Biology 107, Winter 2024
Topic 5: Central Dogma, Part B
Lecture Notes
This lecture outline is designed to help you take notes as you progress through the
lecture materials for Topic 5B.
Remember: The information from these Lecture Notes will help you answer some of the
Topic 5B Application Activity questions, and the Review Quiz in Mêskanâs!
Learning Objectives:
This section of the course will introduce you to the processes of transcription and
translation, as well as some basic differences between prokaryotes and eukaryotes. At
the end of this lecture topic, you should be able to …
Explain what is meant by the term semi-conservative replication of DNA.
Describe the roles that DNA polymerase, DNA helicase, and the origin of
replication play in DNA replication.
Describe from where the energy to power phosphodiester bond formation
comes.
Predict the complementary sequence of DNA, given the sequence of one
strand.
Describe the Central Dogma, and explain the different roles played by
transcription and translation in this process.
Describe the difference between transcription and DNA replication.
Define the term gene and use it correctly to describe the organization of
information within the DNA.
Describe the process of transcription, including the specific function of the
RNA polymerase enzyme.
Identify from where the energy comes to power transcription.
Describe the function of the promoter and terminator, and explain how they
determine the boundaries of a gene.
Transcribe a DNA sequence into an mRNA sequence.
Describe the differences between pre-mRNA and mature mRNA in
eukaryotes.
Identify and describe the three modifications made to pre-mRNA in
eukaryotes, and outline the functions of each modification.
Distinguish between an intron and an exon.
Explain why the reading frame is important for the translation of proteins.
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Use the genetic code table to predict a peptide sequence based on an mRNA
sequence.
Identify the appropriate codon(s) for specific amino acids, and for starting and
ending translation.
Identify all of the molecules needed for translation.
Describe the structure of the tRNA and ribosomes, and explain the role that
each of these play in translation.
Describe the process of translation that attaches amino acids together in the
correct order to produce a polypeptide
Describe the differences in gene expression between prokaryotes and
eukaryotes, and explain why these differences exist.
Background Reading for Topic 5B Lecture Notes
The information covered in these lectures is based on your textbook:
Sections 11.3b and 11.3c, and Sections 12.1, 12.2, 12.3 (parts a and b only), and
12.4 (parts a through f only). For additional supplementary reading on these topics,
you can consult the following website:
https://www.visionlearning.com/en/library/Biology/2/DNA-III/180
https://openstax.org/books/biology-2e/pages/15-1-the-genetic-code
https://openstax.org/books/biology-2e/pages/15-2-prokaryotic-transcription
https://openstax.org/books/biology-2e/pages/15-4-rna-processing-in-eukaryotes
https://openstax.org/books/biology-2e/pages/15-5-ribosomes-and-protein-synthesis
Note that there is information in this reading that we do not cover in this course. You
are only responsible for the information identified in the reading questions and in the
Topic 5B Lecture and Lecture Notes.
Lecture Notes:
Note: Be sure to complete Topic 5B Reading Activity, Part 1 (available on Mêskanâs).
DNA Replication
“It has not escaped our notice that the specific pairing we have postulated
immediately suggests a possible copying mechanism for the genetic material.”
Watson and Crick (1953)
DNA
______________________
dependent synthesis of new DNA
divides
o Must occur every time a cell ________________
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two identient copies
o Must produce __________________________ of the DNA
Basic Process:
Hbond
1. _________________ between bases of the parent DNA molecule break
strand of ____________________
template
2. Each parent molecule is used as a ______________ to synthesize a new
DNA
Complementary
SemiConservative
DNA replication is ____________________
Each daughter helix composed of:
o One strand of __________________
Parental DNA
o One strand of _______________________
newlysynthesized DNA
Overview of Replication:
origin ofreplication
o Begins at: ___________________
o Key enzymes:
DNAponsmr.se
Helicase
DNA
o Template: _________________
o Monomers: _________________
INTPS
Deoxyribonucleotide triphosphates
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Fig. 11.7 (left) Fig. 11.10 (right)
Where does replication start? Origin of replication (ori)
o Specific DNA
________________
Sequence where replication begins
o DNA helix separates (________________________)
bondsbreak to produce two
___________________________
Sinstestrandtemplate
havemultiple ori
Eukaryotes
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Prokaryotes Eukaryotes
Dehydration
HH Reaction H
0
H H
DNA Polymerase:
o Catalyzes synthesis of new strand of DNA
newnucleotide
o Adds ____________________ at the 3’-end of the growing DNA molecule
synthesis 5 73
template
o Uses complementary base pairing to _________________ to select new
nucleotide
Phosphodiester
o Enzyme catalyzes formation of new __________________________
bond
between 3’-OH and 5’-phosphate
Dehydrationreaction
o Energy for synthesis comes from hydrolysis oftriphosphate
___________________
group
group of incoming nucleotide
DNA helicase:
DNAdouble helix
o Unwinds ____________________
o Exposes more _______________________ template
single strand
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What is the Central Dogma?
How do we get from DNA to protein?
o DNA: Polymer of ____________________
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nucleotides
o Protein: Polymer of _____________________
20 AA
Answer: The Central Dogma
Flow in the cell
o A description of _______________________
information
o How information in DNA is decoded
transcription translation
intermediate
Step 1: Transcription
RNA
o Synthesis of ____________ using DNA as a template
o Nucleic acid → nucleic acid
Step 2: Translation
o Synthesis of a ______________ using the information encoded in mRNA
Polypeptid s
o Produces a _________________ of amino acids
Pecificseavence
o Nucleic acid → polypeptide
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DNA Replication vs. Transcription: Transcription occurs ___________________
onegene at atime
RNA
protein
DNA Replication Transcription
Gene: A unit of hereditary information consisting of a specific sequence of
nucleotides in DNA
o Each gene has a ________________
uniarve
Sequence
RNA
o All genes can be transcribed to produce _______________
Proteins
o Many (but not all!) genes encode ______________________
Gene Expression: The process by which DNA directs the synthesis of proteins
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Transcription
What is transcription? DNA-dependent synthesis of RNA
o Process is similar to DNA replication
o Two strands of parental DNA separate by breaking H-bonds
o Single-stranded DNA acts as a template to create complementary strand
of RNA
o Uses complementary base-pairing rules:
In RNA: G C A U
In DNA: C G T A
DNA Replication:
Transcription:
U not T
U not T
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Transcription Overview:
RNA Polymerase
o Key enzyme: ______________________
o Template: __________________
Ifrs
o Monomers: _____________ (Ribonucleotide triphosphates)
o Begins at: __________________
Protiminator
o Ends at: ___________________
Main enzyme is RNA polymerase (RNAP):
o Incorporates new RNA nucleotides onto the 3’ end of a growing RNA
molecule
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o Forms _____________________________
Phosphodester
bonds
o Requires a ____________________ DNA template
singlestrant
o Follows base-pairing rules
Energy comes from hydrolysis of the triphosphate group of the incoming
nucleotide
Promoter:
o Specific sequence of DNA where RNAP binds and begins transcription
o
Tell RNAP wheretostart
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Terminator:
o Specific sequence of DNA where RNA polymerase falls off template and
ends transcription
o
RNATranscriptreleased
promoter
A gene can be defined as the sequence beginning at a _____________ and
ending at a terminator
___________________
single RNA
o Transcribed by RNA polymerase to produce a _____________________
molecule
Only one strand of DNA is the template
non codingstrand
o Template strand
ReadbyRNAPolymerase
RNA synthesized by complementary base pairing
o Non-template strand (coding strand)
not read6s RNAPomerase
Has _______________
SameSearunce as RNA produced
DNA Coding strand 5’ CTG CCA TTG 3’
DNA Template strand 3’ GAC GGT AAC 5’
mRNA 5’ CUG CCA UUG 3’
Transcription Summary:
1. RNA pol binds promoter
2. Uses template strand of DNA to synthesize RNA
3. Dissociates from (falls off) from template at terminator
All RNAs are produced by transcription:
o mRNA: ________________
messenger RNA
Carries information for translation, translated into proteins
Ribosome
o rRNA: _________________ RNA
Structural and enzymatic component of the ribosome
transfer
o tRNA: _________________ RNA
Guides amino acids to the ribosome during translation
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mRNA Processing in Eukaryotes
Eukaryotes modify their RNA prior to translation
o Not done in prokaryotes
ents interior
o Changes made to ____________ and ______________ sequences
pre-mRNA: The initial RNA transcript before modifications have been made
Mature mRNA: An RNA transcript that has been modified
Alterations to mRNA ends
o 5’ Cap:
Modified guanine (G) nucleotide added to 5’ end
Protects mRNAfromdegradation
Airsinattering ribosome
o 3’ Poly-A tail:
50-250 adenine (A) nucleotides added to 3’ end
mRNAfromdegradation
Protects
Aitshedportfromnucleustocytoplasm
mRNA splicing
o Introns: Non-coding or intervening sequences
RuntencoreProtom
o Exons: Coding or expressed sequences
Encote Protein
introns
o Spliceosome enzyme cuts out ____________ from pre-mRNA, and joins
together __________________
exons
mature
o Produces _____________ mRNA with continuous protein coding
sequence
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Note: Be sure to complete Topic 5B Reading Activity, Part 2 (available on Mêskanâs).
The Genetic Code
Remember: Translation is the synthesis of polypeptide using an mRNA sequence
as a template
How can 4 nucleotides specify 20 amino acids?
UAA
o 1 letter code could encode _________
o 2 letter code could encode _________
o 3 letter code could encode _________
Codon: A three-nucleotide sequence of RNA that specifies a particular
______________________
AminoAcid
o Read 5’ to 3’
o one cotont 3rucleotity one AA
Reading Frame:
o The way a cell’s translation machinery groups the mRNA nucleotides into
codons
overlap
o Codons do not _______________
butonlyonemakessense CencotesProtem
o 3 possible frames per sequence ________________________________
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61 of 64 codons encode amino acids
o Each codon = __________________
only one AA
each AA
o More than 1 codon for ______________________
3rdPosition
o Synonym codons differ in _________________________
AUG = Start codon
starttranslation
o Tells ribosome where to ______________________
o Defines reading frame ___________________ nexttime yousee G
msn.es
o Encodes a methionine (met) amino acid
midterm o All proteins start with _________________
2 Three codons are stop codons
AA's
o Do not encode ____________________
o Tells ribosome where to steptranslation
_________________________
Structure of a mature mRNA:
o 5’ untranslated region (UTR):
Before start codon → not translated
Involved in ribosome binding
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o Open reading frame (ORF):
Encodes the protein
No stop codons present
o 3’ untranslated region (UTR):
After stop codon → not translated
start codon
5’- G 5’ UTR ORF 3’ UTR AAAAAA -3’
stop codon
The genetic code is universal
Sam
o ____________________ in all organisms
o Genes can bemonethetween
_________________________
organisms
Translation
Translation Overview:
o RNA-dependent synthesis of a polypeptide
Ribosome Rrna
o Enzyme: _______________
o Key component: __________________
ERNA
o Template: ____________________
MRNA
AA's
o Monomers: ______________________
Start Coton
o Begins at: ____________________
o Ends at: ______________________
stepahfept.in
bonts
Amino acids are linked by __________________
o Created by __________________
dehydration reaction with release of water
o Attaches ________ group to __________
carboxyl group
amine
Ingredients for Translation:
information (order of amino acids)
o mRNA carries _________________
AA's
o tRNA delivers the ____________________
o Ribosome (contains rRNA) uses information in mRNA to attach amino
acids in the correct order
GTP
o Energy from __________ (like ATP, but with a G base instead of an A)
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N C
The tRNA
Delivers amino acid to the ribosome during translation
Structure:
o Small RNA molecule
internetlesserairing
o 3D shape due to _________________________
o 2 key parts
1. Anticodon:
o 3 nucleotide sequence
Cohen
o Base pairs to complementary ______________ in mRNA
2. Amino acid (AA) attachment site:
AA
o Where ________________ is covalently attached to the tRNA
o Each tRNA carries only one AA
o Which AA depends on anticodon
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The Ribosome
enzyme
_______________ that catalyzes peptide bond formation between amino acids
Contain two subunits (large and small)
Both are complexes of:
o rRNA
o RibosomalProteins
Contains several binding sites:
o One mRNA binding site
o Two tRNA binding sites
A site: Where _______________ (carrying amino acid) binds
newtina
P site: Where tRNA holding growing polypeptide binds
______________________
leave Ribosome
o Exit (E) site: Allows empty tRNA to ______________________
16
What does the ribosome do?
o Holds mRNA and tRNA together
o Positions new amino acid for addition to growing polypeptide chain
Partitebonds
o Catalyzes formation of __________________
Mechanism of Translation:
Start codon initiates translation
Amino acids added to growing polypeptide:
o tRNA delivers new amino acid to ribosome by base pairing to mRNA
codon in A site
o Ribosome (rRNA) creates peptide bond between new amino acid and
existing chain
o Ribosome moves 5’ → 3’ down mRNA to read next codon
o Empty tRNA is released
Recognition of stop codon terminates translation
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Prokaryotes vs. Eukaryotes
Similarities between prokaryotes and eukaryotes:
o Transcription: Synthesis of RNA using DNA as a template
o Translation: Synthesis of polypeptide using mRNA sequence as a
template
o Ribosome is translation enzyme
o
uses same sent.ie co k
Eukaryotic vs. Prokaryotic ribosomes
o Same function
o Different size
rRNA Proteins
o Different types of ______________________
antibiotics
o Bacterial ribosomes are susceptible to __________________; eukaryotic
ribosomes aren’t
Transcription and translation are coupled in prokaryotes
o Translation starts before transcription finishes
o Allows _________________________
Rolyribosomes to form
o Reasons:
inthecytoplasm
Transcription and translation both occur ____________________
processed
Transcripts are not ________________
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Transcription and translation are separated in timing and location in eukaryotes
nucleus
o Transcription occurs in _____________
o Translation occurs in _______________
Cytoplasm
o Why are they separated?
processedbeforetranslation
Transcripts are _______________________
exported
mRNA must be _______________________
meters
from
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