Pre-Unit Homework

Watch : DP Hickman 3.2 Video (19min)

Lesson 1
3.1 - Genes
3.2 - Chromosomes
Draw and label a prokaryotic cell (review)
Prokaryotes have one chromosome consisting of a circular DNA molecule.

● Bacteria have circular

chromosomal DNA (genophore)
which, unlike eukaryotes, is not
associated with any histone
proteins

● There is one copy of each gene

except when the cell and its DNA
are replicating

● DNA identical to parent cell

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.

● Because of its negative charge,

DNA is attracted to the positive
charge on the amino acids of the
histone proteins
Eukaryote chromosomes are linear DNA molecules associated with
histone proteins.
In a eukaryote species there are different chromosomes that carry different
genes.
Eukaryotic chromosomes vary in:
● length
● the specific sequence of genes along the
linear DNA molecule
● position of the centromere that holds the
sister chromatids together

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.

● Read Kognity 3.2.6

● Take point form notes on:
○ autoradiography
○ Cairns technique
https://www.philpoteducation.com/pluginfile.php/1200/mod_book/chapter/1136/3.2.2a.j
pg

● Answer the following questions:

○ What was the purpose of using “tritiated thymidine” (3H)?
○ How did he release the DNA onto slides?
○ What happened while the DNA was left to sit exposed to the photographic emulsion?
○ What were the two main revelations of Cairns images?
 Cairns’ technique for measuring the length of DNA molecules by
autoradiography.
Answer the following questions:
○ What was the purpose of using “tritiated thymidine” (3H)?
Radioactive hydrogen decay allowed to visualize thymines (dark spots)

○ How did he release the DNA onto slides?

He then lysed the cells (ruptured their cell walls and membranes)

○ 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

○ What were the two main revelations of Cairns images?

measuring the length of DNA molecules and that prokaryotes have circular DNA/chromosome
When the E. coli cells replicated their DNA, they used the radioactive thymine, creating radioactive
DNA.
Homework:
Watch : DP Hickman 3.1 Video - 0-14min only

❏ Watch : DP Hickman 3.3 Video (20min-end (about 10min))

Lesson 2
Compare prokaryotic & eukaryotic chromosomes

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.

● DNA consists of the base pairs adenine, guanine,

cytosine and thymine

● Humans have between 21,000-23,000 protein coding

genes
A gene occupies a specific position on one type of
chromosome.

Locus (plural loci): the specific location/position

on a chromosome that a gene occupies

● Each chromosome contains many different

genes often linked in groups.

Example of human chromosome 7

fromhttp://users.rcn.com/jkimball.ma.ultranet/
BiologyPages/C/Chromo7.gif
The various specific forms of a gene are alleles.
Allele: One specific form of a gene
- differs from other alleles by one or a few
bases only
- occupies the same gene locus as other
alleles of the same gene.

● There can be two or more (multiple)

alleles of a specific gene
○ The gene that influences human blood
type has three different alleles that
code for blood types A, B and O.
The various specific forms of a gene are alleles.

● Each human cell consists of two

copies of each chromosome & two
copies of each gene (except X and
Y)
○ Sometimes a person can have two of
the same allele (homozygous) or two
different alleles (heterozygous)
Alleles differ from each other by one or only a few bases. New alleles are
formed by mutation.
● Genes consist a specific sequence of DNA bases which can be 100’s to
1000’s of bases long
○ different alleles of the gene vary from one to a couple of different bases

● New alleles are created by random changes in the base sequence called
mutations

● There are a variety of different types of

mutations that can be either harmful, neutral
or beneficial

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

● One chromosome came from an individual’s

mother and one from the father

● Although they carry the same genes, they could

have different alleles
https://i.stack.imgur.com/16QyG.jpg
Draw & label a pair of homologous chromosomes
including: allele, centromere, chromatid, chromosome,
gene, locus
The genome is the whole of the genetic
information of an organism.
Genome: The whole of the genetic information
of an organism
● Prokaryotes have a circular chromosome http://www.sanger.ac.uk/sites/default/files/ideogram_grch38p4.png

and plasmids in their genome

● In animal cells, the genome consists of the

chromosomes and mitochondrial DNA
○ In humans, the genome consists of 46 chromosomes plus
mitochondrial DNA

● In plant cells, the genome also consists of

chloroplast DNA + their chromosomes and
mitochondrial DNA
http://science.sciencemag.org/content/sci/344/6188/1168/F1.large.jpg?download=true
Comparison of the number of genes in humans with other species. (compare
plant & one bacterium; species with more genes & fewer genes than human)

Genome size: total amount of

DNA = total number of base
pairs in an organism
Number of Genes: varies from
species to species & is not
always proportional to genome
size
● eg. how many genes does a
fruit fly have compared to it’s
genome size (millions of base
pairs)
https://www.nature.com/scitable/content/ne0000/ne0000/ne0000/ne0000/6906609
/EssGen5-4_ComparingGenomes_MID_0.jpg
Evaluate the statement: Species with a larger genome are always more
complex organisms.

https://images.slideplayer.com/17/5340582/slides/slide_13.jpg
Exam tip - Kognity 3.1.3 - Take note if you want a 7!

You should be able to compare

the number of genes in humans

with:

● A named species with more

genes than humans
● A named species with fewer
genes than humans
● A named bacterial species
● A named plant species
Comparison of genome size in T2 phage, Escherichia coli,
Drosophila melanogaster, Homo sapiens and Paris japonica.
Organism Genome Size Description
(million base pairs)

T2 phage 0.18 Virus that attaches to E. coli

Escherichia coli 5 Gut bacterium

Drosophila melanogaster 140 Fruit Fly

Homo Sapiens 3,000 Human

Paris japonica 150,000 Woodland plant

Identify what the genome size of eukaryotes depends on.

The entire base sequence of human genes was sequenced in the Human
Genome Project. Techniques used for genome sequencing vary.

● Most of the genome does not code for proteins

(originally labeled “junk DNA”).
○ Some of these regions consist of areas that can affect gene
expression
○ Some are highly repetitive sequences called satellite DNA.

● Scientists can now predict which sequences code for

each protein (approximately 21000-23000 sequences)

● The Human genome project can be found at

http://www.genome.gov/10001772

Video: How to Sequence the Human Genome

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.

In humans, 22 pairs are autosomes, and 23rd pair is sex chromosome

Comparison of diploid chromosome numbers of 5 species. (Kognity 3.2.3
reading - take note if you want a 7!)
Species Name English Name Diploid Chromosome Number

Paracaris equorum Horse threadworm 4

Oryza sativa rice 24

Homo sapiens human 46

Pan troglodytes chimpanzee 48

Cani familiaris dog 78

● All eukaryotic species contain a minimum of two different pairs of

chromosomes (diploid chromosomal count >4)
○ eg. jack jumper ants have one pair of autosomal chromosomes + 1 pair
of sex chromosomes
● most organisms contain more than two pairs!
Sex is determined by sex chromosomes and autosomes are chromosomes
that do not determine sex.
● The X and Y chromosomes determine the
sex of an individual
○ The X chromosome is quite large; centromere is
located near the centre of the chromosome
○ The Y chromosome is relatively small; centromere
located near the end of the chromosome
● An individual with two X chromosomes (XX)
will be a female
○ The X chromosome carries many genes essential
to human development
TedEd: Secrets of the X Chromosome

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.

An individual with an X and a Y chromosome

(XY) will be a male
○ The Y chromosome has a small number of genes
(some shared with X chromosome, some necessary for
male development)
○ The SRY gene codes for a protein called the
testis-determining factor (TDF). TDF is a regulatory
protein responsible for the initiation of male sex
determination in humans

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

● Chromosomes are arranged in pairs

according to their size and structure
○ eg. largest at chromosome pair 1 and
smallest at chromosome 22
○ The 23rd pair are the chromosomes -
females (XX) and males (XY)

● The stained image of the

chromosomes is called a Karyogram
Chromosomes and Karyotypes
https://teaching.ncl.ac.uk/bms/wiki/images/e/e9/Figure-1-Normal-male-chromosomes-and
-karyogram-46XY.ppm.png
 Description of methods used to obtain cells for karyotype analysis
Karyotyping is performed by collecting
cells using one of two methods:
1) chorionic villus sampling (CVS)
2) amniocentesis

● Used for prenatal diagnosis of

genetic chromosome abnormalities
such as:
○ Down syndrome (trisomy 21)
○ Edwards syndrome (trisomy 18)
○ Patau’s syndrome (trisomy 13)
○ Turner syndrome (XO)
○ Klinefelter syndrome (XXY).
Amniocentesis & Chorionic villus sampling
● Cells are obtained from the embryo (not the mother) allowing doctors to
analyze the DNA/genome of the embryo

● Amniocentesis involves extracting a small amount of amniotic fluid (contains

fetal tissues) with a needle through the mother’s
abdominal wall
○ Can be carried out after 15 weeks of pregnancy
○ 1% risk of miscarriage

● Chorionic villus sampling involves removing a

sample of the placental tissue through the vagina
○ CVS can be carried out 8-12 weeks into the pregnancy
○ 2% risk of miscarriage
❏ Refer to Kognity: 3.3.6 Fetal karyotyping: methods and risks
❏ Compare: the two techniques for obtaining cells for a karyotype

Amniocentesis Chorionic villus sampling

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

Fetal age 14–20 weeks 10–13 weeks

Risk ≤1% of miscarriage ≤2% of miscarriage

Non-disjunction can cause Down syndrome and other chromosome abnormalities.

● Non-disjunction is an error in meiosis

○ the chromosome pairs fail to split during cell division
○ results in too many or too few chromosomes in the final gamete cell
■ one gamete could have 22 chromosomes and one could have 24
chromosomes. The resulting zygote will have 47 or 45 chromosomes.

● Can occur in anaphase I OR anaphase II

○ the homologous pairs fail to split OR the sister chromatids fail to split

An example of a non-disjunction is Down syndrome (Trisomy 21)

○ Some Down syndrome symptoms include impairment in cognitive ability and
physical growth, hearing loss, oversized tongue, shorter limbs and social
difficulties.
 Use of karyotypes to diagnose Down syndrome in humans
● Downs syndrome occurs is a genetic disorder
caused by trisomy of chromosome 21

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.

● They also showed that 75% of

the maternally originated Down
syndrome cases arose from
non-disjunction during the first
meiotic division, and 25%
originated in the second meiotic
division.
https://www.philpoteducation.com/pluginfile.php/1200/mod_book/chapter
/1138/3.2.3f.jpg
Evaluate the hypothesis that the risk of non-disjunction
increases with parental age
❏ Evaluate: the hypothesis that the risk of non-disjunction increases with parental age
using the graphs provided

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

Living with Down's syndrome

Caring for a 47year old son with Down's syndrome

TOK - What would you do if you had that choice?

Pretend your
friend was absent
from class today…
Write what you would say if you had to
explain a karyotype to your friend.
Homework:
❏ Refer to Kognity: 3.1.1 Chromosomes, genes and alleles
❏ Refer to Kognity: 3.1.3 Human Genome Project
❏ Refer to Kognity: 3.1.5 Using databases (EXTENSION)
❏ Watch : DP Hickman 7.1 Video (14-44min)
 2.6 - Structure of DNA and RNA
2.7 - DNA replication, transcription, translation
Unit 7 (HL) - Nucleic Acids
Lesson 4
Teams of 2
Pick 1 ‘box’ each for either

- Erwin Chargaff/Franklin OR Watson&Crick experiment,

- read through and briefly explain to your partner.
Analysis of results of the Hershey and Chase experiment providing evidence that
DNA is the genetic material.

- Labelled viral proteins with

radioactive 35S
- Labelled viral DNA with radioactive
32
P
- Infected bacteria with labelled viruses
- Blended everything to release DNA
- Centrifuged to separate cell “pellet”
from liquid supernatant
- Measured how much 35S compared
with 32P was found in supernatant
- Labelled protein did not get passed
on
- Labelled DNA did get passed on …
so DNA must be genetic information
https://upload.wikimedia.org/wikipedia/commons/thumb/3/32/Hershey_Chase_experiment.png/357px-Hershey_Chase_experiment.png
Making careful observations—Rosalind Franklin’s X-ray diffraction provided crucial evidence
that DNA is a double helix. Rosalind Franklin’s and Maurice Wilkins’ investigation of DNA
structure by X-ray diffraction.
- Learned crystallography & x-ray diffraction in Paris
- Improved resolution of a camera for clearer images
- Analysed diffraction patterns to calculate dimensions
of DNA double helix
- Deduced:
- Cross in the centre indicates helical shaped
molecule
- Angle of cross shows pitch (angle) of helix
- Distance between bars shows turn of helix 3.4nm
apart
- Repeating pattern turned out to be vertical
distance between base pairs
- Watson & Crick were given her data without her
permission before she published her work
https://undsci.berkeley.edu/images/us101/xray.jpg
- Added to their model that bases and hydrophobic
& would point to centre of helix
Crick and Watson’s elucidation of the structure of DNA using model making

-
- 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

● each nucleotide is linked to the

next nucleotide between the
phosphate of one and the
pentose sugar of the next
nucleotide
Review:
4min-end
quiz
questions
only
 DNA RNA
Sugar Deoxyribose Ribose (carbon 2 has
(carbon 2 - no oxygen –OH attached)
attached)

Guanine (G) Guanine (G)

Nitrogenous Adenine (A) Adenine (A)
Bases Cytosine (C) Cytosine (C)
Thymine (T) Uracil (U)

Number of Double-stranded Single-stranded

Strands
RNA
- Single strand polymer
- Phosphate linked to C3 of next pentose
sugar
- Leaves C3 open at one end (3’ terminal)
and C5 open at the other end (5’
terminal)
❏ Draw: simple diagrams of the structure of single
nucleotides of RNA
● Circles for phosphates
● Pentagons for pentose sugar
● Rectangles for bases
- Base and phosphate are linked to pentose sugar
- Base linked at C1
- Phosphate linked at C5
❏ Draw: ribose … how is this different from
deoxyribose?
❏ Draw: ribose … how is this different from deoxyribose?
DNA is a double helix made of two antiparallel strands of nucleotides
linked by hydrogen bonding between complementary base pairs

DNA Ladder Interactive - options

https://www.labxchange.org/library/items/lb:LabXchange:feb8ec5b:lx_simulation:1

Scroll down to see each steps.

3D DNA : The Double Helix

https://www.labxchange.org/library/items/lb:LabXchange:5c1562b9:lx_simulation:1
Change the highlighted colors, strands visibles, 3D-ladder-sticks

3D Models in the classroom : Observations!

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.

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)

● Nitrogenous bases match up

according Erwin Chargaff’s
Rules (complementary base
pairing)
List: which bases pair together and how many hydrogen bonds
they form
❏ List: which bases pair together and how many hydrogen bonds they
form
G and C : 3 Hydrogen bonds A and T : 2 Hydrogen bonds
Hint: A comes before C so
A=2 and C=3?
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.

● Sides of the ladder made out of repeating

phosphate and deoxyribose sugar
molecules covalently bonded together
● Each deoxyribose molecule has a
phosphate covalently attached to 3’ carbon
and 5’ carbon
○ phosphate attached to 5’-C of one
deoxyribose molecule is covalently
attached to the 3’-C of the next
deoxyribose molecule
○ forms a long single strand of DNA, the
DNA backbone
DNA is a double helix made of two
antiparallel strands of nucleotides linked
by hydrogen bonding between
complementary base pairs

● DNA strands run antiparallel

to each other
○ one strand running in a
5’ to 3’ direction
○ the other strand running
3’ to 5’
○ replication occurs in
different directions on the
DNA strand
❏ Calculate: If a cell is discovered to contain 29% Adenine,
how much Cytosine will the cell contain?
❏ Calculate: If a cell is discovered to contain 29% Adenine, how much Cytosine will the cell
contain?
❏ Draw: simple diagrams of the structure DNA
● Circles for phosphates
● Pentagons for pentose sugar
● Rectangles for bases
- Double stranded polymer
- Draw strand 1 as for RNA
- Draw strand 2 in the opposite direction
- Leave C3 and C5 terminals open at opposite ends
- Add letters to indicate bases (A, T, C, G)
- Pair complementary bases with H-bonds
Homework:
❏ Refer to Kognity: 3.2.3 Diploidy and Haploidy
❏ Refer to Kognity: 3.2.4 Karyotyping: analysis and determining sex
❏ Refer to Kognity: 3.3.6 Fetal karyotyping: methods and risks
❏ Refer to Kognity: 3.3.5 Non-disjunction and other chromosomal abnormalities
❏ Watch : DP Hickman 7.1 Video (44min to 1h04)
Lesson 5
Nucleosomes help to supercoil the DNA (HL)
Utilization of molecular visualization software to
analyse the association between protein and DNA within
a nucleosome. (HL)

In eukaryote cells a nucleosome:

● consists of DNA wrapped around 8
histone proteins (octamer)
○ 2 copies of 4 different histone
proteins

● DNA wraps twice around the histone

protein core
○ Another histone protein (H1) attaches
binds the DNA to the core
Nucleosomes help to supercoil the DNA (HL)
Utilization of molecular visualization software to analyse
the association between protein and DNA within a
nucleosome. (HL)
● Histones are part of the supercoiling process
that occurs during mitosis and meiosis
○ Helps package long DNA into small nucleus
○ Forms a 30nm fibre

● Supercoiling helps regulate transcription

because only certain areas of the DNA are
accessible for the production of mRNA by
transcription.
○ This regulates the production of a
polypeptide.
Visualizing Nucleosomes (3D)
Take 2 minutes to observe the nucleosome structure:

http://www.rcsb.org/3d-view/3MNN/1
The replication of DNA is
semi-conservative and depends on
complementary base pairing

DNA Replication

● Occurs before mitosis in S

phase in preparation for cell
division

● In the nucleus

● The original strands are used

as templates
The replication of DNA is semi-conservative and depends on complementary
base pairing

● Complementary bases are added according to base pairing rules

○ A with T (two H-bonds) and G with C (three H-bonds)
○ ensures two identical DNA strands are formed after replication is
complete
○ important so the two daughter cells have an identical DNA genome to
the parent cell
○ if no mutations occur, gene sequences successfully passed on from
generation to generation

● DNA replication is semi-conservative

○ the new DNA created consists of one old strand (template) and one new
strand (synthesized strand)
Advanced
Simple
DNA replication is carried out by a complex system of
enzymes.

The Role of DNA Ligase in DNA Replication

Interactive:
https://www.labxchange.org/library/items/lb:LabXchan
ge:a21a9b48:lx_simulation:1
Scroll down to see all the steps.
Helicase unwinds the double helix
and separates the two strands by
breaking hydrogen bonds
● occurs at many different places
on the DNA strand called the
origins of replication
○ represented by bubbles
along the strand

1) DNA strand is unwound and

separated (hydrogen bonds
broken) by helicase (enzyme)
a) DNA gyrase (also called
topoisomerase) enzyme
relieves strain on the stand
as it is being unwound by
the helicase
2) Single-stranded binding proteins bind to the open
strands
a) these keep the strands apart long enough to
prevent the strands from re-annealing before
they are copied
DNA polymerase links nucleotides
together to form a new strand, using
the pre-existing strand as a template

3) DNA replication begins at the

different origins in the 5’ to 3’ direction
at the replication fork (where strands
split exposing the two template
strands)
○ DNA polymerase III adds
free nucleotides in the 5’ to
3’ direction of the replication
fork.

The nucleotides added are deoxynucleoside triphosphates (dNTP), the nucleotide

contains 3 connected phosphate groups. As dNTP’s are added, two phosphates are
lost and the energy released is used to bind the nucleotides together on the growing
strand
DNA replication is continuous on the
leading strand and discontinuous on
the lagging strand.

4) The 5’ to 3’ strand is called the

“leading strand” because replication
is continuous
- keeps replicating until it
meets another origin of
replication
5) The other strand is called the “lagging strand”
■ replicated in the opposite direction (3’ to 5’)
■ replication is delayed until helicase opens up available nucleotides
■ replication in this direction is discontinuous.
- lagging strand is made as a series of fragments called “Okazaki fragments”
DNA polymerases
can only add
nucleotides to the
3’ end of a primer.

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.

● The human genome has around

3 billion base pairs per haploid
set of chromosomes, so 6 billion
base pairs have to be replicated
during the S phase of the cell
cycle.
❏ Draw and Annotate: the steps of DNA Replication
❏ Meselson and Stahl’s results to obtain support for the theory of
semi-conservative replication of DNA
❏ Draw the stages of their experiment

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

N14 and N15 used because:

- Nitrogen is a component of DNA (A, T, G, C)
- Bacteria will include N in DNA replication
- 15N is heavier than N14 so it can be separated by centrifuge
- Can stop replication at different times and see how 15N and 14N separate

❏ Explain the significance of their results

The results show that DNA replication is semi-conservative

- This means that during replication, one strand of DNA is used as a template to build
the complementary strand
Some regions of DNA do not code for proteins but have other important functions.(HL)
The promoter as an example of non-coding DNA with a function. (HL)
Coding sequences
Genes within DNA that code for polypeptides created during translation

Non-coding sequences
Most eukaryotic DNA is non-coding (nearly 60% of human DNA is repetitive sequences)

Other functions include:

● Regulate of gene expression
○ Promoters, Enhancers, Silencers

● Introns
○ non-coding regions of mRNA removed before leaving the nucleus

● Guide production of tRNA and rRNA

● 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)

STEM case extension: identify mutations in transcription/translation, stem cells

therapy
Transcription is the synthesis of mRNA copied from the DNA base sequences by
RNA polymerase

Transcription is the formation of:

● a messenger RNA (mRNA) strand complementary to the DNA strand
contained within the nucleus
○ Necessary to relay the DNA code out of the nucleus to the
ribosomes

Eukaryotic DNA wraps around histone proteins and supercoils

● Supercoiling helps regulate transcription because only certain areas of
the DNA are accessible for transcription
Transcription is the synthesis of mRNA copied from the DNA base sequences by
RNA polymerase

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)

Initiation - begins when the RNA polymerase

binds to the promoter
1) Area of DNA that contains the gene is
unwound by RNA polymerase (enzyme)

Elongation - RNA moves along DNA in the 5’

to 3’ direction
2) RNA polymerase adds mRNA
nucleotides found in the nucleus to the
DNA template strand according to
base-pairing rules Termination - RNA polymerase
a) remember mRNA contains Uracil (U reaches a terminator region of the DNA
with T; T with A; C with G) 1) Once gene has been transcribed,
b) creates covalent bonds between the mRNA strand falls off
nucleotides of mRNA strand
Eukaryotic cells modify mRNA after transcription. (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

In prokaryotes, once the mRNA is synthesized, translation begins

immediately
● There is NO post-transcriptional modification of mRNA
❏ Draw and annotate: the steps of Transcription
Gene expression is regulated by proteins that bind to specific base sequences in DNA. (HL)
Eukaryotic cells modify mRNA after transcription. (HL)
Splicing of mRNA increases the number of different proteins an organism can produce. (HL)

Gene expression or repression

can be regulated by the environment surrounding the gene

● Specific proteins regulate how much transcription of a particular gene will occur

Promoter-proximal elements Enhancers Silencers

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)

Post-transcriptional modification of mRNA

a) The first product of transcription is pre-mRNA
○ Contains exons & introns
b) Non-coding introns are removed as pre-mRNA travels from nucleus to
ribosomes
○ removed through RNA splicing
c) Exons are spliced together to form mature mRNA
○ forms functional, mature mRNA
d) Caps are added to the ends to protect the mature mRNA
○ A poly A tail consisting of approximately 100-200 adenine nucleotides is
added to the 3’ end of mRNA
○ A 5’ cap is added to the other end
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)

The metabolism of lactose by E.coli is a good example

of gene regulation by negative feedback
● The lac operon regulates transcription of enzymes
○ Only happens when lactose is present

● An operon is a set of genes all linked to a single

promoter
● A promoter is a short DNA sequence situated just
before a gene
○ acts as a binding point for the RNA polymerase
enzyme
Gene expression is regulated by proteins that bind to specific base sequences in
DNA. (HL)

In the absence of lactose:

● repressor proteins block the production of the enzymes needed to break
down lactose in the cell

When lactose is present

● repressor protein is deactivated, allowing transcription to occur.
● As transcription occurs, enzymes are made and lactose is broken down into
glucose and galactose

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)

Analysis of changes in the DNA

methylation patterns. (HL)

Looking for patterns, trends and

discrepancies—there is
mounting evidence that the
environment can trigger
heritable changes in epigenetic
factors. (HL)
Transcription can be regulated through methylation or acetylation of histone tails

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

External environment Internal environment

○ In utero (mothers ○ Hormones

experience/choices) ○ Metabolism
○ Temperature ○ Exercise
○ Light exposure ○ Stress / inattentive parents
○ Diet
○ Medication / non prescription
drugs
Example 1:
In Himalayan rabbits, the expression of the C gene is regulated by temperature.
The gene is required for the development of pigments in the fur, skin, and eyes
(Sturtevant, 1913).
● temperature regulation of gene expression produces rabbits with a
distinctive coat coloring
○ the C gene is inactive above 35°C
○ maximally active from 15°C to 25°C
● In the warm, central parts of the rabbit's body, the gene is inactive, and no
pigments are produced therefore the fur color is white
● In the rabbit's extremities (ears, tip of the nose, feet), where the
temperature is lower than 35°C, the C gene actively produces pigment,
making these parts of the animal black.
Example 2:

During embryonic development embryos contain chemicals called

morphogens, which can affect gene expression and the fate of embryonic
cells depending on their position within the embryo.
● In the 1950-60’s Thalidomide was used by pregnant woman for morning
sickness
● It was thought it was harmless for humans but was not thoroughly tested.
● The drug caused severe developmental deformities in approximately
8,000 to 12,000 infants
○ born with stunted limb development
○ continues to be used in certain instances today (treatment of leprosy
& some cancer)
https://helix.northwestern.edu/sites/helix/files/styles/16by9/public/field/image/GettyImages_50674351_helix.jpg?itok=wklBTC54
More information on epigenetics
❏ For more information: watch the videos at Epigenetics - Utah Ed
❏ Complete: the interactive explorations “Gene Control” & “Lick your
Rats”.
❏ Read: Epigenetics and Inheritance, Nutrition and the Epigenome &
Epigenetics and the Human Brain.
❏ Reflect: on some of the
possible evidence that the
environment can trigger
heritable changes in
epigenetic factors
❏ Reflect: on some of the possible evidence that the environment can
trigger heritable changes in epigenetic factors

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)

2. temperature regulation of gene expression produces rabbits with a distinctive coat

coloring
a. the C gene is inactive above 35°C
b. maximally active from 15°C to 25°C

3. Certains drugs caused developmental deformities in children when used during

pregnancy.
Homework:
❏ Read Kognity: 2.7.3 DNA transcription
❏ Read Kognity: 7.2.1 DNA transcription and post-transcriptional modification of mRNA
Lesson 8
Translation is the synthesis of polypeptides on ribosomes

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

● Takes place at ribosomes in the

cytoplasm or on rough ER
○ Ribosomes consist of a large and a
small subunit
○ Ribosomes are made of rRNA and
protein
STEM Case - Protein Synthesis GIZMO
Handbook : DNA transcription and translation (10min?)

STEM case extension: identify mutations in transcription/translation, stem cells

therapy
The amino acid sequence of polypeptides is determined by mRNA according to the genetic
code. Codons of three bases on mRNA correspond to one amino acid in a polypeptide

1) mRNA carries information from specific gene on

DNA to a ribosome
a) mRNA strand consists of triplet bases called
codons
i) each triplet codes for a specific amino acid

2) mRNA binds to small subunit of ribosome

3) Transfer RNA (tRNA) with complementary

three-base anticodon binds to ribosome
a) mRNA codon AUG is called the START codon
because it signals the start of translation
- codes for Methionine
Translation depends on complementary base pairing between codons on mRNA and
anticodons on tRNA
4) tRNA with next complementary three-base
anticodon binds to ribosome
a) Maximum two tRNA bind at one time

5) Ribosome forms peptide bond between two

amino acids
b) first tRNA is released (by an enzyme)
to collect another aa
c) second tRNA holds dipeptide

6) Steps 4 & 5 repeat with tRNA and amino

acids as polypeptide is synthesized
Translation depends on complementary base pairing between codons on mRNA and
anticodons on tRNA

7) Polypeptide synthesis ends when stop

codons are reached
a) The three triplets, UAA, UAG,
and UGA are called STOP
codons
- tRNA do not hold amino acids

8) Completed polypeptide releases off

ribosome into cytoplasm

● There are 64 different triplet codons

that code for 20(ish) amino acids
The use of molecular visualization software to analyse the structure of
eukaryotic ribosomes and a tRNA molecule. (HL)

❏ Visit: Protein Data Bank

● Observe the three
dimensional shape of a
ribosome and its binding
sites
● You can right click on the
image to change different
aspects of how you view
the 3D shape of the
ribosome
tRNA-activating enzymes illustrate enzyme–substrate specificity and the
role of phosphorylation. (HL)
Ribosomes and tRNA facilitate the process of
translation

Ribosomes
organelles made from protein and rRNA that catalyze
the assembly of amino acids into polypeptides during
translation.

Ribosomes consist of two sub-units:

Small sub-unit
● Consists of 1 binding site for mRNA on the
surface of the ribosome
Large sub-unit
● consists of 3 binding sites for tRNA
molecules
tRNA-activating enzymes illustrate enzyme–substrate specificity and the
role of phosphorylation. (HL)
Large sub-unit
● consists of 3 binding sites for tRNA
molecules
○ A site (binds an aminoacyl-tRNA, tRNA
bound to an amino acid)
○ P site binds a peptidyl-tRNA (tRNA
bound to the peptide being synthesized)
○ E site binds a free tRNA (no amino acid
attached) before it exits the ribosome

● The space between the two sub-units of the

ribosome is where the polypeptide is
assembled
 tRNA
Transfer RNA has an anticodon to the mRNA code
on one “end” and carries a specific amino acid at the
other

During translation, tRNA attached to the ribosome

and transfers a specific amino acid to a growing
polypeptide chain

Sections of the tRNA become double stranded

through hydrogen bonds formed between base pairs
creating loops
● A triplet of bases form the anticodon which will
bind to the corresponding triplet codon on the
mRNA strand
● The base sequence of CCA at the 3’ end forms
the amino acid binding site
● Each tRNA binds with a specific amino tRNA
acid in the cytoplasm
○ Each reaction is catalyzed by a
specific tRNA-activating enzyme (21
specific enzymes for the 21 different
amino acids)

● Each specific amino acid binds

covalently to the 3' terminal nucleotide
(CCA) at the end of the tRNA molecule

● The binding of the specific amino acid to

the tRNA requires energy from ATP
❏ Draw and annotate: the steps of
Translation
Homework:
❏ Read Kognity: 7.2.2 Regulation of Transcription
❏ Read Kognity: 7.2.3 Nucleosomes & DNA methylation
❏ Read Kognity: 7.2.4 Epigenetics
❏ Watch DP Hickman Video 7.3 (26min-34min)
Lesson 9
Translation can occur immediately after transcription in prokaryotes
due to the absence of a nuclear membrane. (HL)

(homework later) Translation in Prokaryotes Interactive

https://www.labxchange.org/library/items/lb:LabXchange:049914b8:lx_simulation:1

Scroll down to see the step-by-step process of translation in prokaryotes.

Translation Interactive
Become a tRNA!!
 Initiation of translation involves assembly of the components that carry out the process. (HL)

Initiation (in greater detail)

1) mRNA binds to the small (30s)
ribosomal sub-unit.

2) tRNA carrying Methionine with the

anticodon UAC binds to the codon
AUG (start codon)
- this the initiation complex

3) The large ribosomal subunit binds

to the small ribosomal sub-unit
- the tRNA containing
Methionine binds at the P-site
of large subunit.
Synthesis of the polypeptide involves a repeated cycle of events. (HL)

Elongation (in greater detail)

1) While the first tRNA is still attached, a second
tRNA attaches to the mRNA at the A-site on
the ribosome, carrying the amino acid that
corresponds to the mRNA codon

2) The Methionine amino acid at the P-site binds

to the amino acid carried by the second tRNA
located at the A-site
- the two amino acids are joined together
through a condensation reaction that
creates a peptide bond between the two
amino acids

3) The ribosome moves along the mRNA one

codon shifting the tRNA that was attached to
Methionine to the E-site.
 Synthesis of the polypeptide involves a repeated cycle of events. (HL)

4) The tRNA is released back into the cytoplasm from the

E-site, allowing it to pick up another amino acid
(methionine) to build another polypeptide

5) Another tRNA moves into the empty A-site bringing the

next amino acid corresponding to the mRNA codon

6) The amino acid is attached to the polypeptide forming a

peptide bond, the ribosome slides across one codon and
tRNA at the P-site moves into the E-site releasing it back
into the cytoplasm

7) The ribosome continues to move along the mRNA

adding amino acids to the polypeptide chain

8) This process continues until a stop codon is reached

Disassembly of the components follows termination of translation. (HL)
Termination (in greater detail)
● Termination begins when 1 of the 3 stop codons (UAA, UGA, UAG) moves into
the A site

● These tRNA have no attached amino acids

● 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

The amino acid R group is a

term that refers to the variable
group on each amino acid.

The amino acid backbone is

similar on all amino acids ,
and the R groups are different
on all amino acids.
The biological activity of
a protein is related to its
1o, 2o, 3o & 4o structure.

Denaturing proteins
changes their shape &
disrupts their biological
activity.
The sequence and number of amino acids in the
polypeptide is the primary structure. (HL)

● The amino acid sequence of the polypeptide

chain attached together by peptide bonds
○ can consist of any of the 21 amino acids
○ is coded for by a gene in the DNA

● The sequence of amino acids determines the

shape of the other three levels of protein
structure
The secondary structure is the formation of alpha helices and
beta pleated sheets stabilized by hydrogen bonding. (HL)

● Created when hydrogen bonds form between the

carboxyl (C=O) group and amino group (N-H) of
amino acids in different parts of the polypeptide
○ NOT bonds between the R-groups

● Two main structures formed are the alpha helix and

the beta pleated sheets
○ locally defined so there can be many different
secondary structures present in a single protein
molecule

● Proteins with secondary structure are generally

structural in nature like the secondary structure in silk
The tertiary structure is the further folding of the polypeptide
stabilized by interactions between R groups. (HL)
● Develops a 3-D shape because of the interactions
that occur between the R groups.
○ Disulphide bridges form between sulphur
atoms on the R-groups of cysteine
○ Hydrogen bonds form between two polar
R-groups
○ Ionic Bonds also form between positive &
negative R-groups

● Hydrophobic (non-polar) R-groups turn inwards

away from water and hydrophilic (polar) R-groups
face outwards towards the water
● Protein is globular in nature
The quaternary structure exists in proteins with more
than one polypeptide chain. (HL)

● Refers to the way two or more polypeptides fit

together
○ Insulin (2 polypeptide chains)
○ Hemoglobin (4 polypeptide chains)

● Also refers to proteins that contain additional

components
○ Hemoglobin also contains 4 heme groups
○ Proteins with prosthetic groups are
called conjugated proteins
Protein Folding Interactive
https://www.labxchange.org/library/items/lb:LabXchange:f93a9e87:lx_simulation:1

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

Primary Secondary Tertiary Quaternary

Structure

Shape

Bonds
Formed

Other
❏ Distinguish Between: the different levels of protein structure including structure, shape and type of bonds

Primary Secondary Tertiary Quaternary

Sequence of Polypeptide coils Polypeptide forms an Complex of active 3D

Structure aa’s (α-helix) or folds
active 3D globular protein globular protein
(β-sheet)

Chain-like Made from 2+ polypeptides

Shape α-helix or β-sheet More folding (3D)
sequence

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)

Polysomes attached to a growing

mRNA molecule in a prokaryote.
Identification of polysomes in electron micrographs of prokaryotes and eukaryotes.

In eukaryotes, the mRNA detaches

from the DNA, is transported
through pores in the nuclear
envelope to the ribosomes in the
cytoplasm. Once in the cytosol,
eukaryote mRNA can also form
polysomes (right)

Electron micrograph of polysome in an eukaryotic

cell (salivary gland). The green areas are
proteins, blue are ribosomes and the areas in pink
are mRNA.
Credit: DR ELENA KISELEVA SCIENCE PHOTO LIBRARY
STEM Case - Protein Synthesis GIZMO
STEM case extension: identify mutations in transcription/translation, stem cells
therapy (30min)
Use a table of the genetic code to deduce which codon(s) corresponds to which amino acid.
Use a table of mRNA codons and their corresponding amino acids to deduce the sequence of amino
acids coded by a short mRNA strand of known base sequence.
Deducing the DNA base sequence for the mRNA strand.

The genetic code is considered

“degenerate” because more
than one triplet codon can code
for a specific amino acid
Exam tip
You do not need to know the names

of all the amino acids and their

abbreviations, but you must be able

to:

● Read the genetic code.

● Deduce which codon(s)
corresponds to which amino
acid.
● Deduce the sequence of
amino acids coded by a short
mRNA strand of known base
sequence.
Other example
❏ Transcribe: a strand of mRNA from the DNA
strand below and then identify the correct
amino acids in the polypeptide strand

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

mRNA Strand 5’ AUG 3’

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

AUG AGC GGA AAA UUU CGA UCA UGA UGA

mRNA Strand 5’ AUG 3’

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

Practice the steps to transcribe and translate from a DNA double-helix.

Homework:
❏ Read Kognity: 7.3.4 Ribosomes & Polysomes
3.1-3.2 Study Checklist
1. Draw & label a typical prokaryote cell
2. Draw & label a typical eukaryote cell
3. Compare chromosomes of prokaryotes and eukaryotes
4. Define the following terms and explain their connections
a. allele
b. centromere
c. chromatid
d. chromosome
e. diploid
f. gene
g. haploid
h. karyogram
i. locus
5. Explain the difference between autosomal chromosomes & sex chromosomes
6. Use a karyotype to determine genetic sex & diagnose Down syndrome
7. Explain how sickle cell anemia is caused by a single base mutation
2.6 & 7.1 DNA & RNA Study Checklist
1. Outline the steps of the Hershey Chase experiment
2. Draw and label:
a. RNA
b. DNA
3. Calculate how much Thymine will be present if a DNA strand contains 42% Cytosine
4. Explain how DNA is replicated for cell division
5. Outline Meselson and Stahl’s evidence for semi-conservative replication of DNA
2.7 & 7.2 Transcription Study Checklist
1. Describe the transcription of DNA to form mRNA
2. Including post-transcriptional modification
3. Outline how genes can be regulated with reference to:
a. Promoter-proximal elements
i. Operon
ii. Promoter
b. Enhancers
c. Silencers
d. Repressors
4. Explain the importance of epigenetics with reference to methylation & acetylation
2.7 & 7.3 Translation Study Checklist
1. Describe the translation of mRNA to form a polypeptide
a. Including initiation, elongation and termination
2. Compare and contrast translation in prokaryotes and eukaryotes
3. Correctly use a codon chart to transcribe & translate DNA into a polypeptide (chain of
amino acids)
4. Distinguish between the primary, secondary, tertiary & quaternary structure of a protein
Lesson 12 - Assessment

❏ Complete: 3.1-3.2, 2.6-2.7 & Unit 7 Written Test

Homework after assessment
Prepare for lab activity

DP Hickman Bio Video 3.5 0-7:30min

3.5 Genetic technologies
Prepare for lab activity (homework class before)

DP Hickman Bio Video 3.5 0-7:30min

PCR mechanism DETAILED : https://www.labxchange.org/library/items/lb:LabXchange:f7f6962a:lx_simulation:1

GIZMO DNA Profiling : Actual practice for bands
DNA Profiling

Before BLAST activity

Assign Kognity Reading 3.1.5, 3.2.5 - Databases and genomics analysis

+ DP Hickman Video 3.3 (0-14min)

After BLAST Activity :

Kognity Reading 3.5.1, 3.5.2 and 3.5.3 - Gel electrophoresis, PCR and DNA profiling

+ DP Hickman Video 3.3 (14min-end)

Pro-Teens Making Proteins
IB Biology 11 HL
Goal
● Each amino acid has a specific name and also a specific letter that represents
it.
● At the end of this activity, if you have done the correct code, the single letters
will spell out the correct response to the the following statement:

“This protein codes for the heart of science”

Our job for today…
1. Everyone will be assigned a different role in the theatrical production of
“Translation”
2. You will be using the items provided to your class to correctly build the
polypeptide according to the mRNA codons.
3. Use the safety pins on the styrofoam balls to grow the polypeptide at the
correct sites on the ribosome.
4. Use the role/action table on the next slide to help direct the assembly.
5. You will be directed by the chaperone proteins (Ms. Simard & Mr. Osborne)
Roles and Items

Role Items/Actions

mRNA Controllers Hold each side of the mRNA strand (string)

(2 people) and in charge of moving the mRNA through
the ribosome.

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

tRNA Will hold a ball labelled with an amino acid

(everyone else, randomly assigned) as well as the coordinated anticodon.
Safety pins on each side represent the
peptide bonds.