Proteins and AAs Flashcards
1
Q
What body structure contains the most protein?
A
Skeletal muscle (40%)
2
Q
Give 3 reasons why protein are essential in the diet
A
High protein turnover (synthesis & catabolism)
Amino acids required to synthesis other nitrogen containing molecules
Source of energy via oxidation
(Every cell contains and requires protein)
3
Q
Describe generic structure of an amino acids chemistry
A
central alpha carbon bound to 4 things
an amino group (NH2)
a carboxyl group (COOH)
a hydrogen ion
a unique r-group / side chain
4
Q
What type of reaction is the formation of an amide bond?
A
Dehydration -> i.e. removal of H2O from two amino acids
5
Q
Describe what happens to the two amino acids when they bond together
A
1 Hydrogen from the amino group
1 OH from the carboxyl group
These are removed to form the amide bond & water
6
Q
What is important to note about the equilibrium of amino acids and peptides?
A
Lies on the side of hydrolysis rather than synthesis hence why you need an input of energy
7
Q
How do you break peptide bonds?
A
Hydrolysis (i.e. with water)
8
Q
How do you describe the ends of a peptide chain?
A
C-terminus at the end of the chain with a free carboxyl group
N- terminus at the end of the chain with a free amino group
9
Q
What are the types of amino acids with regards to R-group? Give examples where possible.
A
Non-Polar Amino Acids
Glycine, Proline, (iso)Leucine, (phenyl)alanine, valine, tryptophan
Polar, non-charged Amino Acids
Serine, aspargine, cystine, tyrosine, glutamine
Negatively charged amino acids / acidic
Aspartate, Glutamate
Positively charged amino acids / basic
Lysine, arginine, histidine
10
Q
What two physico-chemical properties are discussed with amino acids?
A
Polarity and net electrical charge
11
Q
Explain net-electrical charge in amino acids
A
Net electrical charge of an amino acids is determined by r-group
An acidic amino acid has an extra COOH group in the r-chain, this can donate a Hydrogen ion when in a pH solution of > 7 resulting in a negative charge
A basic amino acid has an extra NH2 group which can pick up a net positive charge when in a pH solution of <7
12
Q
What amino acid groups are polar and non-polar?
A
Non-Polar amino acids
Polar, non-charged, acidic (negative) , basic (positive)
13
Q
What makes an R-chain polar?
A
Its ability to form hydrogen bonds with water
14
Q
Give 3 examples of a polar and non-polar amino acids
A
Non-Polar = glycine, leucine, isoleucine, alanine, phenylalanine, valine, tryptophan
Polar - serine, cysteine, tyrosine, asparagine, glutamine, aspartate, glutamate, lysine, arginine
15
Q
Define primary structure of a protein.
What does it rely on?
A
Primary structure is the order and sequence of amino acids within the peptide chain.
Relies on gene coding
16
Q
Define secondary structure of a protein
A
Secondary structure is the highly regular local sub-structures produced by regular folds in the polypeptide chain
17
Q
Give the main secondary structures in proteins
A
Alpha helix
B- sheets
18
Q
Define tertiary structure of a protein
A
This describes the overall 3D structure of the protein to maintain maximal stability dependant on reactions of side-chains
19
Q
Give examples of tertiary structure bonds
A
Salt Bridges
Hydrogen Bonds
Disulphide Bridges
20
Q
Define quaternary structure
A
This is the overall 3D structure of a protein that is over result of two or more polypeptides aggregating to form one functional unit
21
Q
What reactions does quaternary structure rely on?
A
Same as tertiary
So non-covalent interactions and disulphide bonds
22
Q
What term is used to describe a protein made up of more than one polypeptide
A
Multimer (e.g. dimer = 2)
23
Q
Give 6 functional types of proteins found within the body
A
Enzymes
Structural: Fibrous & Contractile Types
Transporters (e.g. albumin in the blood)
Immunoprotectors (e.g. antibodies)
Messengers (e.g. hormones)
Buffers (because of charged amino acid residues)
Fluid Balance
24
Q
What are the 3 key stages of protein synthesis?
A
Transcription of gene into mRNA
Translation of mRNA into proteins via ribosomes
Post-translational modifications
or Final conformation adaption
25
What are the 4 bases in DNA?
AT CG
Adenine & Thymidine
Guanine & Cytocsine
```
A&G = Purines
T&C = Pyrimidines
```
26
What codes for amino acids?
3 letter code of DNA bases -> i.e. the codon
27
What is the difference between RNA and DNA bases?
Uracil replaces thymidine
28
What is the 3 types of RNA and their jobs
mRNA - messenger
Carries the codon from the DNA
tRNA - transfer
Carries the amino acid to the mRNA
rRNA - ribosomal
Bulk of the ribosome & synthesises the polypeptide chain
29
What enzyme is responsible for DNA transcription?
RNA Polymerase
30
What is the first type of RNA produced?
hnRNA
31
What is hnRNA?
Heavy Nuclear RNA
This is the initial RNA strand produced when you directly transcribe from eukaryotic cells. This contained all the coding exon regions but also contains lots of non-coding regions called introns. Therefore this must be modified before translation
32
What is the process called when removing non-coding / introns from hnRNA?
Splicing
33
What is produiced following transcription and splicing?
mature mRNA
34
What occurs before translation of mRNA?
A methyl groups gets added to the start of the strand and then adenosine residues are added to the tail (poly A tail)
35
What is the 2nd step of protein synthesis?
Translation (of code from DNA via mRNA)
36
Where does translation take place?
Ribosome
37
What types of molecules are ribosomes composed of?
rRNA & proteins
38
What are the two parts to a ribosome called?
(Larger) 60S subunit
| (Smaller) 40S subunit
39
How does tRNA role work in protein synthesis?
tRNA has an anti-codon sequence which is specific for each amino acid codon so the tRNA acts as the intermediate / mediator between the mRNA and the amino acids to allow for amino acids to come together in the right order coded by mRNA
40
What are the 3 stages of translation?
Initiation
Elongation
Termination
41
What happens at the initiation stage of translation?
Two complexes form:
First complex = eIF2 + tRNA (methionine carrying) + 40S ribosome subunit
Second complex = eIF4 + mRNA (+ poly A tail)
Two complexes come together and the 40S subunit starts working on the mRNA molecule until it reaches the start codon which causes a reaction and eIF2 is chucked out of the picture which signals 60S to come along and bind to form a fully functional ribosome to begin elongation
42
What happens at the elongation stage of translation?
A tRNA molecule binds to next codon site on the mRNA molecule. The ribosome forms the peptide bond between the amino acids. Then the ribosome moves along the mRNA strand by 3 bases to get to the next codon. This process is continued adding an amino acid one at a time, allowing the peptide chain to grow.
EF / Elongation factors are essential for this part
43
What occurs during the termination stage of translation?
After the elongation process and the protein has been coded for there is a 'stop' codon at the end of the mRNA molecule. No tRNA molecule recognises these codes so a 'release factor' (protein) binds to the mRNA which causes the two ribosomal subunits to dissociate. When its breaks up the protein is released.
44
What are motifs?
Conserved sequences/regions of AAs within a protein that perform specific functions or form specific structures
45
What is considered to be the highest level of control for protein synthesis?
Chromatin & Histone structure
46
How does chromatin & histone structure affect protein synthesis?
DNA is packaged into cells as chromatin which is wrapped around histone proteins. Depending on how tightly wrapped DNA is depends on the accessibility of the gene that codes for the protein.
I.e. the tighter the wrap (heterochromatin) the less accessible. The looser the wrap / less dense (euchromatin) the more accessible
Different cells have different chromatin and histone structure depending on what proteins that cell needs to be synthesised
E.g. a hepatocyte will leave albumin genes loosely packed whereas it will tightly pack skeletal muscle / collagen genes
47
What two features can you comment on when discussing chromatin?
Histone acetylation
| DNA methylation
48
Compare euchromatin and heterochromatin
Euchromatin = less dense = hyperacetylation of histones & low DNA methylation
Heterochromatin = more dense = hypoacetylated histones and high DNA methylation
(I.e. acetylation on histones weakens histones to wrap the DNA making is loose)
(I.e. DNA methylation blocks the DNA code therefore higher amounts blocks protein synthesis)
49
What is the name of the region RNA polymerase acts upon on DNA?
Promoter region
50
After chromatin & histone structure, what is the next level of control for protein synthesis?
RNA polymerase ability to bind to the promoter regions and do its job of replicating the code
51
What is functionally important to remember about splicing of mRNA / hnRNA?
Can splice the same molecule two different ways to achieve two very different functional proteins -> so genetic code doesn't always result in same function
52
What is the essential enzyme for tRNA?
Aminoacyl-tRNA Synthase
Binds the appropriate amino acid to the tRNA molecule so it matches the anticodon
53
Working the way through translation, give 4 different things that can regulate / control protein synthesis
Transcriptional Control -> presence of mRNA
Ribosomal Density -> maximum rate of protein synthesis
Initiation -> eIF2 & eIF4
Elongation -> eEF1 & eEF2
(Amino acid supply + mTOR protein)
54
Initiation in the translation step of protein synthesis gives overall control. Why is this? What factors can interact in this step?
eIF2 is essential for the activation / complex formation with 40S subunit.
Inhibition of eIF2 = phosphorylation
This occurs in many situations -> infection, AA starvation, glucose deficiency, drug & heavy metal toxicity, oxidative stress
55
What is the mechanism behind restricted amino acid supply and cessation of protein synthesis?
When there is a lack of AAs, there will be lots of free tRNA (called uncharged) and this builds up
Once built up enough they begin to bin to a protein called GCN2
GCN2 phosphorylates eIF2 stopping initiation of translation switching off protein synthesis
GCN2 is also able to interact with ATF4 which ultimately binds to the AA response element (AAR) within the genome which is for stressful situations like this. It results in the formation of many proteins that do the following:
Further inhibitin of non-essential protein synthesis
Inhibition of anabolism & growth
Increases catabolic mechanisms
56
WHat amino acid is mTOR particularly susceptible to?
Leucine
57
What usually stimulates the mTOR pathway?
Insulin & IGF-1
| These stimulate PKB - phosphoryl-kinase B - which then stimulates mTOR
58
What is the function of mTOR?
Upregulation of mTOR results in the interaction of other proteins which ultimately results in up regulation of protein synthesis
59
What protein down regulates mTOR?
AMPK
60
Why does inflammatory conditions result in sarcopenia>
Inhibition of insulin & IGF-1 on the mTOR pathway
Phosphorylation of eIF2
61
What mechanism is in place to quality control proteins following translation
ERAD - ER associated degradation
This is a process in the ER where damaged, denatured or not properly synthesised proteins are flagged to the cyctosolic 26S proteasome to be degraded
62
How much protein is turned over a day?
250g
63
Why is a high protein turnover important? (3)
Importance of a high turn over is because
we need to regulate metabolic and cellular processes so our protein demands change and are dynamic and we need to be able to match that by switching up proteins
we need a way to prevent the accumulation of damaged or harmful proteins
we need a method to mobilise amino acids in moments of starvation
64
What are the two methods of degrading/releasing amino acids from proteins? Explain each, contrast and compare.
Autophagy & Ubiquitin Proteasome System
Autophagy is non-specific and is 'macrophag-led'. Cells endocytose the proteins, release lysosomes to break down protein via hydrolysis and then release the amino acids.
Ubiquitin Proteasome System is a selective process. Involves ubiquitin (a small molecule in all cells) binding to a protein, acting as a red flag, for the 26S proteasome. This is a complex of proteases which act upon the flagged region to hydrolyse proteins into small peptides and amino acids
65
Give 3 key features of digestion of proteins in the GI tract
```
HCl - denatures proteins
Pepsin - breaks down proteins into peptides & amino acids in the stomach
Pancreatic enzymes (trypsin, chymotrypsin) further break down the protein products into small peptides & AAs
```
66
What hormone releases pancreatic enzymes?
CCK
67
Where in the gut is AAs absorbed?
Along the entire length of the SI but mostly duodenum and upper jejunum
68
How are amino acids & peptides absorbed?
Lots of different types of transporters because of the various amino acids and peptides than can be present in the diet.
(Common theme in a few are Na-dependence)
69
What factor may affect absorption of protein in the diet?
What original protein you begin with
I.e. raw egg protein is absorbed at a rate of 1.3g/h
Whey isolate absorbed at 8-10g/h
70
Why is assessing protein content of foods not the accurate way to measure the consumption of protein in the diet?
Because not all proteins & AAs are digestible
71
WHat happens once AAs are absorbed?
Go to the liver via hepatic portal vein for transamination & utilisation
72
What two options do newly absorbed amino acids have?
Utilised for protein synthesis or oxidation
| use it or lose it
73
Define transamination
Transfer of an amino group from one molecule to another
74
What is a common (generic) transamination reaction
Transfer of an amino group from an amino acid to a keto acid)
75
What enzyme is essential for transamination?
Aminotransferase enzyme
76
What is aminotransferase enzyme dependant on?
Vitamin B6 - pyridoxal phosphate
77
Name 4 essential and 4 non-essential AAs
```
Essential:
Leucine
Isoleucine
Lysine
Methionone
Phenylalainine
Tryptophan
Valine
Histidine
Arginine
Threonine
```
```
Non-Essential (CATS):
Cysteine
Alanine
Tyrosine
Serine
Aspartic acid
Asparagine
Glutamic acid
Glutamine
Proline
```
78
What does protein quality refer to?
Protein quality is when you refer to food stuffs and the amount of amino-acids it requires.
A low protein quality (plant sources usually) only contain limited types of amino acids and therefore you do not get all 11 essential amino-acids
A high protein quality (animal sources usually) contain lots of various amino acids therefore you ca achieve most of the essenital amino-acid consumption
79
What are the two key components of the oxidation of proteins?
Removing the nitrogen
| Oxidation of the carbon skeleton
80
How does the body remove nitrogen from the body from oxidated proteins? Give the two basic steps.
1st need to make ammonia
| 2nd need to convert to urea
81
How does the body form ammonia from nitrogen products from amino acids?
Need to get the nitrogen to the liver as it is the liver that creates nitrogen.
Two methods
1st method: amino groups are transaminated to alpha-ketoglutarate to form l-glutamate which can transfer to the liver via the blood and then l-glutamate is deaminated via glutamate dehydrogenase
2nd method: glucose-alanine cycle
Alanine aminotransferase in muscle combies pyruvate and amino groups to form alanine. THis goes into blood, goes to liver where they go back to pyruvate (which is used for energy metabolism) and amino acids.
Amino acids are then converted to ammonia within the liver
82
How does ammonia get excreted from the body?
Needs to be converted to the less toxic, water soluble urea first via the urea-cycle
83
Why does a high protein diet have high energy costs associated to it?
Each urea molecule made from ammonia requires 3 ATP in the urea cycle - high energy costs associated to the detoxification process
84
Give 4 gluconeogenic amino acids
Glutamate, glutamine, glycine, alanine, cysteine
85
Give 2 ketogenic amino acids
Leucine & Lysine
86
What does gluconeogenic and ketogenic AAs mean?
This is a way to classify amino acids based on their breakdown products
87
What type of amino acid is essential in true starvation, explain why?
Gluconeogenic AAs are essenital as an energy source in true starvation for the obligate carbohydrate metabolisers
88
Give 5 functions of amino acids outwith protein synthesis
Part of the structure for haeme, nucleotides, neurotransmitters, signalling molecules
Sulpher AAs is precursor to S-adenosyl methionine (SAM) which is an essential co-factor for lots of methyl transfer reactions
Precursor to the essential anti-oxidant glutathione
89
What is the easiest way to calculate protein & AA requirements?
Calculating the 'minimum protein required' to achieve nitrogen balance
90
What are obligatory nitrogen losses?
This is the protein and amino acids we loose and have no control or way to prevent them
Mucosal cells and digestive juices, skin losses, oxidative losses urea/ammonia
91
Give 2 reasons why nitrogen balance isnt a good way to assess AA and protein requirements?
Minimum protein requirements varies a lot due to various physiological factors
Protein quality
amino acid requirements change with things like breastfeeding or pregnancy
The protein turnover in the gut microflora
92
Give some benefits of nitrogen balance in assessing protein status
Quick, cheap, easy to perform in theory, no need for fancy equipment
93
Give 2 methods of assessing amino acid and protein requirements in individuals other than nitrogen balance
Carbon balance
Indicator of amino acids
94
Give general description, pro's and con's of carbon balance in assessing protein and amino acid requirements?
Infuse someone with isotopes AAs and assessing output of the isotope.
Pro's - refined & accurate & well studied
Con's - only good for protein synthesis
95
Give a general description, pro's and con's of indicator amino acid in assessing protein and amino acids requirements?
Identify someone with an AA limitation or limit someones specific amino acid intake. Measure someone oxidation level. Infuse amino acid into person and titrate up until oxidation level reaches baseline and that concentration of amino acid is considered the requirement level
Pro's: most accurate
Con's: complex anaylsis, only measure that moment, not good long term
96
Give 3 signs of protein deficiency
stunted growth, poor musculature / muscle wasting, oedema, fragile skin & hair
97
Give two clinicial syndromes associated to protein deficiency
Kwashiorkor - inadequte protein intake
Marasmus -> general dietary deficiency
98
Why is there an estimated maximum protein dietary intake?
The liver has a theoried maximum limit to deaminate proteins and convert ammonia to urea so the theoretical limit is based on the livers ability to excrete nitrogen safely without build up of ammonia
99
How can you maximise protein synthesis with diet?
The timing of consumption of proteins is most important.
Depending on protein absorption rates depends on when you should consume. The slowly digested whole intact proteins should be consumed 90mins before exercise since peak is 120mins following consumption
If you consume amino acid / isolated protein items these reach peak levels within 10-20 mins so consuming them within an hour of training is best
Research suggests the slowly absorbed proteins induce a better post-prandial utilisation than the faster ones
100
Why are elderly at risk of sarcopenia?
Elderly people become less sensitive to the effects of insulin on the mTOR system making muscle less sensitive to amino acids. Research suggests a high protein diet may help acutely stimulate muscle protein synthesis
