Biochemistry and Unity of Life

Question 1

What is Biochemistry

Answer 1

• study of life at a molecular level
• application of chemistry to explain biology

Question 2

Living states can be considered from 4 perspectives:

Answer 2

• Chemical
• Energy
• Genetic
• Evolutionary

Question 3

All living things are made of 4 common ingredients (98% of organisms)

Answer 3

• Carbon
• Oxygen
• Hydrogen
• Nitrogen

Question 4

How does structure dictate function?

Answer 4

• molecules do what they do because of their structures

Question 5

Conformation

Answer 5

flexible changes in structure that don’t break any bonds (spinning things around)

Question 6

Configuration

Answer 6

fixed changes by breaking bonds
- conferred by double bonds and chiral centers

Question 7

Geometric (cis-trans) isomers

Answer 7

have same chemical formula but differ in the configuration of groups with respect to a non-rotating double bond
- once carbons are double bonded they can no longer rotate

Question 8

trans

Answer 8

“across” groups on opposite sides of the bond
- “z” shaped

Question 9

cis

Answer 9

“on this side” groups on the same side of the double bond
- half circle shaped

Question 10

chiral carbon

Answer 10

4 different groups that will attach to the central carbon that are all different
- chemical properties are identical but biological properties are distinct
- double bonds can’t be chiral carbons

Question 11

Construction

Answer 11

often constructed from one stereoisomer
Ex. proteins are built from L-amino acids

Question 12

Interactions

Answer 12

interactions between biomolecules, as well as between biomolecules and small molecules are stereospecific

Question 13

Advantages of constructing biologicals and polymers:

Answer 13

1. Simplicity
2. Recycling
3. Diversity

Question 14

Simplicity

Answer 14

simple and conserved reactions for synthesis and degradation
- single unified system (all be broken down in the same way)

Question 15

Recycling

Answer 15

biomolecules can be digested back to component building blocks
- once protein is used, it can be broken down to amino acids and build a new protein

Question 16

Diversity

Answer 16

Complex molecules can be generated

Question 17

4 major classes of biomolecules:

Answer 17

• Proteins
• Carbohydrates
• Nucleic acids
• Lipids

Question 18

Proteins

Answer 18

• 20 different amino acids
• Peptide bonded linked groups that form linear chains that fold into complex patterns
• side chains differentiate the structures (activity)

Question 19

Carbohydrates (polysaccharides)

Answer 19

• Monosaccharides link together to form linear or branched polymers
• Has lubricate joints and flexible
• serve many important biological roles including structural, energy storage, and cellular recognition

Question 20

Nucleic acids

Answer 20

• Linear polymers of nucleotide building blocks for DNA and RNA
• Aspects of storage and genetic information
• Cytosine, uracil, thymine, adenine, guanine

Question 21

Lipids

Answer 21

• aggregates of building blocks
• aren’t covalently linked to each other or locked into specific positions
• serve in energy storage , formation of membranes, and signalling

Question 22

Prokaryotes

Answer 22

• small, simple, single-celled organisms (bacteria)
• Rapid growth allow adaptation to environment

Question 23

Eukaryotes

Answer 23

• larger complex cells
• make up multicellular organisms
• membrane bound organelles to support specialized functions
• form particular biological functions

Question 24

In vitro (in glass)

Answer 24

• studies behaviour of molecules outside the context of the cell and organism (inside test tube)

Question 25

In vivo (in the living)

Answer 25

- studies occur within the complexity of the cell or organism (inside a living organism)

Question 26

First Law of thermodynamics

Answer 26

Total amount of energy in the universe remains constant, although forms of energy may change - energy cannot be made or destroyed

Question 27

Second Law of thermodynamics

Answer 27

The tendency in nature is towards a greater disorder (continually increasing) Ex. sand castle falling apart

Question 28

Enthalpy

Answer 28

Energy contained within the bonds of a molecule - depends on number of bonds and value of each

Question 29

Entropy

Answer 29

Degree of randomness - temperature dependent

Question 30

Endergonic

Answer 30

Non-spontaneous process, needs input of energy to proceed - Delta G > 0

Question 31

Exergonic

Answer 31

Spontaneous process (occurs without input of energy), releases free energy which can be used to do work, proceeds until equilibrium is reached - delta G < 0

Question 32

Delta G = 0

Answer 32

system is at equilibrium, no change in free energy in the system

Question 33

How can cells drive thermodynamically unfavourable reactions?

Answer 33

By taking a dis-favourable reaction and pairing it with a favourable reactions to make it favourable

Question 34

Catabolic

Answer 34

- Breaking stuff down - releases energy

Question 35

Anabolic

Answer 35

- Builds stuff up - Requires energy

Question 36

ATP

Answer 36

- common energy currency - serves as a link between catabolic and anabolic reactions

Question 37

Perpetuation of life requires that genetic information be:

Answer 37

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

Question 38

Linear sequence in DNA encodes three-dimensional protein structures:

Answer 38

- nucleotide sequence determines sequence of amino acids - amino acid sequence dictates its structure - structure of protein dictates its biological activity - results in an active hexokinase