Biochemistry and its foundations

Question 1

Biochemistry

Answer 1

the Chemistry of Living Matter

• a high degree of complexity and organization
• the extraction, transformation, and systematic use of energy to create and maintain structures and to do work
• the interactions of individual components being dynamic and coordinated
• the ability to sense and respond to changes in surroundings
• a capacity for fairly precise self-replication while allowing enough change for evolution

Question 2

Cellular foundations

Answer 2

• Living organisms are made of cells.
• The simplest living organisms are unicellular (single-celled).
• Larger organisms are multicellular (many-celled), with different functions for different cells.
• Cells have some common features but can contain unique components for different organisms.

Question 3

Eukaryote cells

Answer 3

–> more complexity

• Have a membrane-bound nucleus by definition:
– protection for DNA; site of DNA metabolism
– selective import and export via nuclear membrane pores
• Have membrane-enclosed organelles:
– mitochondria for energy in animals, plants, and fungi
– chloroplasts for energy in plant
– lysosomes for digestion of un-needed molecules
• Compartmental segregation of energy-yielding and energy-consuming reactions helps cells to maintain homeostasis and stay away from equilibrium.

Question 4

Cytoplasm

Answer 4

• Cytoplasm is a highly viscous solution where many reactions take place.

Question 5

Cytoskeleton

Answer 5

• The cytoskeleton consists of microtubules, actin filaments, and intermediate filaments.
– cellular shape and division 
– intracellular organization
– intracellular transport paths 
– cellular mobility

Question 6

The molecular hierarchy of structure

Answer 6

Supramolecular complexes (Chromatin, Plasma membrane, Cell wall)

• -> Macromolecules (DNA, Protein, Cellulose)
• ->Monomeric units (Nucleotides, AA, Sugars)

Question 7

Chemical foundations

Answer 7

Biochemistry aims to explain biological form and function in chemical terms

• Biomolecules Are Compounds of Carbon with a variety of Functional Groups
• The chemistry of living organisms is organized around carbon (more than half of the dry weight of cells)
–> multivalência do carbono –> grande flexibilidade

Question 8

Elements essential for life

Answer 8

• Other than carbon, elements H, O, N, P, and S are also common.
• Metal ions (e.g., K+, Na+, Ca++, Mg++, Zn++, Fe++) play important roles in metabolism.

Question 9

The ABC of biochemistry

Answer 9

1. Some of the AA
   (Alanine, Serine, Aspartate, Tyrosine, Histidine, Cysteine)
2. The components of DNA/RNA:
   - Nitrogenous bases (Uracil, Thymine, Cytosine, Adenine, Guanine)
   - Five-carbon sugars (Ribose, Deoxyribose)
   - Phosphate
3. Some components of lipids (Oleate, Palmitate, Glycerol, Choline)
4. The parent sugar- Glucose

Question 10

Biochemical unity

Answer 10

“What is true of E. coli is true of the elephant.”- Jacques Monod

Biochemical investigations show remarkable chemical similarities in many biochemical processes in many different organisms –> unicidade da vida –> ex possível usar organismos modelo

Question 11

Interactions Between Biomolecules Are Specific

Answer 11

• -> STEREOSPECIFIC
• ex enantiomers are distinguishable by taste receptors
• Macromolecules fold into 3D structures with unique binding pockets
• Only certain molecules fit in well and can bind (non-covalent interactions)
• Binding of chiral biomolecules is stereospecific

Bioquímica assenta na selectividade das interações intermoleculares

Question 12

Physical foundations

Answer 12

• Living organisms exist in a dynamic steady state and are never at equilibrium with their surroundings.
• Energy coupling allows living organisms to transform matter into energy.
• Biological catalysts reduce energy requirement for reactions while offering specificity.
• As the entropy of the universe increases, creating and maintaining order requires work and energy.

Question 13

Energy transductions

Answer 13

Organisms Perform Energy Transductions to Accomplish Work to Stay Alive

Release end-product molecules that are less well organized than the starting fuel, increasing the entropy of the universe
increased order (decreased randomness) in the system in the form of complex macromolecules decreases entropy in the system

Question 14

Energy coupling

Answer 14

• Chemical coupling of exergonic and endergonic reactions allows otherwise unfavorable reactions
• The“high-energy” molecule (ATP) reacts directly with the metabolite that needs “activation.”

Question 15

Pathways

Answer 15

Series of Related Enzymatically Catalyzed Reactions Forms a Pathway
-  Metabolic pathway
produces energy or valuable materials 
- Signal transduction pathway
transmits information

Pathways are controlled in order to regulate levels of metabolites (Inhibition, Activation…)

Question 16

Genetic and Evolutionary Foundations

Answer 16

• Life on Earth arose 3.5–3.8 billion years ago.
• The formation of self-replicating molecules was a key step.
• Could it have been DNA?
• Could it have been proteins?

Question 17

Abiotic production of biomolecules

Answer 17

Miller and Urey Experiments

• demonstrating abiotic formation of organic compounds under primitive atmospheric conditions.
• After subjection of the gaseous contents of the system to electrical sparks, products were collected by condensation.
• Biomolecules such as amino acids
were among the products

Question 18

RNA World?

Answer 18

• RNA can act both as the information carrier and biocatalyst.
• Some viruses use RNA as a primary means of genetic information

Question 19

Evolution

Answer 19

Key metabolic processes are common to many organisms.
The fact that different organisms have macromolecules of similar structure and common biochemical processes suggest that all organisms evolved from a common ancestor.

On the basis of biochemical characteristics, all organisms can be placed in one of three domains (Tree of Life, Carl Woese)

The result of eons of evolution is an enormous diversity of life forms, superficially very different but fundamentally related through their shared ancestry. This fundamental unity of living organisms is reflected at the molecular level in the similarity of gene sequences and protein structures