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DNA and Proteins Flashcards

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1
Q

What are the components of a nucleoside and a nucleotide?

A 
nucleoside= sugar and base
nucleotide= phosphate, sugar and base
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2
Q

Which bases are purine and which are prymidine? What’s the difference in their structure?

A

A and G are purines, C,T and U are prymidines.

Purines have 2 rings, prymidines have one

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3
Q

What is the long name for a deoxynucleotide and a nucleoside containing the base adenosine?

A

nucleoside: deoxyadenosine
nucleotide: deoxyadenosine monophosphate (AMP)

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4
Q

How many H bonds do A-T/U and G-C form?

A 
A-T/U= 2 
G-C= 3
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5
Q

What is significant about the major groove in the DNA helix?

A

It is a more accessible place for proteins to bind.

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6
Q

What is the differences in structure of RNA and DNA?

A

DNA is double stranded

DNA has an OH group on the 3rd carbon of the ribose sugar.

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7
Q

Describe the process of DNA replication

A
  • DNA helicase breaks H bonds to expose both strands
  • DNA primer binds to exposed DNA sequences on both strands
  • DNA polymerase extends fragments 5’-3’
  • On 5’-3’ side okazaki fragments form as DNA polymerase can only extend in bits
  • DNA ligase joins okazaki fragments together
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8
Q

Why do we have 46 chromosomes before and after DNA replication?

A

Because before DNA replication, one chromosome= one DNA molecule, whereas after replication one chromosomes= two DNA molecules.

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9
Q

What is the difference between two sister chromatids?

A

There are no differences, they have exactly the same DNA sequence

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10
Q

What is the difference between two homologous chromosomes?

A

They have the same genes/ loci but different alleles for those genes- one from mum one from dad

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11
Q

What are telomeres? What is their function?

A

Repeating, non- coding sequences at the end of a chromosomes/ DNA sequence. They protect the DNA from degradation because after each DNA replication cycle some DNA is lost. The telomeres therefor protect the coding sequences. They get shorter with ageing.

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12
Q

Where is the centromere located on metacentric, acrocentric, submetacentic and telocentric chromosomes?

A

metacentric: middle
submetacentric: nearer one end
acrocentic: really quite near an end
telocentric: in telomeres (right at the end)

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13
Q

What are the mutations of the genes for cystic fibrosis and sickle cell anemia?

A

sickle cell anaemia= GLU6–> VAL

cystic fibrosis: Phenylalanine deletion

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14
Q

Describe each stage of mitosis

A

Prophase: chromosomes condense, nuclear envelope disappears
prometaphase: centrioles divide and move to poles, spindle fibres attach to centromeres
Metaphase: chromosomes line up on the equator
Anaphase: Sister chromatids separate (thus becoming individual chromosomes) to move to opposite poles
Telophase: Nuclear envelope reforms and chromosomes decondense
Cytokenesis: cleavage furrow forms and deepens, cytoplasm divides

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15
Q

Describe G1, S and G2 and the checkpoints within the cell cycle

A

G1: cell size doubles, cytoplasmic components are made
G1 checkpoint: check for cell size, nutrients, DNA damage, growth factors. If incorrect- senescence- enter stage G0, where cell cycle arrested.
S- DNA is replicated
G2- mitochondira divide, precursors to spindle fibres syntheised.
G2 checkpoint: is cell big enough, is DNA replicated + properly
Mitosis checkpoint: are spindle fibres attached properly.

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16
Q

Describe meiosis 1

A

Prophase is same at mitosis, in metaphase homologous chromosomes line up on the equator of the cell in pairs. Non- sister chromatids then cross over and exchange some genetic material. In anaphase the homologous chromosomes separate (not sister chromatids). You get independent assortment here as the homologous chromosomes line up in random order and so each daughter cell gets a mixture of maternal and paternal chromosomes. Telophase is same as mitosis

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17
Q

Describe mitosis 2

A

Prophase chromosomes condense

prometaphase: spindle fibres attach to chromosomes
metaphase: chromosomes line up on equator in single file
anaphase: sister chromatids separate
telophase: nuclear membrane reformes and chromosomes decondense

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18
Q

Give main differences between mitosis and meiosis.

A

Mitosis creates genetically identical daughter cells.
Mitosis creates cells with 46 chromosomes, meiosis creates one with only 23 chromosomes.
4 daughter haploid cells from meiosis and 2 daughter diploid from mitosis
Process of meiosis 1 differs from mitosis

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19
Q

What are the 3 main principles of the genetic code?

A

Non-overlapping
Degenerate
Universal

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20
Q

How do sex chromosomes find each other to pair up in meiosis?

A

There are small regions that are the same on X and Y chromosomes- PAR1 and PAR2 genes (psuedoautosomal regions).

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21
Q

What would be the consequence of the SRY gene crossing over from the Y chromosmes on the X

A

The offspring could have XY genotype (lost SRY from the X) but have female genotype or have XX and have male phenotype. This is because SRY triggers testicular development.

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22
Q

Describe the steps in spermatogenesis

A

The spermatogonium (stem cell) divides by mitosis into itself and also (from puberty) into two primary spermatocytes. If stimulated, the primary spermatocytes will divide by meiosis, at the end of meiosis 1, each primary spermatocyte will produce 2 secondary spermatocytes- each with 23 chromosomes (in X form)- and so these cells are haploid. The secondary spermatocytes then undergo meiosis 2 for form 2 spermatids. These spermatids then undergo maturation into sperm cells.

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23
Q

Describe the process of oogenesis

A

The oogonium divide into primary oocytes in the foetal stage of development. This means a female only has a finite number of oocytes from birth. The primary oocyte starts meiosis but the process is paused at prophase of meosis 1. When the female reaches puberty, one oocyte will be able to resume meiosis per month. The oocyte divides into a secondary oocyte and a polar body after meiosis 1. The secondary oocyte is then ovulated (the polar body disintergrates) and if it is penetrated by a sperm cell it will very quickly complete meiosis 2 to create another polar body and an ovum. The ovum and the sperms nucleus will fuse to create a zygote.

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24
Q

Why are polar bodies creates in oogenesis?

A

So that the majority of a cells components can go to the oocyte and so it has enough nutrients and mitochondria ect to survive till fertilisation.

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25
Q

Describe the process of transcription

A
  • Transcription factor binds to promotor region (eg TATA box)
  • RNA Polymerase also binds to TR and promotor
  • Transcription activated by enhancer region upstream of promotor region
  • Transcription starts at transcription start sequence (not AUG), helicase unwinds DNA
  • RNA Nucleotides join to bases on template strand (3’-5’) and RNA polymerase joins RNA nucleotides 5’-3’. This means pre- mRNA strand created is complementry to coding strand
  • Transcription continues pasts stop codon and polyA site until it means transcription termination site.
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26
Q

Describe the 3 post transcriptional modifications of pre mRNA

A

Splicing- introns removed by splicosome, which recognises where to cut by splicing sequences at beginning and end of intron.
Capping- methylated guanine is added by 5’-5’ linkage at 5’ end of the pre mRNA strand
Poly A Tailing- Poly A site at 3’ end is recognised and cleaved, PolyA polymerase adds a bunch of AMPs onto the end

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27
Q

Describe the process of translation

A
  • mRNA meets ribosome
  • tRNA with CAU fills P site where it is complementary to the start codon (AUG)
  • the next tRNA in the sequence fills the A site
  • energy GTP breakdown used to form polypeptide bond and break amino alkyl bond between amino acid and tRNA in P site
  • Peptidyl transferase used to move amino acid from P site onto amino acid in A site.
  • tRNA from A site moves into P site
  • Process repeats
  • Water needed to break amino alkyl bond between final amino acid and tRNA when stop codon reached.
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28
Q

What are the differences between prokaryotic and eukaryotic ribosomes?

A

Eukaryotes have 80s type- 60s and 40s subunits

prokaryotes have 70s type- 50s and 30s subunits

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29
Q

What binds the tRNA and amino acid back together?

A

aminoacyl tRNA synthase and ATP

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30
Q

How is the wobble base created on the tRNA meaning one tRNA needed per amino acid not per codon?

A

the base Inosine is present in some tRNA molecules, it can bind to U,C or A meaning the same tRNA can bind to slightly different codons- thus the same amino acid can bind to many different codons (code is degenerate) without needing lots of different tRNA molecules.

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31
Q

State ways that you can classify amino acids side chains

A 
charged/ uncharged
polar/nonpolar
hydrophobic/ hydrophillic
acidic/ neutral/ basic
aliphatic/ aromatic
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32
Q

Where will uncharged/ hydrophobic aminoacid residues tend to reside in a protein

A

on the interior/ within the plasma membrane portion.

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33
Q

Why can amino acids be buffers?

A

because many are weak acids/ bases and so can act to ‘mop up’ excess H+

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34
Q

What is pK?

A

The pH at which an amino acid will have no overall charge

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35
Q

If pH is greater than pK will the side chain be protonated or deprotonated

A

deprotonated- acidic amino acids have very low pK and so pH is usually higher and so usually in deprotonated form

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36
Q

What is pI?

A

the isoelectric point of a protein- the pH at which a protein will have no overall charge. it is basically the avg pK of the amino acids.

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37
Q

Which two amino acids break an a- helix

A

proline (cannot rotate around N-C bond)

Glycine (r-group supports other conformations.)

38
Q

Between which amino acids do disulfide bonds form?

A

cystenine

39
Q

In a dipeptide, do the amino acids take a cis or trans formation?

A

trans (r group is on opposite sides), because cis formation is not stable as they clash

40
Q

State 5 methods of short term regulation of protein/ enzyme activity

A
  • change product conc
  • change reactant conc
  • allosteric regulation
  • covalent modification
  • proteolytic cleavage
41
Q

State 2 long term ways of regulating protein/ enzyme activity

A
  • change rate of protein synthesis

- change rate of protein degradation

42
Q

What are isoenzymes?

A

Different forms of the same protein, they act on the same substrate but have different affinities for the substrate

43
Q

What is the difference between feedback and product inhibition?

A

feeback inhibition is where the product of a pathway inhibits the first enzyme in the pathway
product inhibition is where the product inhibits the enzyme,

44
Q

Give two allosteric activators and 3 inhibitors of PFK (enzyme involved in glycolysis)

A

activators: AMP, fructose
inhibitors: ATP, Citrate, H+

45
Q

Allosteric effectors change the protein from R state to T state/ visa versa, which state is the higher affinity state?

A

T state has lower affinity, R state has higher affinity.

46
Q

Give one example of a method of covalent modification of a protein and describe the process

A

phosphorylation:
By protein kinases transferring terminal phosphate from ATP to the -OH on ser, thr or try
Can activate or de activate proteins
Adds 2 neg charges, gives ability to make H bonds and rate of phosphorylation can be adjusted.
Also leads to amplification as activating one enzyme can activate many more

47
Q

What is a zymogen. Give one example

A

an inactive form of a protein. eg pepsinogen

48
Q

How and why is pepsin activity regulated

A

By proteolyctic cleavage-
released as pepsinogen and then when pH is correct it is cleaved to create pepsin, this is to prevent it from digesting the cell.

49
Q

How is chymotrypsin regulated?

A

chymotrypsinogen (zymogen) is cleaved by trypsin to create chymotrypsin and another chain, this chain is then cleaved by chymotrypsin to create another chymotrypsin and an a and c chain.

50
Q

what is the function of chymotrypsin?

A

to cleave other zymogens and so activate them for digestion

51
Q

How is trypsin activated?

What is trypsins function?

A

by enteropeptidases of trypsin cleaving trypsinogen into trypsin.
to activate, by cleavage, chymotrypsin, elastase, lipase

52
Q

How is prothombin (and other cofactors) localised to the site of damage for clot formation?

A

COOH group added to the Glutamate resiudues post translationally to form carboxyglutumate (Gla). These Gla can bind to the Ca2+ at the site of damadge.

53
Q

How is prothrombin converted to thrombin, what effect does this have?

A

The kingle domains in the prothrombin are cleaved.
Thrombin can then go on to cleave fibrinopeptides from fibrinogen to form fibrin which can aggregate to form a mesh/ clot

54
Q

What cofactor is needed for carboxylation of Glutumate residues in cofactors?

A

vit K

55
Q

How can the clotting cascade be stopped?

A
  • dilution of clotting factors in blood and removal by liver
  • digestion of clotting factors- eg by protein C
  • Antithrombin 3
  • Plasmin (breaks down clots by cleaving fibrin)
  • warfarin (prevents activation of vitK, so lot can’t be localised)
56
Q

If a protein is destined for the cytosol or organelles where is it synthesised? What about if its meant to go to plasma membrane/ secretion?

A 
cytosol= free ribosomes
secretion= ribosomes on RER
57
Q

What sequence targets a protein to a peroxisome? Where is it found?

A

seriene- lysine- leucine (SLK) is the peroxisome targeting sequence (PTS) it is found at the C terminus

58
Q

What receptor is used to target a protein in the cytosol to a peroxisome? How is the protein transported into the peroxisome? What is ATPs role in this movement?

A 
receptor= PEX5 recognises SLK sequence
translocator= 13 PEX proteins in surface membrane of peroxisome
ATP= allows recycling of PEX5 receptor
59
Q

What are the two types of secretion from a cell?

A

constitutive (continuos and unregulated)

regulated- by hormones ect

60
Q

How is a protein targeted to the ER for

secretion?

A

Hydrophobic sequence of 5-30 hydrophobic aminoacids at N terminus (start) is recognised by SRP as soon as it comes out of a ribosome.
The SRP stops translation and binds the ribosome to an SRP receptor on the RER membrane.
Energy from GTP used to open channel
Translation then continues to release the protein into the RER, and the signal sequence is cleaved by signal peptidase

61
Q

What are the roles of the RER in post translational modifications?

A 
Proteolyctic cleavage
glycosylation (adding sugar residues)
forming S-S bonds 
folding
Hydroxylation of lys and Pro residues
62
Q

What are the roles of the golgi in post translational modifications

A 
phosphorylation of ogliosaccarides
adding sugar residues
sulfation of tryosine and carbohydrates
o- linked glycoslation (adding sugar to OH groups)
proteolyctic cleavage
63
Q

How are proteins targeted to ER protein retention

A

Signaled by KDEL sequence at C terminus
KDEL receptor in cis membrane of golgi recognises KDEL sequence
Protein + receptors are packaged into vesicle with COP1 coat
COP1 vesicle moves back to ER
Higher pH in ER lowers affinity between KDEL and KDELr so protein released from receptor and vesicle
Protein is always folded
Energy is needed to set up low pH in golgi

64
Q

How is insulin modified from preproinsulin to insulin

A

Preproinsulin is converted to proinsulin as the RER signal sequence is cleaved from the N terminus as it enters the RER
Proinsulin polypeptide is made up of 3 parts- A,B and C
Disulfide bonds are formed between A and C sequences
Proinsulin transported to glogi
In golgi B sequence is cleaved to make it into insulin. Insulin is packaged and ready for release when stimulated.

65
Q

How is a protein targeted to a lysosome?

A

The signal is a mannose-6- phosphate (M6P) which is added to a signal patch on the polypeptide whilst it is in the golgi.
M6P is recognised by M6P receptor at trans side of golgi.
Clathorin coat forms around vesicle
vesicle takes protein- receptor complexs to late endosome
M6P dissociated from receptor due to pH change
Phosphate removed from the M6P and enzyme complete. M6Pr moves back to golgi in vesicle
Protein is transported folded

66
Q

How is a protein targeted to a mitochondria?

A

Ampiphatic signal at N terminus recognised by hsc70 chaperone proteins that require ATP to bind to the protein.
chaperones keep the protein unfolded
Precursor protein binds to signal receptor on mitochondrial membrane
Receptor takes precursor to TOM protein
When TOM inline with TIM protein can pass through TOM and then through TIM into the matrix of the mitochondrion
hsc70 in matrix helps pull the precursor protein through TIM up conc gradient (ATP needed)
Signal sequence is cleaved, hsc70 is released and protein can fold.

67
Q

How is a protein targeted to the nucleus?

A

Signal sequence called NTS of basic amino acids anywhere in chain but on external surface when folds is bound to importin protein in cytosol
importin-protein complex binds to nuclear pore and moves into nucleus
Ran- GTP binds to complex and causes change which releases protein
Ran- GTP and importin move back into cytosol where ran-GTP becomes ran-GDP and dissociates with importin
ATP needed to reform ran-GTP for it to move back into nucleus
Protein is always folded and signal sequence retained so that it can move back into cytoplasm after mitosis.

68
Q

What cells secrete collagen and is it regulated or constitutive secretion?

A

fibroblasts, constitutive

69
Q

Describe the structure of collagen

A

3 a helixs, interwtining to form a right handed helix
glycine is at every 3rd position, it has a small side chain so allows the polypeptides to intertwine closely together
proline and then hydroxyproline usually follow the glycine.
H bonds form between the 3 polypeptides as a result of the hydroxyprolines

70
Q

What polypeptides does type 1,2 and 3 collagen consist of?

A

type 1: 2x a1(1) and 1x a2(1)
type 2: 3x a1(2)
type 3: 3x a1 (3)
type 4: 3x a1(4)…

71
Q

State what happens to preprocollagen when it enters the RER.

A
  1. Signal sequence is cleaved, so now it is procollagen
  2. Everyother proline residue is hydrocylated to make hydroxyproline by prolyl hydroxylase using fe2+ and vit C
  3. N- linked ogliocaccharides added
  4. Galactose added to some hydrolysines
  5. a helixs created at N termiuns and disulfide bonds formed at C terminus
  6. central body intertwines forming the tripple helix, H bonds from between polypeptides
72
Q

What is the cause of scurvy? How does this cause its symptoms?

A

Vit C deficiancy. This is needed as cofactor with prolyl hydroxylase so add OH to prolines. Without this the procollagen cannot form H bonds, and so the collagen is less stable

73
Q

State what happens after the procollagen moves in to the golgi.

A
  1. O-linked ogliosaccharides added
  2. vesicles form and transport it out the cell
  3. Procollagen peptidases remove N and C termiuses to make it into tropocollagen .
  4. lysyl oxidase and vit B6 cofactor form covelnat bonds between lysine residues on adjacent tropocollagens. (covalent crosslinking) to make stronger collagen fibrils
  5. Type 2 collagen does not aggregate fibrils to fibres but the rest do
74
Q

State the location and features of type 1,2,3,4 collagen.

A

type1: fibrils aggregate to fibres, most common, found in tendons, dermis ect
type2: fibrils dont aggregate to fibres- hyaline and elastic cartilage
type3: reticulin- forms around organs and structures for support (eg lymph nodes)
type4: basement membrane

75
Q

What is Vmax?

A

The maxiumum velocity of a reaction

76
Q

What is Km for an enzyme?

A

The substrate concentration that gives 1/2 the Vmax

77
Q

What factors affect enzyme activity?

A

pH, substrate conc, temperature,

78
Q

What affects do competitive inhibitors have on Km and Vmax?

A

They increase Km (lower rate of activity) but dont affect Vmax- as the inhibitor is surmountable (can be overcome with high [s]

79
Q

What affects do non-competative inhibitors have on Vmax and Km?

A

Doesn’t affect Km, decreases Vmax

80
Q

What is the units for enzyme activity?

A

The amount of enzyme that will produce 1umol of product per min under standard conditions. It is expressed in g or tissue or in L if in serum

81
Q

How can Km and Vmax be easily estimated? (What graph and how do you find each)

A

Lineweaver- burk plot
-1/Km is x axis intercept
1/Vmax is Y axis intercept

82
Q

Describe the structure of myoglobin, its dissociation curve and how its conformation changes when O2 binds.

A

a central Fe co-ordinately bonded to protoporphyrin ring around it and a proximal histidine residue below it.
Its dissociation curve is hyperbolic, and it will only release o2 when PO2 is very low (when muscles are in dire need)
The Fe2+ lies below the protoporphyrin ring until o2 binds, when it is bough up into the same plane

83
Q

Describe the structure of Hba and Hbf

A 
Hba= 2 alpha and 2 beta chains 
Hbf= 2 alpha and 2 gamma chains (higher affinity so taes o2 from mum)
84
Q

Describe the cooperative binding of o2 and why this is important for transport of O2

A

Cooperative binding of o2 is where the binding of one o2 causes conformational change in Hb from T state (low affinity) to R state (higher affinity). This means that where low pO2 there is low affinity and so dissociates from o2 to release o2 at tissues.

85
Q

If the affinity of Hb is increased does the dissociation curve shift to the left or right?

A

pushes to the left- when affinity for o2 is lower, a greater pO2 is needed to fully saturate the Hb

86
Q

What is the normal blood levels of 2,3 Bisphosphate glycerate? How does BPG affect Hb affinity for O2?

A

5mmol

decrease affinity for oxygen- levels increase to 8mmol at altitude so more o2 released at tissues

87
Q

What affect do H+ and CO2 increase have on Hb?

A

bohr effect- decreases affinity for O2, since these are found at tissues, affinity is lower at tissues meaning o2 is released

88
Q

How can someone with 50% of normal Hb levels survive but someone with 50% HbCO (50% of Hb bound to CO) not survive?

A

CO lowers the affinity for oxygen of the subunits around it also.

89
Q

What mutation causes sick cell disease? What does this do the Hb?

A

Glu6–> Val in B globin gene
Val moves in (hydrophobic) causing sticky pocket
HbS can polymerise/ aggregate to make RBC sickle shape. HbS lyse more easily and sickle cells removed by spleen.

90
Q

What are symptoms of sickle cell anaemia?

A 
Anemia
enlarged spleen 
fatigue
crises
swelling in hands and feet
eye damage
necrosis
freq infections
leg ulcers
91
Q

What are the causes of a- thalassaemia and b-thalassemia?

A

a- thalassemia is loss of one/ all of the 4 a globin genes
b- thalassemia is loss of 1/ all of the two b globin genes
Both cause differnt forms of Hb in blood- a chain precitaties or b tetramers ect
how many and what type you loose determines severity of symptoms

92
Q

Give symptoms of thalassemia

A
  • anemia
  • gall stones
  • bone deformities
  • jaundice
  • enlarged spleen
  • still birth

Cell Biology And Genetics (4 decks)

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