Cell biology and genetics Flashcards

Question

mRNA modifications

Answer 1

- polyadenylation signal causes enzymes to add poly - A tail to 3' end - 5' end 5’ Capping modified guanine (methylguanosine) nucleotide is added 5' end (methylation) Modifications work to: - facilitate export of mRNA to cytoplasm - protect mRNA from hydrolytic enzymes - help ribosome attach to 5' end

Answer 2

Catalysed by spliceosomes that recognise splice sites - remove introns - bring exons together - forms mature mRNA

Answer 3

Enzyme that binds Trna and and amino acid

Answer 4

P → holds tRNA that carries growing polypeptide A → amino acid carried E→ exits

Answer 5

- Small ribosomal subunit binds with mRNA and a special initiator tRNA - small subunit moves along mRNA until it finds Aug start codon - large subunit brought in by initiation factors

Answer 6

Codon recognition, peptide bond formation, translocation - A to P to E - exits to be reused

Answer 7

Elongation continues until mRNA stop codon reaches site A of ribosome A site accepts release factor release factor hydrolyses (with water) peptide chain so it is free

Answer 8

Flow of info DNA transcribed to RNA, translated to a protein (feedback loops) Breakdown of processes - disease

Answer 9

``` Cell wall Flagellum 70s ribosomes Plasmids Circular DNA ```

Answer 10

``` Mitochondria Cell membrane Cytoplasm Golgi Smooth er Rough er 80s ribosomes Lysosomes ```

Answer 11

Contains genetic into organized into chromatin | Site of ribosome biogenesis

Answer 12

Captures mRNA begins translation → proteins | Ribosomes

Answer 13

Lipid production, metabolism and hormone production

Answer 14

Post translational modification

Answer 15

Produce all cell types | Necessary to give rise to new organism

Answer 16

Produce nearly all cell types | Form almost all of cells in 3 germ layers

Answer 17

Produce cells of closely related family

Answer 18

Only produce a few cell types of same family

Answer 19

Can only produce one type of cell

Answer 20

Anti parallel Not a perfect double helix - offset major minor grooves Grooves → allow protein interactions, important for gene expression and organisation

Answer 21

DNA → RNA = transcription RNA → protein = translation DNA → DNA = replication RNA → DNA = reverse transcription

Answer 22

One daughter molecule contains both parent strands of DNA | Other daughter molecule contains 2 newly synthesised DNA strands

Answer 23

Parental double helix broken into 2 double stranded segments (horizontally) Synthesis of new double helix molecules with each strand having half new half double helix parent DNA

Answer 24

2 parental strands separate Each strand acts as a template for new strand synthesis DNA has one new strand and one parent strand

Answer 25

5' to 3' DNA polymerizing activity 3' to 5’ Exonuclease activity 5' to 3' exonuclease activity

Answer 26

Destroy DNA by destroying sugar phosphate backbone | Remove nucleotides from the ends of DNA

Answer 27

Can bind to middle of DNA

Answer 28

Proof reading function - corrects mistakes made by polymerase Example 1. DNAPI stalls if incorrect nucleotide is added as next nucleotide can't be added 2. DNAPI has proofreading activity 3. Removes incorrect base

Answer 29

Fast, adds lots of dNTPs before dissociating

Answer 30

DNA wraps round histones, proteins in cell nuclei to form a nucleosome - DNA is packed into chromatin - genetic material composed of DNA and proteins that condense to form chromosome

Answer 31

Enzymes that remove acetal groups from histones - allow DNA to wrap more tightly on histone

Answer 32

Acetal groups added to histone tails - neutralises positive charges - makes it difficult for DNA to wrap around histones - open structure?

Answer 33

Acetal groups are removed from histones - exposing positively charged tails for negative charge DNA to bind to - closed structure

Answer 34

Cancer and aging phenotypes

Answer 35

Clusters of repeated 6 pase pairs - help protect integrity of chromosomes - allow replication of extreme ends - telomerase conserve telomeres

Answer 36

- Protect from physical damage - environment for gene expression - allows DNA to be condensed and stored in cells

Answer 37

Development Repair Growin

Answer 38

Non reproductive | 2 sets of chromosomes = 46

Answer 39

Reproductive cells 23 chromosomes

Answer 40

Made of 2 sister chromatids, with identical DNA attached via cohesions Centromere → bind 2 sister chromatids Kinetochore

Answer 41

Prophase - condensed chromosomes - centrosomes start to form microtubules (asters) move to poles metaphase - sister chromatids position themselves on metaphase plate - kinerochores are bound to microtubeles Anaphase - cohesion’s degraded sister chromatids separate - chromosomes pulled by microtubules to poles Telophase + cytokinesis - nuclear membrane and nucleolus reformed - cleavage furrow

Answer 42

Ordered display of pairs of chromosome, from acell

Answer 43

2 chromosomes in a pair, carry genes controlling same inherited characteristics

Answer 44

Homologous chromosomes line up and separate

Answer 45

Chromosomes line up and chromatids separate

Answer 46

In meiosis 1 → each pair of chromosomes sorts maternal paternal nomolgs into daughter cells independently of other pairs

Answer 47

Any sperm can fuse with any ovum | Genetic variation

Answer 48

part of nucleus that contains proteins + RNA Ribosome biogenesis Ribosomal RNA

Answer 49

Nucleotides contain deoxyribose sugar Base → A G C T 2 polynucleotide chains held together with hydrogen bonds between bases

Answer 50

Ribose sugar Bases → A G C U Single stranded polynucleotide

Answer 51

``` Synthesise - mRNA - ribosomal RNA - small nuclear snRNA - guide chemical modifications of other RNAs - long non coding RNAs - micro RNAs Makes up 5% of cellular RNA ```

Answer 52

15% of cellular RNAs | - synthesise transfer RNA and 5s rRNA (ribosomes)

Answer 53

- make up 80% of cellular RNA | - synthesise rRNA

Answer 54

Single stranded 2d clover leaf structure - anticodon complementary to mRNA - attachment site for amino acid

Answer 55

1. RNA polymerase opens up DNA and transcribes genes for tRNA 2. Transcript is processed properly (remove introns and modify in nucleus) 3. Transfer it outside nucleus to the cytoplasm 4. tRNA used in translation

Answer 56

Catalytic RNA molecules that function as enzymes that can splice RNA Properties that allow it to act as an enzyme: - form ③d structure due to ability to base pair with itself - some bases in RNA contain functional groups that may participate in catalysis - RNA may hydrogen bond with other nuckic acids

Answer 57

Some introns contain sequences that regulate gene expression - alternative RNA splicing = encode more than one kind of polypeptide depending on which segments are treated as exons in splicing

Answer 58

Triplet code Read 5' to 3' Redundant Universal

Answer 59

Gene determines primary structure - determine shape | Folding makes protein functional or non functional

Answer 60

Free ribosomes in cytosol → synthesise proteins that function in cytosol Bound ribosomes (to er) → make proteins of endomembrane system and proteins that are secreted by cell - proteins destined for er or secretion - marked by single peptide - SRP (signal recognition particle) binds to signal peptide, it escorts ribosome to receptor protein in er membrane Proteins move to right place - due to their specific peptide sequences

Answer 61

Multiple ribosomes translating a single mRNA - faster

Answer 62

- Spindle failure - one chromosome lags left out of nucleus - chromosome broken down in cytoplasm

Answer 63

Contains regulatory elements Where polymerase binds to DNA Starts transcribing at +1

Answer 64

Enhances expression of sections for specific genes

Answer 65

Cap site at 5 'end sequence.

Answer 66

1. Sequence recognised by transcription factor 2. Brings bacterial polymerase to gene 3. Regulatory element, place where activators bind

Answer 67

TATA box Initiator -transcription start -site Promoter proximal elements → activators and depressors Enhancers

Answer 68

1. TBP ( tata binding proteins) recognises tata box and binds to it 2. TBP binds to TFII A and TFII B to form TFII D 3. Number of coactivators are part of TFII D to enhance transcription 4. TBP TFII A TFII B - bring down polymerase to right place on the gene 5. once polymerase is recruited, recruit TFII E F AND H

Answer 69

T FII A B D E F H

Answer 70

Regulation of enzyme activity → bind to and inhibit enzyme and stop proceeding steps Regulation of enzyme production Regulate gene expression with negative feed back

Answer 71

Both the genes and promoter with operator in it ( on - off switch for transcription in the promoter) - operators/ operons are controlled by repressors = bind to the operator and block RNA polymerase prevents transcription

Answer 72

Promotor regulatory gene - makes repressor but it is inactive by itself When tryptophan is absent - transcription occurs When tryptophan is present it binds to and activates repressor Operon switched off - no transcription

Answer 73

' Always on + transcribing Only off when activated repressor binds to the operon Example: tryptophan operon

Answer 74

Usually off, until inducer inactivates the repressor and turns on transcription Example: lactose When lactose is absent repressor is active transcription is off When lactose is present reprossor is inactive transcription is on

Answer 75

Operons are switched off when repressor is active Eg tryptophan + lactose

Answer 76

Stimulator proteins like cyclic amp activate transcription When cAMP levels are high → due to low glucose levels It binds to CRP and activates ix Activated CRP goes to promoter drives transcription When cAMP levels are low → due to high glucose Not enough cAMP to bind to CRP CRP is inactive, doesn't drive transcription

Answer 77

Expression of diff genes by cells with same genome | -results in differences in cell types

Answer 78

Regions upstream of the promoter that activator molecules can bind to - DNA bending protein → bend + loop DNA so the enhancer region with activators is closer to the promoter - doing this means transcription complex components can be stabilised - induced transcription Enhancer be specific, one activator specific to one promoter Depends on availability of activators that bind to enhancers

Answer 79

Hormones can induce transcription - activate receptor - GR receptor bound to HSP inactiviates - when no hormone is present gr is inactive - when hormone is present it binds s to gr and removes HSP - conformational change in gr exposes NLS moves gr into nucleus - when in nucleus gr binds to DNA activate basal transcription

Answer 80

Change in bases in RNA c-u Doesn't effect DNA Can induce an early stop codon= shorter protein

Answer 81

Phosphorylation - deactivates enzyme + inhibits translation | Removal of phosphate group = active continue translation

Answer 82

Micro RNA Single stranded microRNA that bind to complimentary sequences in mRNA to block binding of ribosomes for translation - binding of micro RNA can also just cause degradation of mRNA antisense strand 1. Introduce antisense RNA strand that is complementary to target mRNA 2. Enters nucleus and finds target mRNA through complementarity 3. Form double strand RNA that is quickly degraded by enzymes siRNA 1. SiRNA duplexes doubles RNA, goes into cells 2. Reacts with risk protein complexes 3. Target mRNAs and lead to degradation

Answer 83

Nucleoside sliding - conversion of ATP → ADP allows remodeler to push and slide chromatin and unwide from nucleoside Purpose= allow polymerase to move down DNA sequence

Answer 84

Protein that binds to nucleosomes to regulate nucleosome activity - act as remodellers as they can dissociate nucleosome from DNA so it is more accessible to enzymes - reassemble them as new dimers or replace them with Histine Octamer

Answer 85

End terminals of Histone proteins that can be modified, modification can send different signals to cell which can help in gene regulation - methylation = causes nucleosomes to come closer together → compacted - combining modifications can lead to release of histones

Answer 86

Adding acytal group to histone tail | - neutralises positive charge, inhibits DNA wrapping

Answer 87

HDAC histone deacetylases enzyme → removes acetal groups HAT histone acetal transfereases → add acetal groups In cells there is a balance between HAT acetylation and HDAC deacytalation - inhibiting HDAC in cancers = no more deacetylation so there is more acetylation and transcription

Answer 88

Adding methyl groups to specific DNA bases - result in reduced I blocked transcription - can cause long term inactivation of genes 1. Methyl group is added to 5th carbon on cytosine by specific enzymes (DNMT DNA methyltransferases) 2. When this happens to cytosine near promoter areas = blocking of gene transcription downstream to promoters

Answer 89

Enzymes that modify histones = histone modifiers MLL2 Histone methyltransferase is mutated in cancer - cancer imitate histone modifiers to change transcription MLL2 normally binds to RNA polymerase and methylates nucleosomes helping polymerase

Answer 90

- one allele of gene expressed and the other allele is silenced Genomic imprinting X chromosome activation

Answer 91

One allele is silenced/ transcriptionally inactived by DNA methylation 1. Offspring express only one allele from specific imprinted genes 2. Imprinted gene is transmitted to all body cells during development 3. In next generation all imprints are raised in gamete producing allele. Mouse example - 5.2

Answer 92

Both xx chromosomes are NOT expressed one is randomly inactivated in each embryonic cells Either maternal X or paternal X are activated - all mitotic descendants of cell with have same inactive x 1. Inactive X chromosome - compacts into a Barr body 2. once compacted most of the X chromosome genes are not expressed 3. In the ovary, Barr body chromosomes are reactivated and reverse back to normal active X chromosomes so gametes contain functioning X chromosome

Answer 93

Inheritance of traits transmitted by mechanisms not directly altering / involving the nucleotide sequence -modifications are passed to future generations

Answer 94

First part of protein that exits ribosome in protein biosynthesis

Answer 95

Randomly derived change to nucleotide sequence of the genetic material of an organism To be phenotypically effective mutations must alter gene regulation or actions

Answer 96

Spontaneous -caused by chernial instability of DNA Environmental - DNA clamage from environment, physical (radiation) or chemical mutagens Genetic events - rearrangements - recombination of DNA - DNA replication

Answer 97

1. P53 works at g1 checkpoint and detects DNA damage 2. stops cell cycle if DNA is damaged to allow time for repair 3. P53 activates the DNA repair system and induces transcription of p21 4. p21 prevents cyclin and CDK complex formation 5. DNA can't move to S phase for replication

Answer 98

If cells are damaged too much - repair can't cope with amount of DNA damage - apoptosis - necrosis

Answer 99

- Organised / intentional cell death outer membrane is still intact and it can still function 1. Deactivating bcl-1 (protein that inhibits apoptosis) through well controlled chain of enzyme reactions 2. Catabolic processes begin throughout cell - enzyme digests cytosolic components, fragment nuclear Dna, cysteine proteases target proteins 3. Cell is re packaged for safe removal cell shrinks and fragments into stall membrane bound apoptic bodies 4. Compacted cell is phagocytized by adjoining cells

Answer 100

- caused by physical disruption to cell through injury, toxins, deprivation 1. bacteria secrete toxins that disrupt cell function and structure 2. Cell loses control, swelling organelles, clumped chromatin, eventually bursts 3. Cytotoxic cellular components spill out from membrane Issue= tissue damage + inflammation

Answer 101

- DNA is relatively unstable - bond between sugar + base is unstable - random loss of bases - can happen to hundreds, thousands bases

Answer 102

Removal of an amino group from a base - induced by attack by free radicals chemical mutagens eg nitrous acid - can cause base change c→u

Answer 103

Addition of 0, 02, hooh or oh group to a base - these oxygen species are reactive as they try to stick to something when they hit molecules they attach to it and change chemical structure - affect pairing ability of DNA

Answer 104

CPD + pyrimidine pyrimidone 6-4 photoproducts 1. photons reach cells, skin cells are exposed 2. Photon cause 2 neighouring bases to be linked by a covalent bond 3. cause conformational change in DNA 4. replication can't occur until bond is removed

Answer 105

Smoking - insertion and covalent bond formation between benzo[a]pyrene and DNA in middle of DNA ladder - disrupts base pairing

Answer 106

Deposits energy directly in the molecule to break covalent bonds or hycrolyzes water into reactive oxygen molecules that attack DNA - create single strand breaks - base damage - crosslinks - DNA double stranded breaks - Multiple damage sites

Answer 107

Direct repair ( reversal of damage ) Excision and resynthesis of damaged region (only one damaged DNA strand) Strand break repair (breaks in backbone, both strands)

Answer 108

Photo reactivation - directly reverses formation of pyridine dimers (bonds where structure of DNA helix is kinked twist ) → uses enzyme photolyase - absorbs energy from uv light to use in catalysis breaking the covalent bond Only occurs in prokaryotes

Answer 109

Takes advantage of double stranded DNA 3 pathways: - DNA mismatch repair - base excision repair - remove damaged bases - nucleotide excision repair - use undamaged DNA as a template Principles 1. Protein scans DNA for kink 2. Binds to it and removes damage section of strand reveals single stranded region 3. Single stranded region is used as a template to replace damage strand

Answer 110

Break backbone= must join ends correctly to avoid mutation 1. ends recognised by proteins 2. Proteins realign and resynthesises some nucleotides if ends aren't compatible 3. Ligase joins strands together

Answer 111

Repair DNA by conducting excision and replication on the spot - re replicate the strand correctly DNAP can reverse direction of replication and fix damage

Answer 112

When DNA double strand breaks | - based on ability of single DNA strands to find regions of near perfect homology elsewhere in genome

Answer 113

- if DNA damage is efficiently repaired = non problematic viable cell - if DNA can not be repaired due to too much damage - cell death - if DNA undergoes mis repair Where repair is not sufficient - mutation

Answer 114

Mutation in coding sequence

Answer 115

Mutation in non coding sequence

Answer 116

- Erythemia = skin reddening - necrosis of exposed tissue - eye irritation - increased incidences of leukemic Radiation does not produce new unique mutation but simply increases incidence of same mutations that occur spontaneously

Answer 117

Bond breaks occur either: - directly = by direct ionisation of biomolecule - indirectly= through ionization of water and formation of damaging radicals

Answer 118

- treat cancers - proven benefit - long term survival - damage cancerous cells - imaging delivery of treatment

Answer 119

Mutation that only affects a single nucleotide of a nucleic acid - deletion - insertion - substitution

Answer 120

Change one base for another Transition - switch pyrimidine for another pyrimdine (c and t) - switch purine for another purine (a and g) Transversion - switch purine for pyrimidine - switch pyrimidine for purine

Answer 121

Frameshift - change in the codon change one base in reading frame Nonsense- introduce premature stop codon Missense- change entire amino acid, caused by change in one base

Answer 122

Change in one nucleotide in DNA sequence - change from glutamic acid to valine changes folding of haemoglobin Chromosome 11

Answer 123

Dwarfism Adenine replaces guanine Arginine produced instead of glycine Missense mutation in FGFR3 on chromosome 4 - cartilage can't fully develop into bone

Answer 124

Nonsense mutation - substitute g to a which results in premature stop codon Chromosome 12 PKu=phenylalanine build up - neurological defects

Answer 125

Insert or delete any number of bases ends isn't a multiple of 3= frame shift

Answer 126

. Mutation in ctfr gene - Cf transmembrane conductance regulator gene - causes trick secretions - mutation of F508 deletion of one amino acid phenylalanine in position 508 Cloned by positional cloning strategy - 6.2 notes

Answer 127

Cf is good for gene therapy because it is: - a single gene defect - recessive condition - accessible for treatment (pathology in lung) - progressive disease

Answer 128

- large number progeny observe segregation and recombination - well controlled environment - fast - similarity bew human t mice

Answer 129

Normal genes that help cell grow

Answer 130

Any gene that causes cancer

Answer 131

Variation in the number of repeats between people

Answer 132

Satellite DNA Tandem repeats Interspersed repeats

Answer 133

→ type of repetitive DNA with unclear function 2 classes: - alpha repeats = sequence of 171 bp (long) often repeats in clusters up to several Mb long - beta repeats = sequence of 68 bp (smaller) often in clusters of 100 kB to several mb

Answer 134

→ repetitive sequence make up 10% of genome used for positional cloning, genetic markers - Mini satellites - short tandem repeats 2-5 bp overall length 70-200 bp - micro satellites = near telomeres,20 bp core sequence, 1-390 kb - Macro satellites = near centromeres and telomeres megabases long

Answer 135

Up to 5-20% of genome - SINEs -less than 500 bp, short interspersed nuclear elements - LINEs - more than 500 bp, can contain pseudogenes and reverse transcriptase like genes

Answer 136

Necessary for assembly of human genome - rearrangement of genome - duplication and point mutations are key to genomes

Answer 137

Telomeres are repetitive DNA at ends of chromosomes | - protect chromosome ends from degradation

Answer 138

Variable number tandem repeats= short DNA sequences repeated in tandem adjacent to one another - variation in no. Of times sequence is repeated in a given locus - variability is specific to each person (based on inheritance) DNA fingerprinting -if probe is made from VNTR - the size of the pattern of the fragments is the DNA fingerprint Restriction enzyme cuts either side of VNTR - VNTR polymorphism - used in DNA fingerprinting

Answer 139

Restriction enzymes → cut specific DNA sequences - can only cleave specific 4-6 bp palindromic sequences Bacteria 1. Bacterial DNA is methylated 2. Bacterial cells have methylase activity with the same sequence specificity 3. Bacterial re cannot cleave host DNA as it is methylated 4. But if same sequence is present in viral DNA (unmethylated) it will be cleaved

Answer 140

RE will cleave unmethylated DNA → produce sticky ends (overhanging ends offset from eachother) - 2 samples cleaved w same RE will have complementary sticky ends - can be realigned and ligated with DNA ligase to give recombinant DNA

Answer 141

SSLPs (simple sequence length polymorphisms) are used as genetic markers in PCR - they are repeated sequences over varying base lengths - difference in number of repeats between individuals

Answer 142

1. Cut DNA from donors with restriction enzymes 2. reveal polymorphism due to presence or absence of restriction site 3. Resulting fragment will be of different lengths in different people

Answer 143

Use complementarity between probe and target → hybrid probe target complex to identify molecules of interest in complex mixtures

Answer 144

DNA-DNA - single stranded ssDNA = probe - ssDNA forms double stranded base paired hybrid with it's target DNA - RNA - ssDNA probe forms double stranded base paired hybrid with RNA Protein-Protein - antibody = probe - antibody can form complex with a target protein if the antibody’s antigen binding site can bind to target protein

Answer 145

- probe only binds to targets with complementary sequence/shape - reactions occur in the presencence of large quantities of molecules that are similar but not identical to the target.

Answer 146

Form of procedure used to identify specific sequences of DNA - fragments are separated on a gel - transferred directly to a second medium hybridization

Answer 147

- Cut with restriction enzymes + probed with radioactive DNA | - used in genomics

Answer 148

- probed with radioactive DNA or RNA | - used in transcriptomics

Answer 149

Protein probed with radioactive or erzymatically tagged antibodies - in proteomics

Answer 150

1. Separate molecules on basis of molecular weight - gel electrophoresis 2. Transfer separated molecules from gel → solid support (blotting) 3. Hybridization - to detect target sequence using labelleled probes and detecting probe target hybrids

Answer 151

→ making multiple copies of DNA sequence Initiation: polymerase that require heat activation Denaturation: heat to 95° to denature DNA and break h bonds Annealing: temperature lowered to 50 to 70 degrees, primers anneal to target DNA sequence Extension + elongation: raise temp to 72°, enzyme tag polymerase bind to primed sequence and adds nucleotides to synthesise new DNA strand

Answer 152

Design a pair of primers flank a region of DNA that is of interest. Can cause RSP restriction site polymorphism = caused when PCR amplifiers vary in size if primers can snow that DNA region snows size variation

Answer 153

- helps with identification - appearance reflects level of chromatin condensation - dark + light patches

Answer 154

Short arm =p | Long arm=q

Answer 155

Telocentric - no p arms Accrocentric - small p arms Submetacentric - p arms are shorter than q aims Metacentric - centromere in middle arms are in the same place

Answer 156

→ method of gaining banding pattern reproduce able for chromosome analysis 1. Treat with trypsin 2. Stain with Giesma 3. Viewedby light microscope

Answer 157

Branch of genetics about how chromosomes relate to cell behaviour -Specifically in mitosis /meiosis Cytogenetic process: 1. culture the sample 2. Harvest sample induce mitosis to obtain metaphase 3. Prepare bands 4. Analyse preparations -number of chromosomes and banding

Answer 158

Anomalies during embryogenesis | - all tissues hold same anomaly, error present in embryo

Answer 159

Anomalies in cancer | - one organ is involved, other tissues are normal

Answer 160

Exchange of material between 2 chromosomes - balanced= no loss or gain of material - phenotypically normal - unbalanced - loss or gain of material - lead to anomalies

Answer 161

Between 2 Acrocentric chromosomes - loss of sequences from p arms of chromosomes = lost fragment - but amount of DNA lost is negligible - chromosomes break. And rejoin, 2 q arms fused= robersonian chromosome

Answer 162

Trisomy 18 | Failure of organs systems

Answer 163

Trisomy 13 | Congenital abnormalities, polydactyl

Answer 164

Monosamy - one X chromosome | Sterile short female

Answer 165

Trisomy 47 extra X chromosome XXY | Fertile low iq

Answer 166

Trisomy 47 extra X XXY | Sterile male, more woman like in appearance

Answer 167

Trisomy 47 | Sterile violent more manly male

Answer 168

Amine group Carboxyl group H atom Distinctive r group

Answer 169

What remains of amino acid after it has been joined by a peptide bond to form protein Coo- Nh3+

Answer 170

Only a few amino acids in length

Answer 171

Many amino acids

Answer 172

Protonated Nh3+ Cooh

Answer 173

Deprotonated Coo- NH2

Answer 174

pH = pka + log [A-]/[HA] When [HA] = [A-] ph = pka

Answer 175

Positive and negative charges are equal → no net charge | pH = pka

Answer 176

Non polar don't easily dissolve in water | Polar easily dissolve in water

Answer 177

Aliphatic= no rings | Aromatic=rings

Answer 178

R groups - positive= higher pk | High ph - basic solution - less H atoms - deprotonated

Answer 179

Negative r groups- lower pk | Low ph -acidic - lots of hydrogen - protonated

Answer 180

If ph < pk = protonated | If ph > pk- deprotonated

Answer 181

Peptide bonds are planar - restrict rotation of bond | Favours trans formation - more free

Answer 182

Basic protein isoelectric point > 7 - greater than 7 | Acidic protein isoelectric point <7 - less than 7

Answer 183

If ph is less than pl - protonated | If ph is more than pI = deprotonated

Answer 184

3.6 amino acids in a turn H bonds between every 4th amino acid btw carbonyl on one amino acid and amine on another Pro and Gly - helix breakers

Answer 185

Can be parallel or anti parallel (more stable, optimal H bond pattern)

Answer 186

Improperly folded → toxic protein clump - non functional inhibits processes

Answer 187

Takes place - Co translational= while being translated - post translational - after translation finished

Answer 188

- catalysis, regulation cact us enzymes) - several types of secondary structure - compact shape

Answer 189

- Support, shape protection - single type of repeating secondary structure - long strands or sheets eg collagen

Answer 190

Makes up several connective tissue - triple helical arrangement with glycine at every 3rd position - glycine = smallest amino acid, sticks between helixes to stabilize

Answer 191

Linked together with crosslinks - small fibres Collagen formed from tropocollagen fibres Triple helix stabilised by one direct inter chain h bond as well as water mediated h bond

Answer 192

Domains - part of polypeptide chain that fold into a distinct shape with specific rou Water soluble proteins - hydrophobic side chains = inside protein - hydropnillic side chains - outside protein

Answer 193

Allow transport (of water soluble molecules) due to pore present in middle of protein Hydrophilic chains = inside Hydrophobic chain -outside

Answer 194

Protein complexes formed by different types of polypeptide chains Diverse

Answer 195

-protein complexes formed by assembly of multiple copies of a single type of polypeptide chain

Answer 196

When DNA bound to p53 - increases DNA binding activity Low binding= survival High binding = cell death., high binding is due to mutations in p53 which increase DNA binding = too much transcription → cancer Tetrameric p53 = 4 subunits bind to DNA act as transcription factor Tetrameric transcription is beneficial as error in one subunit = decrease binding affinity of complex

Answer 197

1. If protein is correctly folded it goes to Golgi 2. Misfolded protein moves into intercellular space to go to ubiquitin proteasome which degrades it - chaperones use ATP to help protein fold into correct shape

Answer 198

- CF | - alzhemners - aggregated tau proteins - neural dysfunction

Answer 199

Gives an estimate of how distant they are on the chromosome - the more distant they are the more likely that during recombination regions will be recombined - measured by genotyping individuals in a family looking at recombination of both chromosomes

Answer 200

1 unit of recombination = 1 cM centi Morgan -observed in 1 out of every 100 meiosis 1cM is about 1 million bases If distance is close = will not recombine

Answer 201

``` Autosomal dominant Autosomal recessive X linked dominant X linked recessive Y linked ```

Answer 202

Affected individual = one affected parent Present in every generation Males + females are equally likely to be affected Transmitted by either sex Child of affected individual = 50% chance of being affected Eg. Achondroplasia (FGFR3) Marfan syndrome (FBN1) Huntington's(HD protein CAG repeat)

Answer 203

Both genders affected Both parents affected = all children affected Normally children can be affected but parents are not Affected individual t normal partner - normal chil

Answer 204

Mainly affects males Affected males are born to unaffected parents Transmitted to males from mother Only one mutant X needed

Answer 205

Sex affected Usually one affected parent Affected mall only has affected daughters

Answer 206

Only males affected | Affected males - affected father

Answer 207

Intermediate genotypes produce an intermediate phenotype

Answer 208

Mitochondria is inherited by mother | Severity of phenotype - depends on type of mutation, prevalence of abnormal mitochondria

Answer 209

Donor egg, mother egg, father sperm ``` Maternal spindle transfer 1. genetic info from donor egg removed 2. Genetic info from mom w/o mitochondrial defects inserted into donor egg 3. Egg is free from defective gene 4 fertilised ``` Pro nuclear transfer 1. Mothers egg fertilised by sperm 2. Embryo has maternal mitochondria with defective genes parental DNA exists as pronuclei in cell 3. Pro nuclei removed from cell and added to donor cell with normal mitochondria

Answer 210

Loose - more branched spaced out | Fibrous- striated and compacted

Answer 211

Mutation in collagen 2 or 1 - small glycine substituted for bulkier amino acid = cysteine - alter collagen structure - weak and breakable

Answer 212

In cells of fibroblasts 1. Signal sequence on polypeptide chain is used to guide chain to er 2. Signal sequence is cleaved 3. Hydroxylation of proline to hydroxyl proline using vitamin c 4. Add sugar molecules - glycosylation 5. Modifying the amino acid - triple helix N + C terminals held together by disulfide bonds

Answer 213

Collagen fibres spread widely | Elastic fibres

Answer 214

Collagen fibres packed tightly | See fibroblasts and nuclei

Answer 215

Only amino acid with a side chain small enough to fit in the middle of the tropocollagen Must abundant in tropocollagen

Answer 216

Occurs mainly in the cells of fibroblasts 1. Synthesised in the cell in the rough er 2. Collagen passes to Golgi 3. Collagen is transported outside cell - exocytosis 4. Collagen molecules undergo more polymerization to form final collagen fibres

Answer 217

Signal sequence guides polypeptide chain to er - signal sequence is cleaved when it enters the er - hydroxylaction of proline dependent on vitamin c and asorbcate - after hydroxylation there is glycosylation adding sugar molecules occurs in Golgi - after modifications the helix twists with 2 more helices - 2 terminals N and C - - C terminals held together by disulfide bonds

Answer 218

In extracellular space pro collagen peptidase cleave preform peptide on procollagen =tropocolgen - process removes N and C terminals

Answer 219

- cross links between tropocollagen molecules are made by Lysol oxidase - tropocollagen molecules bound together = collagen fibrils

Answer 220

Lysol oxidase acts on 2 lysine residues to form cross links - requires vitamin B6 and copper ions for activity - adds Aldol cross linking that makes collagen stronger

Answer 221

Deficiency of vitamin c and asorbic acid | - symptoms: fatigue, weakness, poor wound healing, anaemia and gum disease

Answer 222

Deficiency of Lysol oxidase - bonding is less strong= stretchy skin Or mutation in collagen type 5 - inherited connective tissue disorder

Answer 223

Breaking peptide bonds to remove part of protein

Answer 224

Addition of functional groups to amino acid residues

Answer 225

Synthesised by ribosomes on rough er or free ribosomes in cytosol → go to cytosol or post translational import into organelles - co translational insertion - synthesis of of polypeptides by ribosomes at border of so protein is contained in er

Answer 226

- Intrinsic signal - like an address that belongs naturally to protein - receptor - that recognises signal and directs it to correct membrane - translocation machinery - helps translocation - energy ATP to transfer protein

Answer 227

Protein targeting sequence- SKL serine lysine leucine 1. Signal intrinsic to protein = SKL signal on c terminus of protein recognised by receptor and binds to it 2. Receptor PTS1R takes protein catalase tetramer to the Pex14p receptor on peroxisome membrane 3. Pex14p receptor on peroxisome membrane helps transport receptor protein complex into cell - first receptor dissociates from protein leaves through membrane 4.PTS1R receptor is moved through cell using ATP

Answer 228

PTS1R receptor- binds to protein intrinsic signal SKL - protein targeting recognition sequence Pex14p receptor- on peroxisome membrane

Answer 229

Regulated secretion - Endocrine cells - secrete hormones - Exocrine cells - secrete digestive juices - Neurocrine cells - secrete neurotransmitters Unregulated - constitutive secretion - secrete proteins continuously like collagen

Answer 230

- Protein with signal sequence - chaperone that carries protein to protein translocater complex - signal peptidases to cleave signal from protein - ATP

Answer 231

1. Proteins translated in er lumen 2. folded into 3d structure 3. Go from er → Golgi 4. Continues post translational modifications in Golgi 5. proteins put into secretory vesicles

Answer 232

- extracellular proteins - membrane proteins - vesicular proteins

Answer 233

1. Protein translated from mRNA -signal sequence translated first 2. Signal sequence recognised by signal recognition peptide - binds to ribosome bringing it to er membrane 3. Ribsome translates protein into er lumen

Answer 234

same process as secretory except: - halfway through translation, there is an anchor sequence that allows hydrophobic amino acids to associate with membrane - then rest of membrane is synthesised

Answer 235

- Insert proteins into membranes - specific proteolytic cleavage - proper folding of proteins - assembly of multi subunit proteins - hydroxylation of selected lys and pro residues - glycosylation - formation of disulfide bonds

Answer 236

Sugars (glucose, galactose etc) are added on asparagine side chain - reaction involves amino group - that is why it is called n-linked - happens in er

Answer 237

- Allows proper protein folding - increases protein stability - facilitates interactions with other molecules - deficiency - severe inherited human diseases, congenital disorders

Answer 238

→ SH groups in two cysteine residues form disulfide bond - facilitated by disulphide isomerase - formed in er lumen - helps protein stability

Answer 239

- Protein may be trapped in misfolded conformation - protein may contain mutation resulting in misfolding - protein may be associated incorrectly with other subunits

Answer 240

Attempt to correct misfolded protein: - retain unfolded proteins in er - act as sensors to monitor extent of misfolding= mediate increased transcription of chaperones, mediate reduction in translation

Answer 241

- Protein returns to cytosol for degradation | - proteins can accumulate at toxic levels in er = disease

Answer 242

Adding sugar to hydroxyl group of serine, threonine

Answer 243

1. Affect substrate and product concentration | 2. Change the enzyme conformation (Shape)

Answer 244

* Allosteric regulation = changing enzyme shape prevent substrate binding * Covalent modification = blocking active site alter shape * Proteolytic cleavage = removing precursor element of protein changes its shape so it interacts with substrate

Answer 245

→ building up then secreting protein stores - change rate of protein synthesis - now much protein made - change rate of protein degradation

Answer 246

- different forms of the same enzyme that have different kinetic properties - active site has different conformation, modified it is even more specific to substrate, so there is better binding efficacy - catalyse same chemical reaction

Answer 247

→ organic non protein compound that catalyse a reaction - not enzymes - limiting coenzyme availability can regulate enzyme activity

Answer 248

→ • Product can become limiting – accumulation of the product of a reaction inhibits the forward reaction (the enzyme) Eg Glucose-6-phosphate inhibits hexokinase activity = negative feedback, by either competitive binding or allosteric regulation

Answer 249

→ allosteric enzymes snow a sigmoidal relationship between rate and substrate conc - affects initial velocity of the reaction as substrate conc may be high but the enzyme shape is not optimal to bind to substrate - Vmax stays the same but Km differs

Answer 250

``` Tense state (T) - low affinity to substrate, closed up like a fist Relaxed State (R) - high affinity to substrate, more open ```

Answer 251

1. Inhibitor/activator binds to another region on the enzyme that isn't the active site 2. causes conformational change 3. Either prevents enzyme binding or promotes enzyme binding

Answer 252

Prevent enzymes binding to substrate | Increase proportion of enzymes in the t state

Answer 253

Promote binding of enzyme to substrate | Increase proportion of enzymes in r state

Answer 254

→ allosterically regulated enzyme that sets pace for glycolysis - Allosteric inhibitors: ATP, citrate and hydrogen ions limit enzyme activity when ATP is high - Allosteric activators: AMP fructose-2,6-biphosphate

Answer 255

PH= pka + log[A-]/[HA]

Answer 256

Acid dissociation constant

Answer 257

Resist large ph changes - equilibrium maintained - added acids h+ are neutralised by base A- to give acid ha - added bases oh- are neutralised by acid HA converted to base a-

Answer 258

Makes protein negatively charged due to added phosphate groups from ATP → change binding ability - phosphoryl groups can make h bonds = affects binding - rates of phosphorylation / dephosphorylation can be adjusted by activating / deactivating enzymes

Answer 259

Adds phosphate groups to protein | - transfer terminal phosphate from ATP to OH of ser, try, thr

Answer 260

Remove phosphate groups | - reverse effects of kinases by catalysing the removal of phosphoryl groups from protein

Answer 261

-> Takes small amount activation and produces amplification of initial signal -enzyme cascade 1. Protein kinase is phosphorylated and activated 2. phosphorylates and activate, another protein kinase 3. Chain continues activating many protein

Answer 262

When glycogen is broken down glycogen synthesis stops - Protein kinase a phosphorylates and activates phosphorylase kinase - Phosphorylase kinase activates phosphorylase a → breakdown of glycogen - phosphorylase kinase phosphorylates glycogen synthase → inactivation of glycogen synthase so glycogen can't be synthesised

Answer 263

- protein kinase a - phosphorylase kinase - phosphorylase kinase a

Answer 264

Phosphorylase kinase | Glycogen synthase

Answer 265

- Used to activate an enzyme 1. start with inactive form of enzyme -zymoyen 2. Enzyme is activated through proteolytic cleavage 3. Releases active form of the enzyme

Answer 266

Inactive form of the enzyme

Answer 267

- Blood clotting - cascade of proteolytic activation - protein hormones - inactive precursors - developmental processes - activation of zymogens for tissue remodelling - apoptosis - mediated by proteolytic enzymes (capases) synthesised in inactive (procapase) form

Answer 268

Chymotrypsin - digestive enzyme that hydrolyse proteins in small intestine Chymotrysingen= zymogen stored in membrane bound vesicles- zymogen granules released when lumen of intestine are activated by trypsin 1. Trypsin is the enzyme that cleaves chymotry psinogen to activate it → chymotrypsin 2. Trysin cuts between Arg15 and lle16 = pi- chymotrypsin l2 amino acid chains) 3. Further modification = alpha-ct (3 amino acid chain)

Answer 269

-> activates pancreatic zymogens Trypsinogen = trypsin zymogen - activated by enteropeptidase membrane bound protease in lining of duodenum - active trypsin can autocatalytically activate trypsinogen – therefore amplification of signal from a few molecules of trypsin

Answer 270

More trypsin activates proenteropeptidase which activates enteropeptidase with activates trypsinogen → trypsin

Answer 271

Plasma protein that inhibits multiple proteases including chymotrypsin and trypsin Deficiency of α1-antitrypsin = emphysema - prevents and inhibits trypsin from being activated - trypsin goes unregulated and continuously activates proelastase → elastase that destroys alveolar walls

Answer 272

Intrinsic → caused by damaged endothelial linking of blood cells - promotes binding of factor xIl - insides circulatory system Extrinsic → trauma release of tissue factor iii from tissue surrounding capillary -outside circulatory system Both pathways lead to factor X activation

Answer 273

Factor X activation leads to thrombin activation - thrombin - fibrin production = causes clot Very small amounts of factors XII and III cause clotting

Answer 274

Activated by phosphorylation and proteolytic cleavage of different factors - once fibrin production becomes cross linked and forms hard blood clot

Answer 275

- 2 Kringle domains = protect actual thrombin and keep it in inactive form - protease function (actual thrombin part) is kept in c terminal domain - gla residues - target appropriate sites for activation, so clots occur in the right place

Answer 276

→ addition of carboxyl groups to glutamate residues = carboxyglutamate gla - using vitamin k - it allows amino acid to interact with sites of damage and brings together clotting factors with calcium binding.

Answer 277

- effects vitamin k and Inhibits process of carboxylation (gla formation) - thins the blood, used for people at risk of heart attack or stroke

Answer 278

Calcium only binds to carboxylated Ga residues as they have calcium binding sites - prothrombin next to site of damage will bind to calcium and activate= thrombin No carboxylation of glutamate - no thrombin activation, no fibrin, no clot

Answer 279

2 sets of tripeptides alpha, beta and gamma joined at N terminal by disulphide bonds

Answer 280

1. Thrombin cleaves fibrinopeptides A and B from central globular domains of fibrinogen 2. Globular domains at c terminal ends of beta and gamma chains interact with exposed sequences at N termini of cleaved beta and gamma chains → fibrin clot or mesh 3. Multiple subunits come together

Answer 281

Factor 13 facilitates cross linking between molecules to produce mesh structure - amide bonds between side chains of lysine and glutamate residues Cross linking reaction catalysed by: - transglutaminase - procransglutaminase

Answer 282

``` - Need constant activation of clotting pathway → ensure sufficient clotting Positive feed back loop enables: Factor XI Factor VIII Factor V Thrombin - to allow for greater fibrin production - no feedback loop = weak clot ```

Answer 283

Localisation of prothrombin - dilute clotting factors by blood flow and remove/ break down in liver Digestion by proteases - Factor Va and VIIIa are degraded by protein C - protein C is activated by thrombin binding to endothelial receptor, thrombomodulin - thrombin acts like a sponge=mop up factors Specific inhibitors - anti-thrombin iii binds to thrombin, prevents thrombin production - heparin binding increases inhibitor specify to thrombin

Answer 284

A - defect in factor VIII reduced thrombin activation B- deficiency in factor ix, protease that activates factor X Treatment- recombinant factor VIII counters defected factor

Answer 285

Inactive zymogen Proteolytic activation Amplification of initial signal by cascade mechanism Clustering of clotting factors at damage site Feedback activation by thrombin ensures continued clotting Termination of clotting by multiple enzymes Clot breakdown controlled by proteolytic activation

Answer 286

Lower activation energy to increase rate at which subserclie is converted into protein

Answer 287

Reception rate when enzyme is fully saturated by substrate | - maximum velocity of enzyme

Answer 288

Concentration of substrate which permits enzyme to achieve half Vmax - lower km - higher affinity

Answer 289

Competitive - straight line | Non competitive - same as normal curve just lower

Answer 290

→ Change rates of chemical reaction - proteases break down proteins - kinases phosphorylate substances - metabolic catalysts

Answer 291

Antibodies - bind to and mark foreign antigens - chains bound together with disulphide bonds • Constant part = sequence is the same for all antibdies of the same class • Variable region – unique to antibody help them to target antigens

Answer 292

1. B lymphocytes express antibodies on membrane 2. Antibodies bind to specific antigen using variable region 3. Binding is strong - causes change in b lymphocytes so they start multiplying and producing antibodies 4. more antibodies

Answer 293

Receptors bind to and find virus Bring virus into all Destroy with lysosomes

Answer 294

``` Macrophages (do phagocytosis) B lymphocytes T lymphocyte - cytotoxic T cells - helper T cells ```

Answer 295

→ build components that cell can use to build other proteins | - act as reservoirs for amino acid that organism can access when necessary

Answer 296

Ferritin. Stores iron | Calmoduin binds calcium and casein (protein of milk)

Answer 297

→ carry molecules, allow entry of molecules into the cell | - transports proteins are in the cell membrane and can transfer molecules into the cell

Answer 298

- Hemoglobin, the iron-containing protein transports oxygen from the lungs to other parts of the body - aquaporins - gated channels - movement of ions - carrier proteins

Answer 299

Active transport Simple diffusion Passive diffusion

Answer 300

- > receptors bound to membranes bind to signals then induce a cascade of actions - second messengers - communicate quickly and effectively

Answer 301

- Receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells. Light (eyes) and olfactory receptors (smells) - growth actors - recognise growth factors - tyrosine kinase receptor - bind to growth factor and are phosphorylated, form heterodimer so they can bind to signal transducer protein - gpcr

Answer 302

→ coordination of an organisms activities

Answer 303

- insulin hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar, concentration

Answer 304

→ movement | Can move part of a cell or whole animals

Answer 305

Actin and myosin proteins = responsible for muscle contraction - myosin fibres move using ATP = power stroke - myosin heads bring actin filaments towards one another

Answer 306

-Support, shape and anchor cells

Answer 307

- Keratin is the protein of hair, horns, feathers, and other skin appendages. - Collagen and elastin proteins provide a fibrous framework in animal connective tissues.

Answer 308

- Make up fibres inside cells - provide structure and support - because eukaryotic cells don't have cell walls

Answer 309

- Microtubules - tubin polymers - microfilaments - actin filaments - intermediate filaments

Answer 310

2 different peptides- alpha and beta - bound to gtp - plus and minus end - microtubules associated proteins - kinesin and dynein proteins - move along micro-tubules and bind to vesicles

Answer 311

Globular action- g Fibre actin- f 1. Actin bound to gtp arrives at plus end 2. Hydrolysis to ATP 3. Actin dissociates at minus end

Answer 312

→ used to correct misfolded proteins -refold them Hsp 70 = chaperonin - bind to hydrophobic residues on protein, sometimes during protein synthesis to prevent misfolding and degradation Hsp 60 = chaperonin -specific structure that polypeptide enters, it is folded correctly in the structure so that it exits the structure as properly folded fully active protein

Answer 313

Forms: - amphorous aggregates - oligomer's - amyloid fibrils These can be dealt with using autophagy

Answer 314

- Formed when misfolded ed proteins stick together with other misfolded led proteins - can contribute to Alzheimer's, Huntington's and Parkinson,

Answer 315

→ misfiled prion proteins responsible for neurodegenerative disorders - has 3 more helixes and beta cells - scrapie - mad cow disease - chronic wasting disease * Can be infectious * If one protein is misfolded this can bind to other proteins of the same kid and transform them to also be misfolded * This chain keeps going

Answer 316

* Regulate gene transcription * Bind to DNA and control what genes are read * Examples: transcription factors TBP or TFIIB

Answer 317

-model of medical practice where care is tailored to specific patient

Answer 318

– Treatment options are based on the precise phenotype of that particular patient. – Biomarkers are used alongside genetic screening. – surgical approaches, taking into account an individual’s unique anatomy, subtle differences to our anatomy

Answer 319

1. Understand what makes the patients difference – medical, family history, lifestyle, gene mutations, biomarkers 2. Stratification – using personal info group patients into different sub groups of patients 3. Now we can think about treatments specific to them 4. Should give positive effects

Answer 320

some patients have - positive effects - adverse effects - no effects

Answer 321

Blood donations - must understand patient blood group and give compatible blood type Tissue typing -Matching HLA antigens – ensure body can tolerate and match donor organ

Answer 322

``` Genomics - genes Transcriptomics - make up of gene Proteomics - proteins Epigenomics - gene regulation Metabolimics - metabolites, how cell functions Nutrigenomics - food, energy and disease ```

Answer 323

Understand mutation → tumour - genotyping CYP2D6, which metabolises tamoxifen, mutated CYP2D6 can't do this Car -t therapy - use patient own immune cells to destroy cancer cells

Answer 324

1. Harvest patient T cells 2. Make CAR in the lap 3. Insert CAR gene using a retrovirus vector into the T cell 4. T cell incorporates CAR gene into its genetic code 5. Select T cells that express CAR receptor 6. Expand that T cell population 7. Reintroduce them into patient – find and destory cancer cells to shrink tumour a lot or enough for tumour to be surgically removed

Answer 325

Patient put on multiple drug regimens (prevent disease progressing) - not all drugs work due to different causes of arthritis - screen patient to find out what causes their arthritis - refine therapeutic treatment

Answer 326

Gut contains microbiome - help digestion and fight infection -understand patient micribiome makeup - understand differences in microbiomes between diseases Can help treatment of gut and gi tract diseases like Ibd

Answer 327

Patients can have significant differences in their anatomy - combine info about patient and info from surgical registries - surgical registries. = info on patient type, materials, outcome, impant type

Answer 328

probe to be attached to implant and all instuments being used to positon implants, computer and cameras that understand patient measurements – allow surgeon to implant the implant replacement within 1 degree of accuracy instead of how it is normally done by eye - Patient metrics taken on surgery day – best inform how to implant the implant

Answer 329

- expensive - time consuming - drugs may not be suitable to target disease - Medical community fails to see reasoning behind this method - relies alot on data - but data should be clear and show same outcome - ethics -collecting data from patients - not necessary to apply to all diseases as some diseases do just have one particular causes presentation and so they have one targeted treatment

Answer 330

Capacity to perform work Exist in many inter convertible forms Can't be created or destroyed

Answer 331

* Biosynthesis – producing stuff * Transport * Mechanical * Electrochemical

Answer 332

Is the processes which derive energy and raw materials from food stuffs and use them to support repair, growth and activity of the tissues of the body

Answer 333

Catabolism - breaks down molecules to release energy, produce reducing power Anabolism - makes large molecules and requires energy, reducing power and raw materials

Answer 334

Breaking bonds releases energy | Making bonds uses energy

Answer 335

Exergonic - more energy released than used | Endergonic - more energy used than released

Answer 336

Metabolism uses energy released from exergonic reactions to supply endergonic reactions

Answer 337

• Carbohydrate – mostly supplies energy (monosaccharides) • Protein – energy and amino acids (deaminate to use for energy) • Fat - energy and essential fatty acids • Vitamins & minerals – essential Essential minerals - sodium, potassium, calcium etc Essential vitamins - fat and water soluble A.B,K.c- D E • Water – maintains hydration, essential solvent and coolant • Fibre – necessary for normal GI function

Answer 338

Transport Nutrients on the way to tissues for: • Utlisation • Storage • Inter conversion And some materials are used by blood • Proteins, clotting factors • Waste products from tissues --> excretion

Answer 339

Fluctuates - rises after a meal - reduces after exercise

Answer 340

Maintains resting activity of body | - maintenance of cells, organs and body temperature

Answer 341

• Body size (SA) bigger = higher BMR • Gener (male BMR is higher than female) • Environmental temperature • Factors tending to change body temperature (e.g. fever) • Endocrine status – Thyroid = underactive thyroid reduces BMR – Reproductive hormones

Answer 342

``` - energy required for this depends on intensity and duration of activity Reflects energy demands of: – Skeletal muscle – Heart muscle – Respiratory muscles ```

Answer 343

- if energy intake = energy expenditure → stable body weight • Incease energy expenditure – energy store increase • If expenditure exceed intake first energy stores will deplete, then other body components (protein) will be utilised to provide energy

Answer 344

- carbohydrates store energy for immediate use - lipids in adipose tissue store energy for long term use - muscle protein can be converted to carbohydrates

Answer 345

``` Weight (kg) / height (m2) - doesn't account for muscle bulk - used for population not individuals <18.5= underweight >35 morbidly obese 28.5-24.9=normal ```

Answer 346

``` Major potentially preventable cause of death Co morbidity: -diabetes - cardiovascular disease -hypertension - gall bladder disease ```

Answer 347

- Damage from low energy intake - deficiency diseases of other nutrients - low protein intake

Answer 348

Arterial end of capillary - high blood pressure - osmotic pressure outside Venous end of a capillary - low blood pressure - osmotic pressure from outside is higher Net movement of fluid into blood vessel

Answer 349

* Some metabollic pathways occur in all cells * Others are restricted to some cell types * Some may be further restricted to compartments within cells – e.g. inside mitochondria

Answer 350

* Break down larger molecules --> smaller one (create intermediary metabolites) * Release large amounts of free energy to be used by cell * Oxidative – release Hydrogen atom * Reducing power

Answer 351

* Synthesise larger important cellular components – from intermediary metabolites * Use energy from catabolism ATP * Reductive – use hydrogen ions from catabolism

Answer 352

1. Digestion 2. Absorption into blood 3. Anabolism - use to make endings 4. Acetal coa breaks substances down to precursors 5. recycle precursor 6. oxidise precursor 7. creates reducing power 8. use reducing power in anabolism 9. Waste =co2, water used '

Answer 353

- building block materials - dynamic state of components = turnover - cell growth, division, repair - organic precursors acetyl coa - biosyntnetic reducing power NADH NADPH - energy

Answer 354

Capacity to do work - biosynthetic - anabolism - transport - transport ions - mechanical - muscle contraction - electrical-action potential - osmotic -kidney

Answer 355

• Exergonic – release energy, delta g< 0 , spontaneous reaction • Endergonic – require energy, delat g > 0, reaction is not spontaneous Gibbs free energy - useful energy

Answer 356

Removal of electrons or protons Or Addition of oxygen

Answer 357

Gaining of electrons or protons Or Losing oxygen

Answer 358

→ transfer electrons and proteins • Total conc o f oxidised and reduced carriers is constant – cycle between both processes Act as carriers for reducing power – used for: • ATP production (NAD+) • Biosynthesis anabolism (NADPH)

Answer 359

NAD+ → NADH NADP+ → NADPH + H+ FAD → FADH2

Answer 360

Via oxidation - exergonic * Directly – using NADPH in biosynthesis (make larger compounds) * Indirectly – using NADH as a carrier in mitochondrial system

Answer 361

ATP --> ADP = breaks ' a high energy phosphate bond which releases a lot of energy (31kj mole) ADP-->ATP = put in 31KJ mole of energy to reform the high energy bond - used as a carrier not storage - constant turnover - ATP is stable in absence of catalysts - control energy

Answer 362

High ATP concentrations – favour anabolic pathways = activated Low ATP concentrations – high ADP, high AMP, catabolic pathways are activated as cells need to make more ATP Adenylate kinase – 2ADP --> ATP + AMP • AMP acts as low energy signal – feedback system high AMP suggest low energy so catabolic pathways are activated = more ATP

Answer 363

---> activate anabolic pathways • High ATP, NADH, NADPH, FAD2H • Signal that energy is high – can make large molecules

Answer 364

---> activate catabolic pathways • High ADP, AMP, NAD+, NADP+, FAD • Signal that energy is low – make more energy

Answer 365

---> store energy when supply exceeds demand | • Stores = polymer macromolecules or fuel molecules – glycogen, triglyceride

Answer 366

converts creatine --> creatine phosphate/ phosphocreatine Move phosphate group onto creatine • Reversible reaction High ATP = form creatine phosphate Low ATP – form creatine and ATP (short term boost)

Answer 367

Creatine + ATP -------> creatine phosphate + ADP

Answer 368

Marker for muscle damage - when muscle bursts it releases ck - measure levelels • Myocardial infarction –region of the cardiac muscle is deprived of blood, cells die and burst = increased CK in blood, analyse CK to determine if it has come from cardiac or skeletal muscle

Answer 369

Oxygen storage protein - in skeletal + cardiac muscle - high affinity for oxygen- slow release - supplies oxygen when oxygencevels are critically low = haemoglobin can't supply enough

Answer 370

Oxygen transport protein - in blood - transports oxygen from lungs → tissues - low affinity to oxygen at tissues -release

Answer 371

protoporphyrin ring and an iron (Fe) atom bound to 4 nitrogen atoms - iron atom is bound to histidine residue on protein - iron from can form 2 bonds to one molecule of oxygen

Answer 372

Monomer, one subunit of 153aa • 75% α-helical • His 93 covalently linked to Fe (proximal histidine) Oxygen is more hidden in structure = slower release

Answer 373

Iron (as it is bound to histidine) sits slightly below the plane of the ring

Answer 374

- The oxygen bound to iron pulls up iron so it sis's in the same plane as everything else - binding of one oxygen can lead to cooperative binding

Answer 375

→ hyperbolic dependence on oxygen - low oxygen pp = high affinity - myoglobin is fully saturated at a lower oxygen pp

Answer 376

* Each haemoglobin has 4 subunits 2 alpha and 2 beta * Each subunit carries 2 oxygen atoms so can carry 8 in total * Each chain contains an essential haem prosthetic group

Answer 377

Exist in 2 states - T (tense) state = low affinity to oxygen - R (relaxed) state = high affinity to oxygen

Answer 378

Conformational change where oxygen binding promotes stabilization of R state

Answer 379

1. Binding affinity for oxygen increases as more oxygen molecules bind to Hb subunits 2. Binding of 1st O2 molecule to 1 subunit is hard – low affinity (high pp) 3. Binding of last O2 molecule to 4th subunit is very easy – high affinity 4. Due to confirmation changes to Hb 5. Conformational changes – changes shape pull subunits making them more relaxed

Answer 380

increased carbon dioxide which reduces haemoglobin affinity to oxygen - Greater the CO2 = greater the change in pH (acidity) CO2 causes low pp of oxygen as it represent oxygen used up for respiration = low affinity release of O2 occurs where CO2 concentration is high

Answer 381

2,3 bisphosphoglycerate – accumulates in RBCs, product of glycolysis - without 2,3 BPG affinity of haemoglobin is similar to affinity of myoglobin - so haemoglobin behaves like myoglobin = bad

Answer 382

contains no 2,3-BPG and so it acts more like myoglobin | - has greater affinity for oxygenat low partial pressures than mother

Answer 383

- Maintains t state in haemoglobin - Binds in centre of tetramer - conformational change causes T state stabilisation - reduce access to haem groups for oxygen to bind to Doesn't stop oxygen binding just reduces oxygen affinity - oxygen can readily dissociate at low tissue conc

Answer 384

2,3BGP concentration increases, promoting oxygen release | - athletes train at high altitudes to train body into releasing more oxygen

Answer 385

H+ and CO2 binding to haemoglobin → lowers haemoglobin affinity to oxygen - High co2 and h+ = lower oxygen affinity (released) - low co2 and h+ = higher oxygen affinity (bound)

Answer 386

* Low pH = low affinity (higher metabolically active cells) | * High pH = high affinity

Answer 387

• CO binds to haemoglobin 250x more readily than O2 - reduces ability of oxygen to bind Fatal – CO combines with ferromyglovin and ferrohaemoglobin and blocks oxygen transport

Answer 388

``` hyperbaric O2 (3x atmospheric pressure) reduces the half-life of CO-hb (carbon monoxide in blood) to ~23 minutes (1/3 of normal half-life) - breathe pure oxygen at higher pressure ``` Hyperbaric treatment also allows direct diffusion of O2 to tissues, bypassing the normal circulation – • Causes oxygen at very high pressures to dissociate into tissues

Answer 389

2 subtypes -alpha2 and beta 2 | 90% of hb

Answer 390

* Higher binding affinity for O2 than HbA which allows transfer of O2 to foetal blood supply from the mother * No 2,3-BPG so curve sits to the left

Answer 391

Measure for diabetes control • Glycosylation of HbA – HbA1c = more HbA1c the higher the blood glucose, can tell you about long term diabetes management

Answer 392

genetic disorders where there is an imbalance between the number of alpha and beta globin chains

Answer 393

* Decreased or absent β-globin chain production * Only α-chains present but they are unable to form stable tetramers – can't regulate oxygen dissociation, reduced ability to carry oxygen

Answer 394

* decreased or absent α-globin chain production, * So only β-globin chain production – but can form a stable tetramer with a greater affinity for oxygen but a problem dissociating oxygen

Answer 395

- activators - shift curve left and enhance high affinity R state - inhibitors - shift curve right and enhance low affinity t state

Answer 396

Increased affinity = better loader - shift left | Decreased affinity = better released - shift right

Answer 397

One protein has many different functions that are mediated by different domains with different structures and functions

Answer 398

* Proteins are targeted to different compartments of the cell * Proteins have different and multiple functions – cell must organise these and regulate which proteins are active

Answer 399

-> control time and place where the protein functions

Answer 400

→ localisation sequences Specific amino acid sequences code signals to direct proteins to specific regions → post translational modification Signal transduction pathway receptors signal for modifications of proteins within the cell → binding to scaffolding proteins specific proteins with no enzymatic activity, but allow other proteins to bind and join together -relay signals and induce separate pathways

Answer 401

Lysosomal proteases that are only active at ph 5.5 1. At normal pH active centre of protein is blocked has 2 aspartic acids 2. At high pH (normal) they are deprotonated – so N terminal binds to active centre of protien = inactive 3. If pH changes (e.g. addition of a lysosome) = protonation of aspartic acids, release N terminal and free up centre of protein --> activation

Answer 402

Toxin has 2 domains A catalytic and B regulatory 1. B domain binds to the human receptor 2. Endocytosis – brings protein into cell 3. Vesicel combines/ fuse with lysosome = pH chanage 4. Low pH breaks disulphide bond between A and B domains 5. T domain changes conformation, inside goes outside, so hydrophobic amino acids move to the outside of protein and bind to vesicle membrane 6. A domain is released into cytoplasm using T as a channel 7. A domain binds to EF-2 and blocks translation 8. Fatal for cells

Answer 403

Active when bound to protein once hydrolysed - inactive Once released = inactive 3 phosphate groups

Answer 404

Protein that bind to gtp -active-induces signalling transduction pathway * GTP bound = active * GTP hydrolysed to GDP = inactive * GTP released = inactive

Answer 405

1. Rho bound to GDP and an inhibitor (GDI) = inactive 2. Inhibitor is released, Rho still bound to GDP is still inactive 3. GEF helps Rho to be activated by binding the protein from GDP --> to GTP = active 4. Effect many other proteins 5. GAP inactivates protein by transforming GTP ``` GEF = activated protein binds to GDP - promotes dissociation of GDP from the gtpase GAP = inactivates protein by hydrolysing GTP bound form to inactive GDP bound form ```

Answer 406

GEP - gtp binds to gtpase = active = signal transduction pathway promoted GAP - gtp hydrolysed to GDP = inactive = signal transduction pathway inhibited

Answer 407

* GPCR transmembrane receptors activated by signalling molecules * When activated there is a change in the protein * Protein bind to GPCR * Release GDP bind to GTP * Affect other proteins (g protein -cause dissociation of alpha subunit ) * Signalling cascade

Answer 408

- Works in elongation during translation, carries tRNA to ribosome - but can only bind to and carry tRNA when bound to gtp - tRNA is released when gtp hydrolysed to GDP

Answer 409

→ move motor protein (myosin and actin fibres) pushing myosin head along actin 1. ATP binds to ATP binding site on protein 2. Conformational change in protein 3. Hydrolysis of ATP 4. Conformational change 5. Release ATP 6. Protein returns to original state

Answer 410

→ controls movement of molecules in t out of cell Molecule binds to receptor * Binding of ATP = conformational change * Protein opens up and releases molecules (push molecule out of cell) * ATP hydrolysis – protein returns to normal conformation

Answer 411

1. PKA phosphorylates regulatory domain and opens it up so allows ATP to bind to secondary domains 2. Opens up channels so ions can move through WITH CF – mutation in receptor = malfunctioning channel ende can't open so no moveoment of ions out of cell, water moves out of cell → thick mucus WITH CHOLERA = toxin removes phosphorylation via of PKA

Answer 412

1. bind with 3 sodium from cytoplasm 2. With ATP = phosphorylates transporter 3. Change in conformation 4. Sodium molecules released 5. Potasssium molecules bind - dephosphorylation - change in conformation 6. Potassium moves into cell

Answer 413

Protein kinases - add phosphate group to protein (amino acids - serine, threonine tyrosine) Protein phosphatases - remove the phosphate group from proteins

Answer 414

1. When inactive SH2 is normally bound to phosphorylated amino acid = keeping it inactive 2. Removal of phosphate – opens up protein loosens structires 3. SH3 binds to specific ligands 4. Kinase can now phosphorylate tyrosine itself and self active 5. Active kinase can phosphorylayte other things

Answer 415

→ activate by binding with amp and phosphate - using protein kinase A 1. Binding of AMP (when cells are running out of ATP) - activates enzyme to work with glycogen 2. Phosphorylation via phosphorylase kinase phosphorylates the enzyme and activates it

Answer 416

4 subunits: - 2 regulatory (r) - 2 catalytic (C) When bound together -inactive → activated by binding to cAMP causes regulatory and catalytic to dissociate - catalytic subunits - phosphorylate things

Answer 417

-controlling protein degradation controls the amount of protein Proteasome – protein complex with many proteolytic residues

Answer 418

Labelling proteins for degradation by binding to lysine in protein Monoubiquitylation - add 1 ubiquitin - hormone regulation Multiubiquityation - few molecules of ubiquitin bind to proteins -endocytosis polyubiquitylation - multiple molecules of ubiquitin one after the other - add to lysine 63= Dna repair - add to lysine 43 - proteasom degradation

Answer 419

post-translational covalent addition of sugar molecules (oligosaccharides) to asparagine, serine or threonine residues on a protein molecule. Glycosylation can add a single sugar or a chain of sugars at any given site.

Answer 420

Add lipid acids to protein → direct proteins to membranes

Answer 421

- Repair = viable ell - no repair = cell death - mis repair = repair causing mutation leading to cancer or cell dean

Answer 422

Accumulation of mutations

Answer 423

Takes advantage of double stranded nature of DNA molecule | - if one strand is damaged duplicate the other strand to be used as repair

Answer 424

Mismatch repair Base excision repair Nucleotide excision repair

Answer 425

Polymerase may mis incorporate nucleotide - proofreading function = repair most mistakes not all So you can still end up with a base mismatch

Answer 426

1. Damage recognised by specific damage recognition proteins 2. Decide which strand is correct one and which has error (normally done by MutL protein) - determining strand specificity 3. Use exonucleases to cut out damaged DNA 4. Use DNA and undamaged strand as template to make new DNA with polymerase and ligase

Answer 427

Differ in ability to recognise specific type s of DNA structure - insertion loops - deletion loops - mismatches - single base loops

Answer 428

- Early age of onset - very nigh propability that mutation will develop - autosomal dominance = high penetrance - microsatellite instability and accumulation of mutation Repeated microsatellite sequences Tumour cells have almost normal karyotype

Answer 429

Synthesising one/ a few nucleotides 1. Base is chopped 2. Backbone is opened 3. Polymerase incorporate a single/few nucleotides using other strand as a template

Answer 430

Similar damage, damage to a single base 1. Damage recognised by DNA glycosylase - removes base and opens up back bone 2. Assemble DNA with nucleotides and polymerase 3. Remove old strand 4. ligase seals backbone

Answer 431

Depend on: - Nature of damage - nature of glycosylase - nature of DNA polymerase

Answer 432

1. Removal of incorrect organic base by appropriate DNA N-glycosylase to create an AP site 2. AP endonuclease nicks on the 5' side of the AP site to generate a 3' OH terminus Extension of the 3'-OH terminus by a DNA polymerase (fill the gap)

Answer 433

Many types - A specifically damaged base is recognised by specific glycosylase - Eukaryotic glycosylase. Have N terminal additions that specify location and protein interaction

Answer 434

- Removes base but leaves backbone intact | - AP endonuclease is required to break backbone

Answer 435

- Enzyme removes base and opens/ modifies back bone | - Easier for AP endonuclease to work

Answer 436

DNA polymerase b pathway - short patch repair - complex of DNA ligase and protein - DNA polymerase incorporates nucleotide and lipase reseals backbone

Answer 437

Cancers have mutations in ber genes | Demethylation of specific genes dependent on ber

Answer 438

1. Damage recognition 2. Binding of a multi protein complex at the damaged site -recognised by mis shaped DNA 3. Double incision of the damaged strand several nucleotides away from the damaged site, on both the 5' and 3' sides - transcription factor opens and unwind DNA 4. Removal of the damage containing oligonucleotide from between the two nicks -using exonuclease 5. Filling in of the resulting gap by a DNA polymerase 6. Ligation

Answer 439

- Extremely flexible | - corrects damage that distorts and alters chemistry of DNA

Answer 440

Global excision repair Transcription coupled repair - Happens after transcription - DNA repair ensures correct gene transcription

Answer 441

Xeroderma pigmentosum Cockayne's syndrome Trichotniodystrophy

Answer 442

Severe light sensitivity and pigmentation irregularities - frequent neurological defects - early onset of skin cancer and elevated frequency of other cancer

Answer 443

Dwarfism, facial and limb abnormalities - neurological abnormalities - early death - sometimes light sensitivity

Answer 444

``` Sulfur's deficient hair brittle Facial abnormalities Short stature Ichthyosis - fish like scales Light sensitivity ```

Answer 445

- Very distinct phenotypes but still deal with the same gene - strains with same phenotype but mutation found in different genes - 2 mutants can = one normal

Answer 446

Occurs it replication coupled DNA repair goes wrong - higher frequency's of sister chromatid exchanges - chromosomal instability - immune defects - autosomal recessive - pigmented areas

Answer 447

- Essential for survival, - pathways dependent on homologous recombinations - non homologous end joining

Answer 448

DNA damage that can cause a double stranded break - simple double stranded break - easy to connect - complicated double stranded break

Answer 449

Can only occur in damaged cells that nave passed the s phase | - they have 2 chromosomes - one can be used as a template

Answer 450

They don't cause cancer But people with a faulty copy of these genes have a higher than average risk of developing cancers like breast and prostate

Answer 451

1. Break = signaling cascade 2. Complex of proteins brings the ends together 3. Complex of ligase ligates both backbones

Answer 452

Inaccurate * Nucleotides chopped away * Nucleotides are added * Issue is that it is done very quickly * Break in the DNA in coding DNA = bad, breka in DNA no continuation of mitosis don't pass cell cycle checkpoint

Answer 453

* Catalyse formation of covalent bond between juxtapose 5' phosphate and 3' oh groups in DNA backbone * Blunt and sticky ends are ligated

Answer 454

-Isolation - analysing - manipulating Individual genes, gene sets and whole genomes

Answer 455

- Selectively cleaving DNA - Ligating gene sequence into original DNA - new sequence is incorporated within cells via recombinant plasmid - new colony of cells formed containing altered DNA with target gene

Answer 456

1. Preparation of very pure DNA samples 2. Cutting and splicing DNA molecules 3. Analysis of DNA size 4. Getting the DNA into host cells 5. ID of host cells that contain recombinant DNA

Answer 457

1. protect DNA against damaging enzymes - deactivate enzymes by heat or removal of divalent cations using chelating agents 2. Storage of DNA in ethanol at low temperatures to prevent water free radicals attacking DNA

Answer 458

- Blood (must remain unclotted in EDTA tubes) - amniocytes (from amniocentesis fluid) - tissue biopsies - cultured cells - paraffin embedded tissue cells

Answer 459

1. Cell collection – have enough cells to get enough DNA 2. Cell lysis – break cells 3. Removal of cellular proteins – using proteolytic digestion (proteases) 4. Precipitation and washing with alcohol (ethanol)

Answer 460

→ Must get enough cells for success Gently chewing the inside of the mouth combined with a water mouth wash is used to dislodge epithelial cells lining the mouth

Answer 461

→ breaking down cell - disrupt lipid bilayer so DNA can escape -lysis buffer to maintain pH of solution at a level where DNA is stable (7/8) and contains EDTA to protect against endo/exonuclease activity - Use SDS a protein solution – most common one is 1% SDS to break open the cell and nuclear membranes, allowing the DNA to be released into the solution - SDS also denatures and unfolds proteins, making them more susceptible to proteolytic cleavage)

Answer 462

→ Biological powders contain proteases to destroy nuclear proteins that bind DNA and cytoplasmic enzymes that breakdown and destroy DNA. - Then extract the proteins using orgaic solvent (phenol-chloroform-isoamyl alcohol) • Protease treatment increases the amount of intact DNA that is extracted.

Answer 463

- DNA is not soluble in ethanol but proteins are

Answer 464

Most are from bacteria → original function to cleave bacteriophage DNA - bacterial DNA is methylated - external DNA is not methylated = methylated DNA is not cleaved

Answer 465

→ use restriction enzymes to cleave DNA and expose sticky ends - modify DNA ends

Answer 466

• Alkaline Phosphatases – remove 5’ phosphate groups = hydroxyl is left, ligase can't ligate This prevents the rejoining of cut ends and self-ligation * Terminal transferases – transfer nucleotides to the 3’ end of a DNA molecule – useful w blunt ends to change them to sticky ends * Nucleotide kinases – transfer single phosphate group from ATP to the 5’ end of DNA

Answer 467

Use PCR 1. Purify DNA as describe above 2. Design primers 3. Use PCR 4. Amplify fragment

Answer 468

1. Break membrane of host cells with heat shock or electroporation= so recombinant DNA can enter cell through pores 2. Transfer recombinant DNA to cells by direct microinjection to target cells Or 3. Viral transfection = vector using viral DNA, viral vector binds to outside of cell and then injects cell with the recombinant plasmid

Answer 469

- vehicle used to transfer genetic material to target cell - DNA molecule capable of independent replication in host - capable of carrying foreign DNA

Answer 470

- Contains marker or marker gene to observe alls containing recombinant DNA = selection marker - origin of replication = specific sequenced recognised as where replication starts - amplify plasmid - plating and bacteria duplication

Answer 471

Isolate and amplify DNA and express foreign DNA in host cell | - allows on demand expression of protein for studying, generating antigens or vaccine development

Answer 472

Containing everything a cloning vector has plus: - promoter region - Ribosome binding site - polyadenylation site - 2 selection markers - Termination

Answer 473

Induction – promotor is inactive until inducer bind to promoter sequence = produce mRNA Repression – promoter is active and produces mRNA until it binds to a repressor (repressor tends to be protein formed as a result of the mRNA produced) → determines rate at which mRNA is synthesised and how much protein is expressed

Answer 474

Transfection and transformation → all methods create situation where membrane is open-for short period of time due to recombinant DNA * Electroporation = Blast cells with electric current, opens up pores in the membranes * Chemicals * Lipid delivery * Microinjection * Viral delivery

Answer 475

1. Put target recombinant DNA that you have created into a mini vesicle made of a lipid membrane like structure 2. Endocytosis – structure is taken inside the cells 3. Structure releases the DNA

Answer 476

* High jack the viruses as they are good at getting into the cell * Create virus carrying the recombinant DNA inside * DNA is delivered into cells

Answer 477

• Use GFP – green fluorescent protein • Clone the pGLO plasmid which contain GFP and bla Bla gene = this gene gets the protein to grown in the presence of ampicilin GFP gene = bacteria with this gene glow under or near UV light • These are attathced to protein of interest

Answer 478

To find mutations in the diagnosis of genetic diseases - to detect a change in the sequence of a gene

Answer 479

- Determines exact position of mutation within a gene | - determines type of mutation

Answer 480

* Chemical degradation = degradation of DNA, exonuclease approach * Chain termination = sequencing newly synthesized DNA strand and terminating it in different places - modern methods

Answer 481

- DNA polymerase reads and synthesises a new complimentary strand barring a primer and deoxynucleotides present - mix of shorter fragments that all end with T corresponding to A in original strand - dttp - auto-radiography - radioactive dTTP or fluorescently labelled ddNTP can be used to determine the sequence of fragments that are synthesised

Answer 482

5 % of the deoxyTTP (dTTP) nucleotides are replaced by dideoxyTTP (ddTTP), which lacks a hydroxyl group = this causes each strand to terminate randomly when a ddTTP is incorporated at the growing 3’ end of the strand - block replication of DNA by polymerase - Used for mapping

Answer 483

Incorporated radioactive ddTTP is detected by using X ray film (autoradiography) * Radioactive T at the end of each fragment * Run the whole mix of fragments on the gel * Longest fragment at the top near the negative end * Shortest fragment at the bottom near the positive end * Read gel from bottom to top (as it separates fragments by size) you get a sequence of DNA from 5' to 3'

Answer 484

→ Fluorescently labelled ddNTP assigns a chlorophyll to each of the 4 bases - colours appear on fluorescent sequencing gel The use of fluorescently-labelled ddNTP terminators has allowed automation and high-throughput sequencing. 2. This technical advance was essential for the rapid completion of the Human Genome Project. 3. A different fluorescent labelling molecule (“fluorophore”) is used for each of the ddNTPs, each with a different emission colour. 4. All four sequencing reactions can be carried out simultaneously in a single tube, and all four are loaded into a single well of the PAGE gel electrophoresis separates the coloured bands. • time a fragment takes to reach the detector is a direct measure of its size (the smallest ones arrive the most quickly) largest arrive later

Answer 485

* to identify the approximate 100,000 (as believed at that time) genes in the human DNA. * determine the sequences of the 3 billion bases that make up human DNA. * store this information in databases. * develop tools for data analysis. * address the ethical, legal, and social issues that arise from genome research.

Answer 486

→ sequence large stretches of DNA with shotgun sequences 1. Prepare pure DNA – total human DNA cleaved by specific restriction enzyme 2. Clone it, DNA clone – use BAC factors as it can add longer lengths of DNA to itself 3. Approx 20000 bac clones = genome 4. Bacs are sequenced , they can be mapped to previously sequenced known parts of the genome (used as markers) 5. All sequences are assembled in a similar simplified way chain termination method = give sequence of the whole chromosome by looking at overlapping sequences find the sequence within the sequence, find the DNA fragment within the DNA sequence, localize it to assemble Overlapping ends into a continuous sequence

Answer 487

Bac library = collection of bac clones containing entire human genome * BAC clones were ‘mapped’ (order and approx. chromosomal location determined), using microsatellite markers and sequence tagged sites (STSs) * Known position of repetitive sequences in human genome = practical use in mapping of genome

Answer 488

- Better understanding of genetic variance in diseases and human genotypes - pre screening for diseases - storage of genome data in a database for future reference by hospitals

Answer 489

* Map the Rare functional variants (Mendelian diseases) * Pharmacogenetic variants (150 gene-drug pairs in the FDA “Table of Pharmacogenomic Biomarkers in Drug Labels”, but only 40 genes involved) = see which variants of the genes determine the response to drugs * Oncogenomic – study of cancer associate genes

Answer 490

• Neonatal sequencing • Maternal blood sequencing • Direct To Consumer (DTC) genomics brought to doctors DTC based on the simple technical advance that we can sequence long sequences very easily, - USB contain genome data

Answer 491

``` • Single nucleotide variants • Multi-nucleotide variants Small insertions/deletions (indels) Large copy number variants (CNVs) Inversions Translocations Aneuploidy ```

Answer 492

* Fairness in the use of genetic info (how and who can use it) * Privacy and confidentiality * Psychological impact and stigmatization – knowing that you have a mutation * Genetic testing * Reproductive issues * education, standards, and quality control. * commercialization. * conceptual and philosophical implications.

Answer 493

→ induce incorporation of a viral vector carrying healthy gene for the disease - inject vector into cells with mutated genes - healthy gene vector is incorporated with original genes - healthy gene creates functional protein = normall cell

Answer 494

In some cases gene vectors can introduce cancer or some other lethal virus

Answer 495

Cf is ideal for gene therapy because: 1. it is a single gene defect, don't have to correct many or multiple genes 2. It is a recessive condition, with heterozygotes being phenotypically normal (suggesting gene dosage effects are not critical) - can retain one copy of mutated gene in cells 3. The main pathology is in the lung, which is accessible for treatment; 4. It is a progressive disease with a virtually normal phenotype at birth, offering a therapeutic window (develop in the teens)

Answer 496

* the intake of digestion enzymes, nutritional supplements, * percussion and postural drainage of the lungs, improved antibiotics * inhalation of aerosols containing medication. = improve lung conditions

Answer 497

→ selective insertion I deletion/editing of genes to produce different genotypes Combine: * DNA double strand break REPAIR machinery in mammalian cells – non homologous end joining and non homolgous recombination * DNA double strand break INDUCTION machinery from bugs

Answer 498

1. When bacteria detects presence of virus DNA it produces two types of short RNA 2. One of the RNA strands contains a sequence that matches the invading virus 3. Two RNAs form complex with kasnine protein (nuclease) 4. When matching sequence (guide RNA) finds its target in the viral genome = kasnine cuts target DNA disabling virus Research found that this can be done to cut other DNA by changing guide RNA and cut DNA, cell tries to repair cut but the process s error prone – allows researchers to understand function • For more precise mutations researchers can add another piece of DNA with desire sequence that can bind up with cut ends and repair it Either knock out genes (deletion) or replace gene

Answer 499

- Should people be allowed to make genetically perfect off spring Chinese biophysicist He Jiankui's attempt to use CRISPR technology to modify human embryos and make them resistant to HIV, which led to the birth of twins Lulu and Nana.

Answer 500

• Don't store much carbs but we each a lot of it • Lipids = efficient storage molecules Proteins = make up muscles but we don't really store it

Answer 501

• Break down larger molecules into smaller ones (intermediary metabolites) • Release large amounts of free energy – Oxidative – release H atoms – ‘ reducing power’ • Release energy Mainly things like amino acids, glucose, fattyacids,and alcohol can be catabolised = acetyal coa

Answer 502

• Synthesise larger important cellular components from intermediary metabolites • Use energy released from catabolism (ATP) – Reductive (i.e. use H released in catabolism • Need energy

Answer 503

Stage 1 • breakdown to building block molecules Stage 2 • breakdown to metabolic intermediates • Release of ‘reducing power’ and ‘energy’ glycolysis - tiny amounts Stage 3 - kerb cycle/ tca • Tricarboxylic acid (Kreb’s) cycle: • release of ‘reducing power’ and ‘energy’ Input: 2 acetyl coA, 6NAD+, 2FAD, 2ADP, 2 phosphate Output: 4CO2, 6NADH, 2FAD2H, 2ATP Provides reducing power and energy for oxidative phosphorylation Stage 4 - Oxidative phosphorylation: • conversion of ‘reducing power’ into energy currency, ATP efficient Input: 10NADH, 2FAD2H, 6O2 Output: ATP (26-28 per glucose) 6H2O, NAD+, FAD

Answer 504

Convert to molecules that can be takenup by cells - protein - amino acids - lipids - glycerol and fatty acids - Carbonyarates - monosaccharides - alcohol - almond Occurs extracellularly in gi tract - molecules absorbed into circulation - no energy produced

Answer 505

Simple molecules → simpler intermediates ``` Amino acids → ammonium (later urea), Keto acids, pyruvate, acetyl coa Monosaccharides → pyruvate Fatty acids → acetyl cOA Glycerol → pyruvate Alcohol → acetyl coa ``` Occurs Intracellular (cytosolic & mitochondrial) • Many pathways (not all in all tissues) - not in RBC • Oxidative (require coenzymes which are then reduced, e.g. NAD+ → NADH) continous supply of NADH - includes glycolysis in stage 2 - Some energy (as ATP) produced

Answer 506

Occurs in mitochondria * Oxidative (requires NAD+ , FAD) * Some energy (as ATP) produced directly - 32 ATP for every glucose * Acetyl (CH3CO- )converted to 2CO2 – waste product * (Also produces precursors for biosynthesis) - useful compounds for anabolism

Answer 507

Occurs in mitochondria * involves Electron transport and ATP synthesis * NADH & FAD2H reoxidised - donate electrons to etc * O2 required (reduced to H2O by taking election ) without it = death * Large amounts of energy (ATP) produced

Answer 508

General formula - (CH2O)n n- length of carbon chain - consist of oxygen and carbon - contain either aldehyde (-Cho) aldose or keto groups (c=0) ketose

Answer 509

→ Simple sugar units 3-9 carbons - aldose = containing aldehyde (glucose, ribose, galactose) - or Ketose groups = containing ketone (fructose)

Answer 510

Exist as ring structures Carbonyl group reacts with alcohol group = ring Polar – attracts water a lot of hydrogens - water soluble Need a carrier to cross membranes Partially oxidised - Alpha rings = have the oh group on opposite side of ch2oh group - beta rings = have oh group on same side as ch2oh group

Answer 511

Diasachharides → 2 monosaccharides (lactose, maltose, sucrose) Ogliosaccharides → 3-12 monosaccharides (dextrins) Polysaccharides → 10-100 monosaccharides (glycogen, all polymers of glucose)

Answer 512

Disaccharides formed by condensation of 2 monosaccharides • O-glycosidic bond • H2O eliminated

Answer 513

→ Storage molecule in body: stored in liver and skeletal muscle * Glycogen granules liver and skeletal muscle * Highly branched * Alpha 1- 4 straight * Alpha 1 – 6 bond branch * Complex branched molecule = good for storage water can't get in

Answer 514

Polymer of glucose – Major store of glucose in mammals (liver, skeletal muscle) – a1-4 and a1-6 glycosidic bonds (Highly branched) – Highly branched = prevent water binding and allows quick breakdown of glycogen

Answer 515

Polymer of glucose found in plants – Mixture of amylose (a1-4 bonds) amd amylopectin and a1-4 and a1-6 glycosidic bonds (Less branched than glycogen) – GI tract enzymes (amylose) release glucose and maltose -

Answer 516

Structural polymer of glucose in plants – β1-4 linkages – No GI enzymes to digest (dietary fibre adds peristalsis important for GI function) • In animals that can digest cellulose they use bacteria to do this not enzymes

Answer 517

-> eat alot of carbs only store a little ``` Main dietary sources • Starches- glucose • Glycogen- glucose • Sucrose - glucose + fructose • Lactose - glucose + galactose ```

Answer 518

Hydrolysis of glycosidic bonds into glucose galactose fructose – using enzymes: - Saliva = amylase – starch, glycogen ---> dextrins - Pancreas = amylase – major enzyme breaks sown dextrins ---> monosaccharides Small intestine = contains enzymes that breakdown carbs --> diassacharidases on border membrane of epithelial cells breakdown disaccharides • lactase (lactose) – N.B. lactose intolerance • Sucrase (Sucrose) • Pancreatic amylase (a1-4 bonds) • isomaltase (a1-6 bonds)

Answer 519

no lactases to breakdown lactose, lactose isn't broken down in small intesine, goes to colon, draws water into colon = bloating

Answer 520

→ active transport system into epithelial cells then via blood supply to target tissues – uptake into cells facilitated diffusoion using transport proteins: • GLUT1- GLUT5 • GLUTs have different distribution and affinities • can be hormonally controlled (e.g. insulin/GLUT4) - insulin increase number of GLUT4 and activity – take glucose into cells and reduce blood glucose )

Answer 521

Blood from small intestine goes to liver via hepatic portal vein-liver breaks down small molecules - whatever we digest and absorb goes through liver - because they are broken down and sent to the liver

Answer 522

Blood [glucose] regulated (~5 mM) because some tissues (rbc, wbc, kidney medulla, lens of the eye) have an absolute requirement & uptake by these tissues depends on [blood] (approx. 40g/24 hours) ==== 5 millimolar is normal blood glucose level • CNS (brain) prefers glucose (approx. 140g/24 hours) • Some tissues need it for specialised functions (liver, adipose) • Too high = hyperglaecemia = diabetes • Too low = hypoglaecemia = low glucose in blood Dizzy, confused, coma, die

Answer 523

Catabolism of glucose - stage 2 → central pathway of glucose metabolism occurs in all tissues (cystolic) - intracellular Overall outcome glucose → pyruvate Can occur without oxygen with the addition of an enzyme

Answer 524

1. Oxidise glucose / NADH production (reducing power – NADH can donate electrons) 2. Synthesis of ATP from ADP – 2 ATP formed 3. Produces C6 and C3 intermediates (C6 splits into 2 C3 molecules) - no loss of CO2

Answer 525

* Exergonic, (energy releasing) oxidative * C6 → 2C3 (No loss of CO2 ) * With one additional enzyme glycolysis is the only pathway that can operate anaerobically (No O2)

Answer 526

Step 1 (hexokinase) - phosphorylation of glucose by hexokinase Step 3 (phosphofructokinase 1 ) - it is key controlling step of glycolysis Step 10 (pyruvate kinase) - one direction step can be reversed back to previous step

Answer 527

Steps 1-3 Step 1 - glucose is converted to glucose 6 phosphate (G6P) Step 2- isomerisation of glucose 6 phosphate to fructose 6 phosphate. Step 3 - committing step of glycolysis Step 1 and 3 both have large negative free energy values (delta g) and are therefore irreversible

Answer 528

→ Glucose is converted to glucose 6 phosphate via phosphorylation (more reactive) • ATP need for phosphorylation • Polar phosphate group addition = Makes glucose negatively charged (anionic) =Charge prevents passage back across the plasma membrane

Answer 529

Isomerisation of glucose 6 phosphate to fructose 6 phosphate - done by phosphoglucoisomerase - reversible

Answer 530

Committing step: first step that commits glucose to metabolism via glycolysis – glucose 6 phosphate in step 3 is committed to go through glycolysis - further phosphorylation - making glucose even more reactive

Answer 531

Reactions/steps 4 - 10 Step 4- splitting of 2 interconvertible 3 carbon molecules Step 10- irreversible step conversion of phosphophenol pyravate to pyruvate Steps 7 and 10 – produce ATP • Produce 4 but have net gain of 2 ATP • Substrate level phosphorylation – production of ATP by chemical reaction • 1,3-BPG and PEP • Transfer Pi to ADP to give ATP

Answer 532

Steps 1,3 and 10 are irreversible | Can't reverse glyodysis

Answer 533

Cleavage /splitting of C6 into two interconvertible C3 units - c6 splits in either DHAP (dehydroxyacetone phosphate) or glyceraldehyde 3 phosphate (g3p) both are interconvertible c3 units • C3 units interconvertible (occurs in reaction 5) • C6 → 2C3 through phase 2

Answer 534

Phosphophenol pyruvate → pyruvate - Using pyruvate kinase enzyme - irreversible - produces ATP

Answer 535

2 moles of ATP put in at start of pathway • 2 moles of ATP invested at the beginning to get the pathway going • 4 moles of ATP produced per mole of glucose (2 x C3 processed) = net of 2 ATP per mole of glucose

Answer 536

- Glycerol phosphate (produced from DHAP) | - 2.3-bisphosphoglycerate (produced from 1,3 bisphosphoglycerate

Answer 537

Convert Dihydroxyacetone phosphate (DHAP) in adipose tissue and liver → Glycerol phosphate glycerol phosphate is reactive – important for forming lipids (combine with 3 fatty acids) – store in adipocytes • Important to triglyceride and phospholipid biosynthesis • Therefore, lipid synthesis in liver requires glycolysis • (Liver can phosphorylate glycerol directly) - to form glycerol phosphate that isn't made from glycolysis

Answer 538

1,3-Bisphosphoglycerate in RBC → 2,3-Bisphosphoglycerate Uses • 2,3 BPG regulates oxygen affinity of haemoglobin • Present in red blood cells (RBC) at the same molar concentration as haemoglobin (approx. 5 mM)

Answer 539

1. Chemistry Is easier to understand in smaller steps 2. Efficient energy conversation – small changes in molecules, not alot of bond breaking 3. Controlling point – controllable 4. Gives versatility – allows interconnections with other pathways – allows production of useful intermediates – allows part to be used in reverse

Answer 540

Pathway needs NAD+ to be converted to NADH for reducing power • Total NAD+ and NADH in cell is constant, therefore, glycolysis would stop when all NAD+ is converted to NADH = fatal - that shouldn't happen as Normally NAD+ regenerated from NADH in stage 4 of metabolism oxidise NADH in etc BUT 1. RBC have no stage 3 or 4 of metabolism – no mitochondria – can't reform NAD+ directly 2. Stage 4 needs O2 - supply of O2 to muscles and gut often reduced • Therefore, need to regenerate NAD+ by some other route = lactate dehydrogenase can be used to reform NAD+

Answer 541

converts lactate --> pyruvate reforms NADH • Reversible reaction can go from lactate to pyruvate or from pyruvate to lactate • Reversible reaction depends on conditions demand • Converting lactate -> pyruvate reforms NADH

Answer 542

1. Lactate produced by RBC and skeletal muscle (skin, brain, GI) 2. Released into blood - to deal with build up of lactate and • normally metabolised by liver and heart (via LDH) to remove lactate 3. Liver and heart need NAD+ to be regenerated quickly but have good oxygen supply

Answer 543

Lactic acid --> lactate ions and hydrogen ions = acidifying effects blood acidosis • When it acidifies the blood • Metabolic acidosis – when lactate acidifies blood • Lactate is measures in the blood Normal lactate level in blood <1mM Hyperlactaemia – high lactate 2-5mM Lactic acidosis – above 5mM of lactate

Answer 544

* Production → of lactate, more produced than removed * utilisation → How quickly liver, heart and muscle can get rid of lactate from blood * disposal→Excreting lactate using kidney

Answer 545

2-5mM • Not much acidosis as there is no change in blood pH – blood has buffering capacity • Below renal threshold – here level doesn't exceed renal threshold so lactate can be reabsorbed and doesn't appear in urine

Answer 546

above 5mM of lactate • Above renal threshold - too much of lactate in blood can't be reabsored (saturated) stays in filtrate and leaves via urine • Blood pH lowered – large amount of lacatate overcomes blood buffering ability

Answer 547

reabsorption of things from filtrate can be saturated, too much of something in blood can't be reabsored (saturated) stays in filtrate and leaves via urine

Answer 548

- From glucose via pyruvate - from amino acid alanine • Normal lactate production 40-50g/24 hours Plasma level of lactate can increase tenfold furong strenous exercsie including big meal – 30g/5min • Plasma levels increase • Return back to normal within 90 mins

Answer 549

Conditons where lactate level is elevated and stays elevated • Shock – fall in bp • Congestive heart disease – heart starts to fail and there is a build up of lactate

Answer 550

• Convert back to pyruvate To be converted to acetyl coa and used in kreb cycle • Convert into glucose in liver gluconeogenesis .• heart muscle = LDH enzyme converts lactate --> pyruvate goes into kreb cycle acteyl coA – co2

Answer 551

- Liver disease = insufficient metabolism of lactate - Deficiency of thiamine vitamins needed for this - Alcohol excessive dependence – uses up NAD+ l... do gluconeogenesis - Enzyme deficiences in population – genetic may Prevent Gluconeogenesis

Answer 552

- Regulated in response to demand Allosteric control - activator/inhibitor binds at ‘another’ site - catalytic: promote formation of products - regulatory: binding of specific molecule, affects catalytic activity and can activate or inhibit Covalent modification • Dephoshphorylation or phosphorylation can activate or deactivate the enzyme

Answer 553

Step 1 -Hexokinase Step 3 - Phosphofructokinase-1 Step 10 -Pyruvate kinase

Answer 554

1. Hexokinase Glucose --> glucose 6 phosphate which feedbacks via product inhibition can reduce rate of first step and inhibit hexokinase - elevated levels of glucose 6 phosphate inhibits hexokinase - low levels of glucose 6 phosphate activates hexokinase

Answer 555

3. Phosphofructokinase-1 skeletal Muscle = depends on ATP:AMP ratio, allosteric inhibition - high ATP inhibits enzyme - low ATP stimulates enxyme = more pyruvate Liver = insulin: glucagon - high insulin = more glycolysis remove glucose and form glycogen

Answer 556

10. Pyruvate kinase Insulin: glucagon ratio - High insulin: glucagon ratio more glycolysis = less glucose Dephosphorylation activates this enzyme

Answer 557

Fructose --> glucose 3 phosphate --> glycolysis Galactose --> glucose 1 phosphate (can form glycogen for storage) --> glucose 6 phosphate ---> glycolysis

Answer 558

Sucrose (refined sugars) = glucose + fructose Fructose metabolised in liver • Using fructokinase (move phosphate group to fructose) = Fructose --> fructose 1 phosphate • Using aldolase to convert fructose 1 phosphate --> 2 glyceraldehyde 3 phosphate • Use in glycolysis

Answer 559

Essential fructosuria - caused by fructokinase missing • Fructose builds up in urine, exceed renal threshold and appears in urine no clinical signs Fructose intolerance - aldolase missing =Buildup of fructose 1 phosphate and fructose in liver • liver damage • Treatment - remove fructose from diet • Make too much fructose 1 phosphate not enough phosphate to make ATP • No cure – genetic disorder

Answer 560

lactose milk sugar, = galactose and glucose Galactose metabolised mainly in liver • Galactose--> galactose 1 phosphate – using GALK (galactokinase) • Galctose 1 phosphate --> glucose 1 phosphate – using GALT (galactose 1 phosphate puridyl transferase) - Missing GALT (galactose 1 phosphate puridyl transferase) = big problem • UDP galactose 4 epidermase (GALE) – UDP glucose (acts catalytically) reaction to UDP galactose feeds into conversion above • Deficient in read enzymes = galactosaemia

Answer 561

Elevated levels of galactose in blood transferase deficiency = Accumulation of galactose and galactose 1 phosphate : • High galactose levels – aldose reductase is activated • Galactose --> galactitol (alcohol version) via aldose reductase and use of NADPH - NADPH isa key defense against reactive oxygen radicals – reaction above depletes NADPh stores - Low NADPH = cells are defenseless against reactive ocygen species - Reactive oxygen species denatures critaslin protein in the lens of the eye = cataracts (cloudy lens) • Accumulation of galactose 1 phosphate affects liver kidney and brain

Answer 562

* Detect very early on ASAP after birth * No cure * Tretament is to avoid lactose in diet * Still have cataracts but avoid other damage

Answer 563

Pyruvate does not directly enter stage 3 of catabolism | - must be converted to acetyl coa by pyruvate dehydrogenase enzyme

Answer 564

Pyravate → acetyl coa = irreversible reaction and carbon dioxide is lost activated by: • Pyruvate - a lot of pyruvate = more active • NAD+ - lack of reducing power activates enzyme • ADP – lack of energy activates enzyme • Insulin Activate enzyme by dephosphorylating it ``` inhibited by: • Acetyl coA • NADH • ATP Inhibit enzyme by phosphorylating it ```

Answer 565

Inputs - Oxidative requires NAD+ and FAD which are reduced in cycle - acetyl coa ``` Outputs One molecules of glucose produces: • 6NADH • 2FAD2H • 2GTP - some energy Produces precursors for biosynthesis Produces a lot of reducing power for stage ```

Answer 566

Citrate → fatty acids succinate → haem groups Oxaloacetate → glucose (or amino acids can form oxaloacetate and feed into cycle) Alpha ketogutamate → amino acids

Answer 567

Isocitrate dehydrogenase Isocitrate → alpha ketoglutarate * Ratio of ATP:ADP in cell and NAD+:NADH ratio * Activated by = high level of ADP, produces more electron donors stimulates cycle * Inhibited by = high level of NADH, as there are enough electron donors

Answer 568

Electron transport chain: - Electrons on NADH and FAD2H transferred through a series of carrier molecules to oxygen (ELECTRON TRANSPORT) - Releases energy in steps Oxidative phosphorylation - Free energy released from electrons used to drive ATP synthesis (OXIDATIVE PHOSPHORYLATION)

Answer 569

- Cristae - inner membrane - outer membrane - Matrix Inner mitochondrial membrane • Largely permeable to water and ammonia • Separate protons across the membrane • Slightly leaky tho

Answer 570

→ oxidation of NADH and FAD2H - establish proton gradient, energy from released electrons is used to pump protons into intermembrane space → electrons are supplied to proton translocation complexes = pump protons * Large protein complexes span the membrane – these use the energy from the elctrons to pump protons across membrane into inner membrane space * Electrons move to second complex * Second complex has more electrons fed in by FAD2H – pump more protons * Electrons move to final complex * Build large proton gradient across membrane * Finally electrons combine with oxygen = water

Answer 571

Protons pass through ATP synthase enzyme when there is a significant gradient – energy from movement is used to make ATP • Uses proton chemical concentration gradient • Proton motive force – moving down conc gradient NADH electrons have higher energy (uses 3 proton translocating complexes) – fed in earlier - 2 NADH = 5 ATP FAD2H electrons have lower energy ( use 2 proton translocating complexes) – fed in at lower level - 2FAD2H = 3 ATP

Answer 572

* NADH dehydrogenase = NADH --> NAD+ to release electrons * Coenzyme Q = shuffles electrons to the next protein complex Side effect of statins – reduce production of coenzyme Q = not good • Cytochrome C – shuffles electrons to cytochrome oxidase • Cytochrome oxidase = where electrons react with oxygen to give water • Maintain large proton gradient

Answer 573

* High ATP = low ADP – more difficult to make ATP as there is no ADP substrate that is used to form ATP * No process = inward flow of proton stops, concenttation gradient of protons builds up, harder to pump protons, slows process Reversed = low ATP concentration, high ADP more protons pumped

Answer 574

Cyanide - can block etc • Cyanide inhibits cytochrome oxidase enzyme • Electrons aren't added to oxygen – stop etc = no ATP = death • Inhibitors block electron transport, e.g. cyanide (CN- ) prevents acceptance of electrons by O2

Answer 575

* Normally oxidative phosphorylation and electron transport are tightly coupled → Operate conjointly * Both regulated by mitochondrial [ATP] high ATP = no ADP inward proton flow stops, prevents pumping

Answer 576

→ Uncouplers increase the permeability of the mitochondrial inner membrane to protons = collapse gradient = reduce proton motive force - make it more leaky so protons don't go through ATP synthase - no atp= death

Answer 577

- Inhibition of electron transport - uncouples - ox/phos diseases

Answer 578

* Block flow of electrons - no electron transport * therefore, no p.m.f. - no oxidative phosphorylation * Lethal – cyanide (inhibit cytochrome oxidase), carbon monoxide

Answer 579

* May dissolve in membrane or act as transporters across membrane * Dinitrocresol – herbicide = posion farmers * Fatty acids – dissolve in membrane increasing permeability

Answer 580

* Genetic defects in proteins encoded by mtDNA mitochondrial DNA (maternal line) = improper formation of complexes * (some subunits of the PTCs and ATP synthase) → reduce speed in electron transport and ATP synthesis

Answer 581

→ Contains protein thermogenin (UCP1) uncoupling protein 1 - naturally-occurring uncoupling protein that collapses gradient = heat Response to cold – release noradrenaline (maintain body temp) which activates: 1. Lipase which releases fatty acids from Triacylglycerol (fat stores) 2. Fatty acids activate UCP1. - more fatty acids = more FA oxidation → NADH/FAD2H → electron transport. 3. UCP1 transports H+ back into mitochondrial matrix – collapse proton gradient, make no TP, release heat 4. So, Electron Transport uncoupled from ATP Synthesis. Energy of p.m.f. is then captured as extra heat. Method of making heat without producing ATP

Answer 582

Babies • A lot of brown adipose tissue • Allows them to maintain heat, particularly around vital organs Adults do still have brown adipose tissue to maintain heat Hibernating animals • Over the winter • so they can generate heat to maintain body temperature

Answer 583

Total 32 molecules of ATP from 1 molecule of glucose | • Most of the ATP comes from ETC

Answer 584

* Lipid soluble, generally insoluble in water * Most only contain C, H, O – (phospholipids contain P, N) More reduced than carbohydrates – release more energy when oxidised – complete oxidation requires more O2 - get more energy from lipids than carbs

Answer 585

- Fatty acid derivative.s - hydroxy-methyl-glutaric acid derivatives = c6 compound (hmgs) - Vitamins

Answer 586

Derived from fatty acids * fatty acids - fuel molecules * Triacylglycerols (triglycerides) basically fat – fuel storage and insulation * Phospholipids – components of membranes and plasma lipoproteins * Eicosanoids – local hormones/ mediators 20 carbons chain fatty acids eg. Prostoglandins

Answer 587

* Ketone bodies (C4 ) – water soluble fuel molecules, transported in blood * Cholesterol (C27) – membranes and steroid hormone synthesis from cholesterol * Cholesterol esters – cholesterol storage, they are more lipid soluble forms of cholesterol used for transport in blood * Bile acids and salts (C24) – produced by liver, released by gall bladder lipid digestion (make fat breakdown easier)

Answer 588

A, D, E and K are fat soluble lipids

Answer 589

Made of glycerol (hydroxyl groups) and fatty acids (acidic group) * Esterification = acid groups react with hydroxyl alcohol group * 3 fatty acids and 1 glycerol * Reversible reaction – lipolysis = breakdown triacyclglycerol into 3 glycerol and one fatty acid

Answer 590

* Hydrophobic so they are stored in anhydrous form – droplets that don't need lots of water * Stored in adipose tissue * These stores are only used in prolonged exercise, starvation and during pregnancy - after glucose and glycogen have been used up * Storage and mobilisation of this fat is under hormonal control

Answer 591

1. Hydrolysis of triglycerides (lipids) occurs in gl tract → fatty acids and glycerol 2. Glycerol and fatty acids are absorbed into lymphatic system - and then absorbed into the blood 3. Glycerol is freely transported in blood (as it is polar) to the liver where it is metabolised 4. Fatty acids are not water soluble= transported by chylomicrons (lipoproteins) in the blood 5. Fatty acids are delivered to adipose tissue for storage - but can be remobilized by albumin

Answer 592

→ Fatty acids can be mobilized from adipose tissue – carried in blood to tissues for energy by binding to albumin - Fatty acid can't be used for energy in brain or by cells without mitochondria • Controlled by hormone sensitive lipase – breaks down fats into lipase but is under hormonal control = insulin (promotes storage) = glucagon/ adrenaline (stimulates breakdown of stores to be used for energy)

Answer 593

Formula: CH3(CH2)nCOOH where n= 14-18 * saturated – no double bond * unsaturated ( ie one or more double bonds C=C) * amphipathic (contain hydrophilic (carboxylic acid end) & hydrophobic groups) polar and non polar * Fatty acids come from diet as we can't manufacture them * certain polyunsaturated FA are essential (because mammals cannot introduce a double bond beyond C9), e.g. linolenic acid 18 : 3 (9,12,15)

Answer 594

Occurs in mitochondria Fatty acid → acetyl coa Also known as beta oxidation Requires oxygen Doesn't occur in brain or cells without mitochondria

Answer 595

1. FA is activated – by linking FA (fatty acid) to coenzyme A outside of mitochondria, in cytosol 2. Must transport activated FA across mitochondria inner membrane – using carnitine shuttle ( transport mechanism) 3. FA goes through sequence of oxidative reactions in mitochondria – 2 carbons removed in each cycle until left with acetyl coA (to be used in kreb/ TCA cycle) 4. Oxidative process = This also produces FAD2h and NADH – electron donors for etc and oxidative phosphorylation

Answer 596

* Binding coenzyme A to FA with high energy sulphide bond * Uses enzyme fatty acycl coA synthase * Forms fatty acyl coA – active form of FA * Outside mitochondria in cytoplasm

Answer 597

→ transports activated fatty acid (fatty acyl coa) across inner mitochondrial membrane 1. Carnitine reacts with acyl coA – activated FA to give = acyl carnitine and coA 2. Acyl carnitine – fa bound to carnitine 3. That has a special transporter that transports acyl carnitine across membrane into matrix 4. Acyl carnitine is broken down into carnitine releasing acyl component which is converted back to acetyl coa 5. Carnitine shuffled back across membrane to be reused

Answer 598

CAT1/2 carnitine acyltransferases = synthesis and breakdown of acyl carnation • Convert carnitine to acyl carnitine • Convert acyl carnitine to carnitine Malonyl coa • shuttle Inhibited by malonyl coA - it is an intermediate in FA production, stopping newly made FA being immediately oxidised

Answer 599

→ difficulty providing energy to muscles over a long period of time * Exercise intolerance * Lipid droplets in muscle

Answer 600

→ glycerol is transported to liver where it is metabolised 1. Form an active form of glycerol by recating with ATP = glycerol phosphate • Using enzyme glycerol kinase – adding phosphate group to glycerol 2. Use glycerol phosphate in one of 2 ways • Use it to form triacylglycerides – triacylglycerol synthesis fats for storage • If there is demand it can be fed into glycolysis by being converted to dihydroxyacetone phosphate DHAP

Answer 601

Depends on energy demands * Use it to form triacylglycerides – fats for storage * If there is demand it can be fed into glycolysis by being converted to dihydroxyacetone phosphate DHAP ( and form NADH)

Answer 602

→ convergence point for anabolic and catabolic pathways • Converted to fatty acids – anabolism • Breakdown down of fatty acids – catabolism Structure: • Acetly coA = acetly group linked to coenzyme a via sulfide bond – high energy bond • like an activated acetyl group • CoA contains vitamin B5

Answer 603

* used as an intermediate for Fatty acid synthesis = that can then form triglycerols and phospholipids * converted to Carbon dioxide – when oxidised in kreb cycle * Go into Hydroxymethyl glutaric acid pathway: that can either form ketone bodies or cholesterol which gives rise to steroid hormones (depends on demand)

Answer 604

- Water soluble - permit high plasma concentrations - ketonuria= when above renal threshold, excreted in urine

Answer 605

• Acetoacetate - (produced in liver- breaks down spontaneously to give acetone) - CH3COCH2COO- • Acetone - (produced when acetoacetate is broken down spontaneously) - CH3COCH3 - volatile, breathed out smelt on breath = sign for type 1 did bites • Beta hydroxybuterate - (produced in liver) - CH3CHOHCH2COO

Answer 606

- Normal to have in blood at low levels = <1mM - Produce more ketone bodies under starvation conditions – so there are higher physiological levels (physiological ketosis) = 2-10mM - Pathological ketosis = level above 10mM happens in untreated type 1 diabetes – level of ketone bodies builds up to high and dangerous levels

Answer 607

→ synthesised by liver mitochondria 1. Convert acetyl coA to hydroxy methyl gluterol coA using enzyme synthase HMG-coA 2. HMG coA can either be: • Converted to cholesterol with HMG coA reductase • Lysed by lyase enzyme and converted to ketone bodies (acetoacetate, acetone, beta hydroxybutyrate)

Answer 608

1. Fatty acids are broken down to acetyl coA 2. Acetyl coA is converted to acetoacetate and beta hydroxybutyrate (ketone bodies) 3. These leave the cells and are carried in the blood as ketone bodies are water soluble 4. In blood acetoacetate are broken down into acetone 5. Acetone and beta hydroxybutyrate are taken up by tissues that need ketone bodies 6. Beta hydroxybutyrate is converted back to acetoacetate which is converted to acetyl coA - which goes into kreb cycle

Answer 609

---> ketone bodies = are a way of delivering acetyl coA from liver to tissues that need energy Acetyl coA is too large to directly transport it

Answer 610

Regulated by insulin/ glucagon ratio - Insulin – storage hormone, eating enough, good insulin supply, storage of fuel molecules = occurs in fed state - Glucagon – breakdown hormone, not enough food low insulin levels, high glucagon levels, low ratio – mobilise ketone bodies – occurs in starvation

Answer 611

Starvation = low insulin: glucagon ratio 1. Acetyl coA to HMG coA 2. Lyase enzyme activated forming ketone bodies 3. HMG coA reductase inhibited Ketone body synthesis

Answer 612

1. Acetyl coA to HMG coA 2. Lyase enzyme activated forming ketone bodies 3. HMG coA reductase inhibited Low insulin: glucagon ratio

Answer 613

1. High insulin to glucagon ratio 2. Lyase enzyme inhibited 3. HMG coA reductase enzyme stimulated – cholesterol synthesis 4. Favours anabolism – no need for ktone bodies

Answer 614

Act to inhibit HMG CoA reductase to reduce cholesterol synthesis

Answer 615

• Acetoacetate and β-hydroxybuterate are relatively strong organic acids →ketoacidosis - acidify blood at high levels can be fatal

Answer 616

* genetic component * Majority of patients have translocation between chromosome 9 and 22 * Results in a small chromosome = Philadelphia chromosome