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
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
3
Q
What nutrients are necessary during cell division?
A
- Energy
- Proteins to create new structures and motors
- Lipids to create cell membranes
4
Q
Define nutrigenetics.
A
Genes control the metabolism of nutrients
5
Q
Define nutrigenomics.
A
Nutrients influence the expression of genes
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
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
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
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)
10
Q
What are the three genes that are known to be involved in the metabolism of lactose?
A
- B-Galactosidase
- Permease
- Transacetylase
11
Q
Lactose is an example of a ______________, while the lac operon is an example of a _____________.
A
dietary constituent
responsive gene
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
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
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
15
Q
Where do responsive genes reside in Eukaryotic cells? What about in Prokaryotic cells?
A
- Eukaryotic: nucleus
- Prokaryotic: nucleoid body
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
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
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
19
Q
Explain how cofactors and vitamins regulate gene expression.
A
Translation cannot occur if they are not present
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
21
Q
Concerted Regulation of Protein and Lipid Biosynthesis occurs by which pathway?
A
The Akt/mTORC1 pathway
22
Q
What are the four proteins involved in the Akt/mTORC1 pathway?
A
- AMPK
- Akt
- mTORC1
- SREBP
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
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
25
What does the Akt/mTORC1 pathway affect?
Regulates protein and lipid biosynthesis
26
True or False: if you increase your mass of cells, you increase your lipid content. Why or why not?
- True
| - Due to the Akt/mTORC1 pathway, which regulates cell growth through protein AND lipid biosynthesis
27
Why is glucose uptake necessary for the Akt/mTORC1 pathway?
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
28
What is SREBP responsive to?
To the status of cholesterol in the environment
29
Explain what happens to SREBP when you have low sterol concentrations.
- 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
30
Explain what happens to SREBP when you have high sterol concentrations.
- SREBP remains bound to SCAP, which is bound by INSIG, and remains in the ER
31
Give examples of abundant elements.
Carbon, hydrogen, nitrogen, oxygen, phosphorus
32
Give examples of trace elements.
Calcium, chlorine, cobalt, copper, iodine, iron, manganese, magnesium, potassium, sodium, sulphur, selenium, zinc
33
Are there few or many functional groups?
Few (12) functional groups composed of reorganized elements exist
34
Describe the 6 levels of organization of life.
- Macromolecule
- Supramolecular Assembly
- Organelle
- Cell
- Tissue
- Organ
- Organism
35
What are the two requirements for life?
- Energy: light, heat, chemical
| - Raw materials
36
What raw materials are necessary for life?
- Carbon source
- Nitrogen source (protein and DNA)
- Water
- Oxygen
- Salts
37
Which terminal of an amino acid corresponds to the 5'-end of the gene that encodes it? What about the 3'-end?
- N-terminal (+) = 5'
| - C-terminal (-) = 3'
38
What is hydrolyzed protein used for?
- Common in some large scale food manufacturing
| - Texturizer, flavour enhancer
39
Explain how hydrolyzed proteins may be hypoallergenic.
If you break up a protein, our immune system might not recognize its different three-dimensional structure
40
What is the function of glutamic acid as a neurotransmitter?
Involved in long-term potentiation (learning and memory)
41
What symptoms has MSG been suggested to cause?
- Headaches
- Numbness
- Tingling sensations
- Obesity
42
What are the three kinds of MSG manufacturing? Are they L or D amino acids?
- Hydrolysis of proteins (L-amino acids)
- Chemical synthesis (DL-glutamate; synthetic)
- Fermentation (L-glutamate)
43
How does L-glutamate made by chemical synthesis differ from L-glutamate made by fermentation?
They are the same despite chemical synthesis being synthetic
44
Which foods contain MSG?
- Anything that contains "protein hydrolysate" (prepared foods, protein supplements)
- Fermented food products (soy sauce, Worcestershire sauce, vegemite)
45
Define homeostasis.
- Homeostasis occurs when the rate of input is equal to the rate of output
- Disease states occur when there is dysregulation in homeostasis
46
What is gout? What is the cause?
- 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.
47
Is RNA or DNA easier to degrade?
RNA is easier to degrade; DNA is sequestered in the nucleus anyways
48
Explain how high uric acid concentration leads to the irritation and inflammation of joints.
Leads to the formation of uric crystals
49
Why is gout aggravated by an animal-based diet?
- 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
50
What is uric acid synthesized from in humans?
Adenine and guanine
51
How do lipids differ from other macromolecules?
- 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
52
What are the two sections of fatty acids?
- Carboxyl-end (hydrophilic)
| - Methyl-end (hydrophobic)
53
Describe the varying lengths of fatty acid chains.
- Short-chain (2-6 carbons)
- Medium-chain (8-10 carbons)
- Long-chain (12-20 carbons)
- Very long-chain (>20 carbons)
54
How does palmitic acid compare to stearic acid?
Palmitic (16:0) is bad, stearic acid (18:0) is better
55
What is olive oil rich in?
Oleic acid (C18:1)
56
What is safflower oil rich in?
Linoleic acid (C18:2)
57
What is lard and beef tallow rich in?
Palmitic (C16:0) and stearic (C18:0) acids
58
What are the dangers of trans fatty acids?
- 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
59
What are the three different uses of fatty acids?
- Energy source
- Structural component
- Substrate for the synthesis of signalling molecules
60
Describe myristillation.
- 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
61
Why can phosphorylation active enzymes?
- Conformational changes
- Serine/threonine/tyrosine become much more hydrophilic, which will pull out that region of the protein, and ultimately changes the shape
62
Why is fat a good energy source?
- They are highly reduced molecules, meaning they have lots of available energy.
- Their hydrophobic nature serves as good packing energy.
63
How are fatty acids stored?
In triacylglycerols
64
Is cholesterol a fat?
No, because solid fats and liquid oils are made of triacylglycerols
65
Differentiate saturated and unsaturated fatty acids.
- No double bonds; can be packed tightly; solid at RT
| - One or more double bonds; can't be packed; liquid at RT
66
Are all fatty acids the same within one TG?
They can be, but they can also be different
67
Describe the structure of phospholipids.
- Phosphate attached to a unique head group (X)
- Glycerol backbone
- Two fatty acids
68
How can phospholipids arrange themselves in water?
- Micelles
| - Lipid bilayer
69
Give examples of interactions occurring within the lipid bilayer.
- Integral membrane proteins
- Peripheral membrane proteins
- Glycoproteins
- Carbohydrate side chains of glycoproteins
70
What are nuclear pores necessary for?
- Proteins
- RNA
- Nutrients
71
What is the role of phospholipases?
- Release fatty acids
| - Leaves you with a lysophospholipid (missing a fatty acid)
72
What is the driving force of the increasing prevalence of both obesity and undernutrition?
- 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
What disorder is responsible for most deaths associated with a high body-mass index?
- Cardiovascular diseases
| - Lipid deposition in arteries and complicating disorders
74
Describe the trends of sugar consumption over the past years.
- Increasing overall
- Decrease in sugar
- Increase in High-Fructose Corn Syrup (HFCS)
75
Give examples of foods sweetened with HFCS.
- Ketchup
- Energy bars
- Ice cream
- Soda
- Chocolate milk
76
What are the major contributors to the development of metabolic syndromes?
- Excessive caloric intake
- Poor quality nutrition (HFCS)
- Sedentary lifestyle
77
Give examples of acquired metabolic syndromes.
- Obesity
- Atherosclerosis
- Fatty liver disease
- Gallstones
- Hypertension
- IBD
- Diabetes
78
What does the sentence "food components are bioactive" mean?
- 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
Do plant-based foods have cholesterol?
No, they have sterols
80
What is particular about plant-based sterols?
They are poorly absorbed because transporters are configured to solely recognize cholesterol
81
What is needed to synthesize cholesterol?
- HMG-CoA reductase
| - The quantity of HMG-CoA reductase is a rate-limiting enzyme, which dictates the efficiency of the pathway
82
What is the function of statins?
Inhibit HMG-CoA reductase, and blocks cholesterol synthesis
83
________ is a lipid that is a precursor of highly bioactive molecules.
Cholesterol
84
Can cholesterol be oxidized to produce energy?
No, ATP spent synthesizing this molecule cannot be recovered
85
Cholesterol is a substrate for the synthesis of what?
- Steroid hormones
- Vitamin D
- Bile acids
86
What is cholesterol required for?
- 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
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?
- 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
Define a nutrient.
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
What are macronutrients?
- Needed in large quantities
- Carbohydrates, proteins, fat
- Nucleic acids are not a source of energy
90
What are micronutrients?
- Small quantities
| - Vitamins and minerals
91
What is the criteria for nutrient essentiality?
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
What are the essential amino acids?
- 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
What are the essential fatty acids?
- Fatty acids with double bonds located at positions 8 or less (counting from the methyl end)
- Linoleic acid
- Linolenic acid
94
What are the essential fat-soluble vitamins?
- A
- D
- E
- K
95
What are the essential water-soluble vitamins?
- B1, B2, B3, B5, B6, B7, B9, B12
- C
- Choline
96
What is vitamin A?
Retinol
97
What is vitamin D?
Ergocalciferol, cholecalciferol
98
What is vitamin E?
Tocopherol
99
What is vitamin K?
Naphthoquinoids
100
What is vitamin B1?
Thiamine
101
What is vitamin B2?
Riboflavin
102
What is vitamin B3?
Niacin
103
What is vitamin B6?
Pyridoxine
104
What is vitamin B5?
Pantothenic acid
105
What is vitamin B9?
Folic acid
106
What is vitamin B12?
Cobalamin
107
What is vitamin B7?
Biotin
108
What are the four functions of choline?
- 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
What is the mechanism that spares choline when it is deficient?
The body will recover and reabsorb all the choline it secretes in the bile
110
Describe the de novo synthesis of choline.
- Three successive methylations (recovers methyl groups) of the phosphatidylethanolamine headgroup generates phosphatidylcholine
- Choline can be released from phosphatidylcholine
111
What are the essential macrominerals? What is their function?
- Calcium
- Chloride ion
- Phosphorus
- Important in forming active enzymes needed to support metabolism
112
What are phytochemicals?
- A broad and diverse group of plant-derived compounds
| - Compound that you can't find anywhere else other than plants
113
Which phytochemicals are thought to have beneficial effects on health? Are all phytochemicals good?
- Flavonoids
| - No, some are very toxic
114
Define malnutrition.
- Refers to improper to insufficient diet
| - Nutrient deficiency and nutrient excess
115
What are essential fatty acids substrates for?
A class of molecules called eicosanoids
116
Give examples of eicosanoids.
- Prostaglandins
- Leukotrienes
- Thromboxanes
117
What are the functions of essential fatty acids?
- Immune function
- Inflammatory response
- Blood clotting
- Vasodilation
- Kidney function
- Cognitive function
118
What are the consequences of essential fatty acid deficiency?
- 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
What are the consequences of essential fatty acid excess?
- Currently, does not appear to cause severe problems.
| - May cause excessive bleeding (slow blood clotting)
120
What is the essential function of vitamin A?
Maintenance of epithelial cells
121
Vitamin A and other retinoids are ________. What does this mean?
- Teratogenic
| - Disturbs the development of the embryo or fetus
122
Vitamin A is the ligand for which receptors? What happens if you supply too much vitamin 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
Where is vitamin A found? How does overdose usually occur?
- Coloured fruits and vegetables
- Difficult to overdose on fruits and veggies
- Overdose usually occurs with supplements and drugs (e.g. Acutane)
124
How does vitamin A deficiency lead to xerosis? What is xerosis?
- Abnormal dryness
| - Causes mucus-secreting cells to be replaced by keratin producing cells
125
What is the consequence of vitamin A deficiency?
- Primarily affects eye function
- Eye blindness
- Eye xerosis causes ulcerations and leads to blindness
126
People with diseases involving the absorption of lipids are at risk for which deficiency?
Vitamin A
127
What are the consequences of vitamin A excess?
- Birth defects
- Reduced bone mineral density
- Weight loss, headache, vision problems, dry itchy skin, hair loss, anemia, teeth discolouration, enlarged liver and spleen
128
Is iron a macromineral or a micromineral?
- Transition metal
| - Micromineral
129
What is iron's main function?
- 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
How much iron does the average person contain? Where is it largely found
- 3-4 grams of iron
| - 60% in the blood
131
What is the average intake of iron? What is the average absorption?
- 15 mg
| - 2 mg
132
What % of the world is deficient in iron?
80
133
What individuals are at risk for iron deficiency anemia?
- Alcoholics
| - Patients with infectious, inflammatory, or neoplastic diseases
134
What are the symptoms of iron deficiency anemia?
- Pale skin
- Tired and weakness
- Difficulty maintaining body temperature
- Shortness of breath
- Inflamed tongue
- Diminished cognitive function
- Decreased immune function
135
How does iron loss occur?
- Shedding of epithelial surfaces
- Through occult blood loss in the intestine
- Menstruation
- Lactation
136
What is the cause of secondary hemochromatosis?
- Excessive alcohol consumption
| - Excessive use of dietary iron supplements
137
What other disorders can iron excess lead to?
- 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
Is iodine a macromineral or a micromineral?
- Halogen
| - Micromineral
139
What are the major functions of iodine?
- Necessary for normal thyroid function
| - Essential substrate for the synthesis of thyroid hormones
140
What are the functions of thyroid hormones?
- 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
What are sources of iodine?
- Seafood (cod, sea bass, haddock, perch)
- Kelp
- Dairy products
- Iodized table salt
142
What are the consequences of iodine deficiency?
- Increased fetal and infant mortality
- Neurological defects
- Mental retardation (cretinism)
- Decreased reproductive fitness
- Hypothyroidism
- Goiter (hypertrophy of the thyroid gland)
143
What are secondary thyroid related disorders?
- Anemia
- Arthritis
- Eye enlargement and inflammation
- Hair loss and premature graying of hair
- Inflammatory bowel diseases
- Depression
144
What is the cause of goiter?
- Iodine deficiency; impaired by thyroid hormone synthesis
| - Also caused by excessive iodine, which results in the inhibition of thyroid hormone production
145
Does an excess of iodine develop more or less problems than iodine deficiency?
Excess iodine develops less problems than iodine deficiency
146
What are the consequences of an excess of iodine?
- 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
What is the lacZ region associated with?
B-galactosidase
148
What is the lacY region associated with?
Permease
149
What is the lacA region associated with?
Transacetylase
150
What does the inhibitor protein of the lac operon bind to in order to shut down transcription?
lacO
151
How do statins function?
- 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
What binds to HMG-CoA reductase? What is produced?
- HMG-CoA binds
| - Mevalonate is produced
