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bmsc 200 > module 1 > Flashcards

module 1 Flashcards

1
Q

what is the definitions of biochemistry?

A

-the study of life at the molecular level
-the application of the principls of chemistry to explain biology
-the common sets of reactions and principles that underlie all living organisms
-the study of the molecular logic of life

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2
Q

what do all organisms use?

A

-a common repertoire of building blocks to create common categories of biomolecules (nucleic acids, proteins, polysaccharides, and lipids)
-a common core of essential biochemical processes

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3
Q

what are the four foundations of the living state?

A

-chemical
-energy
-evolutionary
-genetic

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4
Q

what are the four elements that make up 98% of most organisms?

A

-carbon
-hydrogen
-oxygen
-nitrogen

-water accounts for much of O and H

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5
Q

what are all known life forms?

A

-carbon based

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6
Q

what are the readily available elements in the biosphere?

A

-carbon (from air through plants)
-oxygen (from air)
-hydrogen (from water)

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7
Q

who was fritz haber?

A

-allowed for 3 billion more people to eat
-created technique to get nitrogen from air and convert into nitrates to use in fertilizer

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8
Q

what was fritz haber’s downside?

A

-repurposed his method into gunpowder, mustard gas, chemical weapons
-responsible for thousands of soldiers death
-was a jew, later used in concentration camps
-wife committed suicide

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9
Q

what is the availability of nitrogen?

A

–N in soil limits growth of plants, limits the amount of food we can produce
-naturally occurring N in soil, only enough food for 4 billion people
-

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10
Q

how much are we worth?

A

-chemicals in body are worth less than a dollar
-sum of parts (tissues, organs, biomolecules) are estimated 45 million dollars

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11
Q

why is carbon so versatile?

A

-number and variety of chemical bonds it can form
-enables to create wide array of complex molecules
-ex: amino acids, sugars, nucleotides

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12
Q

what is silicon?

A

-the next best candidate as a chem found for life
-also can form four covalent bonds
-highly abundant in the earth’s atmosphere

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13
Q

why are we based in carbon rather than silicon?

A

-C to C is stronger than S to S (more stable)
-more energy released on combustion (c to c)
-combustion products of carbon (CO2) are soluble and remain active in the biosphere
-silicon dioxide is insoluble, cant be recycled

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14
Q

why are functional groups unique?

A

-their size, shape, charge, reactivities, and hydrogen bonding capacity
-the properties of the functional groups determine the structure, function and properties of the biomolecule (anticipate behavior)

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15
Q

why is it important to understand the structure?

A

-structure dictates function
-do what they do bc of their structures
-allows to predict molecular function, understand complex biology and rationale development of treatments

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16
Q

what is conformation?

A

-flexible spatial arrangement of atoms within a molecules (can be changed without breaking covalent bonds)
-Ex: piece of paper example

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17
Q

what is configuration?

A

-fixed spatial arrangement of atoms within a molecule (cannot be changed without breaking covalent bonds)
-conferred by either double bonds or chiral centers
-much more dramatic
-ex: cutting off a finger

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18
Q

what are geometric (cis-trans) isomers?

A

-have the same chemical formula but differ in the configuration of groups with respect to a non-rotating double bond
-configuration double bond perspective
-can have very diff biological properties

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19
Q

what are cis and trans?

A

-cis= on this side groups on the same side as the double bond
-trans=across groups on opposite sides of the double bond

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20
Q

what is a chiral carbon?

A

-has 4 diff substituents attaches: may be arranged in diff ways in space yielding two stereoisomers that differ in their configuration

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21
Q

what is a stereoisomer?

A

-chemical properties tend to be identical
-biological properties are often distinct

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22
Q

how are stereoisomers diff during chemical reactions vs biochemistry?

A

-chem= not usually stereo specific
-biochem= stereo specific in terms of chemical reactions

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23
Q

what is contruction?

A

-biomolecules often constructed exclusively from one stereo isomer
-ex: proteins are built entirely from L-amino acids

24
Q

what are interactions? (biochem=stereospecific)

A

-interactions between biomolecules and between biomolecules and small molecules are stereospecific
-reaction with diff receptors change sensation

25
Q

where does chemistry meet biology?

A

-synthesis of chemical compounds which have asymmetric carbons result in a mixture of all the chiral forms
-these forms may have different biological activities (therapeutic benefits, pathological side affects differ)

26
Q

what is an example of how two different chiral forms can cause different effects?

A

-thalidomide has two chiral forms, one causes birth defects
-Frances Kelsey (canadian physician working for FDA) saved children after she refused approval

27
Q

how are biomolecules similar to words in a sentence?

A

-the structure and function of the resulting biomolecules are more complex than their precursor molecules
-the whole is greater than the sum of parts

28
Q

what are the advantages of constructing biologicals as polymers?

A

-simplicity: simple and conserved reactions for synthesis and degradation (body has 20000 diff proteins, all from same building blocks)

-recycling: biomolecules can be digested back to component building blocks which are reusable

-diversity: incredibly complex molecules can be generated

29
Q

what are the four classes of biomolecules?

A

-proteins
-carbohydrates
-nucleic acids
-lipids

30
Q

what are proteins?

A

-linear polymers of amino acids
-20 different amino acids
-carboxyl links to amino group of next amino acid
-aminos link to form linear chains that fold into complex patterns with distinct biological activities

31
Q

what are polysaccharides?

A

-made of sugars
-monosaccharides linked together to form linear or branched polymers
-biological roles include structural, energy storage, and cellular recognition
-linked through glycosidic linkages
-form branch points (can form more than 1 covalent bond)

32
Q

what are nucleic acids?

A

-linear polymers of nucleotide building blocks (5 building blocks for DNA and RNA)
-involved in all aspects of storage and utilization of genetic information
-linked through phosphodiester bonds

33
Q

what are lipids?

A

-are aggregates (rather than defined polymers) of building blocks
-serve in energy storage, formation of membranes and signaling
-not joined through covalent bonds (only 1)
-use non-covalent forms which allows freedom of rotation

34
Q

what are prokaryotes?

A

-small (1 nano meter in diameter), simple, single cell organisms (bacteria)
-rapid growth, quick adaptations to changing environmental conditions
-a single compartment, the nucleoid, which contains nucleic acid. Other biomolecules (proteins, etc) in a complex, organized mix

35
Q

what are eukaryotes?

A

-large, complex cells (100 nanometers)
-make up multi-cellular organisms
-organelles (mitochondria, nucleus, etc) to support specialized functions
-differentiation of cells to unique and specialized cell types

36
Q

how many euk and pro cells do we have in our bodies?

A

-30 trillion euks
-100 trillion pros

37
Q

why are pros critical for our health?

A

-bacteria in the gut helps digest food and maintain a functional immune system
-our second brain (the gut), including the microflora, may impact mental health, obesity and intelligence

38
Q

what are some ways to influence the microbiota?

A

-diet
-pro and prebiotics
-fecal transplants

39
Q

what is a major challenge of biochemistry?

A

-studying molecules in isolation simplifies experiments but may be at the expense of biological significance
-experiements which are siccessful in vitro often fail in vitro

40
Q

what are the two experimental appraoches?

A

-in vitro: studies the behavior of molecules outside the context of the cell and organism
-in vivo (in the living) : studies occur within the complexity of the cell or organism

41
Q

how expensive is the energy we use in one day?

A

-to purchase all the ATP from our body in one day would be about 4.5 million dllars

42
Q

what can cellular energy conversion be considered in the context of?

A

-laws of thermodynamics

43
Q

what is the first law of thermodynamics?

A

-in any physical or chemical change, the total amount of energy in the universe remains constant, although the forms of the energy may change
-can’t be created nor destroyed

44
Q

how are cells related to the first law of thermodynamics?

A

-cells are highly effective transducers of energy, converting the energy of metabolized nutrients, or the energy of the sun, into work, heat, or the generation of complex biomolecules

45
Q

what is the second law of thermodynamics?

A

-the tendency in nature is toward ever greater disorder: the total entropy (disorder) of the universe is continually increasing

-however, living systems and their biomolecules require a high degree of organization

46
Q

what is free energy?

A

-willard gibbs developed the theory of energy change during chemical reactions

-free energy of any closed system can defined as:
Free energy: G=H-TS
Free energy change: change of G=change of (enthalpy)-(temperature)(change in entropy)

-enthalpy (H)= reflects the number and kinds of bonds
-entropy (S)= the degree of randomness
-temperature= in degrees kelvin

47
Q

what does free energy mean?

A

-change in G >0: non-spontaneous process, needs input of free energy to proceed, endergonic
-change in G<0: spontaneous process, releases free energy which cane be used to do work; proceeds until equilibrium is reached, exergonic
-change in G=0: system is at equilibrium, there is no change in free energy in the system

48
Q

how does energy coupling link to reactions in biology?

A

-cells can drive thermodynamically unfavorable reactions by coupling energy requiring (endergonic) to energy releasing (exergonic) reactions
-if the sum of the free energy changes is negative, then the overall process is exergonic

49
Q

what is the central role of ATP in metabolism?

A

-energy extracted to the form of adenosine triphosphate (ATP) which serves as a common energy current
-ATP serves as the link between catabolic reactions and anabolic (building things up) reactions

50
Q

what does the perpetuation of life requires that genetic information be:

A

-stored in a stable form
-expressed accurately in the form of gene products
-reproduced with minimal errors

51
Q

for many organisms, DNA provides:

A

-the instructions for forming all other cellular components
-a template for production of identical DNA molecules to be distributed to the progeny when a cell divides

52
Q

what is the central dogma of biochemistry?

A

DNA ->RNA -> proteins
transcription->translation

53
Q

what is the structure of DNA?

A

-two complimentary strands
-each strand is a linear polymer of four different types of building blocks
-it is a linear sequence within the strands that encodes information

54
Q

what does amino acids have to do with genetic foundations?

A

-the nucleotide sequence of genes dictates the sequence of amino acids incorporated into the corresponding protein
-the amino acid sequence of the proteins dictates the structure->dictates its biological activity

55
Q

how does the changes in hereditary instructions allow evolution?

A

-random changes in genotype can result in a change in phenotype
-of this change offers a survival advantage, it will be selected over time
-fuel for evolution

56
Q
A

bmsc 200 (10 decks)

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