Respiration, Muscles and the Internal Environment

Respiration

This is comprised of four steps.

Respiration can happen in the presence of oxygen [aerobic] or in its absence [anaerobic respiration], each involving
different steps.

Glycolysis

 It is the beginning of both aerobic and anaerobic respiration.

 It takes place in the cytoplasm

 2 ATP are used, and four produced, so there is a net [overall] gain of 2 ATP

 A 6-carbon hexose glucose molecule is phosphorylated [has two phosphate groups from ATP added to it] and
produces two 3-carbon pyruvates

 2ADP + Pi → 2ATP and 2NAD → 2NADH for each pyruvate

Link reaction

 It takes place in the mitochondria

 A 3-carbon pyruvate is oxidised

 An NAD molecule reduced to reduced NADH

 This is then decarboxylated as CO2 is released

 coenzyme A + pyruvate → acetyl coenzyme A

Krebs cycle

 Also known as the citric acid cycle.

 It takes place in the mitochondria.

Oxidative phosphorylation
  Electrons are transferred from NADH and FADH2 to protein complexes and electron carriers such as NAD, FAD,
and cytochrome and move through the electron transport chain

 Electrons are used to create an electrochemical gradient as they are pumped across the intermembrane space

 H+ travels to ATP synthase, powering it to make ATP [phosphorylated]

==What is the difference between substrate-level phosphorylation and oxidative phosphorylation?==

Substrate level Oxidative

A phosphate group is transferred from the It uses energy released from electron transfer in the transport
substrate to ADP chain to generate ATP

in mitochondrial matrix in the inner mitochondrial membrane

involved in glycolysis and Krebs cycle involved in the electron transport chain

direct phosphorylation indirect

The process of anaerobic respiration

 pyruvate from glycolysis converted into lactic acid

 lactic acid dissociates to form lactate and H+

 produces 2ATP per glucose molecule respired

Respiratory quotient = vol of CO2 produced/vol of O2 used

Muscles

Key terms

 Tendons are inflexible and connect muscle to bone, while ligaments are flexible and connect bone to bone.

 Bones may be compact [dense and heavy, long bones, RBCs are made here] or spongy [open structure]. They are
made of collagen and calcium salts in a matrix.

 Joints allow movement and locomotion, producing synovial fluid to reduce friction.

 Ball and socket joints [e.g., shoulder and hip] allow movement in 3 planes, while hinge joints [e.g., knee and
elbow] allow movement up and down.

 Antagonistic muscle pairs consist of a flexor and extensor working in opposite directions, so when one contracts,
the other relaxes.

Q) Compare the structure and function of slow twitch and fast twitch muscles.

Slow twitch muscles have:

 many mitochondria→ allow more aerobic respiration to take place

 many myoglobin molecules→ allows a greater store of O2

 larger capillary network→ allows a good supply of oxygen and glucose

  slow sustained contraction → allows longer periods of training/exercise

 more aerobic respiration, less glycogen, smaller capacity of sarcoplasmic reticulum

The electrical activity of myogenic cardiac muscle

 impulses are sent [frequency varies] from the cardiac control centre in the medulla

 the sinoatrial node in the right atrium establishes a wave of electrical excitation/depolarization→ The atria begin
contracting

 the atrioventricular node is excited

 there is a slight delay before depolarization passes into the bundle of His in the septum

 bundle of His splits and carries excitation to Purkyne fibres, which distribute excitation throughout the heart

Definitions

 cardiac output=stroke vol x heart rate= vol of blood pumped in a single unit of time

 tidal volume=vol of air that enters and leaves the lungs at each natural resting breath

 residual volume=vol of blood left in lungs after strongest possible exhalation

 vital capacity = the maximum volume of air that can be discharged from the lungs following maximum inhalation

 stroke volume=vol of blood per beat

 Respiration minute ventilation=vol of gas inhaled [inhaled minute vol] or exhaled from lungs per minute

 breathing rate=number of breaths taken in one minute

Sliding filament theory

 Depolarisation

 Action potential from a motor neuron triggers an impulse from neurotransmitters.

 Triggers the release of acetylcholine, which stimulates Ca2+ ions to get released by the sarcoplasmic reticulum

 Calcium ions bind to troponin and change its shape

 This shifts tropomyosin away and exposes the myosin-binding sites so that actomyosin cross-bridges can be
formed

 The hydrolyzed ATP on the myosin head gets released, so action slides over the myosin

 Another ATP binds to the myosin head, and the cross-bridge breaks

 The repeated reorientation of the myosin heads drags the actin filaments along the length of the myosin,
shortening the sarcomere.
The role of adrenaline in the fight or flight response

 Baroreceptors in carotid arteries are sensitive to pressure changes and detect when adrenaline is needed

 Sympathetic nerves stimulate the adrenal gland to release adrenaline

 Adrenaline stimulates the cardiac control centre in the brain

 This increases heart and breathing rate, vasodilation, and blood flow and decreases insulin production.

Homeostasis

 Positive feedback = effectors work to increase the effect/change that triggered the stimulus.

 Negative feedback = results in a decrease in the change of the variable that triggered the response and maintains
systems within narrow limits.

 Homeostasis = the process of maintaining a stable internal environment despite changes in the external
environment [e.g., insulin, glycogen, and blood glucose]

 Hormones = organic chemicals produced in endocrine glands and released into the blood, which travel to target
organs to cause changes.

 Exocrine gland = group of cells that release a substance [e.g., enzymes] into a duct that carries it to where it is
needed

 Endocrine gland = ductless releases hormones directly into the blood [e.g., pituitary, thyroid]

Control of heart rate

 Chemoreceptors detect changes in blood pH due to CO2 concentration, and baroreceptors in the carotid artery
detect changes in blood pressure.

 Impulses are sent along a sensory neuron to the cardiovascular control centre in the medulla.

 The cardiac control centre increases/decreases the frequency of impulses down sympathetic nerves to the heart.
  The sinoatrial node [SAN] is stimulated to generate more
impulses

 Heart rate increases, and blood flow to lungs increases, causing

a shorter cardiac cycle

 More CO2 is removed from the blood

 The parasympathetic nervous system then decreases the heart

rate if it goes too high beyond specific limits.

Control of breathing rate

 Chemoreceptors in blood detect pH increase or decrease

 Impulses are sent along a sensory neuron to the ventilation centre in the medulla

 Impulses travel along sympathetic nerves

 Intercostal muscles and diaphragm contract, and lungs inflate, increasing the impulses sent

 Eventually, the respiratory centre is inhibited and stops stimulating breathing muscles so frequently.

 Muscles relax and exhale, giving the resting rhythm.

The loop of Henle

It consists of three sections:

1. freely permeable to water, not permeable to NaCl, no active transport, water

moves out through osmosis, hypertonic solution, only this step happens in the
descending limb

2. very permeable to NaCl, not permeable to water, Na+ and Cl- move out through
facilitated diffusion
3. impermeable to water, NaCl pumped out through active transport, more
dilute/possibly hypotonic solution

Control of mammalian plasma concentration and blood volume

This is an example of negative feedback.

Given below is the process that occurs when plasma concentration is high.

 Plasma concentration changes

 Osmoreceptors in the hypothalamus send impulses to the pituitary

 The pituitary gland releases ADH

 ADH binds to receptors in the distal convoluted tubule [DCT] and collects duct

 Cyclic AMP is produced as 2nd messenger, and aquaporins move into the cell
  The distal tubule and collecting duct become more permeable to water

 More water is reabsorbed.

Urea is produced by the deamination of excess amino acids and removed through the ornithine cycle [water in, CO2
in→water out].

Selective reabsorption

 It takes place in the proximal convoluted tubule [PCT]

 80% of filtrate reabsorbed

 Necessary substances [e.g., Na+] are reabsorbed through active transport

 Water and Cl- are reabsorbed through facilitated diffusion and osmosis, respectively, down a concentration
gradient

 Only urea, salt, and some water are not reabsorbed

The layers of the PCT:

1. endothelium of capillaries

2. basement membrane with collagen and glycoprotein network

3. epithelial cells [podocytes] of the inner lining of Bowman’s capsule

Adaptations for reabsorption:

1. covered in microvili→ increases the surface area

2. large number of mitochondria → provide ATP

3. constant blood supply into capillaries → to maintain a concentration gradient

Q) How does the loop of Henle act as a countercurrent multiplier?

A) In the loop of Henle, the flow of filtrate in tubules is in opposite directions, because sodium ions are actively
transported out of the ascending limb therefore water moves out from the descending limb and solutes move out from
the ascending limb due to an increase in the concentration gradient between tubular and interstitial fluid.
The Nervous System

Neurons are nerve cells that help transmit impulses or nerve signals throughout an organism.

There are three types of neurons with varying structure and function.

 Neurons may be coated in a myelin sheath that increases the

rate of electrical conduction because impulses can
leap from one unmyelinated junction [node of
Ranvier] to the next.

 This is known as saltatory conduction.

 Schwann cells do not produce impulses but help

conduct impulses to transport them through the
nervous system.

 There are two types of Schwann cells:

myelinating and non-myelinating.

 The CNS contains both grey matter [unmyelinated] and white matter [myelinated] neurons.

How a nerve impulse is conducted along an axon

How a nerve impulse passes through a neuron

==Step 1-Resting potential==

 At rest, the neuron is polarised.

 The sodium-potassium pump sends Na+ out and K+ in through

active transport.

 K+ moves out through the normal potassium pump.

 The potential difference inside the neuron is negative (voltage -

70mV), and the outside is positive.

 The membrane is impermeable to Na+ and permeable to K+.

==Step 2-Action potential==

 A change in the membrane's permeability is stimulated before an impulse passes through a neuron.

 Voltage-gated Na+ channels opemembrane'smoves out.

 K+ move out through the normal potassium pump.

 The inside of the neuron is positive (voltage +40mV), and the outside is negative.

 The neuron is depolarised, and the impulse passes through.

==Step 3-Refractory period==

 The impulse passes, and voltage-gated Na+ channels close while voltage-gated K+ channels open, through which,
through normal potassium channels, K+ move out.
  The neuron is hyperpolarised.

==Step 4-Return to resting potential==

The K+ channels close, and the membrane is repolarised.

The transmission of an impulse is an all-or-nothing response where +40mV is the threshold that needs to be met for
an impulse to pass through.

Transmission of an impulse along a synapse

 A synapse is a junction across which an impulse is transmitted.

 Calcium ion channels open in the pre-synaptic membrane

 Ca2+ move into the pre-synaptic knob down a concentration gradient

 Vesicles filled with neurotransmitters [e.g., acetylcholine] merge with the cell membrane through exocytosis

 Neurotransmitters are released along the synaptic cleft using energy from mitochondria

 Receptors on the post-synaptic membrane receive neurotransmitters

 One of two responses is triggered:

o Sodium ion channels open and send Na+ into the fibre

o The threshold is reached or exceeded

o Sets up action potential due to a change in potential difference [excitatory post-synaptic potential]

o The impulse is transmitted

 Or:

o Different channels open in the membrane, allowing negative ions in

o An inhibitory post-synaptic potential is set up

o The action potential will not occur

Spinal reflex arc

This is the pathway through which a reflex travels.

A reflex action is usually involuntary and responds to a specific stimulus.

 A receptor detects a specific stimulus

 An impulse is transmitted to a sensory neuron

 This impulse is then passed on to a relay neuron [in the spinal cord in most higher animals]

 The impulse then reaches a motor neuron.

 This signals an appropriate response to be carried out by an effector [e.g., a muscle]

A monosynaptic reflex arc involves only a sensory and motor neuron, but most reflex arcs follow the abovementioned
process and are polysynaptic.
Neurotransmitters

1. Acetylcholine- used by nerves, rapidly hydrolysed and re-synthesised

2. Noroadrenaline

3. Dopamine

Drugs and their effects on nerve impulse transmission

Drugs may either increase or decrease a response.

1. Nicotine

1. binds to acetylcholine receptors in post-synaptic membranes

2. triggers an action potential in the post-synaptic neuron but receptors remain unresponsive for some
time as nicotine binds and doesn’t release for some time

3. causes raised heart rate and down pressure, stimulates the release of dopamine

4. in low concentrations, it has a stimulating effect; in high concentrations, it can kill as acetylcholine is
unable to bind

2. Lidocaine

1. blocks voltage-gated sodium channels

2. prevents the production of an action potential in the sensory nerve

3. prevents you from feeling pain so that it may be used as a local anesthetic or to prevent cardiac
arrhythmia

3. Cobra venom alpha toxin

1. acts as an electron carrier

2. Na+ is not taken up, causing hyperpolarisation

3. decreases the response

4. in small doses, is used to treat asthma by dilating bronchi

5. in large doses, paralyses muscles as they are unable to contract

Response

Receptors

 Primary- a dendrite is sensitive to one stimulus, and an action potential is caused in the neuron.

 Secondary- a receptor on a separate cell synapses with a sensory neuron and transmits an impulse to the CNS.

 Generator potential does not follow the all-or-nothing law.

o Na+ moves along concentration and electrochemical gradients when a receptor cell receives a stimulus.

o A generator potential is set up.

o The greater the frequency of impulses, the greater the generator's potential

 Convergence- when generator potentials from several different receptors add up and trigger an action potential
The Eye

Rods and cones

The retina is comprised of rod and cone cells.

Rods

 are spread evenly across the retina except in the fovea [blind spot]

 provide black-and-white vision

 very sensitive to light and movement

 not very tightly packed together

 produce an unclear image as several rods need to be stimulated at the

same time to create an action potential, but only a small stimulus is needed

 due to synaptic convergence, low acuity but high sensitivity to light

Cones

 densely packed across the fovea

 great visual acuity [very clear vision] because each cone synapses with a single bipolar neuron

 give colour vision

 needs direct light, not very sensitive to light as there is no convergence

The Cranial Reflex

 On the rods, the visual pigment rhodopsin comprises opsin and retinal.

 Retinal exists as cis-retinal in the dark

 When light hits, this is converted to trans-retinal

 Rhodopsin then experiences bleaching and splits into opsin and retinal

 This causes a generator's potential

 Sodium ions are not taken up, causing hyperpolarisation in rod cells

 Cation channels in bipolar cells open and become depolarised

 This generates an action potential in the neuron of the optic nerve

If a person enters dim light from bright light, nothing is seen until cis-retinal is regenerated and rhodopsin is formed from
opsin and retinal using ATP

Habituation

Habituation is the decline in response to a stimulus due to repeated exposure to said stimulus.

Plant hormones

1. Auxin -

1. is present in a high concentration on the side of a shoot or plant, getting less light
 2. regulate gene expression through transcription factors [choosing which genes are expressed and
switched off]

3. cause cell elongation in the side of a plant getting less sunlight, causing it to grow towards the light

2. Gibberellin -

1. responsible for seed germination

2. cause hydrolysis of stored starch by triggering amylase synthesis

3. stored in the aleurone layer

3. Phytochrome -

1. is a blue-green pigment that has two forms

2. phytochrome red is the inactive form, while phytochrome far red is the active form

3. Phytochrome red absorbs red light in the region 660nm and gets converted to phytochrome far red,
which is present at the end

4. Similarly, phytochrome far-red absorbs far-red light in the region 730nm and gets converted to
phytochrome red, which is present at the end

5. Normal daylight has more red light, so more P FR is present as more P R is rapidly converted.

6. A surplus of P FR induces rapid responses, promotes flowering in long-day plants, and inhibits flowering
in short-day plants

7. A surplus of P R induces long-term responses such as internode elongation and inhibits chlorophyll
formation, leading to etiolation

Nervous vs. hormonal control

Nervous Hormonal

Quick response Varying response speed

Information is transmitted as nerve impulses Transmitted through hormones

Impulse transmission occurs through nerve

Hormone transmission occurs through blood
fibres

Targets a specific direction [e.g., effector, Released to blood and taken to the specific receptor through
CNS] circulation

Short term effect Long-lasting effect

The Human Brain

Function

 Cerebral hemisphere - voluntary control of the body

 Cerebrum - control of voluntary behaviour

 Cerebellum - muscle movements, coordination of voluntary

movements, and balance

 Medulla oblongata - controls heart rate/beat, breathing rate and

blood pressure

 Hypothalamus - thermoregulation, hormone production [e.g., ADH]

 Pituitary gland - endocrine gland that produces and releases hormones

Types of brain scanning

1. CT Scan

1. uses X-ray radiation

2. produces cross-sectional images

3. shows damaged/abnormal areas

2. MRI Scan

1. uses a magnetic field and radio waves

2. images soft tissues

3. investigates brain structure and function

3. fMRI Scan

1. the brain is seen in action, performing tasks

2. the oxygen uptake of respiring areas is monitored

4. PET Scan

1. radioactive tracer with glucose is administered to the patient and taken into respiring cells

2. positrons emitted from glucose produce gamma rays that are detected and converted into an image

3. shows cancerous cells clearly as they absorb more radiation

Illnesses caused by an imbalance of brain chemicals

==Parkinson’s disease==

Characterized by a loss of dopamine-secreting nerve cells in the midbrain.

Symptoms:

 begins with a tremor in one hand

 muscle stiffness and slowness of movement spread throughout the body

 dopamine-secreting cells in the basal ganglia die

Treatment:

1. Monoamine Oxidase B inhibitors [e.g., selegiline] inhibit MOB, breaking down dopamine

2. Drugs [e.g., L-Dopa] can cross the blood-brain barrier due to a transport protein [unlike dopamine] and increase
the dopamine levels in the brain

3. Dopamine agonists activate receptors by binding at synapses and triggering an action potential

==Depression==

A decrease in serotonin levels in the brain

Symptoms:

 loss of interest in day-to-day activities

 changes in behaviour

 changes in mood and feelings

Treatment:

1. Medication, e.g., Selective Serotonin Reuptake Inhibitors, slow down serotonin reuptake into the pre-synaptic
neuron so more impulses travel along the post-synaptic neuron.

2. Psychotherapy

Gene Technology

How recombinant DNA is produced [e.g.: insulin]

 Isolate insulin gene

 Isolate bacterial plasmid

 Use the same restriction enzyme to cut gene and plasmid

 Insert gene into the plasmid using DNA ligase

 Insert recombinant DNA into the bacterium

How the DNA is inserted

Vectors:

1. Plasmids

2. Gene guns

3. Liposome wrappings

4. Microinjections

How drugs can be produced from GM organisms

 Microorganisms - can be used to produce insulin utilising the method to make recombinant DNA

 Banana vaccines - genetically modifying plants to produce vaccines for common diseases such as hepatitis B,
would be easier, cheaper and more efficient in preventing diseases in vulnerable individuals
  Transgenic plants - a plant infected by a genetically modified bacterium [contains a specifically extracted plasmid]
will be genetically engineered to develop the new gene

 Transgenic animals - a ewe whose milk produces alpha-1 antitrypsin was dev loped. The process involved
introducing a promoter sequence and a copy of a human gene which coded for the desired protein into the egg
of the ewe

How microarrays are used to identify active genes

 Active genes are transcribed to produce mRNA

 mRNA molecules are collected from the sample being tested, and a reference

 cDNA forms, using mRNA as a template and catalyzed by reverse transcriptase

 a fluorescent marker is added [a different colour is used for each sample, e.g.: red for experimental and green for
sample]

 the samples are added to spots in the microarray slide

 the cDNA is added and hybridizes to the sample DNA

 the microarray is scanned with a laser to measure gene expression

 fluorescent light is produced by the different spots, with the positions identified as known genes

 if both samples express a gene equally, the light will appear yellow (a mixture of red and green light). If the
expression of a particular gene is higher in the experimental sample than in the reference sample, then the
corresponding spot on the microarray appears red. If vice versa, the light will be green.

 the higher the expression of a gene, the higher the fluorescence

Bioinformatics uses software and computing tools to organize and analyze raw biological data.

Using genetically modified organisms

Risks Benefits

Could be used for biological warfare [e.g.: GMOs] Resistant to pests and adverse weather changes

Invasive species/monoculture Improved yield

Consumer resistance Increased nutrition

Allergies and long-term health concerns They may be resistant to herbicides, so weeds can be killed