chapter 1 The foundations of biochemistry

Question 1

Biochemistry: What & Why:

Answer 1

Biochemistry describes in molecular terms the structures, mechanisms and chemical processes shared by all organisms. It provides organizing principles that underlie life in all of its diverse forms- we call this ‘the molecular logic of life’.

Biochemistry provides important insights that can be applied in medicine/industry/agriculture- the ultimate concern is with the wonder of life itself.

Question 2

The Features of Living Organisms:

Answer 2

1. High degree of chemical complexity and microscopic organization.
2. Systems for extracting, transforming and using energy from the environment.
3. Defined functions for each of their components and regulated interactions between them.
4. Mechanisms for sensing and responding to alterations in their surroundings.
5. Capacity for precise self- replication and self assembly.
6. Capacity to change over time by gradual evolution.

Question 3

Cellular Foundations

Answer 3

Cells- eukaryotic vs prokaryotic
Basic cell structures & molecular hierarchy

Question 4

three domains of life

Answer 4

bacteria, eukarya, archer

Question 5

size hierarchy

Answer 5

water, glucose, antibody, virus, bacteria, cancer cell, period, baseball

phospholipid, sugar(amino acid), nucleotide, ATP, NAD

Question 6

All cells are bounded by a

Answer 6

plasma membrance; have cytosol containing metabolites, coenzymes, inorganic ion, and enzymes; and have a set of genes contained with a nucleoid (bacteria and archaea) or nucleus (eukaryotes)

Question 7

bacteria vs. animal cel

Answer 7

both: cytoplasm, membrane, ribosome

nucleus: animal
Nuecleoid: bacteria

Nuclear membrane and membrane bound organelles: animal cell

Question 8

Bacteria cell structure

Answer 8

The simplest form of life, usually without organelles. But, bacteria do compartmentalize their cytoplasm.

fact: about 800 time longer than the cell

nucleiod, pili, cell envelope, flagella, ribosomes

Question 9

Eukaryotic Cells

Answer 9

Includes plants, animals, fungi, protozoans, yeasts and some algaes
Large cells (10-100 μm diameter) – 10x bigger than prokaryotes
Plasma membrane
Cytoplasm
Cytoskeleton
Internal membranes and compartments (organelles)
Organelles contain organized complexes of macromolecules that perform a certain biological function
Most enzymes are compartmentalized

Question 10

Nucleus

Answer 10

-Largest organelle in eukaryotic cells
-Bound by double membrane
-Storage of genetic info
-Site of most DNA synthesis and repair
-RNA synthesis
-Nuclear pores for transport of -RNA and proteins
-Nucleolus – transcription of rRNA; ribosome biogenesis; processing of RNA

Question 11

Endoplasmic Reticulum (ER)
Network of interconnected, closed,
-Extends from
-Two types
-Ribosomes (ribonucleoprotein particles) made up of

Answer 11

-Network of interconnected, closed, membrane-bounded vesicles
-Extends from nuclear envelope to plasma membrane
-Two types (morphologically and functionally):
smooth (SER, to make cellular products like hormones andlipids) and rough (RER—ribosomes attached on cytosolic side, for protein synthesis)
-Ribosomes (ribonucleoprotein particles) made up of RNA and proteins, not bounded by a membrane

Question 12

Mitochondria

Answer 12

-Have double membrane (inner and outer, outer membrane is smooth, while inner membrane forms elaborate folds called cristae)
-Place where most oxidative energy production occurs = “powerhouse” of cell
-Perform cellular respiration; form ATP
-Urea and heme synthesis
-Contain own genome; circular mtDNA

Question 13

structure to molecular hierarchy

Answer 13

supramolecular complexes->Macromolecules->monomeric units

chromatin->DNA->nucleotides

Plasma membrane->protein->amino acids

cell wall->cellulose->sugars

Question 14

bacterial cytoplasm is full of

Answer 14

molecules
cell envelope, flagellum, outer membrane, inner membrane, ribosome, DNA (nuclei)

Question 15

Molecular Weight or Mass

Answer 15

Biochemistry uses both Molecular Weight (Mr) or Molecular
Mass (m) in “Daltons”

Carbon has Mr = 12 or m = 12D

Very Small Proteins have a mass of 10,000D = 10kD
Very Large ones have mass of >1million D = 1,000kD
(Titin a muscle protein ~3 million D)
kD= 3zeros

Question 16

lipids monomer, polymer, supramolecular structure

Answer 16

monomer: fatty acid
Polymer: phospholipid
Supramolecular structure: membrane

Question 17

proteins monomer, polymer, supramolecular structure

Answer 17

monomer: amino acid
Polymer: protein subunit
Supramolecular structure: protein complex

Question 18

carbo monomer, polymer, supramolecular structure

Answer 18

monomer: glucose
Polymer: cellulose
Supramolecular structure: cell wall

Question 19

nucleic acid monomer, polymer, supramolecular structure

Answer 19

monomer: nucleotide
Polymer: DNA
Supramolecular structure: chromosome

Question 20

Biological Monomers
What to Look For = What’s Important:

Answer 20

What to Look For = What’s Important:
Functional Groups: amino, carboxyl, carbonyls (both), alcohol, methyl, phosphate, sulfhydryl, and others.
Covalent Bonds – single, double, triple.
Ionization state, or not.
Solubility
How Monomers are Polymerized
Weak Bonds = H-bonds, Ionic bonds, hydrophobic interactions, van der Waals forces.

Question 21

Key points for cellular foundations:
-Cells:
-Bacterial & archaeal cells contain
-Cytoskeletal proteins assemble into
-There are many supramolecular complexes held together by

Answer 21

Cells: a plasma membrane; a cytosol (metabolites, coenzymes; inorganic ions; nucleoid (bacteria & archaea) or nucleus (eukaryotes).

Bacterial & archaeal cells contain cytosol, a nucleoid, and plasmids, all in a cell envelop. Eukaryotic cells have nucleus and specific organelles; organelles can be separated andstudies in isolation.

Cytoskeletal proteins assemble into long filaments that give cells shape and rigidity, facilitate cellular organells move in the cell.

There are many supramolecular complexes held together by noncovalent interaction, as part of a hierarchy of strutures.

Question 22

Biochemistry is all about the

Most four abundant elements

Answer 22

Bulk elements for most biological polymers and major inorganic, physiological salts. We will add in the trace elements mainly as enzyme cofactors.

CHON

Question 23

It is not important to know individual bond strengths, but rather to know ranges.

Single bonds are rotatable, double bonds

Answer 23

It is not important to know individual bond strengths, but rather to know ranges. Single bonds are 200 to 450 kJ/mole, double bonds are 500-700 kJ/mole and triple bonds are ~900 kJ/mole (hardest to make or break).

Single bonds are rotatable, double bonds not so.

Question 24

Single bonds are rotatable, double bonds

Answer 24

Single bonds are rotatable, double bonds are not

Question 25

Polar Covalent Bonds

Answer 25

The absolute value of the difference in electronegativity of two bonded atoms gives a rough measure of the polarity of the bond.

-When this difference is small (less than 0.5), the bond is nonpolar.
-When this difference is large (greater than 0.5), the bond is considered polar.
-If the difference exceeds approximately 1.8, sharing of electrons is no longer possible and the bond becomes ionic.

Question 26

Bonds that hold things together

Answer 26

-Covalent
-Ionic interactions (weak or strong?)
-Hydrogen bonds

-Hydrophobic/hydrophilic interactions
-van der Walls interactions

Question 27

bond energy of Van Der Waals

Answer 27

(dipole-dipole, London)

0.1 to 10 kJ/mol

Question 28

bond energy of Hydrogen bonding

Answer 28

10 to 40 kJ/mol

Question 29

Ionic energy

Answer 29

100-1000kJ/mol

Question 30

Covalent energy

Answer 30

100 to 1000 kJ/mol

Question 31

Stereoisomer

Answer 31

molecules with the same chemical bonds but differing spatial arrangement

Question 32

cis/transisomerism(geometric isomerism)

Answer 32

s a form ofstereoisomerismdescribing therelative orientation offunctional groupswithin a molecule.

Question 33

Chirality-
enantiomers

Answer 33

In chemistry, chirality usually refers to molecules.

Two mirror images of a chiral molecule are calledenantiomersoroptical isomers. Pairs of enantiomers are often designated as “right-“ and “left-handed”.

Question 34

Naming conventions-
By configuration
By optical activity
By configuration, configuration standard Glyceraldehyde

Answer 34

By configuration:R- andS-
By optical activity: (+)- and (−)-
By configuration:D- andL- (configurational standard Glyceraldehyde)

Question 35

thesis established optical rotation of compounds having the same empirical chemistry other than crystal shape and optical properties.

Answer 35

Pasteur’s Doctoral

Question 36

Interactions between biomolecules are

Answer 36

specific

Question 37

Stereoisomers Have Different

Answer 37

Biological effects

This is why colas sweetened with aspartame have a limited shelf life.

Question 38

Living Organisms Exist in a

Answer 38

Dynamic Steady State, Never at Equilibrium with Their Surroundings

Question 39

Pathways of metabolism

Answer 39

dynamic steady-state

Question 40

Organisms Transform Energy and Matter from Their Surroundings
Two ways for energy:

Answer 40

Two ways for energy:
1) Absorb energy from sunlight (photosynthetic organisms (autotrophs)

2) Take up chemical fuel (e.g. glucose) and extract energy by oxidization (chemotrophs or heterotrophs)

Question 41

Organisms Transform Energy and Matter from Their Surroundings

Answer 41

The biochemical process for energy in living cells contains multiple-step reactions:

C6H12O6 +6O2-> 6CO2 +6H2O +energy

Question 42

ATP(Adenosine triphosphate ), ADP and AMP

ATP provides what

Answer 42

Adenosine triphosphate (ATP) provides energy. Here, each represents a phosphoryl group. The removal of the terminal phosphoryl group (shaded light red) of ATP, by breakage of a phosphoanhydride bond to generate adenosine diphosphate (ADP) and inorganic phosphate ion ( ), is highly exergonic, and this reaction is coupled to many endergonic reactions in the cell. ATP also provides energy for many cellular processes by undergoing cleavage that releases the two terminal phosphates as inorganic pyrophosphate ( ), often abbreviated PPi.

Question 43

Basic thermodynamics
G
H
S
change ofG=change of
change of G=G
Reactants=
change of G*=
free energy is related to the
Keq=
change of G>0=
change of G=0=
change of G<0
endothermic/exothermic does not equal to

Answer 43

G-free energy
H-enthalpy
S-Entropy

change ofG=change ofH-t(change of S)

change of G=Gproducts-Greactnats

Reactants=substrates

change of G*=standard free energy change

free energy is related to the equilibrium Constant (Keq)

Keq=products over reactants

change of G>0= endergonic
change of G=0=equilibrium
change of G<0exergonic

Note: endothermic/exothermic does not equal to endergonic/exergonic

Question 44

∆G +
∆G -
∆G 0

Answer 44

unfavorable
favorable-goes forward, to the right
equilibrium

Question 45

exothermic
endothermic

exergonic
endergonic

Answer 45

release of heat
absorption of heat

exergonic-release of energy
endergonic-use of energy

Question 46

∆S increase ∆H?
∆H increases ∆G?

Answer 46

∆H decreases, nonproprtional
∆G increases, directly proptional

Question 47

How to speed reactions up

Answer 47

Higher temperatures
Stability of macromolecules is limiting

Higher concentration of reactants
Costly as more valuable starting material is needed

Change the reaction by coupling to a fast one
Universally used by living organisms

Lower activation barrier by catalysis
Universally used by living organisms (e.g. Enzymes)

Question 48

Series of related enzymatically catalyzed reactions forms a pathway

Metabolic Pathway

Signal Transduction Pathway

Enzymes’ roles in Pathways

Answer 48

Metabolic Pathway
-produces energy or valuable materials

Signal Transduction Pathway
-transmits information

Enzymes’ roles in Pathways
-Enhance reaction rates (high selection; not being used up; no change for Keq)
-Decrease activation energy

Question 49

Pathways are controlled in order to 
regulate levels of metabolites

Answer 49

Example of a negative regulation:
Product of enzyme 5 inhibits enzyme 1

Question 50

phototrophs and chemotrophs

Answer 50

phototrophs-energy from light
–autorophs-carbon from CO2-example: cyanobacteria, vascular plants
–heterotrophs-carbon from organic compounds- example:purple bacteria, greed bacteria

Chemotrophs-energy from oxidation of chemical fuels (reduced fuel->oxidized fuel)
–lithographs- inorganic fuels-example: sulfur bacteria, hydrogen bacteria
–organotrophs-organic fuels-example: most bacteria all nonphotorophic eukaryotes

Question 51

The single DNA molecule of E. coli, leaking out of a disrupted cell, is

Answer 51

hundreds of times longer than the cell itself and contains all the encoded information necessary to specify the cell’s structure and functions. The DNA contains about 4.6 million nucleotides, weighs less then 10-10 g, and has undergone only relatively minor changes during the past several million years. Right: Chromosome

Question 52

The Structure of DNA Allows for its
AT bonds
CG bonds

Answer 52

Replication and Repair with Near-Perfect Fidelity

Complementarity of two strands of DNA. DNA is a linear polymer of covalently joined 4 deoxyribonucleotides: deoxyadenylate (A), deoxyguanylate (G), deoxycytidylate (C), and deoxythymidylate (T). Each nucleotide can associate very specifically but noncovalently with one other nucleotide in the complementary chain: A with T, and G with C. The two strands, held together by H bonds to form the DNA double helix. In DNA replication, the two strands (blue) separate and two new strands (pink) are synthesized.

AT-2 h bonds
C-G- 3 h bonds

Question 53

Central Dogma

Answer 53

DNA code ->Transcription -> Translation -> Protein

Question 54

Central Dogma extended:

Answer 54

: DNA -> RNA-> Unfolded Protein-> Folded Protein

Question 55

Changes in the Hereditary Instructions Allow

Answer 55

evolution

FIGURE 1–33 Gene duplication and mutation: one path to generate new enzymatic activities. In this example, the single hexokinase gene in a hypothetical organism might occasionally, by accident, be copied twice during DNA replication, such that the organism has two full copies of the gene, one of which is superfluous. Over many generations, as the DNA with two hexokinase genes is repeatedly duplicated, rare mistakes occur, leading to changes in the nucleotide sequence of the superfluous gene and thus of the protein that it encodes. In a few very rare cases, the altered protein produced from this mutant gene can bind a new substrate—galactose in our hypothetical case. The cell containing the mutant gene has acquired a new capability (metabolism of galactose), which may allow it to survive in an ecological niche that provides galactose but not glucose. If no gene duplication precedes mutation, the original function of the gene product is lost.

Question 56

Homolog, Ortholog, Paralog

Answer 56

Homology is the blanket term, both ortho- and paralogs are homologs.
Orthologs are homologous genes that are the result of aspeciation event. same function
Paralogs are homologous genes that are the result of aduplication event. different function

orthologs are genes that are related by vertical descent from a common ancestor and encode proteins with the same function in different species. By contrast, paralogs are homologous genes that have evolved by duplication and code for protein with similar, but not identical functions.”

Question 57

____can be edited nowadays

Answer 57

Genomic DNA with CRISPR

Question 58

Evolution of Eukaryotes through

Answer 58

Enosymbiosis

The earliest eukaryote, an anaerobe, acquired endosymbiotic purple bacteria, which carried with them their capacity for aerobic catabolism and became, over time, mitochondria. When photosynthetic cyanobacteria
subsequently became endosymbionts of some aerobic eukaryotes, these cells became the photosynthetic precursors of modern green algae and
plants.

Question 59

Key points for physical foundations:
-Living cells are
-ATP and its importance
-The tendency for a chemical reaction to proceed toward equilibrium can be expresses by
ΔG < 0, the reaction is
-The standard free-energy change, ΔG° is dependent on the
Enzymes are

Answer 59

-Living cells are open systems, exchanging matter and energy with their surroundings, maintain themselves in a dynamic steady state distant from equilibrium.
-ATP and its importance in energy transfer.
-The tendency for a chemical reaction to proceed toward equilibrium can be expresses by ΔG, and ΔG = ΔH - TΔS.
ΔG < 0, the reaction is exergonic and tends to go toward completion; ΔG > 0, it is endergonic and tends to in the reverse direction.
-The standard free-energy change, ΔG° is dependent on the equilibrium constant, Keq, ΔG° = -RTln Keq.
-Enzymes are biocatalysts, can increase the reaction rate by many orders of magnitudes, but the catalytic activity is enzymes in cells is regulated.

Question 60

Key points for chemical foundations:
-Carbon bonding versatility, a variety of functional groups, can form different types
-Molecular configuration can be changed only by
For C with 4 different substituents (a chiral C), the substituents groups can be arranged in
Only one stereoisomer
-Molecular conformation is the
-Interactions between biological molecules are

Answer 60

-Carbon bonding versatility, a variety of functional groups, can form different types of biomolecules.
-Molecular configuration can be changed only by breaking covalent bonds. For C with 4 different substituents (a chiral C), the substituents groups can be arranged in two different ways, generating stereoisomers with distinct properties. Only one stereoisomer is bologically active.
-Molecular conformation is the position of atoms in space that can be changed by rotation about single bond, without breaking covalent bonds.
-Interactions between biological molecules are almost invariable stereospecific.

Question 61

Key points for cellular foundations:

Answer 61

-Cells: a plasma membrane; a cytosol (metabolites, coenzymes; inorganic ions; nucleoid (bacteria & archaea) or nucleus (eukaryotes).
-Bacterial & archaeal cells contain cytosol, a nucleoid, and plasmids, all in a cell envelop. Eukaryotic cells have nucleus and specific organelles; organelles can be separated andstudies in isolation.
-Cytoskeletal proteins assemble into long filaments that give cells shape and rigidity, facilitate cellular organells move in the cell.
-There are many supramolecular complexes held together by noncovalent interaction, as part of a hierarchy of strutures.