Exam 1 Flashcards
structure of water
1 atom oxygen 2 atoms hydrogen H20 covalently linked polar molecule dipole moment
water
dipole moment
partially positive hydrogen
partially negative oxygen
water is liquid at room temp because of hydrogen bonds
why does surface tension happen
the interaction between the hydrogen bonds
ion solubility
ions are charged
hydrophilic
dissolves in water because of the interaction with the water
shell of hydration
the sodium ions have one with O facing them
the chloride ions will have one with the H facing them
because of the charges
diffusion across a barrier
know the randomness of diffusion across the barriers
know how we end up reaching equilibrium
know how things move from higher to lower concentration
osmosis
the water goes back and forth across channels called aquaporins until it reaches equilibrium
hydrophobic
uncharged
water fearing
triglycerides are an example
hydrophilic
charger
polar
water loving
Na+, Cl-, Ca2+ etc.
triglycerides
starts out with a 3 carbon structure glycerol which is the backbone of the triglyceride
to form a fatty acid there may be 16,18,20 carbons liinked to each other
uncharged
all of this then goes through dehydration synthesis
the H from the carboxylic acid and the OH from the glycerol go together to form a ester bond
does the same for all three
*highly insoluble in water
phospholipids as amphipathic molecules
- characteristics of a lipid which makes one portion hydrophobic
- start with a typical phospholipid with its 3 carbon backbone
- # 3 carbon creates a covalent bond, then take the oxygen and link it to O,P,O which is a phosphodiester bond–causes the end to be charged
phosphate head group
head is hydrophilic
tail is hydrophobic
short name for a phosphodiester bond
micelle
circle organization of phosphate head groups with their heads pointed outward and tails pointed inward
if water goes in the middle they will explode because the inside is hydrophobic and the outside is hydrophilic
not stable
liposome
same sort of structs as a micelle except there are two layers of phosphate head groups and the two layers of tails are pointing towards eachother making the whole molecule hydrophilic so there can be water in the middle and there can be water on the outside
stable
the inner layer is the phospholipid bilayer
lipid mosaic model of biological membranes
-has transmembrane proteins interspersed into the phospholipid bilayer that provide communication pathways for proteins
protein
- polymer of amino acids linked together by peptide bonds
- we create proteins from weaving them across the phospholipid bilayer
- to make sense we look at an amino acid
amino acid structure
- 20 different R-groups
- the term amino comes from the amino terminal on the left side and the carboxyl terminal on the right side
how to determine R-groups
- non-polar, uncharged, hydrophobic
- polar, hydrophilic
- charger, hydrophilic
peptide bonds
amino acid sequence: determines the primary structure sequence
the peptide bonds happen by amino acids strung together like pop beads on a string
primary structure of proteins
amino acid sequence
secondary structure of proteins
- derives from the hydrogen bonding of the protein
- do not require R-groups instead arise from hydrogen bonding within the protein
- hydrogen bonding occurs between the amine hydrogen and the carboxyl terminal
- creates two structure shapes
2 helix
- steps up a spiral staircase
- hydrogen bonding occurs every 4th on the way up the staircase
beta sheet
sheet like structure
tertiary structure of proteins
- when the proteins fold into geometric shapes with the hydrophobic on one side and the hydrophilic on the other side
- they fold in a way the the hydrophobic go on the inside away from the water and the hydrophilic go on the outside
- these form binding pockets which are a substrate for enzymes
- they need to be perfect in order to create these enzymes
transmembrane proteins
- the phospholipid bilayer when we thread a protein across it while following the hydrophilic and hydrophobic rules
- this region is configured as a helix
- there are hydrophobic amino acids that weave through the membrane which means there is a single alpha helix across the membrane
Hydrophilic pathway (channel)
- this is where we link 4 alpha helix across the membrane to form a channel across
- where some of the R-groups are pointed outward towards the other head groups and some inward
- the hydrophobic R-groups are pointed inward to form a hydrophilic pathway
prokaryotes
- bacteria, archaea
- lack intracellular membrane bound compartments
- obey the rules for DNA to RNA to protein
eukaryotes
- nucleus in the middle of the cell
- all DNA is confined to the nucleus
- each chromosome is a molecule of DNA
- there is a DNA binding protein called a histone
histone
- DNA binding protein
- form a spool where the DNA wraps
- organize into a set of 8 octomers
ribosomes
- used for proteins synthesis
- composed mostly of RNA
- factory to make proteins (mostly RNA)
- responsible for making synthesis of cytoplasmic proteins
- cytoplasmic structure
ER
-smooth ER
-rough ER with ribosomes attached to it
-free ribosomes
-membrane bound compartment inside the cell
-synthesize the three types of proteins:
secreted
lyposomal
transmembrane
**plastic bag example
nucleus
- has nuclear pores that assist the several hundred proteins regulate traffic into and out of the nucleus
- very descriptive
- highly structured organization
- the chromosomes are always confined here
- the biology happens around the central dogma
- helps regulate the movement of RNA
golgi
final processing of the proteins arriving from the ER
mitochondria
- makes ATP
- 2 phospholipid bilayers
- uses an O2 receptor to generate adenosine triphosphate from adenosine diphosphate
- there are enzymes called glycolytic enzymes which generate ATP called glycolysis
microtubules
- self assemble from tubulin molecules
- has an alpha end and a beta end
- will self assemble next to eachother
- 13 tubulins generated side by side in a tube
- the +end is where tubulins add
- the -end is where tubulins break off
filimentous actin
-self assembles from actin monomer G-actin
intermediate filament protein
- micofilament
- keratin
kinesin
- walks down the microtubule toward the plus end
- cleaves ATP into ADP+Pi
dynein
-negative end directed motor
rewatch lecture 7
!!!
DNA
- double stranded helix with 2 complimentary strands
- depends on the hydrogen bonding between purines and pyrimidines
- hydrogen bonding is where the bases are linked together and the 1 carbon
- there are phosphodiester bonds at the 5 carbon
purines
- adenine
- guanine
pyrimidines
- cytosine
- thymine
DNA replication
- replicates in a semiconservative fashion because part of it is an old strand and the other part is a new strand
- helicase comes in and unzips the strand
- breaks the hydrogen bonds
- which then begins the process of transcription
RNA structure
- # 3 carbon can link to the #5 carbon and create a phosphodiester bond
- all of the #1 carbons have one of the bases attached
- the #2 carbons have a hydroxyl because of the ribose
- doesn’t have to have another structure to bind to
- single stranded molecule
transcription
- the TATA box which is the promotor box comes in and the transcription factor comes in and finds the promoter region and binds a protein
- generates RNA 5’ to 3’
- which creates a complimentary RNA molecule
- it goes all the way down the strand until it comes to a stop signal
- this new RNA strand will then be spliced
RNA editing
- rRNA is the one that gets mostly edited
- the introns will be cut away and the exons will be expressed
- this new strand will then determine the sequence of amino acids in protein
- *all of this is confined to the nucleus
- the new strand of RNA will then be transported through the nuclear pores to the cytoplasm
RNA’s working to synthesize protein
- taking the edited mRNA strand it will reach a “start codon” –> AUG
- the small ribosomal subunit will attach to the bottom and the large ribosomal subunit will attach to the top
- the transfer RNA comes in and attaches to the start codon with the anticodon and form the amino acid MET
- this will continue down the cell until it reaches a stop codon
- the amino acid strand will then be let go and create a protein
- the ribosomes will then go free to start making a new protein
- *theres a poly a tail and a 5’ cap
- if the protein has 20 hydrophobic amino acids it will form a signal peptide
- if not it will go to the lyposome to get killed
hydrophobic amino acid
- the amino acids will then attach to the SRP which has a receptor in the ER that will attach the ribosomal subunit to the ER creating a rough ER
- the “translocon” has hydrophobic amino acids which allows the signal peptide to be put into the ER
- they then attach to the protein inside the ER in a process called gylcolation
- they will then be carried down to be secreted into the outside world or lysosomal which means they will go to get killed
- *how we make transmembrane proteins
what are the 4 types of tissues?
epithelia: form boundaries
connective: ties things together
muscle: allows us to move
nervous
epithelia
- continuous layer of cells that form a boundary
- sit on the basal lamina
- the layer attached to the basal lamina is the basalar surface the other layer is the apical surface
- epithelial cells form a lining of tubes that extend to the outside of the body
- the blood vessels are lined with a cellular layer called an endothelium
- they maintain the ability to divide and replicate
hemidesmonsomes
-anchoring junctions that attach to the epitical cells to the basal lamina
desmisomes
anchoring junctions that attach their neighbors to each other
occluding junctions (tight junctions)
prevent movement in between the gaps of cells
gap junctions
has a cytoplasmic bridge which extends across the cells
- for very small molecules
- is made up of hundreds of connexons which are made up of 6 connexins
glandular epithelium
- salvitory glands
- mammory glands
- pancreatic
- allows the cells to move things in and out
4 types of connective tissue
CTP: fibrocytes (tendons, ligaments, dermis)
cartilage: chondrocytes (hyaline, elastic, fibrous)
bone: osteocytes (secretes calcium phosphate)
blood: hematopoietic stem cells
Skin (connective tissue)
- composed of an epithelium on a layer of connective tissue
- epithelium: keratinocytes
- connective tissue: CTP in the dermis
- only the SS and the SB are really alive
meloncytes
-secrete pigment called melanin which is taken up by kerationcytes called tyrosine
what are the 4 layers of skin (top to bottom)
- stratum granulosum
- stratum cornieum
- stratum spinosum
- stratum basale
diaphysis
the shaft of the bone
epipysis
the ends of the bone
hylaine cartilage
on the articular surface of the ends of the bone
periosteum
on the diaphysis of the bone
where tendons and ligaments attach (CTP)
medullary cavity
the center cavity of the bone
spongy bone
has trabecular “struts”
where do we bear force and weight?
the spongy bone
compact bone
- organized into osteons which contain many osteocytes
- osteocytes will secrete collagen
growth plate
- occurs between the diaphysis and the ephysis
- they chondrocytes secrete a cartilage section and when growth is completed they will with hydroxyapatite which will end growth
osteoclasts
-bone breakers: they settle on the bone and make a “dam” type structure which will then mobilize the bone
osteocytes
-bone makers
endocrine system
-communication between molecules using chemicals
autocrine
-self
paracrine
-nearby
endocrine
-when the hormone is released into the blood and finds the specific receptor
kd
the concentration at which half of the hormones respond
the higher the kd the lower the affinity
steroid hormone
- cytoplasmic hormone receptor
- built from cholesterol
steroid hormone receptor
- steroid hormone binding domain
- nuclear access domain (has the keys to the nuclear pores)
- DNA binding domain (once in the DNA bind to just the right set of bases)
- transactivator domain
