bioex3 Flashcards
three classical experiments to show DNA is the genetic material
1928: Griffith
1944: Avery and McLeod (and McCarty)
1952: Hershey and Chase.
which is the smallest amino acid
describe r group
glycine
r group a simple hydrogen
osteogenesis imperfecta, what happens
a bigger AA is substituted for the glycine
alpha chains of collagen are braided (TRIPLE HELIX – 3 α chains) with glycine at the core sticking the molecules together more closely
collagen depends on tensile strength. not as tightly bound = not as strong
exact width of double-stranded DNA
2nm
two types of aromatic bases
purines and pyrimidines
pyrimidines are which bases
C, T, and U
what do pyrimidines look like
single hex ring (4 C 2 N)
what do purines look like
1 hex 1 pent – rings
which bases are purines
adenine and guanine
more info about purines?
common type of heterocyclic compound
heterocyclic – carbons and nitrogens at corners
one of the rings is a pyrimidine ring
U subs for
T
name the base pairs in DNA and RNA
adenine thymine cytosine guanine uracil
A & T
C & G
A & U (RNA)
what happens in the thymus (2 things)
WBCs mature
immune factors learn to ignore self-antigens
which nucleotides bind to which, and is one stronger
A binds to T with 2 hydrogen bonds
C binds to G with 3 hydrogen bonds
C and G are bound a bit more tightly
MMP-3, aka:
matrix metalloproteinase-3
Stromelysin-1
enzyme which
breaks down ECM proteins
–>during tissue remodelling and pathological processes such as arthritis
degrades collagen types II, III, IV, IX, and X, proteoglycans, fibronectin, laminin, and elastin
ECM glycoprotein which binds to integrins
fibronectin
other functions of fibronectin
cell adhesion
growth
migration, and differentiation
altered fibronectin associated with pathologies such as
cancer, arthritis, fibrosis
laminins
proteins part of basement lamina which is a layer of basement membrane which is a part of the ECM α β Υ chains
Tight junctions also block lateral movement of lipids and proteins in the plasma membrane
Movement of integral membrane proteins is completely blocked
Gap Junctions Allow
Direct Electrical and Chemical Communication Between Cells
three types of ECM
bone
cartilage
connective tissue
Three Classes of ECM Molecules
- Structural proteins such as collagens and elastins, which provide strength and flexibility
- Protein-polysaccharide complexes, proteoglycans, that provide the matrix
- Adhesive glycoproteins, fibronectins and lamins, that allow cells to attach to the matrix
connective tissue: Collagen and Elastin Fibers Are Embedded in a Matrix of Proteoglycans
PROTEOGLYCAN STRUCTURE
proteoglycans integrate into_____
gel-like network of proteoglycans, glycoproteins with a lot of glycosaminoglycans (GAGs)
GAGs bound to proteins
core protein, GAG chains
the plasma membrane
glycosaminoglycans (GAGs)
attach to core protein where?
large carbohydrates with repeating disaccharide units
serine residues
most common types of GAGs
chondroitin sulfate, keratan sulfate, and hyaluronate
Most GAGs in the ECM exist only as components of proteoglycans
_______ is an exception that occurs:
Hyaluronate is an exception that occurs both as a backbone of cartilage proteoglycans and as a free molecule
where is hyaluronate most important?
joints
It has lubricating properties and is most abundant where friction needs to be reduced, such as in joints
Direct links between the ECM and the plasma membrane are reinforced by a family of adhesive glycoproteins
which are the most common types
laminins and fibronectins
list four domains on fibronectin
these are which types of domains
BINDING DOMAINS
RGD (cell surface)
collagen
HEPARIN AND FIBRIN
what is interesting about fibronectin binding to both heparin and fibrin
heparin is an anticoagulant
fibrin is a key component of clots (insoluble protein – fibrous mesh that impedes blood flow)
clotting factor 1, ________, forms _______-
clotting factor I, fibrinogen, forms the fibrin clot
many cancer cells don’t produce fibronectin :(
:(
another random fact, fibronectin attaches platelets to fibrin
laminins do what
bind cells to basal lamina
distinctive anchor shape
give a quick sketch of what basement membrane comes between
EPITHELIUM (top let’s say)
BASEMENT MEMBRANE (of which basal lamina is a part)
underneath, CONNECTIVE TISSUE
basement membrane give basic structure
[[epithelium]]
[[basement membrane:
basal lamina
(lamina lucida, lamina densa)
reticular lamina]]
[[connective tissue]]
give 3 properties of basal lamina
structural support
permeability barrier
Cells can alter the properties of the basal lamina by secreting enzymes that catalyse changes in the lamina
give one important class of Enzymes That Alter the Basal Lamina
metalloproteinases (MMPs) that require metal ions as cofactors
what do MMPs do
They degrade the ECM locally, allowing cells to pass through
This is important for leukocytes to invade injured tissues and may be a factor in cancer cell invasiveness
describe integrins
transmembrane proteins –anchored in cytoskeleton
cell surface receptors
bind to laminins and fibronectins
1928: Griffith
Frederick Griffith, studying a pathogenic bacterial strain that caused pneumonia in animals, found two forms of the bacterium
S-strain caused a fatal infection when introduced into mice
R-strain was unable to do so
When dead S-strain and living R-strain were mixed and used to infect mice, the mice died
Griffith found many live S-strain bacteria in the dead mice
He concluded that the R-strain had been converted into S-strain, a process called genetic transformation
1944: Avery and McLeod (and McCarty)
fractionated extracts of the S-strain bacteria and found that only the nucleic acid fraction was able to transform the R-strain
Digesting the DNA from the extract prevented transformation
1952: Hershey and Chase.
Phage T2, T4, and T6 are the best studied
==>T2 Phage
to distinguish protein from DNA
They labelled proteins with radioactive sulphur, 35S, and the DNA with radioactive phosphorus, 32P
In two separate experiments, they allowed the labelled phages to infect bacteria
Once the genetic material is injected into the bacteria, the empty phage protein coats (“ghosts”) were removed by agitating cells in a blender
Cells were recovered by centrifugation
They then measured the radioactivity in the supernatant (phage coats) and the cells at the bottom of the tube
DNA and not protein had been injected into the bacterial cells
Therefore, DNA was the genetic material of the phage T2
temperate phages
incorporate their dna into bacterial dna
bacterium reproduces normally – both child cells have phage dna incorporated
Infection by T4 Phage
Phage DNA and capsid proteins self-assemble into hundreds of new phage particles
The infected cell breaks open and releases the new phage particles into the medium
Chargaff’s Rules Reveal
A = T and G = C
DNA basic structure
a sugar phosphate backbone with nitrogenous bases attached to each sugar
at physiological pH, the nucleobases would be able to form ______ bonds with each other
hydrogen
The Double Helix Model
The critical evidence came from :
X-ray diffraction data produced by Rosalind Franklin
It revealed that DNA was a long thin helical molecule
Based on Rosalind Franklin’s structural information, Chargaff’s rules, etc, Watson and Crick used wire modelling which
produced the double helix model
Watson-Crick Model
ten nucleotide pairs per complete turn, and 0.34 nm per nucleotide pair
The 2-nm diameter of the helix is too small for purines and too large for pyrimidines, but just right for one of each
The two strands of double helix are held together by
hydrogen bonding between bases on opposite strands
orientation of the two strands of double helix
antiparallel
5’ to 3’ but going opposite ways
5’ 3’
to to
3’ 5’^
(left of the above goes down)
two strands could separate so that each could act as a template to dictate
synthesis of a new complementary strand
The ______ bonds that join the 5′ carbon of one nucleotide to the 3′ carbon of the next are oriented _________ in the two DNA strands
phosphodiester
in opposite directions (antiparallel)
DNA length is measured in ____________
Larger stretches are measured in:
base pairs (bp)
multiples of a single base pair—for example, the kilobase (kb) is 1000 bp
The right-handed helix is called
left-handed helix?
B-DNA
Z-DNA
the main chirality of DNA is
right
B-DNA
A-DNA is
a right-handed helix, shorter and thicker than B-DNA
A-DNA is created artificially; there is very little naturally occurring A-DNA
However, most RNA double helices are of the
A type
Supercoiling occurs in both linear and circular DNA molecules but is more easily studied in circular DNA
A DNA molecule can go back and forth between the supercoiled state and the _________ state
Extensive supercoiling helps make chromosomal DNA _______
nonsupercoiled, or relaxed
more compact
___________ can both induce and relax supercoils
Topoisomerases
what do topoisomerases basically do
break DNA, thereby removing supercoils
Type I topoisomerases: introduce __________ _________ ____________
Type II topoisomerases: introduce __________; one example in bacteria is ________
Type I topoisomerases: introduce transient single-strand breaks in DNA
Type II topoisomerases: introduce double-strand breaks
one example in bacteria is DNA gyrase
base stacking (2 aspects)
1) stabilizes the double helix by:
2) interactions between adjacent aromatic rings — hydrophobic and van der Waals interactions
DNA renaturation aka**
reannealing
Reformation of the DNA double helix is called __________; it is accomplished by:
DNA renaturation (or reannealing)
lowering the temperature to permit hydrogen bonds to reform
denaturation of DNA, describe, include temp
native DNA breaks into two single strands
it’s ‘native DNA’ – not denatured – up to about 80C