cell bio flashcards

what are the components of basic cells theory?

all living organisms are made out of cells, the cell is the basic structural unit in organisms, all cells arise from cell division

what is cohesion?

the glue that holds the sister chromatids together

features of phase contrast microscopy

good for observing live, unstained transparent cells

features of differential interference contrast (DIC) microscopy

good for observing live, unstained transparent cells like phase contrast but more of a 3D image and better resolution

features of transmission electron microscopy (TEM)

for very small structures, high magnification, used to study internal structures of a sample, cells are fixed- not live

features of scanning electron microscopy (SEM)

used to examine surface details of a sample, cells are fixed- not live

features of fluorescent microscopy

specific molecules are visible, multiple labels possible, can do live imaging

what are the bonds in DNA and where are they?

the 5’ carbon of the new nucleotide bonds the the 3’ carbon of the strand via a phosphate bond. the bases bond with hydrogen bonds

which are the two larger bases in DNA?

the purines - adenine and guanine

how many bonds between AT and GC?

AT = 2 hydrogen bonds, GC = 3 hydrogen bonds

why do cells have chromosomes?

to fit DNA into a cell nucleus, to avoid tangling and breaking DNA, so after replication DNA is equally divided

what is the structure of chromosomes?

telomere at the top and bottom, p arm (always shorter arm), centromere, and q arm

what is the name of a chromosome with two arms the same length?

metacentric

what is the name of a chromosome with one long and one short arm?

submetacentric

what is the name of a chromosome with only one visible arm and what number are these human chromosomes?

acrocentric, humans have 5 autosomal- 13, 14, 15, 21, 22

mitochondria make their own..

DNA, RNA and proteins

what are some features of mitochondrial DNA?

has its own genome, circular double stranded DNA, 16,500 kb long, 37 genes coding for rRNA, tRNA, proteins

what is semi-conservative DNA replication catalysed by?

(DNA-dependent) DNA polymerase

what does helicase do?

uses ATP to break the hydrogen bonds

what does topoisomerase do?

breaks DNA, unwinds then fixes the break to stabilise the DNA

what does primase do?

generates an RNA primer 10-30 nucleotides

what does DNA polymerase do?

joins nucleotides together, proof-reads as it moves along

how many DNA nucleotides does the human genome contain?

3 billion

what percentage of the genome codes for proteins

1%

how many genes does the human genome have?

nearly 20,000

what is the start of a gene called?

the promoter sequence

what is the TATA box?

a region of the promoter where the transcription factors bind

which strand does RNA polymerase use in transcription?

template strand (3’ to 5’) so the RNA is synthesised in the 5’ to 3’ direction

what are regulatory elements?

enhancers and repressors which are upstream or downstream DNA sequences which bind to specific transcription factors and change the amount of RNA being made- loop over and interact with the promotor

when do regulatory elements control gene expression?

during development and differentiation and the response of cells to hormones and growth factors

what does each RNA polymerase do?

I transcribes rRNA, II transcribes mRNA and small regulatory RNAs, III transcribes small RNAs such as tRNA

what is a termination signal?

a sequence in the DNA that signals for the transcription complex to dissociate from the DNA

why is DNA used for the genome and RNA for transcription?

DNA is for storage, is highly stable, needs to be copied. RNA is to get genetic information to the cytoplasm to make proteins but stop when we don’t need them to allow environmental adaption (highly dynamic, responsive process)

when is the chemical difference between DNA and RNA?

DNA has a H (stability) where RNA has an OH (flexability)

what is alternative splicing?

the various combinations of exons which generates different protein sequences

what is mRNA processing?

the addition of a 5’ cap and 3’ polyA tail to protect degradation of the RNA, facilitate transport out of the nucleus and the stabilise the mRNA

what is involved in translation initiation?

at least 10 proteins- eukaryotic initiation factors (eIFs) help the 40s subunit find the mRNA and dissociate when the 60s subunit binds

how does translation termination work?

when a stop codon is reached, a release factor binds to the A site which hydrolyses the bind between the polypeptide chain and the tRNA; the chain is released from the P site. the remaining parts of the translation complex dissociate

why are the 5’ and 3’ untranslated regions (UTRs) important?

to initiate and regulate the speed of translation

what are the three types of filaments?

actin (microfilaments), intermediate filaments, microtubules

what are the functions of actin/microfilaments?

stabilise the cell membrane, cell protrusions (microvilli, pseudopedia, lamellipodia, filopodia), cell migration, cytokinesis contractile ring, muscle contraction

what are the types of intermediate filaments?

keratin, lamin, vimentin, neurofilament

what are the anchoring sites of the cytoskeleton parts?

actin- focal adhesions and adherens junctions, intermediate filaments- desmosomes and hemidesmosomes, microtubules- centrosome (MTOC)

what is the structure of microtubules?

alpha- and beta-tubulin dimers with a plus (GTP bound) and minus (GDP bound) end

what is the structure of actin filaments?

made by joining G actin subunits together, they have a plus end (actin bound to ATP) and a minus end (ADP actin)

what is the difference between filopodia and lamellipodia?

filopodia- finger like extensions, lamellipodia- sheets that follow behind the filopodia and draws the cell forwards

what is pseudopodia?

temporary arm like extensions of the cell membrane to engulf bacteria (phagocytosis)

what is the role of microtubules in mitosis?

metaphase- the MT spindle aligns the chromosomes, anaphase- DNA separated by shortening MT

what are the microtubule motor proteins?

kinesin moves towards + end (anterograde) dynein moves towards - end (retrograde)

what is the length stability of each cytoskeleton component?

actin = dynamic, intermediate filaments = more stable, microtubules = very dynamic

what is the polarity and motor ends of each cytoskeleton component?

actin- polarity via ATP-actin, +end motor is myosins. intermediate filaments- no polarity or motor ends. microtubules- polarity via GTP-tubulin, +end motor is kinesins, -end motor is dyneins

what are the parts of the extracellular matrix?

epithelial cells, basal lamina, connective tissue, blood vessel, fibroblasts

what are the functions of the extracellular matrix?

attaching tissue layers, signalling via ECM receptors, enclosing organs, attaching muscles, skeleton

what does collagen have to do with scurvy?

caused by lack of vitamin C with is needed for the activity of prolyl hydroxylase (turns proline into hydroxyproline) more than 10% of collagen amino acids are hydroxyproline

what is significant for basement membrane?

trimer called laminin- makes a meshwork with collagen IV fibres (the basal lamina)

what are polysaccharides made up of?

chains made of sugar dimers called glycosaminoglycans (GAGs)

what are proteoglycans?

polysaccharides joined to a core protein

what is the primary defect in sanfillipo syndrome?

lysosome failure due to buildup of heparan sulfate

what are the types of cell junctions?

tight junctions, adherens junctions, desmosomes, gap junctions, hemidesmosomes

what are tight junctions?

most apical, make a watertight barrier

what are adherens junctions?

made of cadherins (transmembrane molecule) which connects cortical actin between adjacent cells. (on the inside surface they are attached to actin filaments, hold epithelial layers together) they regulate cell signalling and cell division

what are desmosomes?

connect intermediate filaments between adjacent cells with desmocollin and desmoglein (basically cadherens), primary function is structural stability

what are hemidesmosomes?

attach cells to basement membrane, (connect intermediate filaments to basal lamina). have adhesion molecules (integrins) which bind ECM molecules like laminin and collagen

what are gap junctions?

pores that connect the cytoplasm of adjacent cells, made by connexons, vital for passing currents (small things, not proteins)

what are integrins?

transmembrane receptor proteins on the surface of cells that mediate their adhesion to other cells and the ECM, exist as a heterodimer (one alpha and beta integrin)

what does the nucleus do?

houses chromosomes and machinery for DNA repair and copy, contains all proteins that regulates gene expression

what does the nucleolus do?

is the sight of ribosomal RNA expression and ribosomal RNA processing

what does the nuclear envelope do?

provides a selectively permeable barrier between the nuclear compartment and cytoplasm, keeps pre-mRNA inside nucleus until fully processed

what are the molecules leaving the nucleus?

mRNA, ribosomal subunits, tRNA

what are the molecules entering the nucleus?

transcription factors, chromatin components, regulators of DNA repair

what is a NLS?

nuclear localisation sequence, proteins actively imported into the nucleus must bear it

what is an example of something controlling gene expression?

histone tail modifications- e.g. acetylation of lysine which reduces the net positive charge of the histone tail and promotes more open chromatin

how does chromosome position correlate with the level of gene expression?

silent chromatin tends to be concentrated near the nuclear periphery

what are the general functions of the rough ER?

protein translocation, folding and modification

what are the general functions of the smooth ER?

lipid metabolism, calcium release

explain protein synthesis and the rough ER

proteins that are translocated into the ER have a signalling sequence that recognise the ribosomes and synthesise the protein directly into the ER lumen

what is added to proteins in the ER?

polar oligosaccharides make proteins more hydrophilic and less likely to aggregate so they have a higher probability of folding correctly

what directs correct protein folding?

disulphide bond formation on cysteines and oligomerization

what happens to improperly folded proteins?

the degradation process, ER-associated degradation (ERAD), misfolded glycoproteins transported across ER membrane to cytoplasm then degraded

what are the primary functions of the golgi apparatus?

complex chains of carbohydrates added to proteins, a protein-sorting station

what happens to the golgi during cell division?

stacks undergo scattering, allows equal segregation of golgi into each daughter cell

what is glycosylation?

sugar modification of glycoproteins, a primary function of the golgi

what are lysosomes?

membrane bound compartments that sequester various hydrolases to degrade cellular constituents

what is mitochondria fusion and fission?

fusion: form long networks to protect against autophagosomes which would degrade the mitochondria during starvation

fission: opposite of fusion

what is the plasma membrane?

a selectively permeable barrier made of lipids and proteins between the external of the cells and the cells inner organelles

what is the main constituents of membrane bilayers?

phosphoglycerides - made up of two fatty acid chains (hydrophobic) and a phosphate group head (hydrophilic) 

how do different types of lipids form?

based on what alcohol group is added to the phosphoglyceride

what do integral membrane proteins do?

ion and nutrient transport, signalling, pathogenesis, defence and adhesion

what are the types of plasma membrane transport?

proton pumps, ATP-binding cassette (ABC) transporters, sodium-potassium pumps, Na-Ca carrier, K-channel

what do proton pumps (chemiosmosis) do?

use ATP, moves protons (H+) out of cell from low to high concentration

what do ABC transporters do?

an example of ATP-dependant pumps; move substrates in (influx) or out (efflux) of cells

what do sodium-potassium pumps do?

moves 3 Na+ out of cell and 2 K+ into cell, both moved from low to high concentration

what do Na-Ca carriers do?

transports Ca2+ out of cell in exchange for Na+ (typically in ratio 3 Na+ : 1 Ca2+) driven by electrochemical gradient for Na+ across plasma membrane

what do K-channels do?

role in neuronal excitability, duration of AP, secretion of hormones, smooth muscle relaxation, repolarisation of cardiac muscles

describe membrane pumps

active (uses ATP), moves ions and other solutes across membrane at relatively modest rates

describe membrane carriers

passive, work based on gradient, only transport few molecules at a time, open in and open out configuration, get energy to change configurations by proton gradients generated by pumps

what are the types of membrane carriers?

uniporter: one compound

antiporter: exchange two compounds in opposite directions

describe membrane channels

selective, when open millions of molecules in or out, some open all the time (active), some close when other molecules bind in filter or gate, some have ball mechanism

what are the three components of the secretory pathway?

the ER, golgi apparatus, plasma membrane

what does the secretory pathway allow eukaryotic cells to do?

modify protein and lipid molecules, distribute proteins and lipids, facilitate protein secretion