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Val 307 > 1. Biochemistry of Life (Part I) > Flashcards

1. Biochemistry of Life (Part I) Flashcards

1
Q

What is human nutrition?

A

Making sure that our composition (from a molecular to an organismal level) is functioning properly

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2
Q

Why do cells require ATP for maintenance?

A

Resting cells still require ATP to maintain their cellular structures through cell division, which utilizes energy and, thus, needs nutrients

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3
Q

What nutrients are necessary during cell division?

A
  • Energy
  • Proteins to create new structures and motors
  • Lipids to create cell membranes
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4
Q

Define nutrigenetics.

A

Genes control the metabolism of nutrients

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5
Q

Define nutrigenomics.

A

Nutrients influence the expression of genes

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6
Q

What happens if lactose is present in the culture media of E. coli?

A

Induction of the gene (lac operon) involved in lactose metabolism

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7
Q

Explain how the nutrient-gene interaction between lactose and the lac operon gene is a homeostatic mechanism.

A

You don’t want to waste your energy to produce enzymes for metabolizing lactose, if there is no lactose to metabolize in the first place

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8
Q

Explain what happens on a molecular level to the lac operon when there is a lack of lactose.

A
  • lacI encodes the repressor protein
  • The repressor protein binds to the lac operator, present in the promoter region of the lac operon
  • This ultimately shuts down the transcription of the operon
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9
Q

Explain what happens on a molecular level to the lac operon when there is lactose.

A
  • Lactose binds to the repressor protein, which causes a conformation change
  • The changed repressor is unable to bind to the lac operator region
  • RNA polymerase can see the promoter, and make RNA for the lacZ, lacY, and lacA regions (genes known for their role in lactose metabolism)
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10
Q

What are the three genes that are known to be involved in the metabolism of lactose?

A
  • B-Galactosidase
  • Permease
  • Transacetylase
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11
Q

Lactose is an example of a ______________, while the lac operon is an example of a _____________.

A

dietary constituent

responsive gene

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12
Q

What is a responsive gene?

A
  • Either be induced or repressed by a dietary constituent

- If it does not do either, it is not a responsive gene

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13
Q

What do secondary mediators have an impact on in nutrient-gene interactions? What are they affected by?

A
  • They have an impact on their own responsive genes

- They are indirectly affected by dietary constituents

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14
Q

What are the five ways dietary constituents can interact with genes, either directly or indirectly?

A
  • Responsive genes (direct)
  • Physiological modulation (indirect)
  • Regulation of transcription
  • Regulation of translation
  • Modification of proteins
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15
Q

Where do responsive genes reside in Eukaryotic cells? What about in Prokaryotic cells?

A
  • Eukaryotic: nucleus

- Prokaryotic: nucleoid body

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16
Q

Explain how amino acids and fatty acids regulate gene expression indirectly.

A
  • Interact with a protein embedded on a cell membrane, which will initiate a signal transduction pathway (e.g. phosphorylation-chain)
  • When the signal reaches the nucleus, the protein interacts with a promoter region of a gene to induce or repress RNA transcription
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17
Q

Explain how fat-soluble vitamins, trace elements, fatty acids, phytochemicals, and sterolsregulate gene expression.

A
  • Find their way inside the cell through nutrient transporters
  • Interact with specific transcription factors
  • Nuclear receptors act on target genes, affecting transcription
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18
Q

Explain how folic acid, vitamin B12, and methionine regulate gene expression.

A
  • Affect DNA methylation
  • Impacts the ability of the cell to utilize genetic information
  • Renders it unaccessible for transcription
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19
Q

Explain how cofactors and vitamins regulate gene expression.

A

Translation cannot occur if they are not present

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20
Q

Explain how nutrients can affect proteins directly.

A
  • Certain proteins find their way inside the cell and interact directly with proteins and enzymes
  • This affects their conformation, their binding capacity, and their interactions
  • These influence metabolism by either increasing or decreasing efficiency
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21
Q

Concerted Regulation of Protein and Lipid Biosynthesis occurs by which pathway?

A

The Akt/mTORC1 pathway

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22
Q

What are the four proteins involved in the Akt/mTORC1 pathway?

A
  • AMPK
  • Akt
  • mTORC1
  • SREBP
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23
Q

AMPK and Akt are components of a signalling pathway. What are their functions?

A
  • AMPK: responds to cellular energy status

- Akt: responds to growth factors, including insulin

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24
Q

What is the role of mTORC1?

A
  • Integratesthe information related to the kind:
  • Nutrients available
  • Cellular energy status,
  • Growth factors interacting with the cell receptor
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25
Q

What does the Akt/mTORC1 pathway affect?

A

Regulates protein and lipid biosynthesis

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26
Q

True or False: if you increase your mass of cells, you increase your lipid content. Why or why not?

A
  • True

- Due to the Akt/mTORC1 pathway, which regulates cell growth through protein AND lipid biosynthesis

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27
Q

Why is glucose uptake necessary for the Akt/mTORC1 pathway?

A

Since the production of protein and lipid biosynthesis is an energetically expensive process, which requires the production of ATP through glycolysis and the TCA cycle

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28
Q

What is SREBP responsive to?

A

To the status of cholesterol in the environment

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29
Q

Explain what happens to SREBP when you have low sterol concentrations.

A
  • SREBP, interacting with SCAP and COPII, migrates from the ER towards the Golgi
  • At the Golgi, the SREBP protein is processed by specific proteases of the Golgi
  • The proteases liberate a portion of SREBP, which migrates to the nucleus and binds to the Sterol Response Element (SRE)
  • SRE stimulates the target genes involved in cholesterol and fatty acid biosynthesis
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30
Q

Explain what happens to SREBP when you have high sterol concentrations.

A
  • SREBP remains bound to SCAP, which is bound by INSIG, and remains in the ER
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31
Q

Give examples of abundant elements.

A

Carbon, hydrogen, nitrogen, oxygen, phosphorus

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32
Q

Give examples of trace elements.

A

Calcium, chlorine, cobalt, copper, iodine, iron, manganese, magnesium, potassium, sodium, sulphur, selenium, zinc

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33
Q

Are there few or many functional groups?

A

Few (12) functional groups composed of reorganized elements exist

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34
Q

Describe the 6 levels of organization of life.

A
  • Macromolecule
  • Supramolecular Assembly
  • Organelle
  • Cell
  • Tissue
  • Organ
  • Organism
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35
Q

What are the two requirements for life?

A
  • Energy: light, heat, chemical

- Raw materials

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36
Q

What raw materials are necessary for life?

A
  • Carbon source
  • Nitrogen source (protein and DNA)
  • Water
  • Oxygen
  • Salts
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37
Q

Which terminal of an amino acid corresponds to the 5’-end of the gene that encodes it? What about the 3’-end?

A
  • N-terminal (+) = 5’

- C-terminal (-) = 3’

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38
Q

What is hydrolyzed protein used for?

A
  • Common in some large scale food manufacturing

- Texturizer, flavour enhancer

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39
Q

Explain how hydrolyzed proteins may be hypoallergenic.

A

If you break up a protein, our immune system might not recognize its different three-dimensional structure

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40
Q

What is the function of glutamic acid as a neurotransmitter?

A

Involved in long-term potentiation (learning and memory)

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41
Q

What symptoms has MSG been suggested to cause?

A
  • Headaches
  • Numbness
  • Tingling sensations
  • Obesity
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42
Q

What are the three kinds of MSG manufacturing? Are they L or D amino acids?

A
  • Hydrolysis of proteins (L-amino acids)
  • Chemical synthesis (DL-glutamate; synthetic)
  • Fermentation (L-glutamate)
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43
Q

How does L-glutamate made by chemical synthesis differ from L-glutamate made by fermentation?

A

They are the same despite chemical synthesis being synthetic

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44
Q

Which foods contain MSG?

A
  • Anything that contains “protein hydrolysate” (prepared foods, protein supplements)
  • Fermented food products (soy sauce, Worcestershire sauce, vegemite)
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45
Q

Define homeostasis.

A
  • Homeostasis occurs when the rate of input is equal to the rate of output
  • Disease states occur when there is dysregulation in homeostasis
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46
Q

What is gout? What is the cause?

A
  • A painful genetically-predisposed disorder characterized by joint inflammation.
  • Caused by high uric acid concentration in the body due to high production or inefficient disposal of uric acid.
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47
Q

Is RNA or DNA easier to degrade?

A

RNA is easier to degrade; DNA is sequestered in the nucleus anyways

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48
Q

Explain how high uric acid concentration leads to the irritation and inflammation of joints.

A

Leads to the formation of uric crystals

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49
Q

Why is gout aggravated by an animal-based diet?

A
  • They contain a higher proportion of purines (nucleic acids) than plant-based diets
  • By unit-mass, there is more DNA compared to plant-based diets
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50
Q

What is uric acid synthesized from in humans?

A

Adenine and guanine

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51
Q

How do lipids differ from other macromolecules?

A
  • They are not defined as polymers, but detain a functional classification
  • Lipids are all hydrophobic molecules (fatty acids, cholesterol) and do not have a common subunit
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52
Q

What are the two sections of fatty acids?

A
  • Carboxyl-end (hydrophilic)

- Methyl-end (hydrophobic)

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53
Q

Describe the varying lengths of fatty acid chains.

A
  • Short-chain (2-6 carbons)
  • Medium-chain (8-10 carbons)
  • Long-chain (12-20 carbons)
  • Very long-chain (>20 carbons)
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54
Q

How does palmitic acid compare to stearic acid?

A

Palmitic (16:0) is bad, stearic acid (18:0) is better

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55
Q

What is olive oil rich in?

A

Oleic acid (C18:1)

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56
Q

What is safflower oil rich in?

A

Linoleic acid (C18:2)

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57
Q

What is lard and beef tallow rich in?

A

Palmitic (C16:0) and stearic (C18:0) acids

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58
Q

What are the dangers of trans fatty acids?

A
  • Mimic the structure of saturated fatty acids
  • Body does not know how to metabolize these structures, so they are unknown to the body
  • Their shape is different, thus, they do not fit the proper configuration in the enzymes
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59
Q

What are the three different uses of fatty acids?

A
  • Energy source
  • Structural component
  • Substrate for the synthesis of signalling molecules
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60
Q

Describe myristillation.

A
  • Covalent modification of proteins
  • Attach myristic acid to a portion of a protein residue, which renders it hydrophobic
  • It will tend to insert its hydrophobic residue in a membrane, along with the attached protein
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61
Q

Why can phosphorylation active enzymes?

A
  • Conformational changes
  • Serine/threonine/tyrosine become much more hydrophilic, which will pull out that region of the protein, and ultimately changes the shape
62
Q

Why is fat a good energy source?

A
  • They are highly reduced molecules, meaning they have lots of available energy.
  • Their hydrophobic nature serves as good packing energy.
63
Q

How are fatty acids stored?

A

In triacylglycerols

64
Q

Is cholesterol a fat?

A

No, because solid fats and liquid oils are made of triacylglycerols

65
Q

Differentiate saturated and unsaturated fatty acids.

A
  • No double bonds; can be packed tightly; solid at RT

- One or more double bonds; can’t be packed; liquid at RT

66
Q

Are all fatty acids the same within one TG?

A

They can be, but they can also be different

67
Q

Describe the structure of phospholipids.

A
  • Phosphate attached to a unique head group (X)
  • Glycerol backbone
  • Two fatty acids
68
Q

How can phospholipids arrange themselves in water?

A
  • Micelles

- Lipid bilayer

69
Q

Give examples of interactions occurring within the lipid bilayer.

A
  • Integral membrane proteins
  • Peripheral membrane proteins
  • Glycoproteins
  • Carbohydrate side chains of glycoproteins
70
Q

What are nuclear pores necessary for?

A
  • Proteins
  • RNA
  • Nutrients
71
Q

What is the role of phospholipases?

A
  • Release fatty acids

- Leaves you with a lysophospholipid (missing a fatty acid)

72
Q

What is the driving force of the increasing prevalence of both obesity and undernutrition?

A
  • The composition of the foods we eat (fast foods, convenience foods)
  • Altering the nutrient content to make cheaper sources
  • Decrease in nutrient diverse
  • Alteration in macronutrient content
73
Q

What disorder is responsible for most deaths associated with a high body-mass index?

A
  • Cardiovascular diseases

- Lipid deposition in arteries and complicating disorders

74
Q

Describe the trends of sugar consumption over the past years.

A
  • Increasing overall
  • Decrease in sugar
  • Increase in High-Fructose Corn Syrup (HFCS)
75
Q

Give examples of foods sweetened with HFCS.

A
  • Ketchup
  • Energy bars
  • Ice cream
  • Soda
  • Chocolate milk
76
Q

What are the major contributors to the development of metabolic syndromes?

A
  • Excessive caloric intake
  • Poor quality nutrition (HFCS)
  • Sedentary lifestyle
77
Q

Give examples of acquired metabolic syndromes.

A
  • Obesity
  • Atherosclerosis
  • Fatty liver disease
  • Gallstones
  • Hypertension
  • IBD
  • Diabetes
78
Q

What does the sentence “food components are bioactive” mean?

A
  • Nutrients are not solely needed to build muscle, bone and energy
  • Nutrients are a part of what makes cells work, regulate their activity, and are the components of what they are made of
79
Q

Do plant-based foods have cholesterol?

A

No, they have sterols

80
Q

What is particular about plant-based sterols?

A

They are poorly absorbed because transporters are configured to solely recognize cholesterol

81
Q

What is needed to synthesize cholesterol?

A
  • HMG-CoA reductase

- The quantity of HMG-CoA reductase is a rate-limiting enzyme, which dictates the efficiency of the pathway

82
Q

What is the function of statins?

A

Inhibit HMG-CoA reductase, and blocks cholesterol synthesis

83
Q

________ is a lipid that is a precursor of highly bioactive molecules.

A

Cholesterol

84
Q

Can cholesterol be oxidized to produce energy?

A

No, ATP spent synthesizing this molecule cannot be recovered

85
Q

Cholesterol is a substrate for the synthesis of what?

A
  • Steroid hormones
  • Vitamin D
  • Bile acids
86
Q

What is cholesterol required for?

A
  • The control of membrane fluidity
  • Required for proteins to move and undergo conformational changes, respond to temperature changes, and allow substances to pass through
87
Q

Cholesterol is a highly bioactive molecule that needs to be regulated to be kept within an optimal range. What homeostatic mechanism occurs when there is too much cholesterol?

A
  • Cholesteryl esters (inactive) are synthesized and stored in an oil droplet
  • Choleseteryl esters can’t be used to make steroid hormones or bile acids
  • They need to be converted to cholesterol to become bioactive again
88
Q

Define a nutrient.

A

A nutrient is either a chemical element or compound that is used in the metabolic processes of, or forms an integral component of the physiology of an organism

89
Q

What are macronutrients?

A
  • Needed in large quantities
  • Carbohydrates, proteins, fat
  • Nucleic acids are not a source of energy
90
Q

What are micronutrients?

A
  • Small quantities

- Vitamins and minerals

91
Q

What is the criteria for nutrient essentiality?

A

That absence of the nutrient from the diet results in characteristic signs of a deficiency disease and these signs are prevented only by the nutrient itself, or a specific precursor of it

92
Q

What are the essential amino acids?

A
  • Valine
  • Phenylalanine
  • Histidine
  • Leucine
  • Methionine
  • Tryptophan
  • Isoleucine
  • Threonine
  • Lysine
  • Arginine (in children and special cases; preterm infants are unable to synthesize or create Arginine internally)
93
Q

What are the essential fatty acids?

A
  • Fatty acids with double bonds located at positions 8 or less (counting from the methyl end)
  • Linoleic acid
  • Linolenic acid
94
Q

What are the essential fat-soluble vitamins?

A
  • A
  • D
  • E
  • K
95
Q

What are the essential water-soluble vitamins?

A
  • B1, B2, B3, B5, B6, B7, B9, B12
  • C
  • Choline
96
Q

What is vitamin A?

A

Retinol

97
Q

What is vitamin D?

A

Ergocalciferol, cholecalciferol

98
Q

What is vitamin E?

A

Tocopherol

99
Q

What is vitamin K?

A

Naphthoquinoids

100
Q

What is vitamin B1?

A

Thiamine

101
Q

What is vitamin B2?

A

Riboflavin

102
Q

What is vitamin B3?

A

Niacin

103
Q

What is vitamin B6?

A

Pyridoxine

104
Q

What is vitamin B5?

A

Pantothenic acid

105
Q

What is vitamin B9?

A

Folic acid

106
Q

What is vitamin B12?

A

Cobalamin

107
Q

What is vitamin B7?

A

Biotin

108
Q

What are the four functions of choline?

A
  • Susbtrate for phosphatidylcholine biosynthesis
  • Ensures the structural integrity and signaling functions of cell membranes
  • Source of methyl groups
  • Used to make a variety of very important metabolites (e.g. acetylcholine, platelet-activating factor, betaine)
109
Q

What is the mechanism that spares choline when it is deficient?

A

The body will recover and reabsorb all the choline it secretes in the bile

110
Q

Describe the de novo synthesis of choline.

A
  • Three successive methylations (recovers methyl groups) of the phosphatidylethanolamine headgroup generates phosphatidylcholine
  • Choline can be released from phosphatidylcholine
111
Q

What are the essential macrominerals? What is their function?

A
  • Calcium
  • Chloride ion
  • Phosphorus
  • Important in forming active enzymes needed to support metabolism
112
Q

What are phytochemicals?

A
  • A broad and diverse group of plant-derived compounds

- Compound that you can’t find anywhere else other than plants

113
Q

Which phytochemicals are thought to have beneficial effects on health? Are all phytochemicals good?

A
  • Flavonoids

- No, some are very toxic

114
Q

Define malnutrition.

A
  • Refers to improper to insufficient diet

- Nutrient deficiency and nutrient excess

115
Q

What are essential fatty acids substrates for?

A

A class of molecules called eicosanoids

116
Q

Give examples of eicosanoids.

A
  • Prostaglandins
  • Leukotrienes
  • Thromboxanes
117
Q

What are the functions of essential fatty acids?

A
  • Immune function
  • Inflammatory response
  • Blood clotting
  • Vasodilation
  • Kidney function
  • Cognitive function
118
Q

What are the consequences of essential fatty acid deficiency?

A
  • Growth retardation
  • Sparse hair growth, dry skin and scaling (excema)
  • General weakness
  • Depression
  • Poor wound healing, increased susceptibility to infection
  • Edema
  • Vision problems
  • Neurological problems (particularly in severe cases).
119
Q

What are the consequences of essential fatty acid excess?

A
  • Currently, does not appear to cause severe problems.

- May cause excessive bleeding (slow blood clotting)

120
Q

What is the essential function of vitamin A?

A

Maintenance of epithelial cells

121
Q

Vitamin A and other retinoids are ________. What does this mean?

A
  • Teratogenic

- Disturbs the development of the embryo or fetus

122
Q

Vitamin A is the ligand for which receptors? What happens if you supply too much vitamin A?

A
  • Retinoic acid receptor (RAR) and retinoid x receptor (RXR)

- If you supply too much vitamin A, you inappropriately induce the expression of genes, which may cause damage

123
Q

Where is vitamin A found? How does overdose usually occur?

A
  • Coloured fruits and vegetables
  • Difficult to overdose on fruits and veggies
  • Overdose usually occurs with supplements and drugs (e.g. Acutane)
124
Q

How does vitamin A deficiency lead to xerosis? What is xerosis?

A
  • Abnormal dryness

- Causes mucus-secreting cells to be replaced by keratin producing cells

125
Q

What is the consequence of vitamin A deficiency?

A
  • Primarily affects eye function
  • Eye blindness
  • Eye xerosis causes ulcerations and leads to blindness
126
Q

People with diseases involving the absorption of lipids are at risk for which deficiency?

A

Vitamin A

127
Q

What are the consequences of vitamin A excess?

A
  • Birth defects
  • Reduced bone mineral density
  • Weight loss, headache, vision problems, dry itchy skin, hair loss, anemia, teeth discolouration, enlarged liver and spleen
128
Q

Is iron a macromineral or a micromineral?

A
  • Transition metal

- Micromineral

129
Q

What is iron’s main function?

A
  • Used by a prosthetic group by many biologically important proteins (ex: heme groups of hemoglobin, myoglobin)
  • Generally found in enzymes involved in carrying or metabolizing oxygen
130
Q

How much iron does the average person contain? Where is it largely found

A
  • 3-4 grams of iron

- 60% in the blood

131
Q

What is the average intake of iron? What is the average absorption?

A
  • 15 mg

- 2 mg

132
Q

What % of the world is deficient in iron?

A

80

133
Q

What individuals are at risk for iron deficiency anemia?

A
  • Alcoholics

- Patients with infectious, inflammatory, or neoplastic diseases

134
Q

What are the symptoms of iron deficiency anemia?

A
  • Pale skin
  • Tired and weakness
  • Difficulty maintaining body temperature
  • Shortness of breath
  • Inflamed tongue
  • Diminished cognitive function
  • Decreased immune function
135
Q

How does iron loss occur?

A
  • Shedding of epithelial surfaces
  • Through occult blood loss in the intestine
  • Menstruation
  • Lactation
136
Q

What is the cause of secondary hemochromatosis?

A
  • Excessive alcohol consumption

- Excessive use of dietary iron supplements

137
Q

What other disorders can iron excess lead to?

A
  • Arthritis
  • Liver disease leading to liver failure
  • Damage to the pancreas causing diabetes
  • Cardiac function abnormalities
  • Impotence
  • Abnormal skin pigmentation (making it look grey or bronze)
  • Thyroid deficiency
  • Damage to the adrenal glands
138
Q

Is iodine a macromineral or a micromineral?

A
  • Halogen

- Micromineral

139
Q

What are the major functions of iodine?

A
  • Necessary for normal thyroid function

- Essential substrate for the synthesis of thyroid hormones

140
Q

What are the functions of thyroid hormones?

A
  • Control many aspects of energy (carbohydrate and fat) metabolism
  • Ligands of TR receptor (transcription factor belonging to the nuclear receptor superfamily of transcription factors)
141
Q

What are sources of iodine?

A
  • Seafood (cod, sea bass, haddock, perch)
  • Kelp
  • Dairy products
  • Iodized table salt
142
Q

What are the consequences of iodine deficiency?

A
  • Increased fetal and infant mortality
  • Neurological defects
  • Mental retardation (cretinism)
  • Decreased reproductive fitness
  • Hypothyroidism
  • Goiter (hypertrophy of the thyroid gland)
143
Q

What are secondary thyroid related disorders?

A
  • Anemia
  • Arthritis
  • Eye enlargement and inflammation
  • Hair loss and premature graying of hair
  • Inflammatory bowel diseases
  • Depression
144
Q

What is the cause of goiter?

A
  • Iodine deficiency; impaired by thyroid hormone synthesis

- Also caused by excessive iodine, which results in the inhibition of thyroid hormone production

145
Q

Does an excess of iodine develop more or less problems than iodine deficiency?

A

Excess iodine develops less problems than iodine deficiency

146
Q

What are the consequences of an excess of iodine?

A
  • Skin ulceration (“kelp acne”, high incidence in Japan where kelp is consumed in large quantities)
  • Impairs thyroid hormone production and causes goiter in response to decreased thyroid hormone concentration
147
Q

What is the lacZ region associated with?

A

B-galactosidase

148
Q

What is the lacY region associated with?

A

Permease

149
Q

What is the lacA region associated with?

A

Transacetylase

150
Q

What does the inhibitor protein of the lac operon bind to in order to shut down transcription?

A

lacO

151
Q

How do statins function?

A
  • By competitively inhibiting to HMG-CoA reductase

- Competitive binding to the active site of HMG-CoA reductase prevents HMG-CoA from binding to produce mevalonate

152
Q

What binds to HMG-CoA reductase? What is produced?

A
  • HMG-CoA binds

- Mevalonate is produced

Val 307 (15 decks)

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