BIO130 Midterm Study Guide
Table of Content
Unit 1: Week 1
1.1 Introduction to Cells
1.2 Evolution of Eukaryotes
1.3 Information Flow
1.4 Introduction to Nucleic Acid
1.5 Molecular Interactions in the Cells
1.6 Model Organisms and Humans
Unit 2: Week 2
2.1 Introduction to Protein Structure
2.2 Amino Acid Structure
2.3 Peptide Bonds and Alpha Helix
2.4 Tertiary Structure
2.5 How Proteins Might Be Studied
Unit 3: Week 3
3.1 Genomes
3.2 Eukaryotic DNA Packaging and Chromosome
3.3 Nucleosome Structure
3.4 Chromatin Structure
3.5 Conservative vs. Semiconservative DNA Replication
3.6 Direction of DNA Replication
3.7 Origins of Replication
Unit 4: Week 4
4.1 Binding of Initiator Proteins
4.2 Unwinding DNA by Helicase
4.3 Binding of Single-Strand Binding Proteins
4.4 RNA Primers Made by Primase
4.5 DNA Polymerase
4.6 Sliding Clamp Holds Polymerase Onto DNA
4.7 Nick Sealing by DNA Ligase
4.8 Issues in DNA Replication and DNA Repair Mechanisms
4.9 Telomerase
,Unit 5: Week 5
5.1 Transcription 1 (Bacteria)
5.2 Transcription 2 (Eukaryotes)
Unit 6: Week 6
6.1 Genetic Code and Redundancy
6.2 Reading Frames and Mutations
6.3 tRNA and Quality Control
6.4 Ribosomal Structure
6.5 Protein Synthesis
6.6 Post-Translational Modification and Protein Degradation
6.7 Antibiotics
, Unit 1
1.1 Introduction to Cells
Cell Theory
• The cell is the basic organizational unit of life
• All organisms are comprised of 1 or more cells
• cells arise from pre-existing cells.
Theory of Cells
Prokaryotic:
• No nuclei
• Usually, single celled
• Bacteria (eubacteria) and Archaea
o modern genome sequencing tells us that these two groups are different.
o Bacteria are found in a variety of environments while Archaea are found in hostile
environments.
Eukaryotic
• They have a true membrane bound nuclei.
• Single Celled or multicellular
• Plants, fungi, animals, humans
o algae, yeast, protozoan, paramecium,
Prokaryotes
1. No membrane bound organelles
a) There are ribosomes
2. Smaller size than eukaryotes (few micrometers)
3. Less DNA than eukaryotes
a) DNA will congregate in an area called the nucleoid
• Some have a plasma membrane for filtering what gets in and out of the cell.
• Many have a protective cell wall.
• They are very successful from an evolutionary point of view.
1.2 Evolution of Eukaryotes
Fossil Evidence
• Fossil evidence suggests that prokaryotic cells appeared first.
• Prokaryotic and Eukaryotic cells share many complex traits so it doesn’t make sense
that they would evolve independently.
, Origins of Mitochondria
Early Anaerobic Eukaryotic Cell
• derived from an Archean ancestor
• Signs of a nucleus forming.
• fairly large cell with a flexible membrane
• some type of cytoskeleton so that it could move and possibly eat.
• oxygen levels are rising at this point.
Aerobic Bacterium
• oxygen levels are rising at this point
• if it was engulfed by the early anaerobic eukaryotic cell, a symbiotic relationship could be
set up.
• the aerobic bacterium could provide some energy to the bigger cell.
• The larger eukaryotic cell provided protection but did not digest the aerobic bacterium.
• Loses its bacterial plasma membrane
Early Aerobic Eukaryotic Cell
• Over evolutionary time.
• Mitochondria with a double membrane corresponds to the original double membrane of
the bacterium.
Origins of Chloroplast
Early Aerobic Eukaryotic Cell
• All eukaryotes have mitochondria but not all have chloroplasts. Thus they evolved later.
• photosynthetic bacterium is engulfed to set up a biosynthetic relationship.
• photosynthetic bacterium created food for the eukaryote.
Photosynthetic Eukaryotic Cell
• For the bacteria: Loss of membrane derived from the plasma membrane of the engulfing
early eukaryotic cell
• Together, they are a photosynthetic eukaryotic cell.
• ancestor to modern day plant cells.
Endosymbiont Hypothesis
• Mitochondria and chloroplasts still have remnants of their own genomes, and their
genetic systems resemble that of modern day prokaryotes.
• Mitochondria and Chloroplasts have their own circular genome.
• organelles proliferate in a similar way to bacteria. (Double in size, then divide)
• Mitochondria and chloroplasts have kept some of their own protein and DNA synthesis
components and these resemble prokaryotes too.
• sensitive to many of the same antibiotics
• Mitochondria is less like bacteria.
Table of Content
Unit 1: Week 1
1.1 Introduction to Cells
1.2 Evolution of Eukaryotes
1.3 Information Flow
1.4 Introduction to Nucleic Acid
1.5 Molecular Interactions in the Cells
1.6 Model Organisms and Humans
Unit 2: Week 2
2.1 Introduction to Protein Structure
2.2 Amino Acid Structure
2.3 Peptide Bonds and Alpha Helix
2.4 Tertiary Structure
2.5 How Proteins Might Be Studied
Unit 3: Week 3
3.1 Genomes
3.2 Eukaryotic DNA Packaging and Chromosome
3.3 Nucleosome Structure
3.4 Chromatin Structure
3.5 Conservative vs. Semiconservative DNA Replication
3.6 Direction of DNA Replication
3.7 Origins of Replication
Unit 4: Week 4
4.1 Binding of Initiator Proteins
4.2 Unwinding DNA by Helicase
4.3 Binding of Single-Strand Binding Proteins
4.4 RNA Primers Made by Primase
4.5 DNA Polymerase
4.6 Sliding Clamp Holds Polymerase Onto DNA
4.7 Nick Sealing by DNA Ligase
4.8 Issues in DNA Replication and DNA Repair Mechanisms
4.9 Telomerase
,Unit 5: Week 5
5.1 Transcription 1 (Bacteria)
5.2 Transcription 2 (Eukaryotes)
Unit 6: Week 6
6.1 Genetic Code and Redundancy
6.2 Reading Frames and Mutations
6.3 tRNA and Quality Control
6.4 Ribosomal Structure
6.5 Protein Synthesis
6.6 Post-Translational Modification and Protein Degradation
6.7 Antibiotics
, Unit 1
1.1 Introduction to Cells
Cell Theory
• The cell is the basic organizational unit of life
• All organisms are comprised of 1 or more cells
• cells arise from pre-existing cells.
Theory of Cells
Prokaryotic:
• No nuclei
• Usually, single celled
• Bacteria (eubacteria) and Archaea
o modern genome sequencing tells us that these two groups are different.
o Bacteria are found in a variety of environments while Archaea are found in hostile
environments.
Eukaryotic
• They have a true membrane bound nuclei.
• Single Celled or multicellular
• Plants, fungi, animals, humans
o algae, yeast, protozoan, paramecium,
Prokaryotes
1. No membrane bound organelles
a) There are ribosomes
2. Smaller size than eukaryotes (few micrometers)
3. Less DNA than eukaryotes
a) DNA will congregate in an area called the nucleoid
• Some have a plasma membrane for filtering what gets in and out of the cell.
• Many have a protective cell wall.
• They are very successful from an evolutionary point of view.
1.2 Evolution of Eukaryotes
Fossil Evidence
• Fossil evidence suggests that prokaryotic cells appeared first.
• Prokaryotic and Eukaryotic cells share many complex traits so it doesn’t make sense
that they would evolve independently.
, Origins of Mitochondria
Early Anaerobic Eukaryotic Cell
• derived from an Archean ancestor
• Signs of a nucleus forming.
• fairly large cell with a flexible membrane
• some type of cytoskeleton so that it could move and possibly eat.
• oxygen levels are rising at this point.
Aerobic Bacterium
• oxygen levels are rising at this point
• if it was engulfed by the early anaerobic eukaryotic cell, a symbiotic relationship could be
set up.
• the aerobic bacterium could provide some energy to the bigger cell.
• The larger eukaryotic cell provided protection but did not digest the aerobic bacterium.
• Loses its bacterial plasma membrane
Early Aerobic Eukaryotic Cell
• Over evolutionary time.
• Mitochondria with a double membrane corresponds to the original double membrane of
the bacterium.
Origins of Chloroplast
Early Aerobic Eukaryotic Cell
• All eukaryotes have mitochondria but not all have chloroplasts. Thus they evolved later.
• photosynthetic bacterium is engulfed to set up a biosynthetic relationship.
• photosynthetic bacterium created food for the eukaryote.
Photosynthetic Eukaryotic Cell
• For the bacteria: Loss of membrane derived from the plasma membrane of the engulfing
early eukaryotic cell
• Together, they are a photosynthetic eukaryotic cell.
• ancestor to modern day plant cells.
Endosymbiont Hypothesis
• Mitochondria and chloroplasts still have remnants of their own genomes, and their
genetic systems resemble that of modern day prokaryotes.
• Mitochondria and Chloroplasts have their own circular genome.
• organelles proliferate in a similar way to bacteria. (Double in size, then divide)
• Mitochondria and chloroplasts have kept some of their own protein and DNA synthesis
components and these resemble prokaryotes too.
• sensitive to many of the same antibiotics
• Mitochondria is less like bacteria.
