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Foundations of Nutrition > Proteins and AAs > Flashcards

Proteins and AAs Flashcards

1
Q

What body structure contains the most protein?

A

Skeletal muscle (40%)

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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)

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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

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4
Q

What type of reaction is the formation of an amide bond?

A

Dehydration -> i.e. removal of H2O from two amino acids

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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

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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

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7
Q

How do you break peptide bonds?

A

Hydrolysis (i.e. with water)

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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

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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

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10
Q

What two physico-chemical properties are discussed with amino acids?

A

Polarity and net electrical charge

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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

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12
Q

What amino acid groups are polar and non-polar?

A

Non-Polar amino acids

Polar, non-charged, acidic (negative) , basic (positive)

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13
Q

What makes an R-chain polar?

A

Its ability to form hydrogen bonds with water

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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

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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

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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

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17
Q

Give the main secondary structures in proteins

A

Alpha helix

B- sheets

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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

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19
Q

Give examples of tertiary structure bonds

A

Salt Bridges
Hydrogen Bonds
Disulphide Bridges

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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

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21
Q

What reactions does quaternary structure rely on?

A

Same as tertiary

So non-covalent interactions and disulphide bonds

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22
Q

What term is used to describe a protein made up of more than one polypeptide

A

Multimer (e.g. dimer = 2)

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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

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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

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25
Q

What are the 4 bases in DNA?

A

AT CG

Adenine & Thymidine
Guanine & Cytocsine

A&amp;G = Purines
T&amp;C = Pyrimidines
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26
Q

What codes for amino acids?

A

3 letter code of DNA bases -> i.e. the codon

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27
Q

What is the difference between RNA and DNA bases?

A

Uracil replaces thymidine

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28
Q

What is the 3 types of RNA and their jobs

A

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

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29
Q

What enzyme is responsible for DNA transcription?

A

RNA Polymerase

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30
Q

What is the first type of RNA produced?

A

hnRNA

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31
Q

What is hnRNA?

A

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

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32
Q

What is the process called when removing non-coding / introns from hnRNA?

A

Splicing

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33
Q

What is produiced following transcription and splicing?

A

mature mRNA

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34
Q

What occurs before translation of mRNA?

A

A methyl groups gets added to the start of the strand and then adenosine residues are added to the tail (poly A tail)

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35
Q

What is the 2nd step of protein synthesis?

A

Translation (of code from DNA via mRNA)

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36
Q

Where does translation take place?

A

Ribosome

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37
Q

What types of molecules are ribosomes composed of?

A

rRNA & proteins

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38
Q

What are the two parts to a ribosome called?

A

(Larger) 60S subunit

(Smaller) 40S subunit

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39
Q

How does tRNA role work in protein synthesis?

A

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

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40
Q

What are the 3 stages of translation?

A

Initiation

Elongation

Termination

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41
Q

What happens at the initiation stage of translation?

A

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
Q

What happens at the elongation stage of translation?

A

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
Q

What occurs during the termination stage of translation?

A

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
Q

What are motifs?

A

Conserved sequences/regions of AAs within a protein that perform specific functions or form specific structures

45
Q

What is considered to be the highest level of control for protein synthesis?

A

Chromatin & Histone structure

46
Q

How does chromatin & histone structure affect protein synthesis?

A

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
Q

What two features can you comment on when discussing chromatin?

A

Histone acetylation

DNA methylation

48
Q

Compare euchromatin and heterochromatin

A

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
Q

What is the name of the region RNA polymerase acts upon on DNA?

A

Promoter region

50
Q

After chromatin & histone structure, what is the next level of control for protein synthesis?

A

RNA polymerase ability to bind to the promoter regions and do its job of replicating the code

51
Q

What is functionally important to remember about splicing of mRNA / hnRNA?

A

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
Q

What is the essential enzyme for tRNA?

A

Aminoacyl-tRNA Synthase

Binds the appropriate amino acid to the tRNA molecule so it matches the anticodon

53
Q

Working the way through translation, give 4 different things that can regulate / control protein synthesis

A

Transcriptional Control -> presence of mRNA

Ribosomal Density -> maximum rate of protein synthesis

Initiation -> eIF2 & eIF4

Elongation -> eEF1 & eEF2

(Amino acid supply + mTOR protein)

54
Q

Initiation in the translation step of protein synthesis gives overall control. Why is this? What factors can interact in this step?

A

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
Q

What is the mechanism behind restricted amino acid supply and cessation of protein synthesis?

A

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
Q

WHat amino acid is mTOR particularly susceptible to?

A

Leucine

57
Q

What usually stimulates the mTOR pathway?

A

Insulin & IGF-1

These stimulate PKB - phosphoryl-kinase B - which then stimulates mTOR

58
Q

What is the function of mTOR?

A

Upregulation of mTOR results in the interaction of other proteins which ultimately results in up regulation of protein synthesis

59
Q

What protein down regulates mTOR?

A

AMPK

60
Q

Why does inflammatory conditions result in sarcopenia>

A

Inhibition of insulin & IGF-1 on the mTOR pathway

Phosphorylation of eIF2

61
Q

What mechanism is in place to quality control proteins following translation

A

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
Q

How much protein is turned over a day?

A

250g

63
Q

Why is a high protein turnover important? (3)

A

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
Q

What are the two methods of degrading/releasing amino acids from proteins? Explain each, contrast and compare.

A

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
Q

Give 3 key features of digestion of proteins in the GI tract

A 
HCl - denatures proteins
Pepsin - breaks down proteins into peptides &amp; amino acids in the stomach 
Pancreatic enzymes (trypsin, chymotrypsin) further break down the protein products into small peptides &amp; AAs
66
Q

What hormone releases pancreatic enzymes?

A

CCK

67
Q

Where in the gut is AAs absorbed?

A

Along the entire length of the SI but mostly duodenum and upper jejunum

68
Q

How are amino acids & peptides absorbed?

A

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
Q

What factor may affect absorption of protein in the diet?

A

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
Q

Why is assessing protein content of foods not the accurate way to measure the consumption of protein in the diet?

A

Because not all proteins & AAs are digestible

71
Q

WHat happens once AAs are absorbed?

A

Go to the liver via hepatic portal vein for transamination & utilisation

72
Q

What two options do newly absorbed amino acids have?

A

Utilised for protein synthesis or oxidation

use it or lose it

73
Q

Define transamination

A

Transfer of an amino group from one molecule to another

74
Q

What is a common (generic) transamination reaction

A

Transfer of an amino group from an amino acid to a keto acid)

75
Q

What enzyme is essential for transamination?

A

Aminotransferase enzyme

76
Q

What is aminotransferase enzyme dependant on?

A

Vitamin B6 - pyridoxal phosphate

77
Q

Name 4 essential and 4 non-essential AAs

A 
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
Q

What does protein quality refer to?

A

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
Q

What are the two key components of the oxidation of proteins?

A

Removing the nitrogen

Oxidation of the carbon skeleton

80
Q

How does the body remove nitrogen from the body from oxidated proteins? Give the two basic steps.

A

1st need to make ammonia

2nd need to convert to urea

81
Q

How does the body form ammonia from nitrogen products from amino acids?

A

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
Q

How does ammonia get excreted from the body?

A

Needs to be converted to the less toxic, water soluble urea first via the urea-cycle

83
Q

Why does a high protein diet have high energy costs associated to it?

A

Each urea molecule made from ammonia requires 3 ATP in the urea cycle - high energy costs associated to the detoxification process

84
Q

Give 4 gluconeogenic amino acids

A

Glutamate, glutamine, glycine, alanine, cysteine

85
Q

Give 2 ketogenic amino acids

A

Leucine & Lysine

86
Q

What does gluconeogenic and ketogenic AAs mean?

A

This is a way to classify amino acids based on their breakdown products

87
Q

What type of amino acid is essential in true starvation, explain why?

A

Gluconeogenic AAs are essenital as an energy source in true starvation for the obligate carbohydrate metabolisers

88
Q

Give 5 functions of amino acids outwith protein synthesis

A

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
Q

What is the easiest way to calculate protein & AA requirements?

A

Calculating the ‘minimum protein required’ to achieve nitrogen balance

90
Q

What are obligatory nitrogen losses?

A

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
Q

Give 2 reasons why nitrogen balance isnt a good way to assess AA and protein requirements?

A

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
Q

Give some benefits of nitrogen balance in assessing protein status

A

Quick, cheap, easy to perform in theory, no need for fancy equipment

93
Q

Give 2 methods of assessing amino acid and protein requirements in individuals other than nitrogen balance

A

Carbon balance

Indicator of amino acids

94
Q

Give general description, pro’s and con’s of carbon balance in assessing protein and amino acid requirements?

A

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
Q

Give a general description, pro’s and con’s of indicator amino acid in assessing protein and amino acids requirements?

A

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
Q

Give 3 signs of protein deficiency

A

stunted growth, poor musculature / muscle wasting, oedema, fragile skin & hair

97
Q

Give two clinicial syndromes associated to protein deficiency

A

Kwashiorkor - inadequte protein intake

Marasmus -> general dietary deficiency

98
Q

Why is there an estimated maximum protein dietary intake?

A

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
Q

How can you maximise protein synthesis with diet?

A

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
Q

Why are elderly at risk of sarcopenia?

A

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

Foundations of Nutrition (13 decks)

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