation

Lack of DNA strand rejoining after irradiation

Accelerated ageing (atherosclerosis)

Usually die by 13

131
Q

What is werner syndrome?

A

Mutation in WRN, DNA helicase family

‘caretaker of the genome’: DNA repair and transcription

Baldness, hair and skin ageing, calicification of vessels, cancers, cataracts, arthritis, diabetes

Die by age 50

Central control of ageing?

132
Q

How many times do normal cell approx divide?

A

50 times

133
Q

What type of cells have no limit in dividing?

A

Cancel cells

134
Q

What are telomeres?

A

DNA sequences
Protect the ends of chromosomes
Progressive shortening with age

135
Q

What is telomerase?

A 
Reverse transcriptase
 Stabilizes telomere
length
 Telomerase activity
 in 90% tumours
136
Q

How can lifestyle affect ageing?

A

Leading a sedentary lifestyle may make us genetically old before our time (BBC news Jan ‘08)

Twins who were physically active during their leisure time appeared biologically younger than their sedentary peers.

Telomeres shortened more quickly in inactive people.
Could signify faster cellular ageing.

137
Q

Why does molecule ageing occur?

A

Intrinsic thermodynamic instability of biomolecules

3D structure cannot be maintained

Conformational change, aggregation, precipitation, amyloid formation

Ageing: catabolic chance driven?

138
Q

How does molecule ageing occur?

A

Free radicals

Accumulation of oxidative damage in proteins & DNA

Damage to mitochondrial DNA:
e- leak from e- transport, form free radicals leading to more DNA damage

Flies expressing superoxide dismutase (free-radical scavenger) live longer

Antioxidants to counter ageing (Vit C, E, β-carotene, 2-deoxy glucose)

139
Q

What is extrinsic skin ageing?

A

Wrinkles, pigmented lesions etc.

Sun exposure, air pollution, alcohol, poor nutrition

Smoking- increase in metalloproteinase enzymes which break down collagen

140
Q

What is calorific restriction and why may it lead to living longer?

A

Reduced oxidant production by mitochondria- less ROS damage

Induction of SIRT1- key regulator of cell defence

Increased protein turnover- lack of accumulation of damaged protein

Inhabitants of Okinawa, Japan: 40% fewer calories, longest lifespan & highest % of centenarians

141
Q

What are oncogenes

A

Genes that code for growth factors etc that promotote autonomous cell growth and proliferation

142
Q

What are tumour suppressors genes?

A

Code for factors which control the cell cycle, regulate apoptosis, transcription and cell interactions
Reduces cell proliferation and maintains tissue integrity
Defects - cell grows too fast and dies

143
Q

What are mismatch repair genes?

A

Genes that code for enzymes that repair damaged DNA

144
Q

What are factors in carcinogenesis?

A

Genetics factors
Environmental factors
Chemicals
Viruses

145
Q

What are the two stages of chemical carcinogenesis?

A

Initiation - permanent DNA damage

Promotion - may be reversible, promotes proliferation

146
Q

What is the latent period?

A

Time from initiation to clinical tumour

147
Q

What is a pro-carcinogen?

A

Chemicals often metabolised to ultimate carcinogen (not carcinogen initially) - body activates it

148
Q

What is a co-carcinogen?

A

Chemical not a carcinogen but when combined with a carcinogen it increases its effect

149
Q

What is direct carcinogenesis?

A

Tumour arises at the site of carcinogen application e.g. smoking and lung cancer
(Indirect - tumour arises at different site from carcinogen application) e.g. aromatic amines

150
Q

What is mesothelioma?

A

Cancer of the plural lining of the lungs

151
Q

What type of tissue is the most sensitive to radiation?

A

Embryonic tissues

152
Q

What is the most common cancer?

A

Basal cell carcinoma

153
Q

How do cancers develop?

A

May be de novo - just appear e.g. salivary gland tumours
Via a benign tumour - adenocarcinoma of colon
Via a premalignant lesion - HNSCC

154
Q

What is dysplasia?

A

Cellular abnormalities and disorganisation of the tissue before invasion

155
Q

What are stem cells?

A

Undifferentiated cells which have the potential for self renewal and can give rise to one and sometimes many different cell types

156
Q

What is used to deliver a gene to patient’s target cells?

A

Vector from a virus carries the gene inside to the target cell

157
Q

What is CRISPR-Cas9? (Fault gene replacement system)

A

CRISPR finds the relevant gene
Cas-9 - cuts gene
Replace with donor gene

MDENT210 (7 decks)

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