BIOL 202 Week 8 Lab 8; Food Microbiology 2024/2025
Protein Responsibilities - 1. Catalyzing most intracellular chemical reactions (enzyme proteins)
2. Regulating gene expression (regulatory proteins)
3. Determining many features of the structures of cells, tissues, and organisms (structural proteins)
Polypeptide Chains - - Long chains of amino acids joined together by peptide bonds
- A protein is composed of one or more polypeptide chains
Amino Acid - Contains a carbon atom (the α carbon) to which is attached one carboxyl group (-COOH),
one amino group (-NH2), and a side chain commonly called an R group
R Group - Generally chains or rings of carbon atoms bearing various distinguishing atoms
Peptide Bond - The chemical bond that forms between the carboxyl group of one amino acid and the
amino group of another amino acid
Creates a peptide
Two Ends of Polypeptide Chain - 1. Amino Terminus: has a free amino group
2. Carboxyl Terminus: has a free carboxyl group
Folding of Polypeptides - Determined primarily by the sequence of amino acids
Protein Subunits - Protein molecules that consist of more than one polypeptide chain
May be identical or different
Transcription - The synthesis of an RNA molecule copied from the segment of DNA that constitutes the
gene
,The Three Stages of Transcription - 1. Initiation
- RNA polymerase recognizes and binds to the promoter, a short sequence typically upstream of the start
site of transcription.
- Unlike DNA polymerase, RNA polymerase does not require a primer.
2. Elongation
- RNA polymerase synthesizes RNA in the 5' to 3' direction, using one of the two strands of DNA as a
template.
3. Termination
- Completed RNA is released and RNA polymerase dissociates from DNA.
Similarities Between Transcription in Prokaryotes and Eukaryotes - 1. The precursors in the synthesis of
RNA are the four ribonucleoside 5′-triphosphates: adenosine triphosphate (ATP), guanosine triphosphate
(GTP), cytidine triphosphate (CTP), and uridine triphosphate (UTP). They differ from the DNA
precursors only in that the sugar is ribose rather than deoxyribose and in that the base uracil (U) replaces
thymine (T)
2. The enzyme used in transcription of RNA is RNA polymerase rather than DNA polymerase. The RNA
polymerase binds to a DNA sequence consisting of 20-200 nucleotides, called a promoter, and then
initiates transcription at a nucleotide in the promoter called the transcription start site.
3. In the synthesis of RNA, a sugar-phosphate bond is formed between the 3′-hydroxyl group of one
nucleotide and the 5′-triphosphate of the next nucleotide in line
4. The linear order of nucleotides in an RNA molecule is determined by the linear order of nucleotides in
the DNA template. Each nucleotide added to the growing end of the RNA chain is chosen for its ability to
base-pair with the DNA template strand.
5. Nucleotides are added only to the 3′-OH end of the growing chain; as a result, the 5′ end of a growing
RNA molecule bears a triphosphate group. Note that the 5′-to-3′ direction of RNA chain growth is the
same as that in DNA synthesis.
RNA Polymerase - An enzyme that makes RNA by copying the base sequence of a DNA strand.
,Promoter - A DNA sequence at which RNA polymerase binds and initiates transcription.
DNA Polymerase vs RNA Polymerase - - RNA polymerase is able to initiate chain growth without a
primer
- Each RNA molecule produced in transcription derives from a single strand of DNA, because in any
particular region of the DNA, only one strand serves as a template for RNA synthesis.
PROKARYOTIC TRANSCRIPTION - PROKARYOTIC TRANSCRIPTION
Requirements for Initiation - 1. The RNA polymerase (the enzyme responsible for RNA synthesis)
2. The promoter sequence (the binding site for RNA polymerase)
Bacterial RNA Polymerases - Large, multisubunit complexes that exist in two forms:
1. the holoenzyme
2. the core enzyme
Holoenzyme vs Core Enzyme - - Presence in holoenzyme of the σ subunit
- This subunit is required for promoter recognition
- Once that has occurred and transcription has been initiated, the σ subunit dissociates from the complex,
and the core enzyme then becomes responsible for elongation
Bacterial Promoters - Typically lie immediately upstream of the starting point for transcription
Method to Find Sequences Required for RNA Polymerase Binding - Alignment of upstream regions of
many different genes and the identification of consensus sequences
Consensus Sequences - - Any generalized base sequence derived from closely related sequences found in
many locations in a genome or in many organisms; each position in the consensus sequence consists of
the base found in the majority of sequences at that position.
- Each nucleotide in the consensus sequence is the nucleotide most often observed at that position in
actual sequences
, TATA box - - A promoter DNA sequence crucial in forming the transcription initiation complex.
- The base sequence 5′-TATA-3′ in the DNA of a promoter.
Elongation - - The DNA template must be locally unwound so that one strand can serve as a template for
RNA synthesis
- The core enzyme of RNA polymerase carries out this reaction.
Core Enzyme Role in Unwinding DNA - The enzyme has to do three things:
1. Unwind the DNA helix
2. Remain associated with both strands of the unwound molecule
3. Catalyze the formation of phosphodiester bonds in the growing RNA transcript.
Termination - When the RNA polymerase complex reaches a chain-termination sequence, both the newly
synthesized RNA molecule and the polymerase complex are released
Intrinsic Termination - - The transcribed DNA strand that is able to fold back upon itself to form a hairpin
loop in the growing transcript
- The hairpin loop alone is not enough for termination of transcription; the run of U's at the end of the
hairpin is also necessary
- The hairpin loop terminates transcription by invading the main channel of the RNA polymerase complex
near the active site, which disrupts the RNA/DNA hybrid and prevents further elongation of the chain
EUKARYOTIC TRANSCRIPTION - EUKARYOTIC TRANSCRIPTION
Important Features of Gene Structure in Eukaryotes - 1. DNA is organized into chromatin, potentially
complicating the process of promoter recognition
2. RNAs are transcribed in the nucleus, but translation occurs in the cytoplasm. Thus, the processes of
transcription and translation are uncoupled
3. The primary transcript of a gene undergoes extensive processing to give rise to a mature, functional
mRNA
Protein Responsibilities - 1. Catalyzing most intracellular chemical reactions (enzyme proteins)
2. Regulating gene expression (regulatory proteins)
3. Determining many features of the structures of cells, tissues, and organisms (structural proteins)
Polypeptide Chains - - Long chains of amino acids joined together by peptide bonds
- A protein is composed of one or more polypeptide chains
Amino Acid - Contains a carbon atom (the α carbon) to which is attached one carboxyl group (-COOH),
one amino group (-NH2), and a side chain commonly called an R group
R Group - Generally chains or rings of carbon atoms bearing various distinguishing atoms
Peptide Bond - The chemical bond that forms between the carboxyl group of one amino acid and the
amino group of another amino acid
Creates a peptide
Two Ends of Polypeptide Chain - 1. Amino Terminus: has a free amino group
2. Carboxyl Terminus: has a free carboxyl group
Folding of Polypeptides - Determined primarily by the sequence of amino acids
Protein Subunits - Protein molecules that consist of more than one polypeptide chain
May be identical or different
Transcription - The synthesis of an RNA molecule copied from the segment of DNA that constitutes the
gene
,The Three Stages of Transcription - 1. Initiation
- RNA polymerase recognizes and binds to the promoter, a short sequence typically upstream of the start
site of transcription.
- Unlike DNA polymerase, RNA polymerase does not require a primer.
2. Elongation
- RNA polymerase synthesizes RNA in the 5' to 3' direction, using one of the two strands of DNA as a
template.
3. Termination
- Completed RNA is released and RNA polymerase dissociates from DNA.
Similarities Between Transcription in Prokaryotes and Eukaryotes - 1. The precursors in the synthesis of
RNA are the four ribonucleoside 5′-triphosphates: adenosine triphosphate (ATP), guanosine triphosphate
(GTP), cytidine triphosphate (CTP), and uridine triphosphate (UTP). They differ from the DNA
precursors only in that the sugar is ribose rather than deoxyribose and in that the base uracil (U) replaces
thymine (T)
2. The enzyme used in transcription of RNA is RNA polymerase rather than DNA polymerase. The RNA
polymerase binds to a DNA sequence consisting of 20-200 nucleotides, called a promoter, and then
initiates transcription at a nucleotide in the promoter called the transcription start site.
3. In the synthesis of RNA, a sugar-phosphate bond is formed between the 3′-hydroxyl group of one
nucleotide and the 5′-triphosphate of the next nucleotide in line
4. The linear order of nucleotides in an RNA molecule is determined by the linear order of nucleotides in
the DNA template. Each nucleotide added to the growing end of the RNA chain is chosen for its ability to
base-pair with the DNA template strand.
5. Nucleotides are added only to the 3′-OH end of the growing chain; as a result, the 5′ end of a growing
RNA molecule bears a triphosphate group. Note that the 5′-to-3′ direction of RNA chain growth is the
same as that in DNA synthesis.
RNA Polymerase - An enzyme that makes RNA by copying the base sequence of a DNA strand.
,Promoter - A DNA sequence at which RNA polymerase binds and initiates transcription.
DNA Polymerase vs RNA Polymerase - - RNA polymerase is able to initiate chain growth without a
primer
- Each RNA molecule produced in transcription derives from a single strand of DNA, because in any
particular region of the DNA, only one strand serves as a template for RNA synthesis.
PROKARYOTIC TRANSCRIPTION - PROKARYOTIC TRANSCRIPTION
Requirements for Initiation - 1. The RNA polymerase (the enzyme responsible for RNA synthesis)
2. The promoter sequence (the binding site for RNA polymerase)
Bacterial RNA Polymerases - Large, multisubunit complexes that exist in two forms:
1. the holoenzyme
2. the core enzyme
Holoenzyme vs Core Enzyme - - Presence in holoenzyme of the σ subunit
- This subunit is required for promoter recognition
- Once that has occurred and transcription has been initiated, the σ subunit dissociates from the complex,
and the core enzyme then becomes responsible for elongation
Bacterial Promoters - Typically lie immediately upstream of the starting point for transcription
Method to Find Sequences Required for RNA Polymerase Binding - Alignment of upstream regions of
many different genes and the identification of consensus sequences
Consensus Sequences - - Any generalized base sequence derived from closely related sequences found in
many locations in a genome or in many organisms; each position in the consensus sequence consists of
the base found in the majority of sequences at that position.
- Each nucleotide in the consensus sequence is the nucleotide most often observed at that position in
actual sequences
, TATA box - - A promoter DNA sequence crucial in forming the transcription initiation complex.
- The base sequence 5′-TATA-3′ in the DNA of a promoter.
Elongation - - The DNA template must be locally unwound so that one strand can serve as a template for
RNA synthesis
- The core enzyme of RNA polymerase carries out this reaction.
Core Enzyme Role in Unwinding DNA - The enzyme has to do three things:
1. Unwind the DNA helix
2. Remain associated with both strands of the unwound molecule
3. Catalyze the formation of phosphodiester bonds in the growing RNA transcript.
Termination - When the RNA polymerase complex reaches a chain-termination sequence, both the newly
synthesized RNA molecule and the polymerase complex are released
Intrinsic Termination - - The transcribed DNA strand that is able to fold back upon itself to form a hairpin
loop in the growing transcript
- The hairpin loop alone is not enough for termination of transcription; the run of U's at the end of the
hairpin is also necessary
- The hairpin loop terminates transcription by invading the main channel of the RNA polymerase complex
near the active site, which disrupts the RNA/DNA hybrid and prevents further elongation of the chain
EUKARYOTIC TRANSCRIPTION - EUKARYOTIC TRANSCRIPTION
Important Features of Gene Structure in Eukaryotes - 1. DNA is organized into chromatin, potentially
complicating the process of promoter recognition
2. RNAs are transcribed in the nucleus, but translation occurs in the cytoplasm. Thus, the processes of
transcription and translation are uncoupled
3. The primary transcript of a gene undergoes extensive processing to give rise to a mature, functional
mRNA
