Cell Processes Flashcards
What bases are pyrimidines?
Cytosine
Uracil
Thymine
How can you distinguish pyrimidine structures from one another?
Cytosine possesses an NH2 group
Uracil has a CH whilst thymine has a methyl group at the same Carbon
What bases are purines?
Guanine and adenine
How can you distinguish between the structures of purines?
Guanine possesses a C=O bond whereas adenine does not
What is the structural difference between deoxyribose and ribose?
Ribose possesses two OH groups on the same side but deoxyribose only has one
What is the structure of a steroid?
4 cyclic groups (usually 3 hexagons + 1 pentagon)
List the three macromolecule types:
Polysaccharides (carbohydrates)
Proteins
Nucleic acids
What is a macromolecule?
Polymers constructed of identical or similar monomers - very large
What are two ways macromolecules can be made/broken?
Via dehydration or hydrolysis reactions
Are lipids soluble in water? Why?
Lipids are not soluble in water as they are non-polar. This is due to the fact that they are mostly composed of non-polar hydrocarbon chains
What is the structure of a lipid?
Glycerol + 3 long chain fatty acids
How does the structure of a lipid differ from that of a phospholipid?
One of the fatty acids in phospholipids is replaced with a phosphorus group
What is the function of lipids?
Essential component of cell membrane (cholesterol)
Stores energy as fat
What kind of linkages are formed when a lipid is created? What kind of reaction is this!
Dehydration reaction - ester linkages x3
What is the difference between a fully saturated fat and an unsaturated fat?
Saturated - no more h able to bind, straight
Unsaturated - double bonds present, bent
What is a polysaccharide composed of?
Simple sugar monomers
Name 3 simple sugars
Glucose
Galactose
Fructose
What are the names for polysaccharides containing 1 simple sugar, 2 simple sugars and 3+ simple sugars?
1 - monosaccharide
2 - disaccharide
3+ - polysaccharide
Give 3 examples of a disaccharide
Lactose - glucose + galactose
Maltose - glucose + glucose
Sucrose - glucose + fructose
What is a glycosidic linkage?
A bond between a sugar and another group (may be another sugar)
What is the function of a polysaccharide?
Energy storage (glycogen in animals and starch in plants)
Structural function (chitin in animals and cellulose in plants)
What is the structure and function of starch?
Function: energy storage for plants - hydrolysed when needed
Structure: glucose polymer
What is the structure and function of glycogen?
Function: energy storage in animals - hydrolysed when needed
Structure: glucose polymer, more extensively branched than starch
What is the structure and function of cellulose?
Function: Structural building block of plants - can hydrogen bond to others to form myofibrils (as strong building material)
Structure: beta-glucose polymer, never branched, has different glycosidic linkages to starch which results in a distinct 3D shape
What is the structure and function of chitin?
Function: structural building block of animals
Structure: similar to cellulose with beta-glucose linkages, but also contains nitrogen
What is the structure of a protein?
Molecules built up from 20 different amino acids linked together via peptide bonds
What is the function of a protein? (7)
Enzymes
Defence
Storage
Transport
Cellular communication
Movement
Structural support
What are the 3 R group side chain properties?
Non polar
Polar
Electrically charged
What part of an amino acids comprises the polypeptide backbone?
Non R group parts (amino group, alpha carbon, carboxyl group)
Are the R groups the same in each amino acid?
No, the R group differs from one type of amino acid to the other
What is the structure of a nucleic acid?
Long unbranched molecule
Backbone made of ribose or deoxyribose linked via phosphodiester bonds
Side groups (bases) are pyrimidines or purines
What is the function of nucleic acids?
Codes for genetic material
All informational processes include these macromolecules
Storage of chemical energy in ATP
intracellular signalling via cAMP
What is the difference between a nucleotide and a nucleoside?
Nucleotide consists of phosphate group, sugar, and base
Nucleoside lacks the phosphate group, and consists of just the sugar and base
Describe the fluid mosaic model for the phospholipid bilayer
Phospholipids + proteins studded throughout membrane (protein placement not random, corresponds to defined specialised patches)
Define amphipathic
Molecules that are both hydrophilic and hydrophobic
Fully saturated hydrocarbon tails lead to an increase in _____ and a decrease in _____
Increase in viscosity
Decrease in fluidity
Unsaturated carbon tails lead to an increase in _____ and a decrease in _____
Increase in fluidity
Decrease in viscosity
What is cholesterol regulation?
“Fluidity buffer”
Cholesterol retains gaps between phospholipids
Reduces fluidity at high temperatures
Prevents solidification at low temperatures
What is the difference between a peripheral and an integral protein?
Peripheral proteins do not penetrate the phospholipid bilayer
Integral proteins do
Name the 6 functions of membrane proteins
Signal transduction
Attachment to cytoskeleton and extracellular matrix
Transport
Intercellular joining
Cell-cell recognition
Enzymatic activity
What types of molecules can easily cross the lipid bilayer?
Non polar molecules - hydrophobic and can dissolve in and cross the lipid bilayer
What kinds of molecules will find it hard to cross the lipid bilayer without assistance? Which will travel across slower unassisted?
Polar molecules - hydrophilic - impeded by hydrophobic interior of lipid bilayer
Ions - cross more slowly than polar molecules
List two types of transport proteins and their functions. Are transport proteins specific for molecules or non-discriminating？
Transport proteins are specific for the substance it translocates.
Channel proteins - provide hydrophilic channel so certain molecules and ions can cross (called ion channels for ions)
Carrier proteins - shuttle molecules across membrane by changing shape
What is selective permeability dependent on?
The discriminating barrier of the lipid bilayer + specific transport proteins built into the membrane
What are two types of transport small molecules can use to get across the lipid bilayer?
Passive transport
Active transport
What is passive transport?
No work done (no energy expended)
Molecules diffuse down its own concentration gradient from high concentration to low concentration
Can be facilitated via the aid of proteins
What kinds of proteins are utilised in active transport? What is active transport?
Carrier proteins are utilised in active transport
Movement of molecules against their concentration gradient (low conc. to high conc.)
Work done (energy used in process of active transport)
Give an example of active transport
Sodium-potassium pump
Describe the cycle of the sodium-potassium pump
An increased affinity for sodium means cytoplasmic sodium bind to the sodium-potassium pump
The binding of sodium stimulates phosphorylation by ATP (atp transfers terminal P group directly to transport protein)
Phosphorylation causes the carrier protein to change shape, reducing its affinity for sodium and increasing its affinity for potassium
Sodium leaves carrier protein, extracellular potassium binds to carrier protein
Binding of potassium triggers the release of the phosphate group
The loss of the phosphate group results in a lowered affinity for potassium and an increased affinity for sodium. Potassium leaves the carrier protein and the process repeats.
What is membrane potential?
The voltage across a membrane - affects charged substances across the membrane
In regards to the extracellular matrix, is the inside of the cell more positively or negatively charged? What does this mean for ions travelling across the membrane? How does this occur?
The cell is more negatively charged, the outside is more positive.
Membrane potential favours the entry of cations and the exit of anions.
Voltage is generated via an electrogenic pump such as the sodium-potassium pump (3Na+ out, 2K+ in results in a net loss of one +ve charge per “pump”)
What are the two ways through which large molecules travel to and from the cell?
Exocytosis - secretion via fusion of vesicles with plasma membrane
Endocytosis - pinocytosis and phagocytosis
List two types of pinocytosis and their processes
Pinocytosis - cell “drinking” - engulfs extracellular fluid - non selective
Receptor mediated endocytosis - appropriate molecule binds to receptors on extracellular side of membrane, surface depresses to form coated vesicle
What is a ligand?
A molecule that binds specifically to a receptor site on another molecule
What is a proteoglycan composed of?
Protein + carbohydrate chain (covalently bonded)
What is a proteoglycan complex?
Proteoglycans noncovalently attached to a single long polysaccharide
What is the function of a fibronectin?
Binds extracellular matrix to the cell
What is an integrin?
A pair of proteins that span the membrane; attachment point for extracellular membrane and microfilaments
Wha is an example of a cell junction in a plant? Describe its structure.
Plasmodesmata - cell walls perforated with channels that connect the cytoplasm of cells (cytosol travels between cells through plasmodesmata)
Name 3 types of cell junctions found in an animal cell and their functions
Tight junctions - plasma membranes pressed tightly together, bound by proteins (occludins and claudins) - seal intercellular space
Gap junctions / communicating junctions - channels between cells composed of 2 connexons (hemichannels) each composed of 6 connexins
Desmosomes / anchoring junctions - fastens cells together in strong sheets via cadherin proteins, intermediate filaments (keratin) anchor the desmosomes to the cell
What are some functions of proteins? (8)
Enzymes
Defensive proteins
Storage proteins
Transport proteins
Hormones
Receptors
Contractile / motor proteins
Structural support
What determines how a polypeptide chain folds and its final structure?
The sequence of side chains in the amino acid monomers
What is the primary structure of proteins?
Linear arrangement of amino acids and side chains in a polypeptide
What is the secondary structure of proteins?
Alpha helix - cook held together by hydrogen binding on every 4th amino acid
Beta pleated sheets - beta strands connected by H binds between parts of two parallel segments of polypeptide backbone
What is the tertiary structure of proteins?
The overall shape of the polypeptide resulting from interactions between side chains (R groups) of the various amino acids.
List three types of interactions found in tertiary proteins
Hydrophobic interactions - non polar sidechains end up in clusters towards core of the protein - van der waals interactions hold them together
H bonds between polar side chains and ionic bonds between +ve and -ve side chains help stabilise structure
Disulphide bridges - further reinforce shape of a protein (-S-S- rivets part of protein together)
What is the quaternary structure of a protein?
Association of two or more polypeptides as a functional molecule.
Not all proteins reach quaternary structure.
What happens to protein structure following denaturation?
Weak chemical binds and interactions disrupted/destroyed - only primary structure retained
Can proteins refold/renature?
Only in some cases, once normal environments have been restored.
What factors can contribute to denaturation of a protein? (5)
pH
Temperature
Salt concentration
Reducing agents
Transfer from an aqueous environment to a nonpolar solvent
What is the difference between the denaturation and hydrolysis of proteins?
Denaturation results in a primary structure
Hydrolysis breaks the structure down even further into monomers
What is a chaperonin/chaperone protein and are some of its functions?
Chaperonins assist in polypeptide folding by protecting the polypeptide from disruptive chemical conditions while it folds spontaneously. May also provide a more favourable environment for folding.
- keeps polypeptide separated
- minute amounts of water present - hydrophilic environment
- molecular systems interact with chaperonin to check for correct folding
- can refold misfolded proteins or mark them for destruction
What is the difference between an anabolic and catabolic reaction?
Anabolic - endergonic - e consumed in reaction, products possess higher E - large molecules from small molecules
Catabolic - exergonic - energy released through reaction - small molecules from large molecules
What does an ATP cycle combine?
The ATP cycle couples endergonic and exergonic reactions to drive one another
Why is ATP used as an energy source for driving cellular work?
ATP possesses a higher reactant energy relative to products (ADP+Pi) due to its negatively charged phosphate groups = increased repulsion forces = decreased stability = increased energy
This results in more net energy released than most molecules undergoing similar reactions
How do enzymes speed up (catalyse) reactions?
Enzymes provide an alternate pathway for reactions to take without lowering the 🔺G
- may decrease E needed to reach transition state by stretching substrates
- may provide a more appropriate environment (e.g pH)
- amino acids in active site may directly participate in the chemical reaction
What is a cofactor?
Many enzymes require non-protein “helpers” called cofactors for catalytic activity
May bind permanently or reversibly alongside substrate
How do cells regulate their metabolic pathways?
Switching on/off genes that encode for particular enzymes
Regulating enzyme activity once made
How do cells regulate enzyme activity once they are made?
Converting between inactive and active forms
Cellular localisation (e.g enzymes locked inside lysosomes)
Allosteric regulation (inhibition or activation) - e.g feedback inhibition
What is allosteric regulation?
Where a protein’s function at one site is affected by the binding of a regulatory molecule to a separate site - may result in inhibition or stimulation of an enzyme’s activity
What is a regulatory/allosteric site?
Where an activating or inhibiting regulatory molecule binds - usually located where subunits join
What does an enzyme complex oscillate between?
The catalytically active and inactive shapes
What is the difference in function between an activator and inhibitor (regulatory molecules) on an enzyme complex?
Activator - stabilises active form of enzyme complex
Inhibitor - stabilised inactive form of enzyme complex
What happens when one unit of an enzyme complex changes shape?
The shape change is transmitted to all other subunits.
What is feedback inhibition?
Where a metabolic pathway is halted by the inhibitory binding of its end product to an enzyme that acts early on in the pathway.
- more product = less demand
- product binds to enzyme, inhibiting further production
- as product is used up by cell, less enzymes are inhibited = more production of the same product
What is the sugar phosphate backbone of DNA composed of?
A phosphate group covalently bonded to deoxyribose via a phosphodiester bond
What is a chromosome’s components?
DNA packed together with proteins
What is a histone
A protein that binds tightly to negatively charged DNA
What is a nucleosome?
DNA would twice around a core of 8 histones
What points outwards from a nucleosome?
The amino end (N terminus) / histone tail extends outward from the nuclesome
How is the 30-nm fibre formed?
Interactions between histone tails of different nucleosomes result in chromatin coiling/folding
What is a looped domain?
Loops formed by 30-nm fibre become looped domains which are attached to a chromosome scaffold composed of proteins ; 300-nm fibre
What is the 300-nm fibre?
Looped domains attached to a a chromosome scaffold composed of proteins
Put the following in order from smallest to largest:
Nucleosome, 30-nm fibre, 300-nm fibre, histone, looped domain, chromosome
Histone
Is the interphase chromosome or metaphase chromosome more condensed?
The metaphase chromosome is more condensed as it is it undergoing mitosis
The interphase chromatin is less condensed than when preparing for mitosis
Is the structure of an RNA molecule more or less variable than that of DNA
More variable than DNA
What specifies the sequence of bases for RNA?
The sequence of bases in DNA specify the sequence of bases for RNA
List the 3 types of RNA and their functions
rRNA - ribosomal RNA: makes up ribosomes and comprises the bulk of cellular RNA as it is a stable RNA, synthesised from highly repetitive DNA in the nucleus
mRNA - messenger RNA: conveys information from DNA in nucleus which specifies amino acid sequences of polypeptides, synthesised and degraded at a fast rate so is present only in small amounts (live fast die young lol)
tRNA - transfer RNA: possesses an anticodon and amino acid attachment site, translocates nucleotide sequence in mRNA into amino acids during protein synthesis. Possesses 4 base paired regions, 3 loops containing anticodon, amino acid attachment site. There is at least one specific tRNA for each of the 20 amino acids
What is an origin of replication?
Where DNA replication initiates (1 in prokaryotes, multiple in eukaryotes)
What is the function of helicase in DNA replication
Helicase breaks H bonds between strands, untwists double helix at replication fork
What is the purpose of single strand binding proteins in DNA replication?
Single strand binding proteins prevent separated DNA strands from reconnecting
What is the role of topoisomerase in the process of DNA replication?
Relives strain of DNA twisting ahead of replication fork by breaking, swivelling and rejoining DNA strands.
What is the role of primate in DNA replication?
Adds primer (complementary RNA chain) to DNA template strand as DNA polymerase can only add to an existing chain
What is the role of DNA polymerase in the process of DNA replication?
DNA polymerase catalysed the synthesis of DNA by adding nucleotides
Can only add to the 3’ end of primer
How are the leading and lagging strands synthesised?
Leading: continuously synthesised in 5’ to 3’ direction
Lagging: discontinuous synthesis of fragments (Okazaki fragments)
Describe the process of the synthesis of the lagging strand
Each Okazaki fragment primed separately
DNA polymerase III adds nucleotides to primer which results in the first Okazaki fragment, detaches when it reaches the next primer
Next fragment primed, DNA polymerase III adds nucleotides, detaches when it reaches the primer of the previous Okazaki fragment.
DNA polymerase I replaces RNA in primers with DNA
DNA ligase forms bond between DNA fragments by joining the sugar-phosphate backbone
Who do the ends of chromosomes get progressively shorter with each cell division?
RNA primer at the end of strand removed but cannot be replaced by DNA as DNA polymerase can only add to the 3’ end of an existing chain
What is a telomere and its function?
A region of repetitive nucleotide sequence at the end of each chromatid
Protects ends of chromosomes by preventing loss of genes near the end
Describe the process of transcription
Transcription - mRNA synthesis
RNA polymerase pries DNA helix apart. Unlike DNA polymerase, it does not need a primer to begin building RNA
RNA polymerase binds to a promoter (nucleotide sequence) and initiates RNA synthesis at start point within promoter
RNA joins complimentary nucleotides and builds RNA in a 5’ to 3’ direction (nucleotides added to 3’ end)
RNA molecule “peels away” from the template DNA, transcribed DNA returns to double helix structure
In bacteria: terminator sequence causes RNA polymerase to detach and release transcript
In eukaryotes: RNA polymerase transcribes a sequence known as the polyadenylation signal sequence (AAUAAA in pre-mRNA) which is automatically bound by certain proteins in the nucleus which cut it free from the RNA polymerase, releasing the pre-mRNA
Pre-mRNA modification (RNA processing) only occurs in _____ cells
Eukaryotic
What occurs during pre-mRNA modification?
5’ end receives 5’ cap (modified guanine)
3’ end receives poly-A tail (50-200 adenine nucleotides)
Introns spliced out from pre-mRNA strand and remaining exams ligated together to form mature mRNA
What is the purpose of the 5’ cap and poly-A tail?
They facilitate export of mRNA from the nucleus and prevent degradation by hydrolytic enzymes as well as helping ribosomes attach to the 5’ end of the mRNA
What is the components and function & process of the spliceosome?
Spliceosomes = proteins + small RNAs (snRNPs, small nuclear ribonucleoproteins)
SnRNA (small nuclear ribonucleicacid) pairs with bases in pre-mRNA intron (splice sites)
Spliceosome cuts pre-mRNA and releases intron for degradation
Spliceosome ligates exon end together - catalysed by snRNA
Releases mature mRNA
What does an aminoacyl-tRNA synthetase do?
It attaches the correct amino acid to a tRNA molecule to form an aminoacyl-tRNA
aminoacyl-tRNA synthetase only fits a specific combination of tRNA and amino acid in its active area
What is “wobble”?
Where base pairing between the 3rd nucleotide base of a codon and corresponding codon is more relaxed than the first two - results in flexible base pairing
What are the three sites of a ribosome and what are their functions?
E site - exit site
P site - holds tRNA attached to existing polypeptide chain
A site - holds tRNA with to-be-added amino acid
Describe the initiation step of translation
tRNA carrying methionine binds to small ribosomal subunit
5’ cap of mRNA binds to small subunit
tRNA “scans” mRNA until it finds a specific initiator (start codon) and then binds to it.
Large ribosomal subunit attaches and completes the translation initiation complex.
Describe the translation step of translation
The anticodon of aminoacyl-tRNA pairs with its complementary codon in the A site
rRNA molecule of large subunit catalysed formation of peptide bond between new and growing polypeptide
Ribosome moves tRNAs into neighbouring sites
Describe the termination step of translation
When ribosome reaches a stop codon, A site accepts a “release factor” which promotes the release of the polypeptide from tRNA
Polypeptide released via the exit tunnel, mRNA and ribosomal subunits dissociate
What are polypeptides destined for secretion or the endomembrane system marked by?
They are marked with by a signal peptide which targets the protein to the ER
What is a signal peptide and how does it work?
A signal peptide is a sequence of ~20 amino acids at/near the leading end (N terminus) of the polypeptide
It is recognised as it emerges by SRP (signal-recognition particle)
SRP “escorts” ribosome to a receptor protein build into the ER membrane
Polypeptide synthesis continues, growing chain crosses membrane into the ER lumen via signal pore
Signal peptide removed by an enzyme, units dissociate
What is the difference between a ribosome and a polyribosome?
Polyribosomes are one mRNA strand with multiple ribosomes travelling along it, making chains.
True or false: transcription and translation occur separately in bacteria
False: transcription and translation occur concurrently with one another in bacteria
What is the genetic code
The means by which DNA and RNA molecules carry genetic information: codons, the triplet code which specifies amino acids
What is meant by “the code is redundant”?
Most amino acids are specified by more than one codon
What is the difference between spontaneous and induced mutations?
Spontaneous mutations occur due to random errors in the processes of transcription/translation
Induced mutations are a result of external agents damaging DNA
What is excision repair? Describe the process.
Excision repair is the repairing of damaged/mismatched DNA by cutting out the affected area and replacing it with new nucleotides.
DNA polymerase proofreads DNA but may miss mismatched pairs.
Nuclear excuses (cuts out) damaged/mismatched section
Gap filled with appropriate nucleotides using undamaged strand as template by DNA polymerase
DNA ligase seals free ends of nucleotides to complete strand
How do prokaryotes control gene expression?
Prokaryotes continually turn genes on and off in response to signals from their external and internal environments
True or false: gene expression in eukaryotes is regulated at a single level.
False: gene expression in eukaryotes is regulated at many levels.
How does chromatin modification (unpacking) influence gene expression?
Condensed chromatin needs to be loosed in order to allow access to DNA for transcription.
How does transcription influence gene expression?
Transcription factors that facilitate RNA polymerase binding can also bind to regulatory sequences and stimulate/repress transcription of a gene
Regulating transcription is the most common way of controlling gene expression
How does RNA processing affect gene expression?
Alternative splicing - different mRNA molecules produced from the same pre-mRNA = proteins of different size and function from the same pre-mRNA
How does translation affect gene expression?
Translation is controlled by regulating factors which mediate initiation of translation
How does degradation of RNA affect gene expression?
The lifespan of RNA in cytoplasm determines how long it can be used for protein synthesis
How does protein processing and degradation affect gene expression?
Modification needed to produce a functional protein regulated
Protein trafficking to correct organelle regulated
Selective degradation influences the lifetime of a protein
Non coding RNA can regulate gene expression by influencing: (3)
Chromatin packing
Translation
mRNA degradation
How do prokaryotes control their metabolic processes? (2)
Adjust catalytic activities of preexisting enzymes
Adjust production of enzyme molecules by regulating expression of genes encoding enzymes
How do prokaryotes adjust the catalytic activities of preexisting enzymes?
The product of the metabolic pathway inhibits the initial enzyme of the pathway which prevents production of final product - rapid response, feedback inhibition
How do prokaryotes adjust production of enzyme molecules by regulating expression of genes encoding enzymes?
An abundance of products represses expression of genes encoding all enzymes in a metabolic pathway - long term response
What is an operon?
Operator + promoter + controlled genes
Promoter: where RNA binds, controls transcription of all genes following it
Operator: found in promoter or between promoter and genes, controls access of RNA polymerase to genes
What is the difference between negative and positive gene regulation?
Negative: repressive protein binds to operator, prevents expression
Positive: transcription factor or activator binds to promoter and enables RNA polymerase to initiate transcription
Describe the process of negative regulation of the lac operon in the absence of lactose
Regulatory gene codes for repressor protein: lac I for lac repressor protein
The repressor protein binds to the operator and obstructs promoter
Transcription of the lac operon cannot occur, and beta galactosidase cannot occur
Describe the process of negative regulation of the lac operon in the presence of lactose
Lactose acts as an induced
Lactose binds to lac repressor protein which induces a change in shape of the repressor
Repressor can no longer bind to the operator
Normal transcription of lac operon continues, 3 proteins produced
When glucose levels are low, what happens to levels of cyclic AMP (cAMP)?
The levels of cAMP rise (accumulates)
What is the function of cAMP?
cAMP binds to and activates the catabolite activator protein (CAP)
Describe the process of positive gene regulation of the lac operon and describe how the results would differ in the presence of glucose/absence of glucose)
Active CAP binds to the promoter and facilitates binding of RNA polymerase to promoter, transcription can occur
Presence of lactose inhibits repressor protein (if no lactose, no lac operon transcription occurs)
In the presence of glucose, there are lower levels of cAMP = lower levels of activated CAP
No CAP = lower level of transcription, even if lactose is present
Mutations in the lac operon may result in: (3)
The production of non-functional proteins
No transcription (e.g promoter mutation = no RNA polymerase binding)
Permanently active transcription
