Biology notes

CHAPTER 1 CELL STRUCTURE........................................................................................2

Cell structure.................................................................................................................2
Organelles......................................................................................................................2
Plant cell........................................................................................................................4
CHAPTER 2 BIOLOGICAL MOLECULES........................................................................6
Monomers, polymers and macromers...........................................................................6
Carbohydrates................................................................................................................6
Disaccharides and glycosidic bonds.............................................................................7
Polysaccharides.............................................................................................................7
Triglycerides and phospholipids...................................................................................7
NUCLEIC ACIDS AND PROTEIN SYNTHESIS................................................................8
Structure of DNA and RNA..........................................................................................8
Structure of ATP............................................................................................................8
DNA replication............................................................................................................9
Protein synthesis............................................................................................................9
Sickle cell anemia..........................................................................................................9
CHAPTER 3 ENZYMES.......................................................................................................10
Lock and key and induced fit hypothesis....................................................................10
THE HEART...........................................................................................................................10
Cardiac cycle...............................................................................................................10
Chapter 1 cell structure

Cell structure

This chart show some organelles that cell like virus, plant and animal have in common.

Main difference between bacteria and plant and animal cells is that bacteria’s

ribosomes are smaller

bacteria don’t have membrane bound organelles such as mitochondria and vacuole,

bacteria doesn’t have a nucleus or a full DNA chain.

Organelles

Nucleus
Definition: a relatively large organelle found in eukaryotic cells, but absent in prokaryotic cells.
It contains the cell´s DNA. The main job/ function of the nucleus is to provide a closed
environment for the genetic material

• The nucleolus is considered as occupying 25% of the volume of the nucleus.

• The nucleus is the house for cells’ genetic material.
• It maintains a closed environment or a compartment inside the cell.
 • Transcription of eukaryotes occurs inside the nucleus (Eukaryotic translation occurs in
the cytoplasm).
• The nuclear pores work by only allowing a molecule with a specific size to come in
The major function of the nucleolus is the ribosome biogenesis.
• Therefore, the nucleus consists of mainly DNA whereas nucleolus consists of RNA.
• The main difference between nucleolus and nucleus is that nucleolus is a sub-organelle
located inside the nucleus whereas nucleus is a membrane-bound organelle in the cell.
Ribosomes
Definition: A tiny organelle found in a large number in all cells. Are made of RIBOSOMAL RNA
and protein. They consist of 2 subunits and they are the SITE OF PROTEIN SYNTHESIS

Functions:

 Create chains of amino acids/ proteins, it works by being able to make pass mRNA and
then tRNA in an exact order, so that amino acids are being left in the right order.
Other information about the ribosomes are:
 Its mainly found in the rough endoplasmic reticulum(RER)
 They are composed of ribosomal RNA and proteins
 The Ribosomal RNA is synthesized in the nucleolus.
 It consist of two unequal subunits a large dome shaped and a smaller ovoid one. The
smaller subunits fits over the larger one like a cap.
 ribosomes are of two types 70s and 80s, the 70s type of ribosome are found in all
prokaryotic cell and 80s type are found in eukaryotic cells.

Cell membrane
Definition: A very thin membrane surrounding all cells, it is partially permeable and controls
the exchange of materials between the cell and the environment.

Is a bilayer of phospholipids made up by more substances that make up the mosaic model

Golgi apparatus
Definition: an organelle found in eukaryotic cells. It consist of a stack of flattened sacs
consistently forming at the end.

The Golgi apparatus is a stack of flattened sacs. The Golgi body collects all sorts of molecules,
mainly the processed proteins that come out of the ER.

Then this molecules are transported by the Golgi vesicles that are circular bubbles much like
the lysosomes, and this are secreted on to their destination.

Mitochondria
Definition: the place where aerobic respiration takes place.

The main function of a mitochondrion is to carry aerobic respiration and release energy as ATP,
although it can do other things like the synthesis of lipids. The ATP is created by the synthesis
of sugars and fats.
The mitochondrion is often referred to have a sausage like shape , it measures between 1
micron.

Endoplasmic reticulum
Definition: a network of flattened sacs running through the cytoplasm of eukaryotic cells. Its
continuous with the outer membrane of the nuclear envelope.

There are 2 parts of the Endoplasmic reticulum

 the rough
 the smooth

The rough endoplasmic reticulum (RER), follows the nucleus and is the place where most of
the ribosomes are found. So it’s the main place where proteins are formed.

The smooth endoplasmic reticulum (SER), produce lipids and steroids (cholesterol) and
reproductive hormones (oestrogen and testosterone)

Lysosomes
Definition: A spherical organelle found in eukaryotic cells. It contains digestive enzymes and
has a variety of destructive functions such as removal of old organells.

Lysosomes are used as a way of transporting enzymes from inside a cell to outside or to the
place where their action is needed. Its surrounded by a single wall membrane and inside
there’s enzyme complex .

Centrioles Microtubules an microtubule organism center (MTOC’s)

Definition: one of two cylindrical structures made from microtubules found just outside the
nucleus in animal cells in a region known as the centrosome

A centriole is a hollow cylinder about 500 nm long and 200 nm wide. Each centriole is made
up of nine triplets of microtubules, that is composed of a series of alpha and beta tubulins.

Then when there’s a pair of centrioles that is called a centrosome. The main function of a
centrosome is to gide the genetic information into a new nucleus by making a spindle shape.

Plant cell
Vacuole
The vacuole is a place surrounded by a membrane called the tonoplast, and it stores the water
in form in cell sap. The way that that water goes in is by diffusion as the tonoplast acts as a
semi-permeable membrane.

Chloroplast
The chloroplast is the main site of photosynthesis.

The light is absorbed by the pigment, then the light is used to brake down water and carbon
dioxide into oxygen and glucose plus energy as ATP, the opposite process than the one used in
the mitochondrion , in animal cells.
Cell wall

The cell wall is an organelle outside the cell membrane that not only gives/ determines a shape
but also prevents the cell from bursting.

This wall is made out of cellulose, in the case of plants as bacteria’s cell wall is not made out of
cellulose.
Chapter 2 biological molecules

Monomers, polymers and macromers

 Monomer: is a relatively simple molecule which is used as a basic building block for
the synthesis of a polymer, usually by a condensation reaction. Examples nucleotides,
amino acids.

 Polymer: is a molecule made up from many similar repeating subunits joined together
in a chain, this subunits are much smaller and are known as monomers.

 Macromer: is a large molecule such as a protein.

Carbohydrates
All carbohydrates are made up from hydrogen, carbon and oxygen and have the same formula
of Cx(H2O)n.

These carbohydrates are separated in 3 groups:

Monosaccharides
Monosaccharides are sugars, that easily dissolve in water it follows the general formula of
(CH2O)n and consist of a single sugar molecule.

The most common monosaccharide is glucose. Glucose has the molecular and structural
formula of C6H12O6 and it has a ring shape. Glucose can have an -OH either above or bellow
its ring structure in carbon nº 1, and this slight change determines weather a glucose is α or β.

This slight change determines if the glucose is going to determine what molecule is going to be
build up.
Disaccharides and glycosidic bonds
Disaccharides is a sugar that consist of 2
monosaccharides joined up by a glycosidic
bond.

The most common disaccharides are

maltose( 2 alpha glucose), sucrose ( glucose
+ fructose),lactose (2 beta glucose)

All of this molecules are disaccharides, which

are connected by a glycosidic bond. When to
OH line up a bridge is created, this bridge is
a called a glycosidic bond, and it happens
trough a condensation reaction, this means
that apart from the disaccharide H2O is a
product from the reaction. In order to brake
a condensation reaction a hydrolytic
reaction has to take place, this means to add
water.

Polysaccharides
A polysaccharide is a polymer made up from many monosaccharides. They themselves are not
sugars, rather it’s a way we can store big amounts of energy in one place, as if glucose itself
accumulated in cells then it would dissolve, which would affect to the cells osmotic properties,
glucose is also a very reactive molecule so it prevents changes in its chemistry.

Starch and glycogen

Starch is a mixture of amylose and amylopectin.

 Amylose is a long continuous chain of alpha glucose with a 1-4 glycosidic bond.
 Amylopectin is a shorter chain of alpha glucose with 1-4 and 1-6 glycosidic bonds.

Starch can be found in vegetables like potatoes, but never found in animal cells. In animal cells
instead of starch the body produces glycogen for the storage of carbohydrates. Glycogen like
amylopectin has 1-4 and 1-6 glycosidic bond but its more branched than starch.

Cellulose
Cellulose it’s a polymer made of beta glucose, that flip 180 degres every 2 glucose. It has a 1-4
linked glucose. They are all parallel and they form a microfibrils in the cell wall.

Triglycerides and phospholipids.

Triglycerides
Triglycerides are a glycerol and 3 fatty acids connected by ester bonds. The fatty acids are
hydrophobic and can be either saturated, no double bond, or un saturated, double bond.
Nucleic acids and protein synthesis
Structure of DNA and RNA
DNA stands for deoxyribonucleic acid, it’s a polymer, made up of nucleotides.

RNA stands for ribonucleic acid, its also a polymer and made up of nucleotides.

Nucleotides are made up of:

 Nitrogen containing base (A, T; G, C, U)

 A pentose sugar ( monosaccharide)
 A phosphate group

This are connected by a covalent bond, in the case of the pentose and the phosphate, and
hydrogen bonding between the sugar and the nitrogenous base.

Nitrogenous base pairs

There are four bases in DNA:

 Adenine (purine)
 Guanine ((purine)
 Cytosine (pyrimidine)
 Thymine (pyrimidine
 Uracil (pyrimidine) only in RNA

This are complementary to each other, adenine with thymine and cytosine with guanine. In A-
T base paring there are 2 hydrogen bonds, and 3 between C and G.

Structure of ATP
ATP stands for adenosine triphosphate, its an adenine molecule, a ribose sugar and 3
phosphate groups.
DNA replication

DNA replicates using a semi conservative method. This means that half is part of the original
strand, and the other half is new.

1. Helicase unwinds DNA molecule.

2. Topoisomerase brakes the hydrogen bonds so that DNA molecule doesn’t coil back
into its original shape.
3. Free nucleotides are activated by the addition of a second phosphate group.
4. Then DNA polymerase joins the free roaming nucleotides and the DNA molecule.
( RNA polymerase in the case of mRNA)

Protein synthesis
Transcription
The first step for transcription is to make a template small enough so that it can exit trough the
nuclear pores. This molecule its called mRNA. Which have the opposite base to the one in the
DNA molecule. Paring up in triplets called codons.

Translation
mRNA diffuses out of the nucleus from a nuclear pore, then attaches to a ribosome in the RER.
Then when both codon and anticodon match in the ribosome then an amino acid binds to the
ribosome, then the ribosome
temporally binds to the
amino acid. As another
amino acid is introduced to
the ribosome the bond
brakes, and a peptide bond
forms between the two
amino acids forms, this
happens over and over until
the stop codon is reached.

Sickle cell anemia

Sickle cell anemia is a genetic
disease, that affects the gene
that codes for a beta
polypeptide.

This change in the gene

cause people with anemia to
have red blood cells that are
less soluble.

Also its very painful and in many cases it can be fatal.

chapter 3 enzymes
Enzymes are globular proteins and molecules that can be defined as biological catalyst.

A catalyst is a molecule which speeds up a reaction without being chemically changed. There
are two main types of enzyme:

 Intracellular: enzymes that act

inside a cell. Ex the enzymes in the
lysosome that break down the
dead organelles.
 Extracellular: enzymes that act
outside the cell. Ex digestive
enzymes.

Lock and key and induced fit

hypothesis
Because enzymes are globular proteins, they have an specific shape to them, this is due to
having hydrophobic parts in its polypeptide chain. Enzymes poses what is called an active site
which is a region where another molecule could bind (fit). The idea that the substrate and the
active site have complementary shapes creates the lock and key concept which means that
each substrate has a different type of enzyme.

Factors that affect enzyme action

When enzyme surpasses its optimal temperature, enzymes become denatured. This is a
process of no return.
Enzyme inhibition
There are two types of inhibitors :

 Competitive reversible inhibitor: the inhibitor has a similar shape to the one that the
substrate has, so it can bind to the active site. So enzyme conc decreases until inhibitor
is broken down.
 Noncompetitive reversible inhibitor: In non-competitive inhibition, the inhibitor
binds to an allosteric site and prevents the enzyme-substrate complex from
performing a chemical reaction. This does not affect the Km (affinity) of the enzyme
(for the substrate).
Mitotic cell cycle

Four main stages in the cell cycle:

 The G1 phase is often referred to as the growth phase, because this is the time
in which a cell grows. During this phase, the cell synthesizes various enzymes
and nutrients that are needed later on for DNA replication and cell division.
 The S phase of a cell cycle occurs during interphase, before mitosis or meiosis,
andis responsible for the synthesis or replication of DNA. In this way, the
genetic material of a cell is doubled before it enters mitosis or meiosis, allowing
there to be enough DNA to be split into daughter cells
  During the gap between DNA synthesis and mitosis, the cell will continue to
grow and produce new proteins. At the end of this gap is another control
checkpoint (G2 Checkpoint) to determine if the cell can now proceed to enter M
(mitosis) and divide.

Mitosis
The heart
The hart is made up of two atria and two
ventricles

Cardiac cycle
Atrial systole muscles in the atria contract,
opening the atrioventricular valves, closing the
semilunar valves
Ventricular systole: muscle in ventricles contract, closing the atrioventricular valves, and
opening the semi lunar valves so blood goes from the heart outside.

Diastole: both muscles in atria and ventricle relax. Atrioventricular valves open and semilunar
valves close, so blood goes into the heart.

Pressure changes in the heart

Initiation and control of a cardiac

cycle
The cardiac muscle is myogenic this
means that it contracts and relaxes
automatically without a stimulation
from the brain. This is coordinated
by a series of electrical impulses.

1. The Sino Atrial Node ( SAN )

sends a wave of excitation
from the right atrium
trough out all the atria. This causes Atrial systole
2. This wave of excitation can’t cross to the ventricles, as tissues in the ventricles are
impermeable to this wave. So this wave has to be detected in the sino ventricular node
( SVN ) in the septum of the heart.
3. The SNV send a second wave of excitation down the bundle of his into the purkyne
fibers, this causes the ventricles to contract, ventricular systole.
4. There’s a short delay until the next wave of excitation so that muscles can relax,
diastole.