Midterm 1 Flashcards
central dogma of molecular biology
DNA -> RNA -> protein
light microscopy
stains produce coloured image; make small phase differences visible
fluorescence microscopy (3)
- used to localize and quantify specific molecs in fixed and live cells
- light absorbed at one walv and emitted at a longer wavl
- fluorescent dyes are used for staining
diff btwn fluorescence and bright-field microscopy
fluorescence microscopes have 2 filters, one that allows only the wavl of light that excites the fluorescent dye thru, and one that blocks all light except that wavl
confocal microscopy
a type of fluorescence microscopy that prevents blurry images by having the beam focused on a single point with a small hole allowing only in-focus light and excluding out of focus light
why does the resolving power of light and electron microscopes differ
light microscopes are limited by the wavl of light
transmission electron microscope (TEM) (2)
- similar to light microscopy but w/ electrons
- 2D image
scanning electron microscope (SEM) (2)
- scatters e-s off the sample surface
- 3D image
nucleus (euk)/nucleoid (bacteria)
contains genetic material
one diff btwn a nucleus and nucleoid
nucleus is membrane-bounded
plasma membrane
tough, flexible lipid bilayer which is selectively permeable to polar substances
cytoplasm
aqueous cell contents and suspended particles and organelles
5 diffs btwn euks and proks
- proks do not have membrane bound organelles but euks do
- proks are smaller and euks are larger
- proks have nucleoids, euks have nucleus
- proks have a single circular chromosome but euks have multiple linear chromosomes
- in proks, the cytoplasm is bound by the plasma membrane, but in euks the plasma membrane is bound by the plasma and nuclear membrane
nuclear envelope
contsins inner and outer mem
nucleolus
large structure in nucleus where ribosomal RNA is transcribed and subunits assembled
nuclear pores
allow the passage of molecs in and out of the nucleus
3 mitochondria functs/characteristics
- contain their own DNA and repro by division
- contains inner and outer membrane
- contributes to cell resp (ATP)
what may have evolved from engulfed bacteria?
chloroplast, maybe mitochondria too
endoplasmic recticulum
major site of protein, membrane lipid and oligosaccharide synth
golgi apparatus
membrane enclosed sacs that modify and packages molecs made in the ER
lysosomes (2)
- contain hydrolytic enzymes activated by proteolytic cleavage in an acidic env
- contain transport proteins which carry the products of macromolec digestion to the cytosol for reuse or excretion
peroxisomes
membrane enclosed vesicles where oxidation rxns occur to prod hydrogen peroxide
cytosol
aqueous portion of the cytoplasm
cytoskeleton
network of protein filaments in the cytoplasm involved in strength, organization, mvmt, shape, cell division
what 3 things mainly make up a cell membrane
- lipids
- proteins
- carbohydrates
4 membrane functions
- maintain integrity of cells and organelles
- have highly selective perm barrier
- control flow of info btwn cells and env
- site of E transformations
model orgs (2)
- fundamental to understand human behaviour (homologous)
- easy to study due to size, genome, etc
covalent bonds
strong bonds formed by the sharing of e-s btwn adjacent atoms
polar covalent bonds
unequal sharing of e-s due to one atom being more electroneg than the others
non covalent interactions
individually weak bonds that do not involve the sharing of e-s
3 egs of non covalent interactions
- hydrogen bonds
- van der waals
- charge-charge electrostatic interactions
ionic bonds
loss/gain of e-s - electrostatic interactions
hydrogen bonds
an interaction btwn a covalently bonded hydrogen atom (donor group) and a pair of non-bonded e-s (acceptor group - on electroneg atom)
carbohydrates/sugars (…saccharides) (5)
- E source (glucose/glycogen)
- structure (cellulose, chitin)
- slime/mucus
- modification of proteins/lipids
- info storage
Fatty acids, triacygkycerols, membrane lipids (3)
- hydrocarbon chains contribute to the makeup of fats and membrane lipids
- fatty acids form triacyglycerols which are E source
- fatty acids form membrane lipids which contribute to membrane structure and function
amino acids -> proteins (2)
- same basic structure with variable side chains -> fold to form protein
- joined with peptide bonds
nucleotide funct
- short term carriers of E like ATP
- storage and retreval of biological info (DNA/RNA)
nucleoside
base + sugar (eg adenosine)
nucleotide
base + sugar + phosphate
3 eg of subunits and macromolecs
- sugar, polysaccharide
- amino acid, protein
- nucleotide, nucleic acid
what dictates the precise shape of a macromolecule?
noncovalent interactions (many points of contact)
1st law of thermodynamics
E may not be created or destroyed, only changed in form
2nd law of thermodynamics
increased entropy, always (heat = peak entropy)
the carbon cycle =
cell resp + photosynthesis
oxidation is the _ of an e- from an atom whereas reduction is the _ of an e- from an atom
removal, addition
if you wanted to obtain E from a molec, would you rather use a reduced or oxidized form?
reduced
a rxn is sponteneous if ? (+ symbol)
it inc entropy by reducing its free E, -deltaG
when calculating deltaG, we
add lines
enzyme definition and function and effect on deltaG
a biological catalyst, lowers activation E so speeds up rxn, no effect
is deltaG dependent on the concentration of substrates and products?
yes
why are cells always in disequilibrium
siphon off products from one rxn to another
Keq is directly proportional to deltaG therefore
- K > 1, neg
- K = 1, zero
- K < 1, positive
how to drive unfavourable rxns
siphon off prod in another favourable rxn
Vmax
max rate of a rxn for an enzyme; how quickly it can catalyse a rxn when fully saturated in substrate
Km
concentration of substrate when enzyme is 1/2 Vmax
what is Km dependent on
the viscosity of the substrate
a double reciprocal plot is used to calc what more precisely?
Vmax
competitive inhibitors
compete with the substrate to bind to the active site
what effect do competitive inhibitors have on the Km and Vmax?
inc, same
activated carriers
small org molecs that store E or chem groups in an easily exchangeable form
3 eg of activated carriers
ATP
NADPH
NADH
how is E captured in activated carriers
coupled rxns ie. an energetically favourable rxn is used to drive an energetically unfavourable one (eg. glycolosis)
how is ATP used to do work?
used to generate a high E intermediate by phosphorylating a reactant
NADH (3)
- has 2 high E e-s and a proton forming a hydride ion, H-
- catabolic rxns that generate ATP
- eg. NAD+ red during citric acid cycle, e-s passes from NADH down the e- transport chain to generate ATP
NADPH (3)
- has 2 high E e-s and a proton forming a hydride ion, H-
- anabolic rxns
- eg. biosynth of fatty acids, cholesterol
what input is req in all synthesis’ of biological polymers?
E
amino acids’ behaviour is dictated by their
side chains
4 types of AA side chains
- nonpolar
- polar uncharged
- acidic
- basic
2 eg of -ively charged AA (acidic)
aspartic acid
glutamic acid
3 eg of +ively charged AA (basic)
arginine
lysine
histidine
5 eg of uncharged polar AA
asparagine
glutamine
serine
threonine
tyrosine
10 eg of nonpolar AA
alanine
glycine
valine
leucine
isoleucine
proline
phenylalanine
methionine
tryptophan
cycteine
peptides (3)
- form as a result of a condensation rxn
- join 2+ AAs together
- have directionality
what affects how a protein folds?
side chains
alpha helixes (3)
- 3.6 residues per turn
- R-group face outwards
- stabilized by hydrogen bonds
what affects alpha helix stability?
electrostatic or steric interactions between adjacent, or 3-4 residues away, wside chains
what 2 AAs are not found in helices
- proline (rigid ring, no amine hydrogen to form hydrogen bonds)
- glycine (too flexible and small)
beta sheets are stabilized with
interstrand hydrogen bonds
parallel vs anti parallel beta sheets
- parallel: connect each AA on one strand w/ 2 AAs on an adjacent strand
- anti parallel: connect each AA on one strand w/ 1 AA on an adjacent strand
R goupd in beta sheets are
perpendicular to the plane of the sheet
tertiary pro structure
folded structure of the peptide (3D)
quaternary structure
arrangement of multiple peptides
protein domains (2)
- distinct, stable, structural units that often have separate functions and fold as independent compact units
- can move as a single entity w/ respect to the entire protein
how is protein tertiary structure generated
folding and packing of secondary structure
what type of interactions help pros fold and maintain shape
noncovalent interactions
1 way of stabilizing pro via covalent bonds
disulfide bonds formed btwn 2 cystine residues
what kind of model would you like to look at if trying to see the side chains?
wire
what kind of model would you like if you are trying to see the secondary structure?
ribbon
2 groups of proteins
- fibrous (strength/flexibility)
- globular (spherical)
alpha keratin (3)
- type of fibrous protein
- right handed alpha helix
- coiled coil composed of 2 alpha keratin chains is left handed
silk (3)
- type of fibrous pro
- antiparallel bets strands held together by H bonds to form stacked beta sheets
- fibroin is rich in ala and gly because they permit the close packing of beta sheets and interlocking of their small R groups
protein native state is
the lowest E state
eg. sickle cell anemia
protein folded wrong - unwanted interactions
5 causes of pro denaturation
- temp change
- ph extremes
- detergents and org solvents
- urea or guanidium chloride
- reducing agents
chaperone proteins help pro folding in 2 ways
- formation of isolation chambers for creation
- may bind to hydrophobic residues of nascent polypeptides preventing unwanted associations with other hydrophobic residues
how can misfolded pros lead to disease
can form large aggregates, affecting cellular funct
how are pros classified into families
each member has an AA sequence and 3D conformation that closely resembles each other
pro-ligand interactions are dictated by
noncovalent interactions; binding site AAs and the ligands dictates specificity
antibodies are so abundant because
they contain 2 antigen-binding sites where the AA seq is highly variable
how do enzymes catalyze a rxn
bind to substrates forming an enzyme-substrate complex; after rxn over, product is released
enzymes lower activation E in 3 ways
- aligns substrates in a favourable orientatiwhon
- rearranges the electron distribution
- physically strain the substrate to induce a reaction
what does a lysozyme do
severs polysaccharide chains that form cell walls in bacteria (hydrolosis rxn)
feedback inhibition
the end product of a chain of enzymatic rxns red the activity of the enzyme earlier in the pathway (-ive feedback loop)
allosteric pros can exist in multiple conformations depending of a molec to a site other than the catalytic site via
positive regulation
phosphorylation regulates pros by
causing conformational changes
motor proteins are able to produce large movements in cells via
nucleotide hydrolysis; couple conformational change to the hydrolysis of ATP
pro machines
large pro complexes that are allosteric and driven by ATP or GTP hydrolysis
fred griffith 1920s
an unknown factor can transform the harmless strain into a harmful one
avery macleod and mccarthy 1944
molec that contains heritable info is DNA
hershey and chase 1952
(e coli) DNA enters bacteria and carries genetic info
primary structure
nucleotide seq
secondary structure
regular, stable structure taken up by some or all of the nucleotides
phosphodiester linkages form ? in primary structure
the backbone (repeating)
pentose in primary structure
covalent bond to a base in a b-glycosidic linkage
DNA secondary structure
double R handed helix, antiparallel
base pairing in DNA occurs
thru hydrogen bonding btwn complementary bases
base stacking in DNA is important for stabilizing the double helix
hydrophobic bases need their contact with water minimized
Watson and Crick 1953
base-pairing specificity, double helix structure
chargaffs rule
A=T and G=C; A+G = T+C
chromosomes are made of
DNA that contains strings of genes
2 broad phases in the cell cycle concerning chromosomes and their definitions
- interphase: when chromosomes are duplicated (extended)
- mitosis: when chromosomes are segregated into two daughter molecules (compact)
3 important sequences in chromosomes and their definitions
- telomeres: repeated sequences at the ends of chromosomes that protect it from degradation
- replication origin: sequence where replication begins
- centromere: sequence that allows DNA to be separated during M phase; region of attachment to mitotic spindle
