Intro To Biochem

Question 0

“The molecular logic of life

Answer 0

Biochem seeks to describe structures, mechanisms, and chemical processes shared by all organisms in molecular terms.

Question 1

Biochemistry

Answer 1

The study of matter that makes up living organisms.

• Bioinorganic: non-C based
• Bioorganic: Hydrocarbon based

Question 2

Properties that differentiate living and inanimate objects

Answer 2

Living organisms:

1: have chemical complexity
2: extract, transform and use energy
3: have capacity for self replication and self assembly
4: have mechanisms to sense and respond to changes in surroundings
5: have defined functions for components

Question 3

Property 1: Living organisms have chemical complexity: General

Answer 3

• Thousands of molecules make up cells intricate internal structures
• Thousands more allow cell to perform functions for life

Question 4

Property 1: Living organisms have chemical complexity: Biomolecules

Answer 4

Are all chemical compounds in living organisms

Question 5

Macromolecules

Answer 5

A molecule having a molecular weight in range of a few thousand to many millions

• molecular weight: dimensionless ratio of mass of a molecule to 1/12th of Carbon
• molecular mass: expressed in terms of Dalton’s or atomic mass unit (amu)

Question 6

Configuration

Answer 6

Fixed spatial arrangement of atoms.

Can only be changed by breaking covalent bonds

Question 7

Confirmation

Answer 7

Spatial arrangement of substituent groups.

Can be changed without breaking covalent bonds

Question 8

4 major classes of bio macromolecules

Answer 8

• Carbohydrates (glucose, glycogen)
• Lipids (fatty acids, cholesterol)
• Proteins (Enzymes)
• Nucleic Acids (DNA, RNA)

Question 9

Dehydration synthesis

Answer 9

Chemical removal of a water molecule.

Bio macromolecule polymers are constructed from smaller monomeric subunits using this process

Question 10

Hydrolysis

Answer 10

Chemical addition of water.

Process used to break down polymers into small monomeric subunits

Question 11

Property 2: living organisms extract, transform, and use energy from environment: General

Answer 11

• Obtained by chemical nutrients or sunlight
• Allows organisms to build and maintain their intricate structures.
• Allows orgs. to do mechanical, chemical, osmotic, and other work
• Inorganic doesn’t do work. Just moves to greater disorder until at equilibrium

Question 12

Property 2: living organisms extract, transform, and use energy from environment: Special Topics

Answer 12

• Bioenenergetics (study of energy transformations and exchanges)
• Organisms vs. Environment (orgs. are open systems and not at equilibrium. (Constantly extract and use energy).
• Available energy to do work is Gibbs Free Energy (G).

Question 13

Entropy

Answer 13

Tendency for systems to decay to highest state of disorder. Orgs depend on constant supply of energy to avoid this.

Question 14

Gibbs Free Energy (G)

Answer 14

Available energy to do work.

^G>0, rxn is endergonic/ non spontaneous, absorbs energy

^G<0, rxn is exergonic/spontaneous, releases energy

Question 15

Property 3: living orgs have capacity for self replication and self assembly: general

Answer 15

• Occurs at molecular (DNA replication), cellular (mitosis), and organismal (sex).
• almost always with near perfect fidelity (exceptions are basis of diseases)
• driving force of this is DNA

Question 16

Property 3: living orgs have capacity for self replication and self assembly: special topics

Answer 16

• Molecular level: flow of genetic info
• Cellular level: cell cycle and division
• Organismal level: all events that are part of orgs life and development are initiated, driven and controlled by genetic and biochemical factors

Question 17

DNA Replication

Answer 17

DNA polymerase uses DNA to make exact copies of itself using complementary strands

Question 18

Transcription

Answer 18

Process to synthesize RNA strands using one complementary strand of DNA via action of RNA polymerase

Question 19

Reverse transcription

Answer 19

Offshoot of central dogma.

Some viruses use their RNA to synthesize DNA via reverse transcriptase

Question 20

RNA replication

Answer 20

Offshoot of central dogma.

Viruses use their RNA to synthesize other RNA with complementary sequences via RNA dependent RNA polymerase.

Question 21

Translation

Answer 21

Using mRNA to synthesize protein molecule with specific amino acid sequences. Ribosome,tRNA molecules and other proteins drive this process

Question 22

Property 4: Orgs have mechanisms for sensing and responding to external alterations by changing internal chemistry: Special Topics

Answer 22

• Chemical signaling
• Gene expression
• Metabolism

Question 23

Chemical signaling

Answer 23

Primary way for cell to detect alterations. Chemical messages can be environmental, produced by other organisms or by other cells in same organism. Prominent use of signal transduction

Question 24

Process of cell signaling

Answer 24

Reception: ability to recognize signal Transduction: transmission of signal to internal molecules Response: change as a result of the signal. Depends on type of signal.

Question 25

Gene expression

Answer 25

Primary way a cell responds to change is by change in expression of key genes. Turning on/off and/or upregulating/downregulating genes

Question 26

Regulation: 1. transcriptional, 2. post transcriptional, 3. RNA transport, 4. translational, 5. post translational, 6. protein degradation

Answer 26

1. Controlling synthesis of RNA 2. Controlling maturation of RNA molecules 3. Controlling movement of RNA molecules from nucleus to cytosol 4. Controlling synthesis of proteins 5. Controlling activity of proteins through chemical modification 6. Controlling stability and half life of proteins.

Question 27

Metabolism

Answer 27

Driven by enzymes. Even for exergonic, non spontaneous rxn. Full complement of chemical reactions that occur in orgs to maintain life

Question 28

Metabolic pathways

Answer 28

Sequence of rxns where product serves as reactant for next. Ultimate product is different molecule than original. Eg. Glycolysis. Original: glucose. Final: pyruvate.

Question 29

Metabolic cycle

Answer 29

Final product is same as original molecule Eg. Citric acid cycle. Original and final: Oxaloacetate.

Question 30

Catabolism

Answer 30

Division of metabolism that is responsible for breakdown of larger molecules into smaller molecules. Process produces energy

Question 31

Anabolism

Answer 31

Division of metabolism that is responsible for formation of larger molecules from smaller ones. Process consumes energy

Question 32

ATP

Answer 32

Links anabolism and catabolism. - Primary molecule used for metabolic energy - not necessarily "high energy." Covalent bonds have the same energy as other similar bonds but range structure of ATP makes it easier

Question 33

Central pathways of metabolism

Answer 33

Ones that deal with carbohydrates (glucose) and lipids. They involve major pathways of energy production. Pathways are driven by eating and fasting cycle. (Flooding body with nutrients, vitamins, minerals, AA's, etc.)

Question 34

Glycolysis and TCA

Answer 34

Breakdown of glucose to produce pyruvate and ATP. Pyruvate is used in TCA to produce more ATP. Electron transport chain utilizes oxidative phosphorylation to recycle metabolites in glycolysis and TCA.

Question 35

Glycogenesis and lipogenesis.

Answer 35

Glyco- production of glycogen from glucose. Lipo- building and storing of complex lipids from simple building blocks.

Question 36

Glycogenolysis and lipolysis

Answer 36

Glyco- breakdown of glycogen into glucose. Lipo- breakdown of complex lipids into simpler lipids.

Question 37

Gluconeogenesis

Answer 37

Anabolic Production of glucose using simple amino acids broken down from proteins.

Question 38

Property 5: living orgs have defined functions for each components: general

Answer 38

Occurs at all levels and all systems work closely together. - Changes in one component leads to change in other. - the whole ensemble of chemical components display a character - Collection of molecules on living off carries out a program to give life