Cell Biology Flashcards
Invagination definition.
The action or process of being turned inside out or folded back on itself to form a cavity or pouch.
Why have a nucleus?
- Separate fragile chromosomes from cytoskeletal cytoplasmic filaments
- Separated RNA transcription (in nucleus) from translation machinery (in cytoplasm)
How does the nucleus protect chromosomes?
The DNA and proteins are highly packed and dense
Why is it important to separate RNA transcription from translation machinery?
- RNA processing (nucleus) - alternative splicing
- Regulation of RNA export
- Regulate the import/export of other proteins
Briefly describe the possible evolution of the nucleus.
- DNA attached to cell membrane at many points (ancient prokaryote cell)
- Membrane invaginate : mesosomes
- Repeated invagination forms nucleus (ancient eukaryotic cell)
What is a mesosome?
An organelle of bacteria that appears as an invagination of the plasma membrane
Describe the structure of DNA.
DNA is a double helix with a sugar phosphate backbone and pairs of bases protruding into the middle
Describe the structure of the sugar-phosphate backbone.
Nucleotides linked together by a covalent bond between 5’ phosphate and 3’ -OH group of deoxyribose
Which bases form how many hydrogen bonds with each other?
Thymine forms 2 hydrogen bonds with adenine
Cytosine forms 3 hydrogen bonds with guanine
Which base pairs contain a purine and which contain a pyrimidine?
A + G contain one large purine
T + C contain one small pyrimidine
Why do the two strands of DNA wind into a double helix?
To maximise the efficiency of base pairing
What is the function of DNA?
Storage of genetic information for replication and gene expression
What is the definition of gene expression?
The process by which the information in a strand of DNA is copied into a new molecule of mRNA
What is splicing?
The process of removing non-coding introns
What is the name of non-sex chromosomes and how many pairs do we have?
Autosomes - 22 pairs
Give some properties of telomeres.
- End of the chromosomes (protective)
- 1000 X GGGTTA
- Special replication mechanism
- Shorten with age
Give some properties of centromeres.
- Hold metaphase chromosomes together
- Attaches to mitotic spindle
- Repetite sequences; highly packaged
How are autosomes ordered and classified.
Ordered by size
Classified by position of centromere
Meaning of metacentric
In the middle
Meaning of submetacentric
Intermediate (slightly closer to one end)
Meaning of acrocentric
Terminal (at the end)
Chromatin structure
Association between DNA and protein
Process of DNA packaging
- Short region of DNA double helix
- “Beads on a string” form of chromatin (nucleosome)
- Chromatin fiber of packed nucleosomes
- Chromatin fiber packed into loops
- Entire mitotic chromosome
What is the net result of DNA packaging?
Each DNA molecule has been packaged into a mitotic chromosome that is 1000-fold shorter than its fully extended length.
Why is important for the DNA to be packaged so tightly
As DNA gets smaller it’s harder for proteins to gain access to DNA to read it for transcription/translation when it’s not required
What protein makes up a nucleosome?
Histone
What makes an octamer?
2 molecules of each of four histones (H2A, H2B, H3, H4)
What bonds form between the DNA and the histone octamer?
Hydrogen
What is the purpose of histone H1?
It acts as a clamp to keep the DNA wound around the histone - this prevents long sections of DNA from being exposed to replication before the cell is ready for it
What is the function of non-histone proteins in a nucleosome?
They attach to the outside of the nucleosome to either make sure the nucleosome binding is not disrupted, of they disband the protection and induce gene expression.
What is a heterochromatin?
Highly packaged DNA; silenced genes
Shows up dark on microscope
What is a euchromatin?
Active genes
Show up light under microscope
Describe the structure of the nuclear envelope.
- Consists of 2 concentric membranes - contiguous with one another but are functionally distinct
- Inner membrane attached to nuclear lamina and chromatin
- Outer membrane is continuous with the endoplasmic reticulum
What goes in and out of the nuclear pore?
- Nuclear proteins (histones, transcription factors) - IN
- RNA molecules (mRNA, rRNA, tRNA) - OUT
- Ribosome subunits (assembled in nucleus) - IN/OUT
How do the molecules enter the nucleus?
Small molecules - free diffusion at different speeds depending on their size
Large molecules - Regulated by the pores for selective active transport in and out of nucleus
To fully get into the nucleus, what do molecules need?
A “key” known as the Nuclear Localisation Signals (NLS’) which is usually an area of the protein that’s positively charged e.g. arg, lys, pro
Describe the actions of the molecules entering the nucleus.
Import receptors (importin) bind to the NLS of “cargo” and they bind to the FG repeats in the nuclear pore complex. Once in the nucleus, the complex dissociates and the importin is recycled.
What can nuclear export be regulated by?
Exportins
What is the structure and purpose of the nuclear lamina?
- Next to inner membrane
- 2D lattices of fibres called intermediate filaments
- Made of proteins called lamins
- Provides support and organisation
Purpose of lamins.
Help keep everything in place, each side of membrane
Structure of lamins.
- Globular head ends
- Rod-like central domain - helix
- Monomers coil to make dimers
Purpose and function of dimers
- Additional strength
- Arrange themselves into “slides” - in pairs they slide next to each other to allow flexibility in shape and organisation
How does the lamina attach to the membrane?
A ‘lipid like anchor’ on the COOH terminus of each lamin attaches the lamina to the inner membrane alongside the phospholipids.
What subunits are ribosomes made up of?
40s and 60s
What does s stand for in subunits and what is it a measure of?
Svedberg unit)a sedimentation co-efficient)
Measure of how quickly a particle/molecule sediments e.g. centrifuge
What s are the subunits in eukaryotes and prokaryotes?
Eukaryotes - 80s
Prokaryotes - 70s
What is the composition of a subunit and describe the structure
2/3 is RNA
1/3 is protein
An RNA core with proteins attached mainly to the surface
How many RNAs make up a large and small subunit in eukaryotes?
Large - 3
Small - 1
How many RNAs make up a large and small subunit in prokaryotes?
Large - 2
Small - 1
Process of ribosome synthesising
- rRNA - synthesis and processing
- Ribosomal proteins - transcription and translation
- Ribosomal subunits - assembly
What is the nucleolus?
A darker area of the nucleus with no additional membrane and is where the ribosomal subunits are produced - forms around parts of chromosomes known as nuclear organisers
How many ribosomes in each cell
10^6 and therefore 10^6 copies of each ribosomal (r) RNA
Components of nucleolus and purpose
oDense fibrillar component - RNA being transcribed
oGranular component - maturing ribosomes
oFibrillar centre - DNA not being transcribed
Processing rRNA precursor RNA
- 45s precursor RNA is made up of rRNA genes and spacer regions
- Chemical modification - binding of RNA proteins leading to the signalling for cleavage into 3 independant rRNAs (18s, 5.8s, 28s)
What do the 3 independent rRNA’s make up?
18s - small ribosomal subunit
28s + 5.8s (+ an extra 5s) - large ribosomal subunit
Summarise translation
- Codon recognition
- Peptide bond formation
- Release of empty tRNA
Functions of the 3 sites on ribosome
A site - new tRNA attaches
P site - growing peptide chain attached to tRNA
E site - empty tRNA is released
Explain how rRNA allows formation of peptide bonds
- The 28s rRNA contains an important adenine for this - it acts to temporarily accept a hydrogen from the tRNA at the A site
- It becomes positively charged
- Amino terminal and carboxyl terminal interact, creating a negative charge in the molecule
- One of the O accepts the H to make a hydroxyl group
- The sharing of electrons between O + H favours a release of the OH group which generates a peptide bond and released the tRNA from the ribosome
What is a ribosome often referred to during the formation of peptide bonds and why?
Ribozyme - it acts as an enzyme by speeding up the process
Describe the initiation of translation.
- Most start codons are AUG
- Large subunit binds
Describe the termination of translation
- Stop codons are - TGA, TAA, TAG
- Release factor binds instead of tRNA
- No more peptide bonds - peptide chain released
- Last codon exits
- Ribosome dissociates - subunits separate
Whats the definition of RNA processing?
Removal of spacer DNA resulting in cleavage and 3 independent rRNAs
What happens if you fail to remove misfolded or damaged proteins?
Damaging - can cause things like progressive neurodegenerative diseases e.g. Alzheimers, Huntington’s
How are regulatory proteins controlled?
- Short half life - way of maintaining them at low levels
- Can be conditional - stabilised when needed but rapidly degraded in response to particular trigger
- E.g. cyclins rapidly degrade at the end of mitosis
What is the proteasome?
Protein complexes which degrade unneeded/damaged proteins by proteolysis
It’s and ATP-dependent protease
Describe the structure and their functions of a proteasome
- Head group regulates entry
- Central part is responsible for destroying
- Bottom part distributes debris
Whats the protein degrading machine and its structure
Has a hollow tube of many subunits, including multiple proteases which face inwards
What’s ubiquitin?
A short peptide which can be attached to the NH3 side chains of lysine residues in proteins targeted for degradation
Explain the control of protein degradation
- Ubiquitin is activated by binding to a Ubiquitin Activating Enzyme
- UAE transfers it to Ubiquitin Ligase
- Ubiquitin Ligase recognises the protein targeted for degradation and transfers ubiquitin to it
- Further ubiquitin molecules are added by UAE
Whats the signal for degradation by the proteasome?
Multiple ubiquitin chains are the signal and it gives access to the head part. At least 3 are needed though
Describe the appearance of the endoplasmic reticulum
- Membranous labrynth
- Continuous tubules and sacs
- ER lumen bounded by ER membrane
- ER membrane is contiguous with outer nuclear membrane
- Can constitute >10% of the cell volume and up to 60% of cell membrane
Why is the rough ER rough?
Due to ribosomes that make:
- Secretory proteins
- Transmembranous proteins (cross membranes)
- ER and Golgi proteins
- Lysosomal proteins
What are the names of each part of the Golgi apparatus from top to bottom?
Endoplasmic reticulum, Golgi vesicles, vesicular tubular cluster, cis Golgi network, cis cisterna, medial cisterna, trans cisterna, trans Golgi network, secretory vesicles, plasma membrane/other organelles
Describe and explain the structure of the Golgi apparatus
- A stack of flattened membrane bound compartments (cisternae)
- Each layer = cisterna - long tube aqueous environment (has proteins and soluble things inside)
- Membrane bound vesicle - aqueous inside and out (in cytoplasm)
What happens in the trans Golgi network
Like a goods outwards
Sorts whats going where
Trans = departing site
What happens in the cis Golgi network
Where everything goes to
Cis = nearest to ER
What is the function of the Golgi apparatus
- Proteins (soluble) destined for secretion and for a variety of organelles/vesicles within the cell are sorted, modified and dispatched from golgi
- Major site of carbohydrate synthesis in the form of glycoproteins and proteoglycans
What is a donor compartment?
Place of origination for the vesicle
What is the target compartment?
Place where vesicle is going to
What is a vesicle and what is its structure?
Membrane covered sac, two layers of membrane, amphipathic phospholipids with head groups on inside and outside
Where do membrane bound vesicles carry their large?
In their lumen and membrane from a donor compartment to target compartment
How do vesicles bud?
From specialised coated regions of the donor compartment, the coat is later discarded allowing the membranes of the vesicle and recipient to interact and fuse
Coat proteins help with the formation of the bud by bending the membrane into a bulb shape and pinches
How is it made sure that cargo is in the right place and right time?
Cargo receptors(proteins)
Purpose of COP||
Coats the vesicles which transport molecules from ER to golgi
Purpose of COP|
Coats the vesicles which transport molecules from the Golgi back to ER (retrograde/retrieval)
Purpose of clathrin
Coats the vesicles which transport molecules between the Golgi, lysosomes and the plasma membrane
Describe the structure of clathrin
Each clathrin subunit contains 3 large and 3 small polypeptide chains which together forms a 3-legged triskeleton
What is adaptin and what does it do?
- It’s a second membrane complex thats needed to attach the clathrin coat to the membrane
- Adaptin can also interact with the transmembranous proteins, including the transmembranous receptors which capture soluble cargo for transport
- There are at least 4 different adaptins, each recognising a different set of cargo receptor
What is dynamin
A protein that pinches of the vesicle, it binds to the neck of the budding vesicle - the coat is rapidly lost and the naked vesicle is ready for transport
What are SNARE’s and how do they work?
- Surface markers of vesicles to help them be identified
- There are complimentary receptors on target membranes
- There are 20 different SNARE’s which work as pairs
- They wrap around each other forming a stable trans-SNARE complex which locks the two membranes together (docking)
Which SNARE is for the vesicle and which is for target membrane?
V-SNARE - vesicle
T-SNARE - target membrane
How does membrane fusion happen?
For two membranes to fuse, they need to be in close proximity that water is completely excluded from between them
The formation of the trans-SNARE complex may act as a winch, using the energy released as the helices warp to end water exclusion and membrane fusion (hemifusion)
What is exocytosis?
The moving of vesicles containing soluble proteins
What does the regulatory secretory pathway I allow?
Concentration of secretory proteins
What are secretory granules?
Special vesicles which some cells concentrate and store secretory products in
In regulatory secretory pathway I, what happens in acidic conditions of the the Golgi?
Secretory proteins aggregate, then leave the trans Golgi network as loosely bound secretory vesicles
What causes the concentration of secretory proteins to increase as the vesicles mature?
- Retrieval of the membrane (coat) back to the Golgi
- Increased acidity in the maturing vesicle lumen, causing tighter aggregation
What does the regulated secretory pathway II allow?
Further processing of secretory proteins and within the. secretory vesicles, proteins may be further processed by proteolysis
What is proteolysis?
Breaking down of proteins
What does proteolysis enable?
Enables very short (5 AA) peptides to be produced (neuropeptides) and also protects the cell from its own hydrolytic enzymes (inactive prior to cleavage)
What does the regulated secretory pathway III allow?
Allows release in response to a trigger. In some cells, vesicles dock with the plasma membrane but fusion only occurs following specific trigger
Explain the process of exocytosis
- Following the release of secretory proteins to the extracellular space, there is a transient increase in the surface area of the plasma membrane
- These extra components must be removed and recycled
- Cells also take up macromolecules and even other cells
What are the three types of endocytosis?
- Pinocytosis
- Receptor-mediated endocytosis
- Phagocytosis
What is pinocytosis?
Clathrin-coated pits rapidly invaginate and form vesicles which lose their coat and fuse with early endoscopes.
In this way, extra cellular constituents are delivered to the lysosomes for digestion and membrane components are recycled
What is receptor-mediated endocytosis?
Binding of a ligand to a receptor, causing a shape change which stimulates the invagination of the membrane - it pinches off and whatever is on the membrane and bounded to the receptor gets taken up
What is phagocytosis?
- Specialised white blood cells (macrophages, neutrophils and dendrite cells) can take up large particles like microoganisms and dead cells,
- Such particles bind to the surface of phagocytes and are recognised by cells surface receptors
- This stimulates the cell to extend pseudopods which fuse to engulf the particles
- The resulting large, endocytic vesicles (phagosomes) fuse with lysosomes so that their contents can be digested
What are lysosomes?
Membrane bound compartments and the major site of intracellular digestion. They contain 40 types pf hydrolytic enzymes
How are all hydrolytic enzymes protected from each other?
They are all acid hydrolyses so protected from each other by a high degree of glycosylation - maintained at around pH5 by a H+ pump in the lysosomal membrane (pH 5 maintains charge of enzyme so protein folds properly)
How is the cell protected from attack by its own digestive enzymes?
- The lysosomal membrane keeps enzymes out of the cystol
- Acid hydrolyses don’t work at cellular pH (7.2)
What are the functions of lysosomes?
- Hydrolytic enzymes are transported from the ER where they are synthesised
- Macromolecules targeted for digestion come from a variety of sources
- Digestion products are transported out of the lysosomes by transporters in the membrane
What are the 3 fates of endocytosed contents?
Recycling, transcytosis and degradation
What happens in the recycling of endocytosed contents?
Membrane and many receptors are sent to the “recycling endosome”
Vesicles return to plasma membrane
What happens in the transcytosis of endocytosed contents?
Vesicles return to different parts of the plasma membrane: transports material across the cell
What happens in the degradation of endocytosed contents?
Cargos (and some receptors) are sent to late endoscopes which mature into lysosomes
Macromolecules are degraded and their components are used to make new molecules
What makes up the structure of mitochondria and what are their percentages?
- Matrix - 67% of mitochondrial proteins
- Inner membrane - 21% of proteins, invaginated into cristae
- Outer membrane - 6% of proteins
- Inter membrane space - 6% of proteins
What are the functions of mitochondria?
- Make most of the energy a cell requires
- Most foods are broken down in the cytoplasm to simple constituents which are then transported to the mitochondria
- Further oxidation occurs to produce Co2, H2O and ATP
What does ATP stand for?
Adenosine triphosphate
How is energy stored?
Energy is stored in ability of phosphoryl groups to be transferred to other molecules
What are the resulting molecules of ATP?
ADP (adenosine diphosphate) of AMP (adenosine monophosphate) and inorganic phosphate
What makes up the structure of mitochondria and what are their percentages?
- Matrix - 67% of mitochondrial proteins
- Inner membrane - 21% of proteins, invaginated into cristae
- Outer membrane - 6% of proteins
- Inter membrane space - 6% of proteins
What are the functions of mitochondria?
- Make most of the energy a cell requires
- Most foods are broken down in the cytoplasm to simple constituents which are then transported to the mitochondria
- Further oxidation occurs to produce Co2, H2O and ATP
What does ATP stand for?
Adenosine triphosphate
How is energy stored?
Energy is stored in ability of phosphoryl groups to be transferred to other molecules
What are the resulting molecules of ATP?
ADP (adenosine diphosphate) of AMP (adenosine monophosphate) and inorganic phosphate
In oxidative phosphorylation, in the cytoplasm, what is converted into what?
Sugars to pyruvate
Fats to fatty acids and glycerol
In oxidative phosphorylation, in the peroxisomes, what is converted into what?
Fatty acids to acetyl CoA
This generates some ATP but not enough - these simples compounds are transported into the mitochondrial matrix
