Biological Psychology
Learning goals, Lectures, Practical lectures, Book chapters
Chandler, Obligatory articles/crash courses, terms
By Kelly van Helvoirt, year 2021/2022
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,Table of contents
Part 1: Basic Biology
Lecture 1: Evolution ~ Dr. Paula Mommersteeg - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - p3
Chapter 2 Chandler: Genetics and evolution
Lecture 2: Communication ~ Dr. Paula Mommersteeg - - - - - - - - - - - - - - - - - - - - - - - - - - - - p20
Chapter 4 Chandler: The Neuron, the Endocrine System and Communication
Lecture 3: Development ~ Dr . Reneé Otte - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - p41
Chapter 3 Chandler: Neural development
Crash courses
Lecture 4: The immune system ~ Dr. Paula Mommersteeg - - - - - - - - - - - - - - - - - - - - - - - - - p56
Practicum 1: The immune system
Online book chapter 17: The Immune System and Disease
Lecture 5: Homeostasis ~ Dr. Paula Mommersteeg - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - p76
Chapter 15 Chandler: The Neural Regulation of Homeostasis: Feeding and Drinking
Part 2: Sex, Drugs and Rock-‘n-roll
Lecture 6: Psychopharmacology ~ Dr. Paula Mommersteeg - - - - - - - - - - - - - - - - - - - - - - - - p90
Chapter 7 Chandler: Psychopharmacology
Lecture 7: Emotions ~ Prof. Dr. Ad Vingerhoets - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - p107
Chapter 17 Chandler: Emotion
Lecture 8: Sex ~ Dr. Dounya Schoormans - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - p121
Practicum 2: Sex
Chapter 14 Chandler: Sex
Lecture 9: Personality ~ Dr. Dounya Schoormans - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - p133
Online Article Smith: Personality as Risk and Resilience in Physical Health.
Part 3: Advanced Psychobiology
Lecture 10: The heart and the brain ~ Prof. Dr. Wijo Kop - - - - - - - - - - - - - - - - - - - - - - - - - - p142
Book chapter Kop & Gottdiener: The interaction between psychologic distress and
biobehavioural processes in cardiovascular disease
Lecture 11: Social interactions ~ Prof. Dr. Wijo Kop - - - - - - - - - - - - - - - - - - - - - - - - - - - - - p166
Online article Cikara & van Bavel: The Neuroscience of Intergroup Relations
Online article Sapolsky: The influence of social hierarchy on primate health
Lecture 12: Depression ~ Dr. Dounya Schoormans - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - p186
Practicum 3: Depression
Chapter 22 Chandler: Affective disorders
Lecture 13: Stress and Anxiety ~ Dr. Dounya Schoormans - - - - - - - - - - - - - - - - - - - - - - - - - - p197
Chapter 23 Chandler: Stress and anxiety
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,PART 1: BASIC BIOLOGY
We focus on basic human physiology. We start at the lowest level; DNA, and work our
way up in gradually increasing complexity such as development, the endocrine system,
the immune system, and homeostasis.
Lecture 1: Evolution ~ Dr. Paula Mommersteeg
Evolution, heredity, and our DNA
Learning goals
- Understand and reproduce support for the evolution theory
- Explain how characteristics are passed on from one generation to another
- Describe and use examples of Mendelian genetics and inheritance
- Understand and describe the function of DNA
- Describe the process from DNA to functional protein
- Understand and describe genetic variation, different forms of genetic variation, mutations, and
tandem repeats
- Explain the basics of epigenetics, behavioural genetics and how this is relevant for psychology
Can you inherit depression:
Is there a depression gene? → no one simply inherits depression from their mother or father. Each
person inherits a unique combination of genes from their mother and father, and certain combinations
can predispose to a particular illness.
Life on earth is about 4,5 billion years old and we as humans have not been around for very long.
Almost 2 million years ago the first human-like figures started life on earth. Before that, there were
other life forms on earth. The interesting thing is that we are made from the same building blocks and
mechanisms.
Modern taxonomic groups from their common ancestor
We can use this to see where we are as humans in
perspective of all life on earth. We are grouped under
animals which means we are more closely related to fungi
and slime molds than all the bacteria. But we all share
some similar characteristic with all of the life groups.
The story about Adam and Eve, which tells us about how we can trace humans back to our ancestral
male and female form via chromosomes or mitochondria.
Descent of humans:
Homo sapiens have evolved about 200000 years ago while other species are around for 2 million
years. All humans belong to the same species – homo sapiens
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, men all have a Y chromosome (XY) and women have 2 X
chromosomes (XX). So you always inherit your Y chromosome from
your father.
Y-chromosomal Adam: our most recent common ancestor who shares
a similar Y chromosome can be traced back. So when differences have
emerged in the Y-chromosome overtime, those differences can be
traced back to ancestral forms until the hypothetical first human male
on earth. Y-chromosomal Adam = most recent common ancestor from
whom all currently living people are descended (patrilineal (=via the
male)).
Mitochondrial Eve: All humans start of as an egg and all eggs contain
mitochondria which are the energy factories of a cell. And all mitochondria are already in the egg
when the sperm enters so it comes from your mother. You can therefore look at the little differences
that have emerged in the mitochondria DNA and trace back the women line of descent. Mitochondrial
Eve = the most recent woman from whom all living humans are descender matrilineally (via the
mother) through transmission of mitochondrial DNA.
Out of Africa Theory:
A theory that the first ancestral human life form started off in Africa and then migrated and spread
across the earth. Then evolved and adapted to their environment
Alternative theory:
Human life started in Eurasia
Human genetic variation:
- All humans are 99.9% genetically identical (we have the same codes for how to construct a
human)
- The 0.1% genetic differences between humans makeup all the differences between people.
The human genome project: identified the genetic makeup of humans completed in 2003. A
collaboration between different scientists. In 2003 they had a first human genome completely
sequenced, so they knew exactly what the letters of that person were (genetic makeup).
In total all this code to make a human are divided into parts that make up genes.
- Gene: a small part of your DNA of your genetic makeup which is a code/instruction for how
to make a protein.
- In total there are 3 billion nucleotides or ‘letters’ that makeup the four letter DNA alphabet
(A-T - C-G). A and T are always a base pair and C and G as a base pair.
- Less than 2% of the DNA are functional genes coding for proteins. (there is a lot of stuff in
our DNA of which it’s unclear what it does there or something else than coding for proteins)
proteins is how humans are build.
Amazing DNA:
Each cell in our body contains about 5cm of DNA.
A human has about 10 trillion cells.
So if all DNA in your body would be stretched out, it would reach the
sun and back four times!
This DNA is tucked neatly inside your cells and not randomly. There is
an exterior boundary with a little ball on the inside (nucleus), inside this
nucleus the DNA is neatly rolled up into chromosomes, the chromosomes
make this rolled up DNA spiral.
Charles Darwin
Described his trip around the globe in his book “the voyage of the beagle” ~ (1831-1836)
And collected a lot of specimen which he observed and described.
1837: He wrote a note about why some species looked more alike than other species. That’s still true
for today (all life is related to each other).
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, ➔ Years later in 1858 Alfred Russel Wallace wrote down an idea: “on the tendency of varieties
to depart indefinitely from the original type”. → same principle as Darwin.
1859: Darwin wrote a short summary of his idea: “on the origin of species by means of natural
selection”.
Evolution: Natural selection steps
Traits becoming more common based on these key steps:
Moths of the same species, in some circumstances e.g. with dark trees its easier for the black moth to
survive and reproduce because it gets eaten less (camouflage).
1) Variation in species: 1 species of moths, but they’re different)
2) Heritable traits: both variation in species can have children with the same traits.
3) Struggle for existence: these moths can go auround and live
their lifes but some moths get eaten by birds earlier than other
moths (depends on the environment) not all species can
survive and reproduce.
4) Survival and reproductive rate: not all moths are eaten
equally and not all moths can therefor reproduce and spread
their traits into the next generation.
Evolution in real-time: bacteria evolving resistance to antibiotics:
Microbiologist Michael Baym explains how bacteria move as they
develop resistance to drugs.
By building a 2 feet by 4 feet petri dish with 9 bands and at the base
of each of these bands a normal petri dish thick agar with
different amounts of antibiotic.
across the top of it pour some thin agar that bacteria can
move around in. First you see that the bacteria spread in the
area where there no antibiotic up until the point they can no
longer survive. Then a mutant appears which is resistant to
the antibiotic and spreads until it starts to compete with
other mutants around it. When these mutants hit the next
boundary, they too have to pause and develop new mutations to
make into ten times as much antibiotic. They repeat this step all the
way and after about 11 days they are resistant to as much as 1000x
more antibiotic. Bacteria that are normally sensitive to an antibiotic
can evolve resistance to extremely high concentrations in a short period of time.
➔ What does this have to do with psychology?
Human karyotype:
= karyotype: (of a human) an organised set of chromosomes
Human cells that start to divide, then all the DNA in the nucleus start to
fold up neatly into chromosomes. You inherited 1 chromosome from each
parent which make matching pairs. If you make a snapshot at the moment
of cell division, you can match up these pairs of chromosomes and align
them and see all 23 pairs of chromosomes (46 chromosomes).
22 identical pairs form mother and father and 1 set of ‘sex’ chromosomes
- Female: X and X chromosome
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, - Male: X and Y chromosome
o X chromosome is a longer stripe and they Y
chromosome is short (the last one in the picture on the
bottom right is a sex chromosome of a male (XY)
In the right visualisation you see a schematical karyotype
This is a karyotype of a human with the condition of down syndrome
→ the human has an extra copy of chromosome 21.
= Trisomy 21
DNA in the cell:
Genome: whole of the genetic information of an organism, in the cell
each nucleus contains a whole genome of an organism. A genome
comprises of more chromosomes in humans 46.
Nucleus: Middle part of the cell, where the DNA is stored
Chromosomes: long strand of DNA wound around histones.
(Inside the nucleus) – this is a chromosome that is about to
divide into different cells.
Centromere: things hook on this part of the
chromosome so every chromosome can be pulled
towards a new cell.
Telomere: region at the end of the chromosome.
Protects the DNA during cell division. With every
cell division the telomere gets shorter till it reaches a
moment that it’s too short to divide and self-
destructs
Histones: proteins used, to fold DNA, so it doesn’t
become entangled
Base pairs: DNA consists of nucleotides (A-T) and (C-G)
Gene: a part of DNA that codes for creating a protein. (instruction)
Allele: two variants of a gene found on the same place on a
chromosome.
Alleles:
Homozygous for dominant allele: When both alleles (on the
chromosome of father and mother) are identical and dominant.
Homozygous for recessive allele: when both alleles are
identical and recessive
Heterozygous: When both alleles are different; one is
dominant and one recessive. The dominant allele will
determine which trait is going to be expressed.
Dominant: you only need 1 copy of the gene in
order to get this trait.
Recessive: you need 2 copies of this gene in order
to get this trait
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,Autosomal dominant trait:
Autosomal dominant: it doesn’t matter if a specific illness is on 1 or
both chromosomes. When there is one allele with the condition, you get
the illness. E.g. Huntington. Huntington will out itself around your 40th
year and you will probably already have children by then, so you could
not know about that gene before that.
In the example on the right:
- The mother is homozygous for the condition (not affected on
both alleles)
- The father is heterozygous for the condition (affected on one
allele)
- The next generation can inherit a combination of alleles 1 from
mom and 1 from dad. When the next generation inherits the
affected allele they automatically will get the condition because
the condition is dominant. 50% chance of passing on the affected allele
X-linked recessive heritability
Recessive: you need 2 copies of this gene in order to have the
condition. (or an absence of the copy).
Heterozygous: 2 different alleles (for the mother)
X-linked: gene not present on the Y chromosome (males)
With 1 copy of the gene on 2 X chromosomes (in women) you don’t
have the condition but you’re a carrier and can give this allele to your
children. (the condition can only take place on the X chromosome). If
these people get offspring. A daughter with 2 X chromosomes can
either get the affected X chromosome of mom with the unaffected
chromosome of dad (carrier but no disease) or the unaffected
chromosome of mom with the unaffected chromosome of dad
(unaffected daughter). However a son can only get the Y chromosome
of dad that cannot be affected and then either the 1 of 2 X
chromosomes of mom. which means this can also be the affected X chromosome of mom in 50% of
the cases. When this is the case, the son will get the disease with only one affected gene, because there
is no dominant variant of the allele on the Y-chromosome.
Genotype and phenotype:
Genotype: genetic makeup of a cell in an organism
Phenotype: observed trait in an organism based on genes and environment
A black and a white moth can have similar genotypes but express different phenotypes.
Selection can occur for certain phenotypes. E.g. a dark moth can survive
better on dark trees than light moths.
Phenotype ca also be sensitivity for food reward, becoming depressed,
tendency to be persistent, chance to develop diabetes.
Why women are stripey:
Epigenetics: changes in gene expression due to factors other than changes in the DNA sequence.
Usually chromosomes just look like a wiggly thread within a nucleus. In order to not get tangled the
DNA is wrapped around proteins called histones. Those histones have wiggly tails. The 23th set of
chromosomes is the sex chromosome (XX = female), (XY=male). Since the male chromosome are
different, both can remain active for the rest of their lives. For females one of the X chromosomes
needs to be inactivated in order for proper development to occur. This happens when a female embryo
is just 4 years old. In a cell both the X chromosome from mom and the X chromosome of dad are
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,active. But through a tiny molecular battle one of the X chromosomes wins and remains active, while
the other X chromosome is inactivated by packing the DNA closes together and making modification
to those histone tails that signal this inactivation. New structural proteins are added to bind everything
closer together and metal groups (tiny molecular markers) are added to the DNA to signal to the cell
that this DNA shouldn’t be read. The active X chromosome DNA is more spread out, which allows
better access to the genes on the chromosome. Histones can be slid along the DNA or removed
entirely and histone tails have a different modification, signalling this DNA is active. All of this makes
it possible for RNA polymerase to access and transcribe this DNA into messenger RNA which then
goes out into the cell and is used to make a protein. It seems random which X chromosome wins
(fathers’ or mothers’). When these cells divide they keep their active X chromosome and will give this
to new cells and continues on into adulthood. So if you could look at a woman’s skin and see which X
chromosome has been inactivated you would see a striped pattern which shows the growth and
migration of all of the cells when this person was only 4 days old.
You can see this phenomenon in calico cats and that’s because the gene for fur colour is on the X
chromosome. So only female cats can be calico cats, because only they can inherit 2 X chromosomes
with 2 different colour genes.
What does DNA do?
DNA: Deoxyribonucleic acid
DNA is a recipe for proteins and consists of 2 chains of nucleotides
that are connected to each other with on the outside a sugar-
phosphate layer. It looks like a double helix.
Nucleotides: the letters ATCG
base pairs: the letters that form pairs where A and T are opposites
and C and G are opposites.
Where do this processes take place?
Transcription: Takes place in the nucleus where the DNA is located.
A piece of DNA, a gene is copied (=transcription) into messenger
RNA (mRNA)
Translation:
Translation takes place in the cytoplasm when the mRNA goes out
of the nucleus. mRNA of the gene is then “translated” into a protein
at the ribosome (huge protein = protein factory)
The genetic code: (how translation takes place)
3 nucleotides/letters combined form a combination which is related to a specific amino acid. This is
called a triplet code/codon
A gene contains information for making a protein and
proteins are made of amino acids which there are 21 of.
Step 1: transcription: DNA to RNA
Transcription of
a gene from the DNA template to primary RNA.
A piece of DNA gets rolled off so on one side proteins can
attach. Then an exact copy can be made of one half =
primary RNA transcript
Difference RNA from DNA: U instead of T nucleotide (T
becomes A in RNA / A becomes U in RNA). RNA is
shorter than DNA (because it only has 1 gene) and can leave the cell nucleus.
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,Step 2: slicing RNA into mRNA
Before those RNA transcripts are ready to exit the
nucleus another process takes place which is called
splicing and is like cleaning up the recipe book and
excluding sections that are not necessary. The primary
RNA transcript has a certain length and parts of it are
combined and are called the exons. The exons leave/exit
the nucleus and form a new piece of (mRNA) and is
then transported to the next phase. Certain parts are
removed (introns). Introns stay in the nucleus and get
recycled.
Step 3: Translation of mRNA into a chain of amino acids
Orange bulb = ribosome
Green things = separate molecules
mRNA is pulled though the ribosome
The primary mRNA that just left the nucleus no goes into
a huge protein factory called the ribosome. On the one
hand the mRNA combines with the ribosome and then the
whole translation process takes place. This happens in a
specific order. The first 3 letters that entered the ribosome
left there other side of the base pair (e.g. U leaves A) the
letters that are left behind of the mRNA are called
transfer RNA (tRNA). Now there are two codons (3
letters combined) that combine with the tRNA anticodon at the ribosome unit which has opposite
codes to the mRNA. On one side the tRNA has an anticodon and on the other side it has an amino acid
attached to it. The mRNA keeps moving an pulling through the ribosome so new codons are displayed
that match with tRNA and make new proteins formed by matching amino acids that form a chain.
tRNA: a protein which can transfer an amino acid on the ribosome to start making a new protein.
Each tRNA molecule has an amino acid on one end and an anticodon on the
other. In this example mRNA: UGG codon combines with tRNA ACC
anticodon, with the amino-acid tryptophan on the other end. Appropriate codon
combinations meet at the ribosome determining the order of amino acids in the
growing protein chain.
Amino acid chain at the ribosome: the protein
Each new amino-acid combines with the previous one and start to
form a chain: the protein
When the mRNA is finished, the primary protein is complete. The
mRNA may combine again with a ribosome to repeat the process.
Step 4: post-translational protein processing
This is not the completion of the protein yet. Sometimes proteins need
to be folded or some newly arrived large proteins have to be cut
into smaller proteins, creating multiple proteins. (proteins do not
always have to undergo these additional steps)
Control of protein synthesis on DNA level:
There are certain processes that decide if a gene gets transcribed
or inhibited:
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, - Promoter region: region prior to the area where
a gene gets cancelled. Molecules (transcription
factors bind to this and determine if a gene gets
cancelled or not.
- It’s also possible that a signal on the outside of
the cell (extracellular signal) binds to a receptor
which causes an activation in the transcription
factor and then migrates to the nucleus where it
binds to the promoter region and cancels a gene
or inhibits a gene so it produces less proteins.
So the process of when we need a certain protein is regulated very carefully via transcription. When
we need a protein it will be activated and when we don’t need it, it will be inhibited.
From mRNA to secreted protein (because proteins need to be either
released to the environment and taken up into the bloodstream and
transported via vesicles all over your body to reach cells where they can do
something. Or some proteins you need in your own cell so its gets build up
within a cell (e.g. to slice)
Summary: from gene to protein
Cell: basic unit of all living tissue in most human cells there is a structure
called a nucleus which contains the genome. In humans the genome is split
into 23 pairs of chromosomes. Each chromosome contains a long strand of
DNA tightly packaged around proteins called histones. Within the DNA
there are sections called genes. These genes contain the instructions for
making proteins. When a gene is switched on an enzyme called RNA
polymerase attaches to the start of the gene. It moves along the DNA
making a strand of messenger RNA (mRNA) out of 3 bases in the nucleus. The DNA code determines
the order in which the 3 bases are added to the mRNA. This process is called transcription. Before the
mRNA can be used as a template for the production of proteins, it needs to be processed. This involves
removing and adding sections of RNA. The mRNA then moves out of the nucleus to the cytoplasm.
Protein factories inside the cytoplasm called ribosomes bind to the mRNA. The ribosome read the
code in the mRNA to produce a chain made up of amino acids. There are 20 different type of amino
acid. Transfer RNA (tRNA) molecules carry the amino acids to the ribosome. The mRNA is read 3
bases at a time. As each triplet is read a tRNA delivers an amino acid. This is added to a growing chain
of amino acids. Once the last amino acid has been added, the chain folds into a complex 3D shape to
form the protein
Proteins, enzymes and what can go wrong
What do proteins do
Proteins: molecules that are made of amino acids.
Examples:
- Building blocks of your body, e.g. muscle fibers are proteins
- Can become part of the cell membrane (fatty layer that encloses the cell) to form receptors for
neurotransmitters or hormones
- Are part of the cell structure and function e.g. cytoskeleton, muscle contraction, connecting
cells
- Combines with other proteins and iron to transport oxygen (haemoglobin) in red blood cells
- Form ribosomes in order to create new proteins
- Products of the immune system to kill invaders
- Some function as hormones or even neurotransmitter
- Can serve as fuel for energy and heat production
- Can be an ENZYME to metabolize chemical reactions (cellular glue or scissors)
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