BM109

What are the most stably stacked proteins?

Transmembrane proteins

Which of the following is not part of the endomembrane system: peroxisomes, mitochondria, Golgi apparatus, nuclear envelope or plasma membrane?

mitochondria

What's one purpose of glycosylation?

to aid in cell surface recognition through determining protein structure

In a plant cell, which organelle provides the cell with a supply of energy?

mitochondria

In Frye and Edidin's experiment to verify the lateral movement of transmembrane proteins using hybrid cells formed from a mixture of mouse and human cells, why did the cells which were cooled to 0oC show no movement of transmembrane proteins?

it was too cold so movement was inhibited due to membrane solidity

How are peripheral membrane proteins bonded to the cell membrane?

hydrogen and/or ionic bonds

what is the main function of the plasma membrane in an animal cell?

controls movement of substances in and out of the cell, site of cell signalling

the plasma membrane is made up of what components?

proteins, lipids and carbohydrates

What allows for the best resolution in a light microscope?

When the illumination source has a shorter wavelength

in TEM, what is true about the stain that is used on the biological sample?

The stain consists of heavy metals

Who discovered cells and how?

Robert Hooke, looking at cork using a self designed compound microscope

What are the 4 basic concepts of cell theory?

Cells only arise through mitosis of existing cells. They are the functioning unit of life, capable of independent life under certain conditions and contain inherited DNA

Compare eukaryotic and prokaryotic DNA

Eukaryotic DNA is linear and contained within a nucleus, whereas prokaryotic DNA is circular and contained within a nucleus and sometimes plasmids. Eukaryotic DNA is associated with histone proteins whereas prokaryotic DNA is not.

Describe the shape and location of squamous epithelial cells

Flat and very thin, found lining surfaces such as bronchioles

Describe the shape and location of cuboidal epithelial cells

cube shaped, found in tissues responsible for secretion and absorption

Describe the shape and location of columnar epithelial cells

long and thin, found in areas which secrete mucus

location and function of simple squamous epithelial cells

found lining blood/lymphatic vessels and air sacs, for lubrication and diffusion

location and function of simple cuboidal epithelial cells

found in ducts and secretory areas of glands and kidney tubules for secretion and absorption

location and function of simple columnar epithelial cells

makes up ciliated tissue in bronchi, uterus and smooth tissue in digestive tract and bladder to absorb and secrete enzymes and mucus

location and function of pseudostratified columnar epithelial cells

lines trachea and most of upper respiratory tract to secrete and move mucus

location and function of stratified squamous epithelial cells

found in oesophagus, mouth and vagina to protect from abrasion

location and function of stratified cuboidal epithelial cells

protective tissue found in sweat, salivary and mammary glands

location and function of transitional epithelial cells

found in bladder, urethra and ureter lining so urinary organs can expand and stretch

describe the structure of connective tissue and where it's found

made up of many cell types and found throughout the body with either no blood supply or is highly vascularised, made up of ground substance, fibres and cells

Connective tissue function

support, protect, insulate, store fuel and transport

define amphiphatic

contains both hydrophilic and hydrophobic parts

basic functions of the cell membrane

protection from surroundings, create optimum environment for cellular functions, cell signalling, cell adhesion to other cells and the ECM

lateral movement of phospholipids

passive, frequent process which occurs within the layer as the phospholipids aren't bound together (semifluid membrane)

flip flop of lipids

active process requiring ATP where phospholipids flip from one leaflet (layer) to the other

what is the function of cholesterol

regulates fluidity of membrane, making bilayer stronger, more flexible and less permeable to hydrophilic molecules

Where are transmembrane proteins found?

part(s) are physically embedded in the fatty acid portion of the membrane. The transmembrane section is folded into an alpha helix

structure of lipid anchored proteins

amino acid is covalently bonded to a lipid

examples of lipid anchored proteins

G proteins and some kinases

where are peripheral/extrinsic proteins found?

on the membrane surface only

are peripheral proteins a permanent part of the membrane?

No, they can attach and remove themselves from the membrane eg hormones

What is the first law of thermodynamics?

energy can be neither created or destroyed, only changed from one form to another. Therefore the total energy content of the universe remains the same

What is the second law of thermodynamics?

the universe tends towards disorder/entropy tends to a maximum

what increases entropy?

increasing temperature and increasing the number of particles in a system

Are cells at higher or lower entropy than their compartments?

the cell is at lower entropy but higher energy level than all its compartments

how do cells gain energy?

by oxidising compounds such as glucose and releasing heat and CO2 to the surroundings, increasing entropy

what is the transition state

has higher free energy than either reactants or products, so is the least stable species in the pathway.

What is the free energy between the substrate and transition state?

activation energy

how do enzymes lower activation energy?

by providing a different route for the reaction to occur, acting as a catalyst

define catalysis

specific stabilisation of the transition state of a reaction

what is metabolism?

conversion of different chemicals in the body by catabolism (break down) or anabolism (build).

What metabolic pathways are most efficient?

Cyclic or spiral metabolic pathways

What are the 4 different structures of metabolic pathway?

linear, branched, cyclic or spiral

How are metabolic pathways regulated?

switching genes which code for enzymes/regulate enzymes on or off, negative and positive feedback

allosteric regulation

molecule binds to one enzyme site to affect another site and either activate or inhibit an enzyme. Binding of activators stabilises the active form whereas inhibitors binding stabilises the inactive form

How do allosterically regulated enzymes differ in structure from other enzymes?

quaternary structure

define cooperativity

Allosteric regulation that increases enzyme activity. A substrate binds making the enzyme more able to bind other substrates at other sites

What is neurospora crassa and what is it used for?

common pink mould often used in genetic research as it can reproduce asexually, creating haploid spores meaning recessive mutations aren't masked

what is minimal medium

contains basic essential nutrients: sugar, nitrogen source, mineral ions and vitamins. Neurospora is able to make all other compounds it needs

what is complete medium?

minimal medium + all amino acids

What did Beedle and Tatum do?

Grew Neurospora on minimal medium and exposed it to xray to induce mutations then cultured each spore in complete medium for a next gen. They took subcultures of the next generation to see if they'd grow in minimal medium. Some couldn't therefore were lacking enzymes to make certain amino acids

depurination of bases

purine base completely detaches from the sugar. This can be caused by heat and could lead to insertion of the wrong bases during replication

What happens in base excision repair?

A damaged base is removed by DNA glycosylase and the sugar phosphate removed by AP endonuclease. New nucleotides are added by DNA polymerase then joined by DNA ligase

polymorphisms

harmless genetic differences usually found outside of coding regions

What causes cystic fibrosis?

mutation in the CFTR gene leading to non functional protein so chloride ions aren't pumped out of lung cells, water remains in the cells and lungs aren't kept moist. Mucus also is very thick leading to infections and other damage

how do some diseases evade natural selection?

Many diseases only show after childbearing age and Sometimes having one copy of a recessive allele is advantageous (sickle cell anaemia)

Sickle cell anaemia

Single amino acid mutation in Hb beta globulin chain creating HbS rather than HbA In low oxygen, HbS forms crystals which distorts RBC shape

What are mitochondria?

Energy-converting organelles found in eukaryotic cells. They produce 2.5% of their own proteins as they contain circular DNA and 70S ribosomes.

describe oxidative phosphorylation

Reduced NAD is oxidised releasing electrons that are transferred to NADH dehydrogenase (complex I). Electrons are transferred to coenzyme Q then complex III. Reduced FAD is also oxidised and electrons transferred to complex II then coenzyme Q. The energy is used to pump H+ across the inner membrane. H+ then moves down its electrochemical gradient via ATP synthase, driving ATP synthesis. The electrons and H+ are transferred to oxygen, which acts as the final electron acceptor, forming water.

how does cyanide affect mitochondria?

Inhibits complex IV, preventing electrons being transported from cytochrome C to oxygen, disrupting the electron transport chain so aerobic production of ATP ceases

what is alkaptonuria?

Lack of homogentisic acid oxidase -> dark brown urine. Tyrosine and phenylalanine aren’t broken down homogentisic acid builds up

What is phenylketonuria?

Lack of phenylalanine hydroxylase so phenylalanine accumulates in blood leading to mental retardation.

which amino acids have aromatic R groups?

phenylalanine, tryptophan, tyrosine, histodine

amino acids with non polar R groups

proline, phenylalanine, tryptophan, leucine, methionine, isoleucine, glycine, alanine, valine

polar R groups

tyrosine, histidine, lysine, arginine, serine, threonine, cysteine, asparagine, glutamine, aspartate, glutamate

positively charged R groups

histidine, lysine, arginine

negatively charged R groups

aspartate, glutamate

essential amino acids

histidine, lysine, threonine, phenylalanine, tryptophan, leucine, methionine, isoleucine, valine

amino acids containing OH

tyrosine, serine, threonine

amino acids containing S

methionine and cysteine

What is pyruvate dehydrogenase complex (PDC)?

multienzyme, supramolecular machine found in both prokaryotes and eukaryotes, involved in converting pyruvate into acetyl CoA, in which pyruvate is oxidatively carboxylated

How is pyruvate's acetate unit activated?

linking it to Coenzyme A, so that it can then undergo further reactions

what happens during mitochondrial oxidative decarboxylation of pyruvate?

carbon atoms of carbohydrates and amino acids committed to oxidation via the TCA cycle or to the synthesis of fatty acids

when does mitochondrial oxidative decarboxylation of pyruvate occur?

only occurs if ATP is needed or two-carbon fragments are required for fatty acid biosynthesis

how is oxidative decarboxylation of pyruvate controlled?

allosterically and by phosphorylation

What are the three reactions of the pyruvate dehydrogenase multienzyme complex?

1) decarboxylation of pyruvate to a 2C alcohol. 2) oxidation of the alcohol to acetic acid with reduction of NAD+ to NADH. 3) esterification to coenzyme A

What are the three subunits of PDC?

pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and dihydrolipoamide dehydrogenase (E3)

advantages of a multienzyme complex

direct transfer from one enzyme to another avoids metabolite dilution in the aqueous environment and increases rate of reaction so diffusion of the substrate isn't rate-limiting.

what are the six major components of human PDC?

pyruvate dehydrogenase (E1), dihydrolipoyl acetyltransferase (E2), dihydrolipoyl,dehydrogenase (E3), E3-binding protein (E3BP), pyruvate dehydrogenase kinase (PDK) , pyruvate dehydrogenase phosphatase (PDP)

how does E2 act as a scaffold to organise and connect the different components?

Two lipoyl domains (L1, L2) are connected by alanine-proline rich linkers. Outer linker regions allow a ‘‘swinging arm’’ active site coupling mechanism between the E1, E2 and E3 components. The lipoic acid prosthetic group, which is covalently bound to the lipoyl domains via a lysine residue, can extend into the active-site channels and perform the substrate channelling. C-terminal part is the inner catalytic domain (IC).

What species have one lipoyl domain per E2?

yeast, chloroplast, or Bacillus stearothermophilus

What species have two lipoyl domain per E2?

mammalian, plant mitochondria, and Streptococcus faecalis

What species have three lipoyl domain per E2?

Escherichia coli or Azotobacter vinelandii

Define cell communication

The process by which cells detect, interpret and respond to signals in their environment

What does cell communication allow?

This allows cells to respond to environmental changes and allows cell-to-cell communication

Why is cell communication important? Use yeast as an example.

Yeast cells have receptors which glucose binds to. Cell responds by increasing expression of glucose transporter proteins and enzymes allowing cell to hydrolyse/use/store glucose

Why is cell communication important? Use plant shoots as an example.

Cells in the growing shoot tip sense light and send a signal (auxin) to cells on the shaded side of the shoot. Cells located below the growing tip receive this signal and elongate, causing the shoot to bend so the tip grows towards light.

What happens in direct intercellular signalling and where is this type of signalling important?

molecules pass through gap junctions from the cytoplasm of one cell to adjacent cells. Important in heart as synchronised contraction of cardiomyocytes essential

What happens in contact dependent signalling and where is this type of signalling important?

Membrane-bound signalling molecules bind to receptors on adjacent target cells, inducing a response. Important in synapses in the brain to allow neurones to know connection has been made with others

What is autocrine signalling?

Cells release signals that affect themselves and nearby target cells. Used to sense cell density in the tissue for control of cell growth

What is paracrine signalling?

Cells release signals that affect nearby target cells. Important in blood vessel dilation

What is endocrine signalling?

Cells in one part of the body release hormones that travel long distances in the bloodstream to affect target cells in another part

What are the three stages of cell communication?

receptor activation, signal transduction and cellular response

What does receptor activation involve?

The binding of a signalling molecule causes a conformational change in a receptor that activates its function.

What does signal transduction involve?

The activated receptor stimulates a series of proteins, forming a signal transduction pathway.

What does the cellular response involve?

The signal transduction pathway affects the functions and/or amounts of cellular proteins, producing a cellular response.

If the intracellular target is an enzyme, what is the cellular response?

Altered metabolism or other cell functions

If the intracellular targets are structural proteins, what is the cellular response?

Altered cell shape or movement

If the intracellular target is a transcription factor, what is the cellular response?

Altered gene expression, which changes the types and the amounts ofproteins in the cell

Why are most receptors found on the cell surface?

Most signalling molecules are hydrophilic (polar) so can't cross the cell membrane. Cell surface receptors are usually enzyme linked, G-protein coupled or ligand gated ion channels

What do protein kinases do?

transfer a phosphate group from ATP to a protein substrate in a process called phosphorylation

How do G protein coupled receptors work?

A signalling molecule binds to a GPCR, causing it to bind to a G protein. The G protein exchanges GDP for GTP. The G protein then dissociates from the receptor and separates into an active α subunit and a β/gamma dimer. The activated subunits promote cellular responses.

When are intracellular receptors needed/important?

Some signalling molecules eg hormones are hydrophobic so can cross the plasma membrane to activate intracellular responses. They are often involved in regulating transcription.

Describe oestrogen receptor signalling

Oestrogen diffuses across the plasma membrane, enters the nucleus, and binds to the oestrogen receptors. The receptors undergo a conformational change and form a dimer, binding to promoter regions of specific genes to activate transcription.

What is a signal transduction pathway?

Stimulated by the conformational change that occurs when a signalling molecule binds to a receptor. May involve a cascade of intracellular kinases or generation of intracellular signals called second messengers

What is epidermal growth factor?

signalling molecule that binds to the EGF receptor to stimulate cell growth and division

Describe the EGF signal transduction pathway.

Two EGF molecules bind to EGF receptor subunits, causing them to dimerize and phosphorylate each other on tyrosines. Grb binds to the receptor then Sos which stimulates Ras to release GDP and bind GTP. Ras activates Raf, which starts a protein kinase cascade where Raf phosphorylates Mek, then Mek phosphorylates Erk. Erk enters the nucleus and phosphorylates transcription factors Myc and Fos.

give 4 examples of second messengers

cAMP, calcium ions, diacylglycerol, inositol triphosphate

signal transduction via cAMP

Activation of GPCR stimulates GTP binding by G alpha subunit, releasing it from G beta gamma. Alpha subunit binds to adenylate cyclase, stimulating cAMP synthesis

How does cAMP activate protein kinase A?

Binding of cAMP to protein kinase A (PKA) activates it. PKA phosphorylates specific proteins, including enzymes, structural proteins and transcription factors

How is signal amplification an advantage of second messengers?

Binding of the signal to one receptor can cause the synthesis of many cAMP molecules that activate PKA, and each PKA can phosphorylate many proteins

How is speed an advantage of second messengers?

large amounts of cAMP can be produced very rapidly following ligand binding to receptor, and can diffuse rapidly through the cell

How can activated G proteins activate signal transduction pathways via IP3 and DAG

Alpha subunit activates phospholipase C which cleaves PIP2, producing diacylglycerol (DAG) and inositol triphosphate (IP3). IP3 opens calcium ion channels in the ER, increasing levels of calcium ions. DAG activates protein kinase C (PKC)

effects of adrenaline in humans

dilates pupils, inhibits saliva production, relaxes airways, increases heart rate, stimulates sweating, stimulates glycogenolysis in skeletal muscle, constricts blood vessels in skin

function of phosphodiesterases

convert cAMP back to AMP

How can HbS be advantageous?

Having HbA and HbS alleles produces 20 to 45% HbS and protects against severe malaria, perhaps as rupturing RBCs disrupts parasite life cycle

Why is it important to diagnose phenylketonuria young?

Important to diagnose in young babies so diet changes to reduce Phe intake can be made and mental retardation prevented

What 5 cofactors does PDC require?

Thiamine pyrophosphate TPP Lipoamide Coenzyme A FAD (prosthetic group of E3; riboflavin or vitamin B2) NAD+ (this is a co-substrate)

What is thiamine pyrophosphate?

prosthetic group of E1, accepts hydroxyethyl group and is derived from vitamin B1

What is lipoamide?

prosthetic group of E2, accepts acetyl group after oxidation of the hydroxyethyl, forming acetyl lipoamide, vitamin N

What is FAD?

prosthetic group of E3: riboflavin or vitamin B2

What is G0?

Also known as quiescence, G0 is when cells can no longer divide but are metabolically and functionally active

What's the longest phase of cell division?

G1 of interphase, average length 11 hours

What's the shortest phase of cell division?

mitosis

Centrosome function

centres of microtubule organisation which duplicate during interphase

What part of the centromere binds to the mitotic spindle fibres?

kinetochore proteins

Function of each type of spindle microtubule

Astral microtubules bind the centrosome to the membrane. Polar microtubules lengthen to pull

When are each of the human cyclins active?

D is active throughout the cell cycle but mainly in S phase, E is most active at the end of G1, A is most active during G2 and B most active in mitosis

What controls CDKs?

Inhibitors such as p21, which is regulated by p53

define senescence

when mitotically competent cells cannot replicate indefinitely

what is the Hayflick limit

In 1961, Hayflick and his colleagues observed that human primary fibroblast cells in culture could divide 50 times and that after this point, the cells remained functional but could no longer divide

telomere structure

repeated DNA sequence (TTAGGG) found at each end of chromosomes which shorten with each cell division due to antiparallel DNA structure

telomere function

Organise our 46 chromosomes in the nucleolus and allow the chromosome to be replicated properly as they prevent sister chromatids from fusing and damage (loss of genetic info). Senescence is induced when all telomeric DNA is lost

How does telomerase overcome telomere shortening and the end replication problem?

by adding telomeric repeat DNA directly to 3' overhang

define aging

slow process which leads to a decline of the biological functions and the ability to adapt to metabolic stress of cells, tissues and organs

difference between embryonic and adult stem cells

embryonic stem cells are pluripotent whereas adult stem cells are multipotent

How does telomerase work?

it uses its own RNA as a template to add telomeric repeats. Telomerase activity is highest in early embryonic cells and stem cells

Why can PET scans be used to detect cancer?

Cancer cells have very high glucose usage to produce ATP so radioactively labelled glucose can be used to show areas of high glucose consumption (tumours)

Describe carcinoma

cancer begins in the skin or in tissues that line or cover internal organs eg adenocarcinoma

describe sarcoma

begins in the connective or supportive tissues such as bone, cartilage, fat, muscle or blood vessels. These cancer types are more rare

describe leukaemia

cancer of the white blood cells. It starts in the tissues that make blood cells such as the bone marrow.

describe lymphoma and myeloma

these cancers begin in the cells of the immune system