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SIMARD 3.1-3.2, 2.6-2.7, Unit 7 - Genes & DNA Slides (HL-2023)
SIMARD 3.1-3.2, 2.6-2.7, Unit 7 - Genes & DNA Slides (HL-2023)
SIMARD 3.1-3.2, 2.6-2.7, Unit 7 - Genes & DNA Slides (HL-2023)
http://lh3.ggpht.com/-QufTg--alis/U6FUBwpKv0I/AAAAAAAABsU/1kScsB0Sr-Q/prokaryotic%25
2520chromosome%25255B9%25255D.png?imgmax=800
Some prokaryotes also have plasmids but eukaryotes do not.
Plasmids are:
● small separate (usually circular) DNA
molecules
● “naked” (not associated with histone
proteins)
● often associated with antibiotic resistance
● able to be transferred from one bacterial
cell to another.
● used by scientists to artificially transfer
genes from one species to another (eg.
gene for human insulin)
https://3.bp.blogspot.com/-xs5q8NXlSXw/ULRo-wNb9AI/AAAAAAAACEQ/
QV2z-JXXd3c/s1600/Prokartoic+chromosimess.jpg Note: prokaryotes divide by binary fission
Draw and label a eukaryotic cell (review)
Eukaryote chromosomes are linear DNA molecules associated with
histone proteins.
● Histones are globular shaped
protein that DNA wraps around
○ DNA wrapped around 8 histone proteins
is called a nucleosome.
○ DNA wraps twice around the histone
protein core.
○ Another histone protein is attached to
the outside of the DNA strand. This
helps maintain the colloidal structure of
the nucleosome.
Note:
- There are no plasmid in eukaryotic cells.
- Most eukaryotes divide by
mitosis/cytokinesis
Cairns’ technique for measuring the
length of DNA molecules by
autoradiography.
○ What happened while the DNA was left to sit exposed to the photographic emulsion?
high energy electrons emitted by the radioactive decay of 3 H within the DNA caused the appearance of
dark spots on the photographic emulsion
https://www.philpoteducation.com/pluginfile.php/1152/mod_book/chapter/1051/3.1.2
a.jpg
A gene is a heritable factor that consists of a length of DNA and influences
a specific characteristic.
Gene:
The basic unit of heredity; a heritable factor that
controls a specific characteristic.
● New alleles are created by random changes in the base sequence called
mutations
https://i.stack.imgur.com/ZcmFo.jpg
Homologous chromosomes carry the same sequence of genes but not
necessarily the same alleles of those genes.
Homologous chromosomes are:
● pairs of chromosomes that carry the same
genes
● the same shape and size
● paired up during meiosis
https://images.slideplayer.com/17/5340582/slides/slide_13.jpg
Exam tip - Kognity 3.1.3 - Take note if you want a 7!
with:
https://bitesizebio.com/wp-content/uploads/2011/03/HGP.jpg
What are some of the
advantages &
disadvantages of
sequencing your
genome?
Would you sequence
yours?
Human Genome Project Pros/Cons (previous question)
Pros:
- Knowledge of your genetic susceptibilities to certain illnesses could allow you to take steps to protect
your health.
- there is the potential to tailor medical treatment to the genetic profile of the individual.
- It is possible that affordable genetic sequencing will begin an era of ‘personalised medicine’.
Cons:
- Genetic medical knowledge could also be used by insurance companies to charge you more or to refuse
to insure you.
- Ethical concerns about who owns the genetic information once submitted to DNA sequencing
companies
EXTENSION WORK : Use of a database to determine differences in the
base sequence of a gene in two species.
Go to GenBank database and follow the procedure of comparing two gene
sequences:
● Refer to Kognity: 3.1.5 Using databases
● Follow the instructions: to compare the cytochrome C gene between two species
(gorilla and human for example)
● Reflect: on the task
○ What was interesting about using the database to compare genes?
○ What did you find tricky?
○ Is comparison of genes & mutations something you would be interested in forming
an IA question around?
Homework:
❏ Refer to Kognity: 3.2.1 Prokaryotic chromosomes
❏ Refer to Kognity: 3.2.2 Eukaryotic chromosomes
❏ Read Kognity: 3.2.6 Cairn’s autoradiography technique
❏ Watch : DP Hickman 7.1 Video (0-14:30min)
❏ Watch : DP Hickman 2.6 Video (6-11min)
Lesson 3
The number of chromosomes is a characteristic feature of members of a
species.
● Chromosome number does not indicate how complicated an organism is
● Humans have 46 chromosomes
○ 22 paired autosomes
○ The 23rd pair determines sex (XX = female; XY = male)
● Organisms with different numbers of chromosomes are unlikely to interbreed
● Chromosome number tends to remain unchanged over millions of years of
evolution
http://ib.bioninja.com.au/_Media/diploid-number_med.jpeg
Explain the difference between
autosomal and sex chromosomes.
❏ Explain: the difference between autosomal and sex chromosomes
Autosomes are chromosomes that do not determine sex. Sex is determined by sex chromosomes
(XX = genetic female, XY = genetic male).
Autosomes are chromosomes that do control the inheritance of all traits except those that are
sex-linked.
Sex-linked traits are found on the sex chromosomes and are therefore not controlled by
autosomes.
https://images.theconversation.com/files/62610/original/bv9fpsk3-1414040470.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip
Sex is determined by sex chromosomes and autosomes are chromosomes
that do not determine sex.
https://images.theconversation.com/files/62610/original/bv9fpsk3-1414040470.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip
A karyogram shows the chromosomes of an organism in homologous pairs
of decreasing length.
● Chromosomes are stained during
mitosis (usually metaphase) and a
micrograph is taken of the stained
chromosomes
Procedure Source of cells obtained: Amniotic fluid Source of cells obtained: chorion
● with a needle through the mother’s (membrane)
abdominal wall ● removing a
sample of the placental tissue
through the vagina
SC - Karyotypes and
gender
https://www2.palomar.edu/anthro/abnormal/images/Down_Syndrome_Karyotype.jpg
Use of karyotypes to diagnose Down syndrome in humans
● trisomy of chromosome 21
● Some Down syndrome symptoms include:
○ impairment in cognitive ability and physical
growth
○ hearing loss
○ oversized tongue
○ shorter limbs
○ social difficulties
https://www2.palomar.edu/anthro/abnormal/images/Down_Syndrome_Karyotype.jpg
Studies show age of parents influences chances of non-disjunction
● Yoon and colleagues (1996)
concluded that 86% of the
trisomy 21 cases from
1989-1993 in Atlanta were
maternal in origin, 9% were
paternal in origin, and 5%
occurred during the mitotic
divisions of the embryo.
Maternal data for non-disjunction supports the hypothesis that the risk
of non-disjunction increases with age. The risk of all non-disjunction
events is 0.5/1000 at material age under 25. This risk doubles to 1/1000
at maternal age above 30-34, with an exponential increase to 6/1000 at
maternal age above 40.
However, paternal data does not support the hypothesis. Paternal data
suggests non-disjunction decreases as male under 25 show greater
non-disjunction than females the same age (1.5/1000), with a decrease to
0.5/1000 for males age 35-39. There is a slight increase in males above
40, which may support the hypothesis.
Studies show age of parents influences chances of non-disjunction
-
- Watson & Crick were given her data without her
permission before she published her work
- Added to their model that bases and hydrophobic
& would point to centre of helix
- Joined ideas of many scientists to create first
model of DNA
- To “fit” Rosalind Franklin’s x-ray dimensions they
paired purine with pyrimidine (C-G and A-T) &
flipped one strand “upside down”
- Model led to hypothesis of semi-conservative
replication
https://www.dnalc.org/content/c16/16430/16430_dna_medalmodel.jpg
❏ Draw & Outline: the
steps & findings of the
Hershey-Chase
experiment
❏ Draw & Outline: the steps & findings of the Hershey-Chase experiment
❏ Draw & Outline: the steps & findings of the Hershey-Chase experiment
The nucleic acids DNA and RNA are polymers of nucleotides
DNA differs from RNA in the number of strands present, the base composition and the type of pentose
Nucleotides
● the monomers of the polymer
DNA
● made up of 3 components
linked by covalent bonds
○ phosphate group (PO4)-3
○ pentose sugar
○ nitrogenous base
DNA Structure
● Double stranded
● Shaped like a ladder
● Two strands are
coiled forming a
double helix
DNA is a double helix made of two antiparallel strands of nucleotides linked by hydrogen bonding
between complementary base pairs
DNA structure suggested a mechanism for DNA replication.
● Rungs of ladder contain two
nitrogenous bases (one from
each strand)
○ bonded by hydrogen
bonds
○ Purines - two ring
nitrogenous bases
(Adenine&Guanine)
○ Pyrimidines - single ring
nitrogenous bases
(Cytosine&Thymine)
http://www.rcsb.org/3d-view/3MNN/1
The replication of DNA is
semi-conservative and depends on
complementary base pairing
DNA Replication
● In the nucleus
6) DNA primase adds a small primer (5-10 RNA nucleotides) on the lagging strand of DNA.
- provides a free 3’ -OH starting point for DNA polymerase III
- DNA polymerase III adds nucleotides again in the 5’ to 3’ direction (opposite direction of
the leading strand because the stands are antiparallel)
7) After the fragment is created, DNA polymerase I replaces the RNA primer with DNA
DNA polymerases
can only add
nucleotides to the
3’ end of a primer.
8) As the strand continues to open, a new RNA primer is added and a new fragment of
DNA is created away from the replication fork
9) As these fragments are made, little nicks are created between the fragments
a) DNA ligase forms a phosphodiester bond between 3’ OH on the growing strand
and the 5’ phosphate on the next fragment
b) this seals the nicks between the phosphates and the sugars
Important Fun Facts
● The rate of replication is
approximately 100 nucleotides
per second in eukaryotes while
it can be as high as 1000
nucleotides per second for
prokaryotes.
DNA after 1st Replication DNA after 2nd Replication DNA after 3rd Replication
❏ Draw the stages of their experiment
DNA after 1st Replication DNA after 2nd Replication DNA after 3rd Replication
❏ Identify why 15N and 14N were used in this experiment
Non-coding sequences
Most eukaryotic DNA is non-coding (nearly 60% of human DNA is repetitive sequences)
● Introns
○ non-coding regions of mRNA removed before leaving the nucleus
● Telomeres
○ repetitive sequences on the ends of eukaryotic chromosomes
○ protect DNA during replication
○ prevents the loss of genes near the end of the chromosomes because enzymes can’t replicate all
the way to the end of the chromosome
Homework:
❏ Read Kognity: 2.6.0 The big picture &
❏ Read Kognity: 2.6.2 Using a model to elucidate the DNA structure and DNA: structure of the double helix
❏ Read Kognity: 7.1.6 The Hershey-Chase experiment
❏ Read Kognity: 7.1.5 Rosalind Franklin and DNA structure
❏ Read Kognity: 2.6.1 DNA & RNA: basic structure
❏ Watch DP Hickman 7.2 Video (all - 30min)
Lesson 6
STEM Case - Protein Synthesis GIZMO
Handbook : DNA transcription and translation (10-15min)
Transcription consists of
3 stages called:
1) Initiation
2) Elongation
3) Termination
Transcription occurs in a 5’ to 3’ direction. (HL)
Nucleosomes help to regulate transcription in eukaryotes. (HL)
Following Transcription
1) mRNA exits the nucleus through a nuclear pore
2) mRNA is transported to a ribosome for protein synthesis
The DNA strand with the same base sequence as the mRNA is the called
the sense (DNA coding) strand and the other (the one the mRNA binds to)
is called the antisense (DNA template - 5’-3’) strand
● Specific proteins regulate how much transcription of a particular gene will occur
have binding sites close to the Regulatory sequences on the Regulatory sequences on the
promoter; their binding is DNA that increase the rate of DNA that decrease the rate of
necessary to initiate transcription when proteins transcription when proteins
transcription bind to them bind to them
Eukaryotic cells modify mRNA after transcription. (HL)
Splicing of mRNA increases the number of different proteins an organism can produce. (HL)
Alternative splicing can also occur with genes that produce multiple proteins
■ some exons may be removed during splicing, producing different
polypeptides
eg. In mammals tropomyosin is a protein involved in muscle
contractions
● the pre-mRNA is spliced to form 5 different forms of the protein
● the mature mRNA that codes for tropomyosin in the smooth
muscle of the intestines is missing exon 3 and 10
● the mature mRNA that codes for tropomyosin in skeletal
muscle is missing exon 2
(You are not expected
to know spliceosome
definition for the exam.)
Homework:
❏ Read Kognity: 7.1.1 Nucleosomes
❏ Read Kognity: 2.7.1 DNA Replication
❏ Read Kognity: 7.1.2 DNA Replication
**assign reading from Lesson 3 today instead as switched for SUB
Lesson 7
Start at
2:44min
Gene expression is regulated by proteins that bind to specific base sequences in
DNA. (HL)
When there are only small amounts of lactose left in the cell, the repressor binds
to the operator once again, blocking transcription from taking place.
Start 2min
The environment of a cell and of
an organism has an impact on
gene expression. (HL)
Methylation
● A methyl (CH3 group) can be added to histone proteins or DNA directly
○ histone proteins pack DNA tightly together
○ can decrease transcription of the gene
○ amount of methylation can vary over an organism's lifetime
○ can be affected by environmental factors
Acetylation
● Histone tails or DNA are modified by addition of acetyl groups (CH3O)
● Creates a less condensed structure of DNA
○ Allows the gene to be transcribed more often
○ If acetylation does not occur, the DNA remains tightly packed and
transcription is inhibited
An organism’s external and internal environment both have an
impact on gene expression
1. Exposing mice during pregnancy to a diet high in folic acid (which contains the methyl
group), increased the proportion of dark mice in their litters. This is indirect evidence that
increased methylation of genes in the fetus can influence the inheritance of a trait. (Kognity,
2022)
Translation is:
● The formation of polypeptides (proteins)
with a specific amino acid sequence
○ Amino acid sequence is determined by
specific base sequence on mRNA
molecule
Ribosomes
organelles made from protein and rRNA that catalyze
the assembly of amino acids into polypeptides during
translation.
● When the stop codon is reached, the ribosome dissociates and the polypeptide
is released.
Story time!
Using your notes as well as the video on Advanced Translation below:
- Watch the video on mute and narrate what is happening to your partner
(teams of 2!).
- Take turns until each of you had a chance to narrate! (maybe 1 partner does
0-1:30min, and the other one does 1:30-3min!)
❏ Explain: the synthesis of a
polypeptide on a ribosome
❏ Explain: the synthesis of a polypeptide on a ribosome [8 marks]
a. mRNA is translated;
b. mRNA binds with ribosome/with small subunit of ribosome;
c. tRNA-activating enzymes/aminoacyl tRNA synthetases attach specific amino acid to tRNA;
d. anticodon of 3 bases/nucleotides on tRNA;
e. start codon/AUG on mRNA;
f. tRNA carrying first amino acid/methionine binds to P/peptidyl site (when large subunit binds);
g. anticodon (on tRNA) binds to codon (on mRNA);
h. complementary base pairing (between codon and anticodon);
i. tRNA for next codon binds to A site/amino acyl site;
j. peptide bond forms between amino acids (on tRNAs) at P and A sites;
k. ribosome moves along mRNA to next codon/by three bases/in 5’ to 3’ direction;
l. tRNA released from E/exit site;
m. process/cycle repeats to elongate the polypeptide/until stop codon is reached;
n. release of polypeptide and mRNA/disassembly of ribosome complex at stop codon;
Marks can be awarded in an annotated diagram.
Accept UAA, UAG or UGA instead of stop codon in mpm or mpn but do not accept terminator sequence.
Do not award mpk for the ribosome moving to the start codon in a 5’ to 3’ direction.
Amino Acid R group
Denaturing proteins
changes their shape &
disrupts their biological
activity.
The sequence and number of amino acids in the
polypeptide is the primary structure. (HL)
Scroll down to see the step-by-step process of protein folding. You can use this to
help you fill the table on levels of protein structure.
❏ Distinguish Between: the different levels of protein structure including structure, shape and type of bonds
Structure
Shape
Bonds
Formed
Other
❏ Distinguish Between: the different levels of protein structure including structure, shape and type of bonds
Form by interactions
Peptide bond, Form by interactions between “R” groups Hydrogen, covalent and
Bonds
Chain joined by ionic bonds between
Formed between H-bonds (hydrogen, covalent and
ribosomes polypeptides
ionic bonds)
Homework:
❏ Read Kognity: 2.7.4 DNA translation and the genetic code
❏ Read Kognity: 7.3.2 Analysis of the structure of eukaryotic ribosomes and tRNA
❏ Read Kognity: 7.3.3 tRNA activating enzymes
❏ Watch DP Hickman Video 7.3 0-12min only
Lesson 10
Free ribosomes synthesize proteins for use primarily within the cell. (HL)
Bound ribosomes synthesize proteins primarily for secretion or for use in lysosomes. (HL)
❏ Read Kognity: 7.3.4 Ribosomes & Polysomes
In Prokaryotes In Eukaryotes
● DNA is not ● The completed mRNA has to be transported from the nucleus, through
compartmentalized the nuclear pore to the ribosome on the ER or in the cytosol
into a nucleus
Free ribosomes Bound Ribosomes
● Once transcription
● Found in the cytoplasm ● Ribosomes attached to rough
begins creating a strand
● Endoplasmic Reticulum (ER)
of mRNA, translation
● Synthesize proteins that will be
can begin immediately ● Create proteins that are
used inside the cell in the
as the mRNA strand is secreted from the cell by
cytoplasm, mitochondria and
created exocytosis OR are used in
chloroplasts (in autotrophs)
lysosomes, ER, Golgi
Apparatus & the plasma
membrane
Bound Ribosomes
are directed to the Endoplasmic Reticulum (ER) by a signal sequence that is part
of that specific polypeptide
● the signal sequence on the polypeptide binds to a signal recognition protein
(SRP)
● the SRP guides the polypeptide and ribosome to the ER where it binds to a
SRP receptor
● Translation continues and the polypeptide is deposited into the lumen of the
ER as it is created for transportation to the correct location
● Proteins perform many functions within specific compartments of the cell or in
other parts of the body after they are secreted out of the cell
Identification of polysomes in electron micrographs of prokaryotes and eukaryotes.
Polysomes
Multiple ribosomes
translating the same
mRNA strand at one
time
● Look like beads on
a string in an
electron micrograph
Identification of polysomes in electron micrographs of prokaryotes and eukaryotes.
In prokaryotes, several
ribosomes can attach
themselves to the growing
mRNA chains to form a
polysome while the
mRNA chains are still
attached to the DNA (top
left)
to:
DNA Template 5’ TAC TAC TCG CCT TTT AAA GCT AGT ACT ACT 3’
Strand
DNA Coding 3’ ATG ATG AGC GGA AAA TTT CGA TCA TGA TGA 5’
Strand
Met
Amino Acids (Start)
❏ Transcribe: a strand of mRNA from the DNA
strand below and then identify the correct
amino acids in the polypeptide strand
Polypeptide : 8 amino acids
DNA Template 3’ TAC TAC TCG CCT TTT AAA GCT AGT ACT ACT 5’
Strand
DNA Coding 5’ ATG ATG AGC GGA AAA TTT CGA TCA TGA TGA 3’
Strand
Met Met Ser Gly Lys Phe Arg Ser Stop Stop
Amino Acids (Start)
Homework:
❏ Read Kognity: 7.3.1 Translation
❏ Read Kognity: 7.3.5 Proteins: conformation
❏ Review Translation in Prokaryotes: https://www.labxchange.org/library/items/lb:LabXchange:049914b8:lx_simulation:1
❏ EXTENSION : Complete GIZMO Protein Synthesis for Homework if not completed during class
Lesson 11 - Review for Assessment
❏ Complete: Kognity Readings & Quizzes
❏ Complete: Class Notes Package
DNA to Protein Interactive
https://www.labxchange.org/library/items/lb:LabXchange:fb468b9e:lx_simulation:1
Kognity Reading 3.5.1, 3.5.2 and 3.5.3 - Gel electrophoresis, PCR and DNA profiling
Role Items/Actions
Small Ribosomal Subunit Join with tRNA carrying Met and scan for
(shortest person in the class) the start codon
Large Ribosomal Subunit Join with small ribosomal subunit and use
(tallest person in the class) hula hoops to make the E/P/A sites