MGD Flashcards
0
Q
Name 2 uncharged amino acids
A
Possible answers: phenylalanine, tyrosine, tryptophan, glycine, alanine, pro line, valine, leucine, isoleucine and methionine
1
Q
What stereoisomer (L or D) of amino acids are naturally found in proteins?
A
L
2
Q
Name a negatively charged amino acid
A
Possible answers: aspartate and glutamate
3
Q
Name a positively charged amino acid
A
Possible answers: lysine, arginine and histidine
4
Q
Name 2 polar amino acids
A
Possible answers: serine, threonine, cysteine, asparagine and glutamine
5
Q
What are the key features of peptide bond?
A
CO and NH bond in trans orientation
Cant rotate due to double bond characteristics
6
Q
What are the difference between a globular and fibrous protein?
A
Globular: water soluble, compact and highly folded. Usually has a regulatory or enzymatic function
Fibrous: water insoluble, elongated, repeating units. Usually has a structural function
7
Q
Define the isoelectric point
A
The pH at which a protein has no overall net charge
8
Q
Define a zwitterion
A
A neutral ion with the positive NH3+ and negative COO- ends. Formed at the isoelectric point
9
Q
What is the primary structure of a protein and what bonds are involved in its formation?
A
The linear amino acid sequence of a polypeptide. Covalent (peptide) bonds
10
Q
What is a secondary sequence of an amino acid, what bonds are involved in its formation and what are the 2 common types?
A
The local special arrangement of the polypeptide backbone.
Hydrogen bonds.
Alpha helix and beta pleated sheets.
11
Q
What is the tertiary structure of a polypeptide and what bonds are involved in its formation?
A
The overall 3 dimensional structure.
Hydrogen, van der waals, hydrophobic, covalent and ionic
12
Q
How many amino acids are there in 1 turn of an alpha helix?
A
3.6
13
Q
If a protein has an isoelectric point of 5.0 and is placed in an electric field at physiological pH would it move towards the positive or negative electrode?
A
Positive
14
Q
What can denature a protein?
A
Heat, pH and detergent
15
Q
What is the pitch of an alpha helix?
A
0.54nm
16
Q
How large is a eukaryotic and a prokaryotic cell?
A
Eukaryotic:10-100 micrometers
Prokaryotic: 1 micrometer
17
Q
What are the differences between a prokaryote and a eukaryote?
A
Prokaryotes have no nucleus, membrane bound organelles or cytoskeleton. They reproduce asexually and divide by binary fission as opposed to mitosis/meiosis. They have smaller ribosomes.
18
Q
Which residues are strong helix formers?
A
Alanine and leucine because they are small and hydrophobic
19
Q
Name two helix breakers and explain why they are helix breakers
A
Proline - the rotation around the N-C bond is impossible
Glycine - the tiny R group supports other conformations
20
Q
In beta strands, what is the distance between each amino acid?
A
0.35nm
21
Q
How is a beta sheet formed?
A
The beta strands run anti parallel to each other and H bonds form between them to stabilise the structure
22
Q
What is a domain?
A
Part of a polypeptide chain that folds into a distinct shape. Usually has a specific functional role
23
Q
What is a motif?
A
Folding pattern that contains 1 or more types of secondary structure
24
What residue are disulphide bonds formed between?
Cysteine
25
What shape would a graph showing the binding of oxygen to myoglobin exhibit?
Hyperbolic
26
What shape would a graph showing the binding of oxygen to haemoglobin exhibit?
Sigmoidal
27
Why does haemoglobin have a sigmoidal shape?
Cooperative binding - the binding of oxygen to one of the haem groups increases the affinity of oxygen to the other ones.
28
Why is the sigmoidal curve of haemoglobin significant?
Because it means that oxygen is easily picked up in the lungs and then easily given up at the tissues
29
What effect does BPG have on oxygen binding, which direction will the curve shift and why is this significant?
BPG decreases the affinity for oxygen binding. The curve will shift to the right. It is significant because more BPG is produced in higher altitudes which promotes oxygen release at tissues
30
How do H+ ions and CO2 affect the affinity haemoglobin has for oxygen, which direction will the curve shift and why is this significant?
Reduce the affinity. Shift to the right. Because metabolically active tissues produce both substances and will need more oxygen. This couples supply and demand. Known as the Bohr effect.
31
Why is carbon monoxide poisonous?
It binds more strongly and irreversibly to haemoglobin than oxygen
32
How do the subunits of foetal haemoglobin differ from the regular form, what effect does this have and why is it significant?
It has 2 gamma sub units instead of the 2 beta ones. This increases the affinity for oxygen. This means that the foetus can get oxygen from the mothers blood
33
What are Thalassaemias?
A condition where there is an imbalance between the number of alpha and beta sub units
34
What are the differences between alpha and beta thalassaemias?
Beta: decreased or absent beta sub units. Alpha chains can't form stable tetramers. Symptoms onset after birth
Alpha: decreased or absent alpha subunits. Different levels of severity but beta chains can form stable tetramers with increased affinity for oxygen. Onset before birth
35
Define Vmax
The maximal rate when all enzyme active sites are saturated with substrate
36
Define Km
The substrate concentration that gives half the Vmax value
37
Does a low Km value represent a high or low affinity for the substrate?
High
38
What are the differences between competitive and non competitive inhibition?
Competitive binds at active site and effects Km but not Vmax.
Non competitive binds at a secondary site and effects Vmax but not Km
39
What is one unit of an enzyme?
The amount of enzyme that catalyses the conversion of 1 micro mole of substrate per minute.
40
What is a zymogen?
An inactive precursor of a proteolytic enzyme
41
What are the 5 main regulatory mechanisms that control enzyme activity
Allosteric, substrate/product concentration, proteolytic, covalent modification and enzyme amount
42
How would an allosteric activator affect an enzyme?
It would make the R state more stable. This shifts the curve to the left
43
What type of enzyme catalyses the attachment of a phosphate group? What catalyses its removal? What amino acids are phosphate groups added to?
Kinase attaches. Phosphotase removes. Can be attached to serine, threonine and tyrosine.
44
Give 2 examples of covalent modification of an enzyme
Attaching one of the following to a protein via an amino acid: phosphoryl, acetyl, adenyl, uridyl, methyl or ribosyl
45
What is proteolytic activation and why is it used?
Activating a protein by removing part of the chain. This is useful, especially for proteases (enzymes that break peptide bonds), because it allows for them to be transported without causing any damage
46
How can the amount of enzyme be changed?
Increase its production by increasing the rate of transcription. Increase its degradation - tag it for destruction by adding a molecule known as a ubiquitin
47
Define feedback inhibition and give an example
End product of a pathway inhibits its own rate of synthesis e.g. ATP inhibits catabolic pathways. Glucose 6-phosphate inhibits hexokinase.
48
Define feed forward activation and give an example
Increased amounts of a substrate increase the rate of the first of the first step of its pathway e.g. Ethanol increases amount of ethanol oxidising enzymes
49
Define counter regulation and give an example
Catabolic degradation of the product inhibits the anabolic production of it e.g. Glycogenesis/glycogenolysis
50
What is an isoenzyme?
Enzymes that catalyse the same reaction but have a different amino acid sequence
51
What is the difference between a nucleoside and nucleotide?
Both have a nitrogenous base and pentose sugar but only nucleotides have the phosphate group
52
List the activators and inhibitors of phosphofructokinase
Activators: AMP and fructose 1,6-bisphosphate
Inhibitors: ATP, citrate and H+
53
What is an enzyme cascade?
An initial enzyme will activate subsequent enzymes which in turn activate even more increasing the magnitude of an initial signal very rapidly
54
What is the zymogen for Pepsin, where is it synthesised and what activates it?
Pepsinogen. Stomach. pH
55
What is the zymogen for Chymotrypsin, where is it synthesised and what activates it?
Chymotrypsinogen. Pancreas. Trypsin
56
What is the zymogen for Trypsin, where is it synthesised and what activates it?
Trypsinogen. Pancreas. Enteropeptidases
57
What is the zymogen for Carboxypeptidase, where is it synthesised and what activates it?
Procarboxypeptidase. Pancreas. Trypsin
58
What is the zymogen for Elastase, where is it synthesised and what activates it?
Proelastase. Pancreas. Trypsin
59
How does a deficiency of a1 antitrypsin cause emphysema?
The deficiency means less trypsin is broken down. This means elastase is produced in excess and breaks down the walls of the alveoli
60
Describe the extrinsic pathway of the clotting cascade
Membrane damages exposes the domain of factor 3. It's activates factor 7 which in turn activates factor 10
61
Describe the intrinsic pathway of the clotting cascade
Factor XI is activated which in turn activates factor IX. This combines with the activated factor XIII and the extrinsic pathway to activate factor X. Factor IX and X are targeted to the damaged membrane by Gla domains. Ca2+ ions play a role.
62
Which factors are get feedback activation from thrombin in the clotting cascade?
Factor XI, VIII and V
63
Outline how a fibrin clot is formed from the fibrinogen
The thrombin cleaves fibrinopeptides A and B from the main fibrinogen (feet and stalks) the domains at the C terminal of the beta and gamma parts (claws) can attach to the cleaved chains
64
Haemophilia is the result of a defect in which factor of the clotting cascade?
VIII
65
How is the clotting process stopped?
Clotting factors are diluted and removed by the liver. Others are degraded by proteases such as protein C and finally some are factors are inhibited (antithrombin)
66
What are the 7 key control points in clotting?
Inactive zymogens present in low concentrations. Proteolytic activation. Amplification of signal by cascade. Clustering of clotting factors at damage site. Feedback activation by thrombin maintains clotting. Termination of clotting by multiple mechanisms. Clot breakdown controlled by proteolytic activation.
67
How many hydrogen bonds form between bases A and T?
2
68
Which bases are pyrimidines and which are purines?
Pyrimidines: C, T and U
Purines: A and G
69
What are the 4 stages of the cell cycle and what happens in each one?
G1 - cellular components except chromosomes are duplicated
S - all 46 chromosomes are duplicated
G2 - chromosomes are checked for errors
Mitosis
70
What enzyme unravels the DNA double helix?
Helicase
71
The new strand created by DNA polymerase grows in which direction? What end is the template strand therefore read in?
The chain grows 5' to 3'. The DNA is read 3' to 5'
72
What are the 3 steps of DNA replication?
Initiation, elongation and termination
73
What is required to initiate DNA replication?
Primers, primase and DNA polymerase
74
Outline the elongation part of DNA replication
Moving replication forks. Helicase unzips double strand. 3' strand (lead) extends continuously and 5' strand (lagging) grows in Okazaki fragments. DNA ligase joins the DNA joins the DNA strands together with phosphodiester bonds
75
How do the roles of DNA polymerase and ligase differ?
Polymerase adds free nucleotides to the 3' end of the template strand. Ligase joins the strands together by forming phosphodiester bonds
76
Outline the termination stage of DNA replication
The replication forks meet and ligase joins them together. Chromosome number stays the same despite now being made up of 2 chromatids
77
What happens in prophase (mitosis)?
Nuclear envelope disappears. Chromosomes condense. Spindle starts to form
78
What happens in metaphase (mitosis)?
The chromosomes attach to the spindle at the metaphase plate
79
What happens in anaphase (mitosis)?
The chromatids are pulled apart to become 2 separate chromosomes.
80
What happens in telophase (mitosis)?
2 nuclear membranes form and chromosomes decondense.
81
What happens in cytokinesis?
At the same time as telophase the cell starts to split into 2
82
What causes variation in meiosis?
Crossing over, random segregation and mutations
83
How does meiosis differ from mitosis?
Produces 4 cells not 2. Cells aren't genetically identical. Cells are haploid. 2 rounds of division.
84
Define heterozygous, homozygous and hemizygous
Homo-both alleles same. Hetero-both different. Hemi-in x sex linked as there's only 1 allele
85
What is a dominant allele and what is a recessive allele?
The dominant allele will be expressed if present. The recessive requires both alleles to be there to be expressed
86
What would a pedigree of an autosomal recessive disease look like and give an example?
Disease can skip generations and appear to have come out of nowhere. Males and females are equally affected. Examples include cystic fibrosis and sickle cell disease
87
What would a pedigree of an autosomal dominant disease look like and give an example?
Disease can't skip generations so every affected individual will have at least one affected parent. Males and females equally affected. E.g. Huntingtons disease
88
What would a pedigree of an x-linked recessive disease look like and give an example?
Affect males more than females. Every affected male has a carrier/affected mother. Every affected female has an affected father and carrier/affected mother. E.g. Haemophilia a
89
What is codominance and give an example?
Neither allele is dominant over the other so they are both expressed. Blood group
90
What is an example of complementation?
Albinism
91
What is stage G0 and why does it exist?
G0 is a stage where the cell is not dividing/preparing to divide. It could be to regulate growth or as the final destination
92
During DNA replication, why can't both strands grow continuously?
During DNA replication a new DNA strand can only grow in a 5’-‐‑>3’ direction (using a 3’-‐‑>5’ template). As the two original DNA strands are antiparallel and are both used as a template, only one of the two templates (the 3’-‐‑>5’ template) can be replicated continuously while the replication fork ‘unzips’ and the other one is replicated in small sections
93
How many chromosomes does every human somatic cell contain in G2, just before mitosis?
46 - despite the chromosome being replicated they are still viewed as 1 chromosome
94
How is recombination frequency estimated?
Number of recombined progeny/number of informative progeny
95
Where does transcription occur and where does translation occur?
Transcription occurs in the nucleus. Translation occurs in the cytoplasm
96
What length does the chain grow in transcription?
5' to 3'
97
What are the 3 types of post transcriptional modification that convert pre-mRNA to mature mRNA
Capping, tailing/polyadenylation and splicing
98
What are endonucleases and exonucleases and how do they differ?
Endonucleases break within the polynucleotide and are either specific or non specific. Exonucleases degrade from the 5' end or the 3' end
99
Briefly describe initiation in transcription
Initiation code is recognised (5' TATA 3') and transcription factors bind here which attracts RNA polymerase to start production upstream.
100
Briefly describe elongation
RNA polymerase travels along the mRNA picking up base pairs and copying them into a complementary RNA strand
101
Briefly describe termination in transcription
When the gene has been transcribed a methyl-guanine cap is added to the 5' end. At the 3' end the stop codon cleaves the mRNA and approximately 200 adenine nucleotides are added. Both of these protect against degradation.
102
What type of RNA polymerase make mRNA, what percentage of RNA is mRNA, how many different kinds are there and how many copies of each kind?
RNA polymerase II, 2%, 100,000s of kinds, few copies
103
What does rRNA do?
Ribosomal RNA binds to the mRNA and provides the location for tRNA
104
Which RNA polymerase produces rRNA, how much of the RNA is rRNA, how many different kinds are there and how many copies of each kind?
RNA polymerase 1, >80%, few kinds, many copies
105
Which RNA polymerase produces tRNA, how much of the RNA is tRNA, how many different kinds are there and how many copies of each kind?
RNA polymerase 3, 15%, 100 kinds, very many copies
106
Describe initiation in translation
The starting codon 5'AUG will bind to a corresponding anticodon 5'CAU on the tRNA. The 5' cap binds to the 40s sub unit and then the 60s sub unit binds
107
What does the P site do and what does the A site do in a ribosome?
P site is for holding the Peptide chain
| A site is for Accepting the tRNA
108
Describe elongation in translation
tRNA occupies P site and another aminoacyl tRNA occupies the A site. Peptide bond forms between them. tRNA leaves
109
Describe termination in translation
Stop codon is read on the mRNA (UAA, UGA, UAG) no corresponding anticodon so the peptide chain is hydrolysed and released.
110
Define a gene
A unit of heredity; a transcription unit, i.e. a length of DNA on a chromosome that contains the code for a protein (or RNA) as well as sequences necessary for its expression, such as promoter and terminator sequences and introns.
111
What are the implications of a degenerate code?
Substitutions can lead to a different primary sequence which affects the tertiary structure. If a stop codon is altered it affects the length of the polypeptide.
112
How would a mutation outside the gene coding area affect gene expression?
It may affect the promoter region where transcription factors bind.
113
How is bacterial gene expression different?
Bacteria have: simpler promoters, different transcription factors, smaller ribosomes (clinically useful as can target the 30s sub unit only found in bacteria), coupled transcription-translation, different translation factors and no post translational modification
114
Describe the key differences between transcription and translation in a human cell
Transcription: makes mRNA, occurs in the nucleus
Translation: makes a polypeptide, occurs in the cytoplasm
115
How are translation and transcription similar?
Both read a "code", consist of 3 stages (initiation, elongation and termination) and both require energy and enzymes.
116
What is a polysome?
A length of mRNA covered in many actively translating ribosomes
117
What length is the mRNA read in translation?
5' to 3'
118
What direction is the DNA read in transcription?
3' to 5'
119
How does constitutive secretion differ from regulative secretion?
Constitutive secretion is a continuous process where the proteins are constantly packaged into vesicles and released by exocytosis. Regulative secretion puts proteins into vesicles but are not released until a signal is received
120
What is the difference between N-linked glycosylation and O-linked glycosylation?
N-linked: carbohydrate is added to the amide nitrogen of Asn in the ER
O-linked: carbohydrate is added to the hydroxyl of Ser or Thr in the Golgi
