LS 2 midterm 1 Flashcards
covalent bonds
two atoms share one, two, or three electrons –> very stable bond
most common
ionic bonds
either give up or accept electron from another atom to achieve a filled outer shell
hydrogen bonds
the attraction of the positive (hydrogen) end of the polar molecule to the negative end of another polar molecule (H - N,O,F) (high electronegativity)
van der waals forces
weak interactions between atos due to movement of negatively charged electrons resulting in formation of dipoles – transient, but in large quantities can cause significant changes
5 properties of water
- solvent - carries nutrients into body and wastes out; oxygen and CO2 can dissolve
- participates in chemical reactions - e.g. digestion
- absorbs and releases heat slowly - maintain homeostasis
- requires a large amount of heat to evaporate - perspiration can assist cooling of body
- provides lubrication - saliva, mucus because of cohesion and adhesion
inorganic compounds
water, inorganic acids, bases, and salts
organic compounds
carbs, lipids, proteins, nucleic acids
property of inorganic acids, bases and salts
all undergo ionization (dissociation) when dissolved in water in the body
how do acids ionize
produce hydrogen ions (protons) H+
how do bases ionize?
release hydroxyl ions (OH-)
how do salts ionize
cations and anions
what is a cation
positive ion
what is an anion
negative ion
importance of inorganic salts in body
components of cells and body fluid – sodium and chloride ions in extracellular fluid and potassium and phosphate ions inside cells
calculate pH
-logbase10[H+]
what pH represents neutral
7
what pH represent acidic
below 7 (1-7)
what pH represents basic
above 7 (7-14)
how does the body maintain constant pH (homeostasis)?
buffer systems
what is a buffer
a solution of a weak acid or weak base which remove excess H+ ions and OH- ions
pH of blood
7.35-7.45
pH of gastric juice (stomach)
1.2-3.0
types of lipids (4)
- fats (triglycerides)
- phospholipids
- prostaglandins
- steroids
what are fats and their purpose
(triglycerides) consist of one glycerol and 3 fatty acids; serve as a source of energy, and protect and insulate
unsaturated fat
fatty acids have a double bond
saturated fat
fatty acids are all single bonds
difference between fat and oil
fat is solid at room temp and oil is liquid
what are phospholipids
components of cell (plasma) membrane – lipid bilayer - polar head outside and nonpolar tail inside
what is amphipathic and example
polar and nonpolar parts - e.g. phospholipids
4 types of phospholipid movement
- rotational (rapid)
- diffusion (rapid)
- flexion (rapid)
- flip flop (rare)
rotational phospholipid movement
rotates along axis like a globe
diffusion phospholipid movement
lateral movement across bilayer (moves to diff spot in line)
flexion phospholipid movement
tails flex side to side
flip flop phospholipid movement
movement across bilayer, requires a special protein (moves to other side of bilayer)
what are prostaglandins
derivatives of fatty acids similar to hormones
what are fatty acids
chain of carbon atoms with a carboxyl group at one end
what are steroids
cholesterol is most abundant steroid in body and a component of cell membranes and steroid hormones are derived from cholesterol - ring structure
3 functions of carbohydrates
- provide energy
- form part of structural elements of some cells
- supply carbon atoms for synthesis of cellular components
what is glycogen
carb - stored form of glucose in liver and skeletal muscles for rapid needs
a polysaccharide that is the man energy source for animals
releases branched polymer of glucose
types of carbs
monosaccharides, disacharides, oligosacharides, polysacharides
molar ratio of carbs
C:H:O 1:2:1
how does the H:O ratio in carbs compare to lipids
much lower
what are monosaccharides
simple sugars - one molecules
3 main types of monosaccharides
glucose, fructose, galactose
what are disaccharides
2 monosaccharides bonded
3 main types of disaccharides & how they’re formed
sucrose, lactose, maltose (condensation reaction –> glycosidic reaction forms covalent bonds)
components of sucrose
glucose + fructose
components of lactose
glucose + galactose
components of maltose
glucose + glucose
what carb is milk sugar
lactose
what causes lactose intolerance
lack of enzyme lactase which breaks down lactose
what is an oligosaccharide
3-20 residues (sugars)
what is a polysaccharide and how can it be broken down
many monosaccharides bonded together (20+); broken down into constituent sugars by hydrolysis
what is cellulose
provides structural support to plants; unbranched polymer of glucose
layers of glucose that have H bond interactions
why is cellulose so strong
bc they lay flat and form h bonds between the layers
what are proteins and how are they linked
large complex molecules made up of amino acids, linked in sequence by covalent peptide bonds
what do amino acids consist of?
an amino group, carboxyl group, and a side chain
what is an amino group and it’s pH
-NH2; basic
what is a carboxyl group and it’s pH
-COOH; acidic
what is a side chain
the r group; different for each of the 20 different amino acids
5 roles of proteins
- cytoskeleton - supports and organizes cell components
- enzymes
- transport and storage of small molecules
- transmit info (hormones)
- defend against infection (antibodies)
what percent of enzymes are proteins
only 95%
what is primary structure of proteins
the amino acid sequence
- depends on specific amino acid at points along the chain and the number of amino acids making up the chain
what is secondary structure
local interactions
interactions between backbone
2 types:
alpha helices: corkscrew held together by hydrogen bonds
beta pleated sheets: protein chain loops back on itself (u-shape) like silk
tertiary structure
the 3d structure/conformation of the protein molecule, resulting from side chain interactions between different parts of the primary structure , all 4 types of bonds are possible e.g. hydrogen bonds, disulfide bridges between cysteine residues
quaternary structure
overall structure in a protein made up of more than one polypeptide chain (not all proteins have this)
interactions between multiple subunits of a protein
what structure is cholesterol
steroid ring structure
cholesterol is plants and animals?
absent from plasma membranes of most places, but present in up to 25% of lipid weight in plasma membranes of animals
do people need to consume cholesterol
no! body makes all cholesterol it needs in the liver
why is cholesterol needed
stabilizes the plasma membrane and helps produce bile salts for digestion
what happens if there’s too much cholesterol
can lead to deposition of excess in the walls of arteries (leads to athlerosclerosis)
why is LDL cholesterol “bad”
carries cholesterol to the tissues for use by cells
why is HDL cholesterol “good”
carries the cholesterol back to liver for excretion
proteins involved in muscle movement
actin and myosin (myosin head group pulls actin globules)
what does it mean to denaturize a protein
unfold the protein until it randomizes
what are nucleic acids
long polymers made up of nucleotides
chemical difference between RNA and DNA
H is in DNA and OH is in RNA
sugar components of nucleotides
deoxyribose is in DNA and ribose is in DNA
5’-3’ and 3’-5’
2 types of bases in nucleotides
purines and pyrimidines
purines
adenine, guanine
pyrimidines
cytosin, thyamine
complementary base pairs
adenine-thyamine and cytosine-guanine
3 types of RNA
messenger RNA (mRNA) transfer RNA (tRNA) ribosomal RNA (rRNA)
where does protein synthesis occur?
ribosomes
what is ribozyme
catalytic RNA, catalyst for making peptide bond between amino acids during protein synthesis
miller and Urey
synthesis of prebiotic molecules in an experimental atmosphere
types of tissue
epithelial tissue, coonective tissue, nervous tissue, muscle tissue
epithelial tissue
forms boundaries between parts of the body and has tight junctions keeping it sealed
connective tissue
cells in some sort of extracellular matrix
e.g. bone in a calcified matrix, blood cells in plasma, adipose cell in triglycerous matrix
nervous tissue
neurons conduct and generate action potentials
muscle tissue
skeletal (bicep), cardiac, smooth (digestive tract)
prokaryotes
cells lacking a nucleus; e.g. eubacteria and archae bacteria
eukaryotes
contain a large, membrane bounded nucleus and DNA
e.g. plants, animals, fungi, protists (algae)
size comparison between eukaryotic cells and prokaryotic cells
euk much larger than prok
polar amino acids
argenine asparagine glutamic acid glutamine histidine lysine serine threonine tyrosine
nonpolar amino acids
alanine cycteine glycine isoleucine methionine phenylalanine choline tryptophan valine
what happens during sickle cell anemia
mutation in beta subunit and part of protein becomes hydrophobic and causes aggregation of hb molecules into a sickle shape instead of usual biconcave
glutamine (P)–> valine (NP)
ideal total blood cholesterol
200 mg/dL
desirable LDL levels
less than 130 mg/dL
borderline high risk of athlerosclerosis LDL levels
130-159 mg/dL
high risk of athlerosclerosis LDL levels
160+ mg/dL
what kind of ratio of HDL:LDL do you want?
high ratio (more HDL)
difference in bases between DNA and RNA
DNA: G-C and A-T
RNA: G-C and A-U (no T)
2 types of microscopy
light microscopy and electron microscopy
characteristics of light microscopy
glass lense, uses visible light, magnified image
resolution: 200 nm
characteristics of electron microscopy
electrons magnets focus a beam of electrons on specimens, more powerful, resolution 2 nm
types of light microscopy
bright field, phase contrast, stained and brightened, differential interference, fluorescence, confocal
bright field microscopy
light directly passes through cells; little contrast and few details
phase contrast microscopy
shows contrast by emphasizing differences in refractive index whih enhances light and dark regions and creates more contrast
stained and brightened microscopy
use a stain to enhance image
sample stains
eosin– binds to + structures like proteins, collagens, and muscle tissue which turns it red/pink
hematoxelyn– binds to negative structures like DNA and turns it blue/purple
differential interference microscopy
2 beams of polarized light enhance contrast
fluorescence microscopy
natural fluorescence; apply dye which will bind to different parts
confocal microscopy
uses fluorescent materials and autofocus light to create a clearer image
types of electron microscopy
transmission, scanning e-, freeze fracture
transmission electron microscopy
if absorbs e- will look darker and if e- pass through, it will look lighter
scanning e- electron microscopy
direct electrons to surface of sample and cause electron to be emitted where a screen catches them and produces a 3d structure
freeze fracture electron microscopy
freeze cells and use a knife to crack open frozen cells and the bumps are protein aggregates
purpose and method of cell fracturization/centrifugation
homogenizes cells
- place in tube and centrifuge
- particles form sediment pellet at bottom
* heavier particles sediment at lower speeds
centrifugation sediment times/masses
500 g for 10 min –> obtain nuclear fraction
10,000g for 20 min –> obtain mitochondria
100,000g for 1 hour –> get ER fraction
what did miller and urey do?
conducted an experiment where they simulated the conditions of early erath
what did miller and urey find from their experiment?
inorganic molecules could convert to important organic molecules and ultimately form life
describe miller and urey’s experiement
heated a solution of gasses to simulate atmosphere of early earth, ran an electric current through it (like lightning), condensed it (like rain), and found amino acids, simple sugar, and other organic compounds
what is the “RNA World” hypothesis
in a world before dna for protein synthesis, rna was used as a carrier of genetic information and to catalyze reactions
theoretical process from RNA to DNA
start with rna (composed of ribose, bases, and phosphates) and some were replicable and eventually began to make catalytic proteins and eventually became double stranded DNA which survived because of the stability it provided for storage of genetic material
now: DNA uses RNA to make proteins
hierarchical organization of life
atoms –> molecules –> organelles –> cells –> tissues –> organs –> orga systems –> organization
5 properties of life
- cellular organization
- sensitivity/response to stimuli
- growth
- reproduction
- homeostasis
are viruses alive?
no!
describe virus structure?
made up of a core of nucleic acids surrounded by a protein sheath (and sometimes a lipid envelope)
lack a cell membrane, nucleii, and organelles
can’t reproduce on own –> need host cell to replicate
do not carry out metabolism on their own
what is cell theory
all organelles are composed of cells
cell is the basic building block of life –> all chemical reactions take place inside of cell
all cells arise through division of a pre-existing cell
why are cells so small
as object increases in size, volume increases more rapidly than surface area and cells need large SA:V ration in order to efficiently transport nutrients and waste
prokaryotes characteristics and examples
lack nucleus, DNA is coiled into a nucleoid some have more than 1 nucleoid small organism dna is in direct contact with cytoplasm E.g. eubacteria and archaebacteria
eukaryotes characteristics and examples
contains a large, membrane bound nucleus (containing DNA)
typically separated into many membrane bound compartments (organelles)
larger organisms
e.g. all plants, animals, fungi, protists
“special features” of prokaryotes (5)
- cell walls (bacteria may have peptidoglycan in them)
- outer membranes may enclose cell wall
- cyanobacteria can cerry out photosynthesis
- some may have flagella
- some have pili (used for mating)
“special features” of eukaryotes (3)
- plasma membranes, cytoplasm, ribosomes
- internal cytoskeleton (maintains shape and moves materials around cell)
- plants have cell walls and large vacuoles for storage of food, water, waste, nutrients, etc
sizes of plant cells
5-30 micrometers
sizes of animal cells
35-80 micrometers
sizes of prokaryotes
0.2-2 micrometers
endosymbiotic theory
explains origin of eukaryotic cels from prokaryotic cells – states that some of the key organelles originated as a symbiotic relationship between 2 prokaryotes (one ingested other and eventually couldn’t survive without)
what is the biggest organelle?
nucleus
what does the nucleus contain
most of the cells dna
how does the nucleus faciltate replication
DNA combined proteins form chromatin
chromatin condenses and coils tightly to form chromosomes connected by a centromere
mitosis to form 2 daughter chromosomes
what do chromosomes contain
contains one long molecule of dna - comprises many genes
what do ribosomes do
synthesize proteins (all cells synthesize them on ribosomes)
where are ribosomes located in eukaryotes (2 locations)
in the cytoplasm (free)
bound to the rough ER
where do higher numbers of ribosomes go
energy producing organelles like the mitochondrial matrix and chloroplast stroma)
what are ribosomes made of?
ribosomal RNA associated with a proton
2 parts of the endomembrane system
- golgi apparatus
2. endoplasmic reticulum (ER)
what is the ER
endoplasmic reticulum - extensive system of folded membranes
2 parts of the ER
rough ER
smooth ER
characteristics of the smooth er
lacks ribosomes, site for glycogen hydrolysis, synthesis of steroids
characteristics of rough er
contains ribosomes, manufactures proteins for export from the cell and incorporate into membranes or to different organelles
what does the golgi apparatus do?
modifies, packages, and sorts proteins
synthesizes some sugars/polysaccharides for the cell wall
how does the golgi synthesize sugars/polysaccharides
vesicles from the rough er fuse with the cis region of the golgi and secretory vesicles pinch off from the trans region
signal sequences operation
approximately 25AA residue long sequence at the beginning of a polypeptide chain directs the polypeptide chain to the ER and then it goes to the golgi and the secretory vesicle sends it out of the cell
example of signal sequence
insulin
how does insulin work
acts to decrease blood glucose by increasing glucose uptake in cells
the secretory vesicles are then exocytosed and stored in pancreatic beta cells until needed
what triggers insulin release
an increase in blood glucose - hyperglycemia
nickname for mitochondria
powerhouse of the cell
what do mitochondria do
convert energy from food to ATP
how are mitochondria sized
pretty small - similar in size to bacteria
what contains mitochondria?
almost all living things except those living in an environment without O2
where do most mitochindria exist
in metabolically active areas - heart, liver
what are plastids present in
plants and some protists like algae
what do plastids do?
carry out photosynthesis
structure of plastid membrane
double membrane without cristae; inner membrane forms stack of thylacoids (grana)
what is contained in thylacoid membranes
chlorophyll
what is stroma
fluid contained within the inner membrane of chloroplasts that suspends ribosomes, dna, elara
what are lysosomes
contain hydrolytic (digestive) enzymes, participate in phagocytosis
example of a pathology of lysosomes
tay sachs disease
what is tay sachs disease
harmful lipids known as gangliosides accumulate in dangerous quantities in the brains heme cells and the lysosomes cannot break down the compound
what are peroxisomes (in plants and animals)
accumulate toxic peroxides such as H2O2
(byproduct of some biochemical reactions); and safely break it down without mixing with other parts of the cell
glyoxysomes
occur in plants and are similar to perixisomes
what are vacuoles
present in plant cells; store waste products and provide turgor
what replaaces lysosomes in plants
vacuoles provide similar role and turgor provided keeps plant rigid
what is the Cytoskeleton
maintains cell shape, facilitates cell movement
what is the Cell wall and where is it found
supports the cell’s shape; present in plants, fungi and some protists (also present in bacteria)
what is the Extracellular matrix?
surrounds animal cells, and is composed of proteins eg. collagen,
glycoproteins, and proteoglycan
3 Components of the cytoskeleton
microfilaments, intermediate filaments, and microtubules
what are microfilaments?
strands of actin, involved in movement during animal cell division, and muscle contraction
3 uses for microfilaments
a. muscle contraction (myosin and actin interactions)
b. cytokinesis (division of cytoplasm)
c. microvilli (epithelial lining of small intestine); increase surface area for absorption
of nutrients across lumen across to the blood
what are intermediate filaments and an examples
tough, fibrous protein molecules twisted into rope-like structures which stabilize cell structure e.g. keratin in hair/nails
what are microtubules
involved in structure and function of cilia and flagella, centrioles, and movement of cellular organelles; important for the mitotic spindle;
microtubule uses
scaffolding
what is the sturcture of microtubules
hollow cylinders made of tubulin; made up of tubulin alpha and beta subunits- 13 subunits arranged in circle
what happens during depolymerization of microtubules
pull sister chromatids to opposite poles of cell
what are cilia
9 sets of microtubules arranged in spoke like pattern (9+2 pattern)
what are CENTRIOLES
microtubule organizing structure
what are Motor proteins and examples
use energy from ATP to use microtubules and facilitate movement of cell e.g. dynein and kinesin
how do flagella move?
Complex protein ring structures anchored in the plasma membrane form a motor unit that rotates the flagellum and propels the cell
how do Sister chromatids separate to form chromososmes
Mitotic spindle microtubules from opposite poles attach to each sister chromatid at the kinetochore in prometaphase. In anaphase, the connection between the sister chromatids breaks down and the microtubules pull the chromosomes toward opposite poles.
golgi apparatus cis region
lies closest to nucleus
where is the golgi apparatus trans region?
closer to cell surface
what act as the target for the signal sequences to latch onto
ribosomes
pH inside a lysosome
acidic - 5.5
what is autophagy
breaking down worn out cell organelles
e.g. worn out mitochondria could fuse with a lysosome and be broken down
what are glyoxysomes
in plants, specialized form of peroxisomes; break down stored lipids
no lysosomes in plants
how do microfilaments participate in cytokinesis (division of cytoplasm)
occurs by loops of actin (microfilaments, which can lengthen or shorten by adding or subtracting individual actins) forming around the middle
why are microtubules important to the mitotic spindle
attach to sister chromatids during cell division; pull them apart and reform the nucleus
size progression of cytoskeleton components
(smallest) microfilaments –> intermediate filaments –> microtubules (largest)
what type of cell lines the small intestine
endothelial cells
what are microvillus
projections used to absorb nutrients, increases surface area for absorption from lumen of gut
what are cilia made of and why are they important
9 microtubules; important in airway which prevent particles from getting into lungs
what causes fluidity of lipid bilayer
movement of individual phospholipids
what are membrane proteins
Carry out most of specific functions
Amount and types of proteins in a membrane are variable
3 classes of membrane proteins
integral, peripheral, and lipid-anchored proteins
integral proteins
(penetrate into the lipid bilayer) - most are transmembrane proteins (contain an alpha-helix of nonpolar amino acids extending across the hydrophobic interior of the membrane)
peripheral proteins
located outside of the lipid bilayer on the cytoplasmic surface attached by noncovalent bonds to the polar head groups of the lipid bilayer, or to integral membrane proteins
lipid-anchored proteins
covalently attached to a phospholipid or fatty acid embedded in the bilayer
Role of membrane proteins (3)
transport proteins
receptors for molecular messengers from other cells
form junctions between cells
what are MEMBRANE CARBOHYDRATES
Project from the exterior surface of the plasma membrane when attached to proteins or phospholipids within the membrane
Serve as recognition sites on the cell surface
what are glycoproteins
carbohydrates (oligosaccharides) in membranes bound to proteins that enable cells to recognize foreign substances
what are glycolipids
form cell identity markers eg. A,B, O blood group markers
types of cell junctions
tight junctions
desmosomes
gap junctions
why are gap junctions important in the heart
allow small molecules (e.g. iron) to move from cell to cell
facilitates spread of action potentials (what tells the heart to beat)
what are plasmodesmata
aqueous pore in plant cells - analogous to gap junctions
what anchors extracellular matrix to exterior cytoskeleton and what is it attached to
integrin and attached noncovalently to fibronectin
what type of mechanism is an ion channel and how does it work
passive and nonmediated - creates an aqueos pore in the membrane
what type of mechanism is a carrier (transporter) and how does it work
passive and carrier mediated; carrier protein allows polar molecule to shuttle through
no aqueous pore is created
moves from high to low - facilitated by mechanism, but still passive because does not require to move against concentration gradient
what is diffusion
random molecular motion from areas of high concentration to lower concentration
what type of mechanism would move molecules against the concentration gradient
active, mediated transport involving a membrane protein carrier and requiring energy
what can diffuse across the lipid bilayer
Small nonpolar molecules, e.g. O2 and CO2
what is osmosis
Diffusion of water molecules across a selectively permeable membrane
why can’t plant cells burst like animal cells can
stability from the cell wall
what is osmolarity
sum of ions in solution
benchmark osmolarity of blood plasma and hyposmotic and hyperosmotic
~300 mosmol/L
300
what regulates channel proteins
- binding of some specific molecule (ligand gated)
2. change in voltage (voltage gated)
graphs of diffusion to see if it experiences saturation kinetics
- linear would indicate it’s not carrier mediated and is 2. simple diffusion (does not experience saturation kinetics)
curved and eventually flattening out means it can saturate andyou will reach max rate of transport
uniport
molecule moves one direction
symport
molecules move same direction
antiport
molecules moving in opposite directions
what does Endocytosis do
transports macromolecules, large particles and small cells into eukaryotic cells
3 types of endocytosis
Phagocytosis, Pinocytosis, and Receptor-mediated endocytosis
what is phagocytosis
large particles or cells are engulfed
what is pinocytosis
small dissolved solutes or fluids enter
what is Receptor-mediated endocytosis
a specific membrane receptor binds to a particular macromolecule at sites called coated pits
what is endocytosis
taking molecules into cells
what is exocytosis
vesicle fusing and dumping outside
what is an exergonic reaction
A reaction whose products contain less free energy than the reactants (delta g is negative); tend to occur spontaneously and release heat; catabolism – cell respiration
what is an an endergonic reaction
products of the reaction contain more energy than the reactants and the extra energy must be supplied for the reaction to occur; anabolism – active transport and cell movements
what is the main carbohydrate store in humans
glycogen
what is the main lipid store in humans
triglycerides
what does metabolism do to energy stores
breaks it down into ATP
2 ways cells make atp
substrate-level phosphorylation
chemiosmosis (most do this way)
how does substrate-level phophorylation work?
direct transfer of phosphate group to ADP from another molecule
why does breaking atp bonds release so much energy
it has negatively charged phosphates which are close to each other which takes a lot of energy, so breaking those binds releases lots of energy
is atp actually a nucleotide?
yes
how do autotrophs synthezise food molecules
using light energy
do heterotrophs or autotrophs extract energy from food?
trick! both do
stages of extracting energy from food
- digestion - enzymes break large moleucles into smaller molecules
- catabolism - other enzymes dismantle fragments extracting energy at each stage
what is harvested to generate ATP
Glucose (C6H12O6); C-H bonds; uses the energy from the electrons making up the bonds
what is glycolysis
conversion of glucose to pyruvate
what is cellular respiration
conversion of pyruvate to CO2 and water in the presence of O2 which releases large amounts of energy
where does chemiosmosis occur
mitochondria
where did the term oxydative phosphorylation come from?
experiment where mitochondria were put in a test tube with ADP and phosphate and oxygen and it makes ATP
what is the more current/accurate way to describe making ATP
chemiosmosis (in mitochondria)
which organelle can you use the terms chemiosmosis and substrate level phosphorylation intrchangeable and which ones can you not
mitochondria can use both, but chloroplasts cannot
how is atp generated by substrate-level phosphorylation
Involves direct transfer of phosphate group to ADP from another molecule
how is atp generated by chemiosmosis
glucose enters cells, converted to pyruvate, converted to CO2
what is NAD+
an electron shuttle; AN ELECTRON CARRIER IN MANY REDOX REACTIONS; Nicotinamide adenine dinucleotide
