Biochemistry A Short Course: Chapter 1-4 & 6-7
Metabolisme en Biochemie
deeltentamen 1
Chapter 1
Unity of biochemistry: all organisms have much in common biochemically
- Ubiquity of water: makes life on earth possible
- Fuel molecules are made up of carbon, hydrogen and oxygen
- Combustion: Fuels react with oxygen to produce carbon dioxide and water
Silicon vs carbon:
- Both four covalent bonds
- Carbon-carbon stronger than silicon-silicon
o Carbon-carbon more stable
o Carbon-carbon release more energy when they undergo combustion
- Carbon is soluble in water: stays in biochemical circulation
- Silicon is insoluble after reaction with oxygen: out of biochemical circulation
Four Major classes of biomolecules
- Proteins
- Nucleic acids
- Lipids
- Carbohydrates
Proteins
- Made from 20 amino acids --> long unbranched polymers
- Are signal molecules and receptors for signal molecules
- Functions:
o Structure
o Mobility
o Defense
, o Catalyst: every process depends on enzymes
Nucleic acids
- Made from 4 nucleotides
o 5 carbon sugar
o Deoxyribose/ribose
o Heterocyclic ring
o 1 or more phosphoryl group(s)
- Information keepers
- Deoxyribonucleic acid (DNA)
- Ribonucleic acid (RNA)
o Additional hydroxyl on sugar group
Lipids
- Hydrophilic tail
- Hydrophobic head
o Has one or more hydrocarbon chains
- Can form intracellular compartments
- Signal molecule
Carbohydrates
- Glucose --> most common form
o Plants: starch
o Humans: glycogen
- Chains highly branched
o Help cells recognize eachother
Central dogma:
- Replication: DNA polymerase1
- Transcription: RNA polymerase
o Selective expression: defines function of a cell or tissue
- Translation: Ribosomes
*Genes are useless in and of themselves
A cell needs:
- A barrier that seperates the cell from its environment (plasma membrane)
- An inside that is chemically different from the environment (cytoplasm)
Eukaryote cells: have membrane-enclosed compartments
Prokaryote cells: don’t have membrane-enclosed compartments
- We need prokaryote organisms (microbiome)
The plasma membrane has selective permeability
The plant cell wall is made of cellulose: long linear polymer of glucose molecules
Cytoplasm:
- Initial stage of glucose metabolism
- Fatty acid synthesis
- Protein synthesis
- Organized by the cytoskelet
o Actin filaments
1
Exists of mutiple proteins
, o Intermediate filaments
o Microtubules
Nucleus
- Punctuated with nuclear pores
Mitochondrion
- Two membranes
- Intermembrane space
- Fuel molecules undergo combustion to create ATP
Chloroplast
- Two membranes
- Photosynthesis: conversion of sunlight into chemical energy
*Cretaceous mass extinction: thought that photosynthesis ceased
Endoplasmic reticulum
- Membranous sacs
Smooth ER: Processing exogenous chemicals (drugs)
Rough ER: Synthesis of proteins for inside and outside the cell
In the lumun of the ER folded in 3D structure by chaperones and are often modified --> go to parts of
the RER without ribosomes --> into transport vesicles --> Golgi
Golgi complex
- Further processing (different set of modifications)
- Sorting of proteins in different fates --> secretory granules bud off after signal is given
Exocytosis --> outside the cell
Endocytosis --> endosome inside
- Often biochemicals such as iron, vitamins, cholesterol
Phagocytosis --> large amounts of material
- Bacteria for instance
By a macrophage cell for example
Lysosomes
- Contain digestive enzymes
- Form the same way as secretory granules but fuse with endosomes
- Release small molecules
- Degrade extracellular material and damaged intracellular organelles
Plant vacuoles
- Occupies 80% of cell’s volume
- Stores water, ions and nutrients
Diseases:
- Hypercholesterolemia
o Inefficient endocytosis of cholesterol
- Tay Sachs
o Improper lysosome function
Chapter 2 Water, Weak Bonds and the Generation of Order Out of
Chaos
Covalent bonds
- In molecules
Metabolisme en Biochemie
deeltentamen 1
Chapter 1
Unity of biochemistry: all organisms have much in common biochemically
- Ubiquity of water: makes life on earth possible
- Fuel molecules are made up of carbon, hydrogen and oxygen
- Combustion: Fuels react with oxygen to produce carbon dioxide and water
Silicon vs carbon:
- Both four covalent bonds
- Carbon-carbon stronger than silicon-silicon
o Carbon-carbon more stable
o Carbon-carbon release more energy when they undergo combustion
- Carbon is soluble in water: stays in biochemical circulation
- Silicon is insoluble after reaction with oxygen: out of biochemical circulation
Four Major classes of biomolecules
- Proteins
- Nucleic acids
- Lipids
- Carbohydrates
Proteins
- Made from 20 amino acids --> long unbranched polymers
- Are signal molecules and receptors for signal molecules
- Functions:
o Structure
o Mobility
o Defense
, o Catalyst: every process depends on enzymes
Nucleic acids
- Made from 4 nucleotides
o 5 carbon sugar
o Deoxyribose/ribose
o Heterocyclic ring
o 1 or more phosphoryl group(s)
- Information keepers
- Deoxyribonucleic acid (DNA)
- Ribonucleic acid (RNA)
o Additional hydroxyl on sugar group
Lipids
- Hydrophilic tail
- Hydrophobic head
o Has one or more hydrocarbon chains
- Can form intracellular compartments
- Signal molecule
Carbohydrates
- Glucose --> most common form
o Plants: starch
o Humans: glycogen
- Chains highly branched
o Help cells recognize eachother
Central dogma:
- Replication: DNA polymerase1
- Transcription: RNA polymerase
o Selective expression: defines function of a cell or tissue
- Translation: Ribosomes
*Genes are useless in and of themselves
A cell needs:
- A barrier that seperates the cell from its environment (plasma membrane)
- An inside that is chemically different from the environment (cytoplasm)
Eukaryote cells: have membrane-enclosed compartments
Prokaryote cells: don’t have membrane-enclosed compartments
- We need prokaryote organisms (microbiome)
The plasma membrane has selective permeability
The plant cell wall is made of cellulose: long linear polymer of glucose molecules
Cytoplasm:
- Initial stage of glucose metabolism
- Fatty acid synthesis
- Protein synthesis
- Organized by the cytoskelet
o Actin filaments
1
Exists of mutiple proteins
, o Intermediate filaments
o Microtubules
Nucleus
- Punctuated with nuclear pores
Mitochondrion
- Two membranes
- Intermembrane space
- Fuel molecules undergo combustion to create ATP
Chloroplast
- Two membranes
- Photosynthesis: conversion of sunlight into chemical energy
*Cretaceous mass extinction: thought that photosynthesis ceased
Endoplasmic reticulum
- Membranous sacs
Smooth ER: Processing exogenous chemicals (drugs)
Rough ER: Synthesis of proteins for inside and outside the cell
In the lumun of the ER folded in 3D structure by chaperones and are often modified --> go to parts of
the RER without ribosomes --> into transport vesicles --> Golgi
Golgi complex
- Further processing (different set of modifications)
- Sorting of proteins in different fates --> secretory granules bud off after signal is given
Exocytosis --> outside the cell
Endocytosis --> endosome inside
- Often biochemicals such as iron, vitamins, cholesterol
Phagocytosis --> large amounts of material
- Bacteria for instance
By a macrophage cell for example
Lysosomes
- Contain digestive enzymes
- Form the same way as secretory granules but fuse with endosomes
- Release small molecules
- Degrade extracellular material and damaged intracellular organelles
Plant vacuoles
- Occupies 80% of cell’s volume
- Stores water, ions and nutrients
Diseases:
- Hypercholesterolemia
o Inefficient endocytosis of cholesterol
- Tay Sachs
o Improper lysosome function
Chapter 2 Water, Weak Bonds and the Generation of Order Out of
Chaos
Covalent bonds
- In molecules
