Cell Ultrastructure & Proteins

Question 1

What is the structure and function of the nucleus

Answer 1

envelope (double membrane) continuous with RER
pores allow for exchange of molecules
has a central nucleolus

F:
store and replication of DNA
control of gene expression and therefore protein production

Question 2

Nucleolus Structure and Function

Answer 2

small spherical found in neucloplasm
fibrillar and granular components forming an ill defined matrix
F:
ribosome assembly
pre rRNA transcription processing and assembly

Question 3

Mitochondria structure and function

Answer 3

Envelope form Inter-membrane space
foldings of inner membrane forming cristae (lots of ATP-synthase
matrix containing mDNA and enzymes for, LR, KC, OP
contains 70s ribosomes

Site of link reaction, Citric acid cycle and oxidative phosphorylation leading to production of ATP

Question 4

Smooth ER structure and function

Answer 4

Series membranes folded to form cisternae held in place by cytoskeleton
site of steroid, lipid synthesis, storage, transport

Question 5

RER structure and function

Answer 5

Series membranes folded to form cisternae
has bound 80s ribosomes
site of protein synthesis proteins enter whilst still being synthesised
post translational folding and modification of proteins, storage and then transport

Question 6

Lysosomes

Answer 6

membrane bound organelles formed by Golgi
contain hydrolytic enzymes (catalase) remove miss-folded proteins and unwanted cell structures
(bigger than peroxisomes)

Question 7

Peroxisomes

Answer 7

small membrane bound organelle
contains oxidative enzymes that break down hydrogen peroxide preventing cellular damage
also involved in fatty acid breakdown and lipid synthesis
derived from RER

Question 8

Golgi apparatus

Answer 8

Convex shaped membranous cisterane
further modification of proteins and lipids addition of glycocalyx to form glycolipids/glycoproteins
Packs proteins into secretory or transport vesicles

Question 9

Centrioles

Answer 9

Pair of cylindrical structures formed out of tubulin to form microtubules (9+0 arrangement)
Contained within the centrosome
Organise spindle fibres during cell division
Duplicates itself during G2 phase of cell division

Question 10

Ribosome structure and function

Answer 10

not membrane bound
made from rRNA two subtypes 80S found in cytosol and on RER
70S only found in the mitochondria
Site of translation and production of ppc

Question 11

Three components of cytoskeleton

Function

Answer 11

Microfilaments (thinnest) actin: muscle contraction cytokenisis
Intermediate filaments keratin fibres (organelle anchoring)
Microtubules (largest) tubuiln

All three:
help to maintain cell shape and structure
enable movement of organelles within cytosol
enable the movement of chromosomes to occur during mitosis/meiosis

Question 12

Motor proteins

Answer 12

Bind strongly to cytoskeletal filaments
allostery
release from filament
conformational relaxation
rebinding

Allows intracellular movement of organelles and molecules

Question 13

Protein Functions

Answer 13

S- structural (Keratin)
T- transport (Hb)
E- enzymes
A- Antibodies
M-membranes and receptors
H- hormones and ligands

Question 14

Primary protein structure

Answer 14

Sequence of amino acids in a polypeptide chain
Amino acids joined via condensation reaction to form a peptide bond and water

Different R groups on amino acids different properties charged, polar, hydrophilic/phobic determines folding

Question 15

Secondary Strucuture

Answer 15

folding of the ppc into a helices or B pleated sheets

Held in place by H bonds between C=O (-) and NH group (+)

Question 16

Tertiary Strucutre

Answer 16

further folding of ppc:
Proteins fold into most energetically favourable formation
Ionic, disulphide (cystine), additional hydrogen bonds, and LDF’s all occur between adjacent R groups. NB (disulfide>ionic>hydrogen>LDF’s)
Polar hydrophilic R groups tend to be on the outside of a protein whereas non-polar R groups are on the inside.
Some proteins may become active at this stage

Question 17

Quaternary Strucutre

Answer 17

When:
two or more ppc chains join together
OR/AND
presence of a prosthetic group e.g. haem group in Hb or the Zn2+ ion
(Zinc fingers suggest DNA regulatory proteins)

Question 18

Differences between fibrous and globular proteins

Answer 18

Fibrous:
long & insoluble
structural roles

Globular:
compact soluble (hydrophilic outside)
metabolic roles e.g. enzymes hormones

Question 19

Features of Enzymes

How do they lower the activation energy of a reaction?

Answer 19

Globular proteins
Biological catalysts
Specific

alternative metabolic pathways bring reactants together to form ESC
puts strain on bonds in reactant meaning they are broken and form more easily

Question 20

What is the turnover rate

Answer 20

amount of molecules that can be converted in a given period of time by a single catalytic site

Question 21

How is protein function regulated?

Answer 21

Synthesis: proteins are only synthesised when they are needed. Are signals in place to trigger and halt synthesis?
Controlled via feedback inhibition catalytic activity of an enzyme lower down in a synthesis pathway is halted by and increase in concentration of a product further up in the pathway prevents unnecessary protein synthesis

Localisation:
Is the protein where it needs to be? Is the sorting signal correct and present? Is it being stored somewhere?

Modification:
Does the protein need to activated or inactivated.

Degradation:
is it needed any more? Are unnecessary and damaged proteins being broken down?

Question 22

What are cofactors?

Answer 22

May be required for some enzymes functions:
Non protein components:
o Organic molecules (coenzymes) e.g. vitamins.
o Inorganic ions (Cu2+ Zn2+).
o Cofactors that are bound permanently= prosthetic groups.

Cause an allosteric change in shape of active site making it more complimentary to the substrate

Question 23

How are proteins activated / deactivated?

Answer 23

Phosphorylation:
Activating, addition of phosphate group to amino acid side chain usually tyrosine threonine or serine.
catalysed by a kinase

Dephosphorylation:
Deactivating, removal of phosphate group catalysed by a phosphatase

Question 24

Cdk and cyclin example

Answer 24

catalytic protein involved heavily in regulating cell division cylclin dependant kinase
binding of cyclin regulatory proteins via cooperative binding to allosteric binding sites on Cdk
conformational change exposes binding site on Cdk activating it.

Question 25

Outline the secretory pathway and the two types of vesicle.

Answer 25

virtually all proteins synthesised on ribosomes in cytosol or on RER.
Each protein contains a strong sorting signal to direct it to correct site in the cell (imperative)
Nearly all proteins move into the RER as they are still being synthesised
Moved to Golgi
packaged into Secretory vesicles or transport vesicles to leave the Golgi

Costitutive Secretion:
regulated uses transport vesicles no external signal is required for protein secretion thus occur continuously

Regulated secretion:
uses secretory vesicles that can hold proteins until an extracellular signal arrives causing rapid release via exocytosis
If they are not needed and become defective over time degraded by lysosomes

Question 26

How can mutations affect protein function?

Answer 26

can result in change in amino acid sequence of DNA –> alter way protein folds and functions

e.g. CFTR deletion of phenyalanine at position 508 on chromosome 7
mutated protein folds incorrectly retained in RER and never reaches the CSM.

Question 27

What is the unfolded protein response?

Associated disseases?

Answer 27

Imbalance in cells folding response leading to ER stress
this leads to accumulations of miss-folded proteins –> formation on aggregates as they are not removed properly
prevents cellular functioning leading to cell death
Alzheimers and Huntingtons

Question 28

Functions of cell membranes

Answer 28

control what substances enter and exit the cell/organelles through selective permeability (hydrophobic core barrier to polar charged molecules)
Allow for compartmentalisation and division of labour
Surface for chemical reactions

Question 29

What does the fluid mosaic model mean?

Answer 29

Fluid PPL can move laterally within monolayer so too can proteins. PPL can also flip between monolayers
Mosaic= protein molecules interspersed within membrane

Question 30

Phosholipids

Answer 30

Amphipathic molecules (polar phosphate head & non polar hydrophobic c tail)

Tails can be saturated (no C double bonds) pack tighter together more van de walls between molecule less fluid
or can be unsaturated resulting in kinky tails and less VDW’s more fluid

Hydrophilic head faces extracellular and intracellular aqueous environments polar tails form hydrophobic core barrier to water soluble charged molecules

Question 31

Name some PPL’s and a sphingolipid which are also found in membranes

Answer 31

Phosphatidylcholine
Phosphatidylserine

Sphingomyelin

Question 32

Cholesterol- role

Answer 32

Short rigid molecule fills in gaps between neighbouring PPL stabilising interactions between them particularity between unsaturated tails
Stiffens the bilayer making it less fluid

Question 33

Glycolipids Glycoproteins

Answer 33

Glycolipids= cell to cell adhesion

Glycoproteins cell to cell recognition

Question 34

Intrinsic protein structure

Answer 34

Tend to be a helices. Polar peptide bonds in hydrophobic core. Atoms in pp backbone form H bonds with each other forming a more stable a helix.

Do occasionally get B pleated sheets spanning core but create B barrels (porins found on mitochondrial envelope) hydrophilic R groups on inside of barrel

Question 35

What can cant pass hydrophobic core?

Answer 35

Small hydrophobic molecules (02 CO2 steroid hormones) can lipophilic

Some small polar molecules can pass in small volumes eg. water

Large Uncharged molecules e.g glucose cannot pass

Any ions and charged molecules (protein hormones) cannot pass

Question 36

What are the two types of transport

Answer 36

Passive molele down its diffusion gradient ion down its electrochemical gradient. no input of energy

Active
moving a molecule against its concentration gradient requiring an input of energy

Question 37

What is an electrochemical gradient

Answer 37

composite of two forces one due to a concentration gradient and one due to voltage differentials.

Question 38

Why must electrochemical gradients be maintained?

Answer 38

To drive transport across membranes

To maintain the osmotic balance of cells

Question 39

Simple Diffusion (passive)

Answer 39

movement of non-polar lipophilic molecules down concentration gradient

Question 40

Facilitated Diffusion (passive)

Answer 40

movement of charged/polar and large molecules down their concentration or electrochemical gradients using either channel proteins or transporter proteins

Question 41

FD channel proteins

Answer 41

Intrinsic non directional channels
hydrophilic R groups outside of protein
Do have some selectivity:
Leak channels (open all time in neurones)
Voltage-gated channels
Ligand gated ion channels Open when ligand binds
Mechanically gated channels

Question 42

Facilitated diffusion transporter proteins

Answer 42

much more selective than CP’s
molecules must have a specific complimentary shape to binding site on transport protein –> binding results in conformational change and the molecule being brought into the cell

Can reverse direction if conc gradeitn changes

e.g. glucose transporters in the gut

Question 43

AT ATP driven pumps

Answer 43

use energy from hydrolysis and dephosphorylation of ATP & subsequent phosphorylation of transporter to move a molecule against its concentration gradient.

e.g. Na+/K+ pump
3Na bind intracellularly moved out of the cell due to phosphorylation and allostery of transport protein
3Na+ released extracellularly allows binding of 2K+ dephosphorylation of protein returns to original conformation and 2 K+ brought into cell.

Movement of Na+ out of the cell essential maintains EC gradients and allows Na+ transporters to work

Question 44

Coupled Transporters

Answer 44

work by coupling the movement of one molecule with its concentration gradient with the movement of another molecule against its concentration gradient
Symporters and Antiporters

E.g Na+/Glucose symporter in PCT
Na= binds to specific cooperatively along with gluose (both must be present for symporter to work). Na+ moved into the cell down its EC gradient and Gluc moved into the cell down its conc gradient.

(must then have uniporters on basal side of cell to move gluc out of cell into blood)

Question 45

what is endocytosis?

Answer 45

cell surface membrane folds to form a vesicle:

Phagocytosis:
cell takes in solid material in large quantities these cells are phagocytes and engulf bacteria surrounding them in a phagocytic vesicle

Pinocytosis:
cell take in liquid material in large quantities
very small vesicles are formed via micropinocytosis e.g uptake of nutrients by an ovum from follicle cells

Question 46

What is exocytosis?

Answer 46

removal of waste products or secretion of useful products out of the cell