Biomolecules + Cell Structure Flashcards
Binary fission
Asexual separation into 2 cells for prokaryotes
Mycoplasma
Smallest known bacteria
3 basic bacterial cell shapes
- Cocci - spheroidal w/70 nm-thick cell membrane
- Bacilli - rodlike w/30-250 nm thick cell wall made from chemically cross-linked polysaccharides
- Spirilla (helicoidal) w/flagella for locomotion
Mitosis
Eukaryotic cells divide by this - each chromosome is duplicated + each copy sent to 1 daughter cell
Meiosis
Eukaryotic cells divide by this - reductive process where each daughter cell contains half the chromosomes of the mother cell
How do the metabolisms of mitochondria + chloroplasts function in opposite directions?
In mitochondria oxygen is used as electron acceptor to extract energy from organic molecules - in chloroplasts solar energy is invested to generate organic molecules + oxygen
Do both chloroplasts and mitochondria contain their own DNA?
Yuh - it’s replicated by binary fission
Glycosylation
Addition of sugar to secreted proteins that occurs in rough ER and then Golgi apparatus
Differences in prokaryotes + eukaryotes in terms of structure/size
- P: 1 large circular chromosome, E: several long chromosomes in duplicate copies (diploid)
- P: chromosome condensed in nucleoid, E: nucleus surrounded by nuclear envelope
- P: plasmids (small circular DNA), E: nucleolus (synthesis of ribosomal RNA)
Differences in prokaryotes + eukaryotes in terms of genetic material
- P: no organelles, E: organelles
- P: no vesicles, E: vesicles
- P: photosynthesis in chloroplasts, E: no photosynthesis
Difference in prokaryotes + eukaryotes in terms of sub cellular elements
- P smaller than E
- E longer doubling times than P
- P unicellular, E multicellular
- P: complex cell wall, E: simpler cell wall + no cell wall in animals
- P: flagella made from single protein, E: flagella made from microtubule complex
Autotrophs
Use simple molecules + external energy source to synthesize organic molecules
Photoautotrophs
Use simple molecules + light via photosynthesis to synthesize organic molecule
Chemolithotrophs
Require organic compounds + oxidizing agents to generate energy via oxide-reduction reactions
Heterotrophs
Extract energy from pre-existing organic molecules
Obligate aerobes
Must use oxygen
Obligate anaerobes
Oxygen is toxic to these
Facultative anaerobes
Can grow in presence or absence of oxygen
Bacteria use in biotechnology products
Easy to introduce foreign genetic material + don’t secrete proteins (ex: food products + nucleic acids)
Fungi use in biotechnology products
Can secrete proteins + perform post-translational modifications but may be diff than those seen in animal cells (ex: food products + antibiotics)
Animal cells use in biotechnology products
Fragile + expensive + able to secrete proteins - post-transcriptional modifications of proteins similar to humans (ex: vaccines + hormones)
mRNA
Intermediate molecule that can be used to convert + amplify info stored in DNA into large amounts of proteins
Central dogma of molecular biology
DNA is transcribed into RNA which is translated into polypeptide sequences
Constitutional isomers
Molecules w/same chemical composition but dif bonds
Stereoisomers
Molecules w/same chemical composition + bonds but dif 3D organization
Beta anomer - when is it an alpha anomer
Used if OH and CH2OH groups are on same side - it’s an alpha when it’s not a beta lol
Glycosidic bond
Forms between 1 anomeric carbon and 1 non anomeric carbon on neighbouring saccharide monomer - condensation rxn of monosaccharide to polysaccharide results in its formation
Glycogen
Acts as energy-storage molecule in mammals - branched polysaccharide made from glucose monomers linked by beta-1,4 glycosidic bonds
Nucleotides
- Nucleic acids are its polymers - comprise of pentose sugar (ribose in RNA, deoxyribose in DNA) + nitrogenous base on 1’ carbon of sugar + P group on 5’ carbon of sugar
Phosphodiester bonds
Bind together chains of nucleotides that make up strands - link each P group to 2 pentose sugars + form between nucleotide and 3’ carbon of another nucleotide so they’re created by linking 2 ribose/2 deoxyribose sugars via their 3’ and 5’ carbons
How are the 2 DNA strands oriented towards each other?
They’re antiparallel - 5’ and 3’ ends of nucleotides face in opposite directions on 2 strands
Where are nitrogenous bases found on the helix? What about the P residues?
Nitrogenous bases found inside as they’re hydrophobic - P residues found outside because they’re charged
tRNA
Converts mRNA sequence into polypeptide chain
rRNA
Involved in catalytic rxn required to produce proteins from mRNA strands
Differences DNA and RNA
- DNA is A T C G, RNA is A U C G
- DNA carries genetic info that’s always present, RNA only expressed when needed
- DNA has long stable double helices w/2 complementary antiparallel strands, RNA usually single-stranded + can form short/temp double helices + can form complex 3D structures
Coding strand
DNA strand chosen to provide sequence info
Template strand
Transcribed to produce complementary RNA strand
Main interactions + effects that stabilize DNA double helix
- Hydrophobic effect
- Hydrogen bond formation between complementary base pairs
- Base stacking - pi stacking interactions between aromatic rings of nitrogenous bases
- Ionic interactions between negatively charged P backbone + ions present in sol’n
What happens if pH of hydration shell in DNA/RNA is lowered below the pKa of the nucleic acid P groups?
P backbone becomes protonated + loses its charge - protonated nucleic acids are less polar so they ppt from sol’n
Salting in
At low salt concentrations the addition of salt leads to cations helping to shield negative charges of P backbone which increases nucleic acid solubility
Salting out
At high salt concentrations the salt molecules compete w/nucleic acids for interactions w/water to form salvation shells so nucleic acids ppt from sol’n
Hybridizing short RNA or DNA sequences with long nucleic acid strands
Exploits the fact that shorter complementary strands anneal faster than longer ones -
Hyperchromic effect
Extinction coefficient of single-stranded DNA is higher than extinction coefficient of double-stranded DNA
DNA melting temperature
- On a DNA melting curve this is the temperature at which slope of relative absorbance of temperature is steepest - molecules w/higher GC content + longer molecules + molecules w/surrounding solvent w/increased salt concentration have higher Tm
- Very low/high pH decrease Tm
Main roles of proteins
- Catalyzing bio rxns
- Cell structure + movement - scaffolding, contractility, motility
- Cell-cell communication
- Transport
- Immune functions w/in organisms
- Modulating gene expression
Amino acids
Make up polypeptide chains
Alpha-carbon of an alpha-amino acid
Surrounded by primary amine group, carboxylic acid group, H atom + side chains
Do proteins consist of L or D enantiomers?
L
O-linked glycosylation
Addition of sugars linked to hydroxyl groups (on amino acids) via glycosidic bonds
N-linked glycosylation
Sugars added to amino acids that have reactive nitrogen atoms on their side chain
Disulphide bonds
2 cysteine side chains react together in oxidizing conditions to form this
Peptide bonds
Join amino acids in linear fashion to make polypeptide chains - form via dehydration rxn that creates covalent bond between amine group of 1 amino acid + carboxylic acid group of next
How is sequence of polypeptide chains normally given?
From free amino/N terminus to free carboxy/C terminus
Why is alpha helix formation favourable?
Their particular conformation allows for establishment of H bonds to stabilize the helix
What’s the difference between the hydrogen bonds in alpha and beta sheets?
In beta the H bonds form between dif polypeptide segments rather than w/in 1 polypeptide segment - beta sheets involve at least 2 interacting beta sheet segments to allow H bonding
Difference between parallel and anti-parallel beta sheets?
Parallel ones have N and C termini of interacting segments on same side - antiparallel have N and C termini of interacting segments opposite from each other
Motifs
Secondary structure arrangement patterns
Interactions that stabilize the tertiary structure of proteins
- Disulphide bonds - covalent bonds forming between side chains of cysteine residues
- Salt bridges - ionic interactions between 2 charged amino acids
- Coordination bonds
- Hydrogen bonds - between secondary structure elements
- Van der Waals interactions - dipole-dipole associations between neutral molecules
Proteoglycans
Heavily glycosylated proteins that include core proteins and glycosaminoglycans
Glycosaminoglycans
Unbranched polysaccharides consisting of repeating disaccharide units - viscous + elastic
Difference saturated and unsaturated fatty acids
Saturated fatty acids have fully hydrogenated chains while unsaturated have double bonds
Glycerophospholipids
Main component of biological membranes - similar to triglycerides but 1 hydroxyl group of glycerol is occupied by phosphatidic head
Sphingolipids
Compose a hydrophilic head + hydrophobic body on glycerol backbone with its central carbon bound to an amine/amide group
Liposomes
Self-sealing solvent filled vesicles bound by single lipid bilayer - also obtained by injecting ethanol-containing phospholipid solution into water/by dissolving phospholipids in detergent then removing detergent by dialysis + used as drug delivery methods
What does the effect of cholesterol on membrane fluidity depend upon?
Test temperature - at body temps it decreases membrane fluidity due to its rigid structure but it broadens T of order-disorder transition by hindering packing of fatty acid side chains to form a paraffin-like crystalline structure
Integral proteins
- Completely/partially embedded in membrane via hydrophobic regions that interact w/hydrophobic region w/in bilayer - amphiphilic + contain transmembrane domains that expose hydrophobic surfaces to membrane
- Relay signals from outside to inside of cell
Peripheral proteins
Linked to membrane via lipid that anchors protein to membrane - presence/absence of diff lipid anchors controls localization of proteins to specific organelles + this impacts function of proteins and their interactions w/other proteins
Peptidoglycan
Polymer consisting of polysaccharide chains cross-linked by peptide chains that composes cell wall
What is cell wall flanked by?
2 permselective lipid bilayer membranes (cytoplasmic membrane + outer membrane)
Lipopolysaccharides
Displayed on outer membrane surface - lipids that include polysaccharide chain + trigger strong immune response as defence against invasion by pathogenic bacteria
Why may an outer membrane be problematic when over-expressing proteins of interest in bacteria using recombinant DNA tech?
Because proteins get trapped in the periplasm which complicates protein recovery
How to distinguish gram positive and gram negative bacteria?
Gram staining - u apply a primary stain + then dehydrate/wash (which is when peptidoglycan layer condenses)
How are gram positive bacteria distinguished from gram negative?
Bacteria w/thick peptidoglycan cell wall retain the primary stain so they’re gram positive
