Week 2 Flashcards
What is the plasma membrane important in?
- Separates intracellular from extracellular environment
- Controls internal conditions of cell
- Important in communication between cells
What comprises the phospholipid (draw + label)
- Hydrophilic head (glycerol and phosphate)
- Hydrophobic tail (two fatty acids, one unsaturated)+
Looks like RC body pin
Draw the cell membrane. Why is it oriented like this?
- Phospholipid bilayer
- Hydrophobic tails face away from aqueous environment, hydrophilic heads face out
What structures/substances are in the plasma membrane?
- Cholesterol
- Glycoproteins/Glycolipids
- Integral proteins
- Peripheral proteins
What is the function of cholesterol in the cell membrane?
Adds rigidity and structural integrity
What is the function of glycoproteins/glycolipids
Cell-cell communication, anchoring, adhesion
What is the structure of integral proteins?
Called integral because they cannot be removed. Transmembrane proteins, act as channels.
What is the function of peripheral proteins?
Can be removed (peripheral)
(e.g. Useful in enzymatic activity)
What are the six classifications of surface proteins?
- Cell-cell recognition
- Anchoring
- Adhesion
- Receptor
- Channel
- Enzymatic activity
What characteristics affect the permeability of a cell membrane (including the substance and the membrane itself)?
Substance: size, lipid solubility, charge
Membrane: presence/arrangement of lipids and proteins
From most easily to least easily, which kinds of substances can cross the cell membrane?
- Hydrophobic molecules
- Small polar molecules
- Large polar molecules
- Ions (can’t without transport protein assistance)
How do non-polar, uncharged molecules cross the cell membrane?
Simple diffusion
How do small/medium charged molecules and macromolecules cross the cell membrane? (passive transport)
Facilitated diffusion
How does water cross the cell membrane
Osmosis
What are the three types of passive transport?
- Diffusion
- Facilitated Diffusion
- Osmosis
What are the types of active transport?
- Primary
- Secondary
- Vesicular transport
Describe primary active transport
- ATP is used to transport a substance across the plasma membrane against the conc gradient
Describe secondary active transport
The energy of one substance moving along its concentration gradient is used to facilitate the movement of another molecule against its concentration gradient (e.g. sodium glucose pump)
What are the three types of endocytosis?
- Pinocytosis
- Phagocytosis
- Receptor-mediated endocytosis
What is the name given to cytoplasmic extensions during phagocytosis?
Pseudopodia
Approximately how many genes in the human genome?
25,000
How do you differentiate between peptides and proteins?
Peptide: <50 amino acids
Protein: >50 amino acids
How can you relate the joining of amino acids back to Greenslade’s chemistry class?
Amino acids are joined by peptide/amide bonds, just like we learned last year:
Recall the four levels of protein organisation
- Primary
- Secondary
- Tertriary
- Quaternary
Which terminus does the polypeptide structure begin an end?
Begins at amino terminus, ends at carboxy terminus (think: alphabet, a before c)
Interestingly, the same alphabet logic applies to afferent vs efferent signals
Why do post-translational protein modification affect the function of a protein?
They affect the strcture of the protein, and therefore the function is altered
What do structural proteins form?
Muscle, bone, skin, connective tissue and the cytoskeleton
What are some examples of structural proteins?
- Muscle Proteins
- Collagens
- Cytoskeletal Proteins
- DNA-Associated proteins (e.g. histones)
What is the most abundant protein in the human body?
Collagen (25%)
What are the three steps of haemostasis?
- Vasoconstriction
- Temporary plug
- Blood coagulation, resulting in a fibrin clot
What are the most important coagulation proteins?
- Thrombin
- Fibrinogen
What is the function of anticoagulation Proteins
Prevents blood clots
What are the two types of coagulation disorders?
- Bleeding disorders (not enough coagulation)
- Thrombotic disorders (too much coagulation)
How can enzymes act as biomarkers?
Tissue destruction due to pathology results in enzyme release into the bloodstream. Pathologists can use this information to detect diseases.
What is another name for signalling proteins?
Ligands
What is the function of cell adhesion molecules?
Hold cells and tissues together.
What three domains do cell adhesion molecules consist of?
- Intracellular domain: interacts with the cytoskeleton
- Transmembrane domain: inserted in membrane
- Extracellular domain: interacts with other molecules outside of the cell
What are the three stages of the central dogma?
DNA → RNA → Protein
What is DNA replication important for?
Development, growth, tissue repair and maintenance
What are the phases of cell replication, and when does DNA replication occur?
G1: Growth - Preparation for DNA synthesis
S: Synthesis - DNA Replication occurs here
G2: Growth - Preparation for mitosis (new organelles)
M: Mitosis (Prophase, metaphase, anaphase, telophase)
True or false: DNA replication occurs from one end to the other.
False, DNA replication occurs in bubbles, which expand into one another until two strands are formed.
Think of this as like two forks of replication moving away from one another.
Which end of DNA strands does DNA replication start and finish?
From 5’ to 3’
What are fragments of the lagging strands called?
Okazaki fragments
What is the role of primase?
Adds a 3’ group for polymerase to start from (binds to hydroxyl group of second nucleotide)
What is the name of the enzyme that ‘unzips’ DNA?
DNA Helicase
What is the role of DNA polymerase?
Adds complementary nucleotides to unzipped original DNA strand
List some external factors that can damage DNA
- UV light
- Thermal damage
- Mutagens
List some internal factors that can damage DNA
- Mistakes in polymerase
- Reactive oxygen species
What are the four types of DNA damage?
- Break (double/single stranded)
- Bond between neighbouring nucleotides
- Nucleotide modification
- ‘Rung’ linkage
MNRB (___ are bad -> damaging)
What occurs during nucleotide excision repair?
Enzyme excises a long piece of DNA that spans a damaged nucleotide. Polymerase then fills in right sequence. Ligation.
What is base excision repair?
Damaged base is removed. Polymerase adds in right one, and ligation occurs.
What is the difference between NER and BER?
BER only acts on one damaged base, whereas NER can act on a section of DNA.
What occurs during mismatch repair?
- Enzyme makes a ‘nick’ upstream
- exonuclease removes the section including the mismatched base
- polymerase and ligase
What occurs during non-homologous end joining?
Ligase simply joins two broken ends
What is non-homologous end joining?
Homologous chromosome is used as a template for repairing the damaged chromosome
Which type of RNA does RNA polymerase 1 make?
rRNA
Which type of RNA does RNA polymerase 2 make?
mRNA
Which type of RNA does RNA polymerase 3 make?
tRNA
Exons vs Introns
Exons: Code for protein
Introns: Don’t code for protein
What is the 5’ cap during post-transcriptional processing?
Modified guanine added to 5’ end for molecular stability and to help it attach to the ribosome.
What is polyadenylation, where does it occur, and why?
Occurs on 3’ end to add molecular stability and helps it get exported to the cytosol. (It’s painful, so at the end it shouts AAAAAAAAAAA!)
Which is the first codon that signals the beginning of translation?
AUG methionine (Cam Chau)
What are the three steps in translation?
- Initiation: mRNA binds to ribosome and tRNA deliver first amino acid
- Elongation: Amino acids are linked by peptide bonds
- Termination: Proteins are released for further modification
What are the three pockets on a ribosome:
APE
A: Amino acid
P: Peptide
E: Exit
Moves from A to E
Which histones pair up?
H2A and H2B, H3 and H4
What happens when two pairs of histones join together?
Tetramer unit is formed
What happens when two tetramer units combine?
Octamer unit is formed
___ Base pairs wrap around an octamer structure to for a _____
146 base pairs to form a nucleosome
What does The Programmed Theory State?
Ageing has an internal clock
What does Error Theory state?
Ageing is a result of the accumulation of errors in vital cellular molecules.
What is cellular senescence?
A permanent block block in proliferation of a cell.
What are some useful applications of senescent cells?
- Immunity (stop viruses from propagating)
- Tumor suppression
- Wound healing (inflammation)
What are some detrimental consequences of senescent cells over time?
- Chronic inflammation
- Tissue degeneration
What is the name given to the type of drugs that can destroy senescent cells?
Senolytics
What is the name given to the type of drugs that can destroy senescent cells?
Senolytics
What are the caps on the end of chromosomes called?
Telomeres