Final Exam Review from list Flashcards
L1: what elements are most common in living organisms
HONC
L1: what is an electron, neutron and proton? how do they affect an element
electron- +1 charge, in nucleus, ID element mass
Neutron- no charge, in nucleus, give isotope mass
electron= -1 charge, in cloud, charge bonding
L1: what is mass number and atomic number
mass number is weight, proton and neutrons
atomic number is how it’s IDed how many protons
L1: characteristics of alpha, beta, gamma radiation
alpha: helium nucleus change atomic mass by 4 and atomic # by 2, penetrate top skin layer
beta: nuclear electron, atomic number +1 , sub-cutaneous
gamma: photon- energy wave, no effect on numbers, penetrate deep
L1: Isotopes vs elements
isotopes are different forms of the same element different number of neutrons. Only mass changes
L1: Radioactive Particles include
alpha, beta gamma
L2: Bohr Model - Absorption, Excitation, Relaxation, Fluorescence
absorption-
excitation -
relaxation -
fluorescence -
L2: Quantum Model – Orbitals and how they are organized
orbital: location and wave-like behavior of electrons
shell, subshell, orbital
L2: shell, subshell and orbital
shell: pathway followed by electrons around an atom’s nucleus ex. the 1st, 2nd, 3rd, 4th,etc shell(everything inside)
subshell: pathway in which an electron moves within a shell ex. s,p,d,f
orbital: describe wave-like behavior of an electron. ex. 1,3,5,7
L2: Electron configurations
where electrons go:
SPDF
L2: periodicity - electronegativity and atomic radius trends
electronegativity trend: right top is highest
atomic radius trend: left bottom
L2: valence shell and octet rule
valence shell: outer most shell that contains electrons
octet rule: elements are most stable when they fill their outermost S and P subshell
L2: Lewis dot structure
how many electrons in outer most shell and draw dots either 8 or less
L3: Ions – Anion vs Cation, from which rows in the periodic table?
cation: ion with pos. charge, gave up electron. first 3 rows
anion: ion with neg. charge, took electron last 3-4 rows
L3: Covalent Bonds – Polar vs Non Polar.
How many bonds does H, O, N, C want?
polar: share bonds, one wants it more non-polar: share bonds, both want it the same amount H: wants 2 bonds o: wants 2 bonds N: wants 3 bonds C: wants 4 bonds
L3: Electronegativity (Ionic, Polar, Non-Polar, how does HONC relate to this?
How bad element wants to steal or give away their electrons. Non-polar equal sharing. Polar- unequal sharing. Ionic: take/give up electron. - O>N>C=H +
L3: Single, Double, Triple bond shapes and properties
single: tetrahedral and freely rotate
double: trigonal planar, can’t rotate
triple: linear, can’t rotate
L3: How and why do chemical reactions occur?
when chemical bonds between atoms are being broken or formed
L3: What does equilibrium mean? What is K? What is G?
equal rates forward and backwards, equal energy add reactant =forward, add product = reverse, remove reactant = reverse. remove product = forward K= rate of reaction G = 0 energy used
L4: what bonds are weak bonds
Hydrogen and VDW and Ionic
L4: Ionic when in water what happens to the charge, strength, etc.
Ionic bonds: electron is taken, in water, bond is weak, breaks and h2o surrounds it. still has partial charges
L4: Hydrogen bonds define
h-bonds: partial charges of a neg. and pos. attract
L4: Van Der Walls define and who bonds together
VDW: temporary attraction when long chains are by each other and the electron is close to outside element, the other side is partial neg. and when the electron goes to the other side, they swap positions
nonpolar weak bonds, induced
L5: Why is water so special?
float when solid, H bonding
L5: Cohesion
water w/ water - hydrogen bonds
L5: Adhesion
water w/polar substance- hydrogen bond
L5: what is specific heat
cal = 1 gram raised 1 degree C cal = g x temp change
L5: % solution
= g solute/100 mL solution
L5: What is a mole?
unit of measurement ex. a dozen = 12 eggs
L5: Molar solution
mole solute/ L solution
L6: How to calculate pH
pH = -log [H+]
L6: How to calculate pOH
pOH- = -log [pH-]
L6: pH and pOH together is equal to what number? What equation
pH + pOH- = 14
[H+] x [OH-] = 1 x 10^ -14
L6: Buffer
resists change
HA(weak acid) dissociates H+(proton) and A-(conjugate base)
L7: what is an isomer
same molecular formula, different structure
L7: difference of Structural, Geometric, Enantiomers, Diastereomers isomers
Structural: same molecular formula, different pattern of bonds, atoms connected in different order
Geometric: same molecular formula, same bond pattern, different spatial arrangement around a double bond (cis or trans)
Enantiomer: mirroring the bonds from the two
Diastereomer: mixture of same bond and mirrored bonds
L8: Alkyl structure,
H
I
R-C-R Non-polar
I
HL8: sulfhydryl structure,
R-S-H
L8: hydroxyl structure,
R- O-H
L8: carbonyl structure
.. O
.. II
R-C-R
L8: carboxyl structure,
.. H
.. II
R-C-OH
L8: phosphate structure,
...... O ... .... I R-O-P-OH Acidic, polar ionic ........ I ...... OH
L8: amino structure
… H
… I
R-N-H
L8: Polysaccharide monomer and bond name
monosaccharides and Glycosidic
L8: Protein monomer and bond name
Amino acids and peptide
L8: Nucleic Acid monomer and bond name
nucleotides and phosphodiester
L8: lipids monomer and bond name
fatty acid and glycerol, and ester
L8: condensation is when what happens
when a bond forms and water is a byproduct
L8: hydrolysis is when what happens
water used to break bonds, put back in
L9: Names3 types of Monosaccharides
Fructose
galactose
ribose/deoxyribose
L9: Names/types of Disaccharides
Maltose=glucose + glucose
sucrose=glucose + fructose
lactose=glucose + galactose
L9: define of Oligosaccharides and function
sugars of 3-40 monomers, many different simple sugars,
highly branched
cell recognition/signaling and cell defense
L9: Names/types of Polysaccharides animals/plants
starch(plants), glycogen(animals), cellulose(plants), chitin(insects)
L9: Chemistry name for a mono saccharides
glucose
L9: Functional Groups common to carbs.
hydroxyl and carbonyl
L9: What are the monomers, polymers, bond between monomers, functional groups used. of carbs
two or more monosaccharides held together by glycosidic bond from condensation between hydroxyl and hydroxyl
L9: Alpha 1-4, alpha 1-6, beta 1-4: structure, polymers, plants vs. animals
storage–> alpha-monomers
structural –> beta monomers
storage:
plants –> 1) amylose alpha 1-4 helical. 2) amylopectin: alpha 1-4 helical and alpha 1-6 branched. 3) animal –> glycogen: a1-4 helical and a1-6 branched
structural:
plants –> 1) cellulose: b1-4 lines (wood). animals –> 2) chitin b1-4 lines (exoskeleton)
L10: functional groups common to fats
carboxyl and hydroxyl
L10: What are the monomers, polymers, bond between monomers of fats
polymer: lipid
monomer: fatty acid& glycerol
bond: ester
L10: Differences between saturated/unsaturated. state at room temp where comes from structure bonding
saturated: solid room temp from animals structure- linear max hydrogen bonds and no double bonds
unsaturated: liquid room temp 1 or more double bonds double bond replace 2 hydrogen crocked if cis/ straight across if trans, in plants
L10: What is a phospholipid?
2 fatty acids (hydroxyl) tails and phosphate (polar head)
create bilayer
L10: What makes a fat more liquid vs. solid?
bonding, if there are max hydrogen bonds it’s solid, if there are bonds missing or double, liquid
L11: Functional Groups common to nucleic acids.
Hydroxyl and Phosphate
L11: monomer, polymer and bond between monomer of nucleic acids
polymer: nucleic acids
monomer: nucleotides
bond: phosphodiester
L11: Differences between DNA and RNA
DNA:
nucleus, long term info storage, double stranded
RNA:
in cytosol, short term info(messenger), single strand, protein synthesis
L11: Purine vs Pyrimidine
purine: two ringed
pyrimidine 1 ring
L11: Central Dogma - DNA to RNA to Protein
DNA split, RNA comes in and reads a little bit and takes out of nucleus and give to ribosomes. Ribosomes translate to protein
L12: Functional Groups common to amino acids.
amino and carboxyl
L12: What are the monomers, polymers, bond between monomers to amino acids
monomer: amino acid
polymer: protein
bond: peptide
L12: Primary, Secondary, Tertiary, Quaternary
Primary: amino acid sequence
Secondary: Hydrogen backbone, helices or sheets
Tertiary: bonds rest of the molecule, 3D structure
Quaternary: associated with 2 or more folded peptides into a protein
L12: What does denaturation do? 4 things
break all weak bonds
don’t break covalent bonds
secondary, tertiary and quaternary
heat, detergent, strong acid/strong base
L13: What makes up a plasma membrane? Asymmetric why?
lipids and proteins, phospholipid bilayer.
asymmetric because lipids from the top can’t 180 and go to the bottom
both sides of the phospholipid are different from each other
L13: Types of proteins and oligosaccharides on the plasma membrane
transmembrane
integral
peripheral
lipid anchored protein
Glycolipids and glycoprotein
L13: FRAP and Hybridomas
FRAP: a cell was coated in a fluorescent color and a part of the cell was bleached. Waited to see if the bleach separated
Hybridomas: part of a human cell (colored) and part of a mouse cell (colored) and waited to see if the color mingled together
L13: How do plants and animals govern membrane fluidity?
plants: chain/tail length
cis unsaturated/ saturated
animals: cholesterol “fluidity buffer”
regulate internal temp
L14: What is part of the endomembrane system? 7 organelles
nucleus, RER, SER, Golgi, Lysosome, Plasma Membrane, Vacuole
L14: Structure and function of the organelles
nucleus: holds DNA
RER: Protein synthesis
SER: phospholipid synthesis
Golgi: receive, ships, processes protein and lipids and exports
Lysosome: break down macromolecules, hydrolases
Plasma Membrane: outer cell membrane
Vacuole: unique to plant cells
L14: Differences between animals and plants?
plant: double membrane, chloroplast, thylakoid, DNA floating around
animal: 1 membrane, dna in nucleus,
L15: Semi-autonomous organelles?
organelles with DNA, plant and animals
L15: Structure and function of peroxisome, mitochondria, chloroplasts
peroxisome: single membrane w/ crystalline core. detox, get rid of Oxygen and oxidizes large fatty acids
mitochondria: powerhouse of cell, make ATP, double membrane, matrix and circular DNA
chloroplasts: solar powerhouse, triple membrane, thylakoid and circular DNA
L15: Structure and function of microtubules, actin filaments, intermediate filaments
microtubules: tube, chromosome separation, cell motility (part of cell move but not whole)
actin filaments: 2 stranded rope, cell division, cell movement and muscle contraction
intermediate filaments: cable/rope(bungee cord) resist pulling forces, give nucleus its shape, connect skin cells
L16: Difference between prokaryotes and eukaryotes
prokaryotes: bacteria, no nucleus (nucleoid)
eukaryotes: animal/plants, circular DNA
L16: Difference between bacteria and archaea
Bacteria contain peptidoglycan in the cell wall; archaea do not
L16: Difference between gram+ and gram-
gram+ thick layer of peptidoglycan, protect cell
gram- thin peptidoglycan layer, less protection
L16: Define the 3 types of DNA sharing
transformation: eats a plasmid
transduction: bacteriophage lands on bacteria, abducts some bacteria DNA, breaking the og DNA, some of the OG DNA gets sent off and gives it to a diff. bacteria
conjugation: attach bacteria together sex pili and transfer plasmid
L17: Structure and types of viruses
Structure
genome: composed of nucleic acids, sd dna, ds dna, ss rna, ds rna
protein coat: called capsid, package and protect genomic material
viral envelope: outer membrane of phospholipids and proteins, stolen from host, still has viral glycoproteins
accessories:proteins essential for viral life cycle
not all viruses need
help virus carry out job
allows virus to do things host can’t do
L17: Stages of Lysogenic and Lytic
Lytic: 1. attachment
- entry
- synthesis
- assembly
- release
Lysogenic: 1. attachment
- entry
- integration
- activation
- synthesis
- assembly
- release
L17: How does a vaccine work?
destroy virus
part of virus
can’t give you the illness
vaccines are preventative doesn’t cure it
L18: Anabolic vs. Catabolic
Anabolic: building something up
Catabolic: a catastrophe
breaking down
L18: Potential vs. Kinetic
Potential energy is the stored energy
Kinetic energy is the energy of an object or a system’s particles in motion
L18: Define 1st and 2nd laws of thermodynamics using enthalpy, entropy, and free energy.
- energy is never created or destroyed
- entropy(chaos) of the universe is always increasing
* *no energy transfer is 100% efficient
enthalpy: total potential energy
entropy: energy/heat lost during reaction
free energy: energy available to do work
useful energy
L18: Delta G >0; <0; =0
ΔG >0:requires energy endergonic-takes energy non-spontaneous = must be forced to happen ΔG <0:give off energy exergonic- releases energy spontaneous- naturally happens ΔG =0: reaction is at equilibrium
L18: How can you get a non-spontaneous reaction to become spontaneous?
- change temp
- add reactants remove products
- couple endergonic with an exergonic reaction
L19: Energy of Activation?
energy needed to go ‘over the hump’/ strain and pull chemical bonds before being broken an formed into new and release energy
L19: How can you change reaction kinetics/rate?
add catalyst
add reactant
remove product
change temp
L19: How can you regulate an enzyme?
phosphorylation
temp
pH
cofactor/coenzyme
L19: How can you inhibit or activate and enzyme? Competitive, Non-Competitive, Feedback
Competitive inhibition: blocks active site
Non-competitive regulation: dont touch active site
if open and an enzyme attaches to it (not in the active site) it will become inactive
BUT
if active site is closed and an enzymes attaches to it (not active site) it will become active
Feedback regulation: if an substrate somewhere in the line comes and binds to the enzyme
if attach to active site its called competitive
if attach to nonactive site it’s called non-competitive
L20: Redox; OilRig
reduction oxidation
oxidation
is
loses electrons
reduction
is
gaining electrons
L21: Where does glycolysis happen?
cytosol
L21: What goes in and what comes out glycolysis?
in:1 glucose 2 ATP 2 Pi 4 ADP 2 NAD+
out: 2 Pyruvate
2 ADP
2 NADH
2 H2O
L21: Where does fermentation happen?
cytosol
L21: What goes in and what comes out fermentation?
in: pyruvate and NADH
out: Lactate or ethanol and co2
NAD+
L21: What is anaerobic vs aerobic? Why would a cell use one or the other?
anaerobic: no oxygen
produce energy without the presence of oxygen
aerobic: has oxygen, energy can continue to other parts of the cell respiration
L21: PFK?
phosphofructokinase (PFK) is negatively inhibited by ATP and citrate and positively regulated by ADP.
L22: Where are Pyruvate bridge, Citric Acid Cycle, Beta Oxidation, electron transport chain
Pyruvate bridge: mitochondria
Citric Acid Cycle: matrix
Beta Oxidation: mitochondria
electron transport chain: inner membrane mitochondria
L22: what goes in and out of Pyruvate bridge, Citric Acid Cycle, Beta Oxidation, deamination…
Pyruvate bridge: in: pyruvate
NAD+
CoA
out: Acetyl-CoA
NADH
CO2
Citric Acid Cycle: in:1Acetyl-CoA
3 NAD+
1 FAD
1 ADP+Pi
out:2 CO2 3 NADH 1 FADH2 1 ATP 1 CoA
Beta Oxidation: in: NAD+ and FAD
out:NADH and fADH2
electron transport chain: in: NADH FADH2 O2 H+ Pi and ADP
out: H2O
ATP
NAD+
FAD
L22: what is deamination
Lysosome through hydrolases will break down protein to amino acids
Remove amino, left with hydroxyl,
Put in kreb cycle based on number of carbons
L23: Where and how are NADH and FADH2 used?
NADH goes to complex 1
FADH2 goes to complex 2
L23: What is the role of Complex 1, 2, 3, 4?
transfer electrons
L23: What does oxygen do?
take H+ and make water
L23: What does the ATP synthase do?
turbine, brings H+ to the inside of matrix and create ATP
L24: What is absorption? Where is light absorbed in photosynthesis?
def: process in which light is absorbed and converted into energy
chloroplast
L24: Where do the light reactions happen?
thylakoid
L24: What goes in and what comes out?
In:H2o
NADP+
light
ADP +Pi
Out: NADPH
O2
H+
ATP
L24: What are pigments and photosystems?
pigment: light capturing molecule
photosystem: gather light, collect energy and pass through complex structure that can collect light and pass that energy alone in excited electrons
L24: What types are light are the best and which are the worst for photosynthesis?
best: purple, red and blue
worst: green
L25: Where does the Calvin Cycle happen?
stroma
L25: What goes in and what comes out?
In: 3 RuBP 3 Co2 9 ATP 6 NADPH
Out: 3 RuBP 1 G3P 9 ADP 6 NADP+
L25: What are the 3 phases?
Fixation: add CO2, enzyme RuBP
Reduction: Add phosphates, something is gaining electrons
Regeneration: Fix NADH, ATP imbalances
L25: What is cyclic electron flow?
when electrons are backed up and FD goes back to PQ and creates a circuit
L26: Diffusion vs. Osmosis
diffusion: movement of particles so that they spread out into avaible space
try to go to equilibrium
osmosis: Diffusion(movement of particles so that they spread out into avaible space) of water
L26: What is an electrochemical gradient?
measure of the free energy available to carry out the useful work of transporting the molecule across the membrane
L26: Hypo, hyper, iso osmotic
Hypoosmotic: lower solute concentration
hyperosmotic: higher solute concentration
isosmotic: equal solute concentration
L26: Hypo, hyper, iso tonic
Hypotonic: cell swells
hypertonic: cell shrinks raisin
isotonic: no change in cell
L27: Differences between active and passive transport? Energy and gradients
energy required: active up/with the gradient [low] –> [high]
no energy required: passive down/against the gradient [high] –> [low]
L27: 3 types of passive transport
Simple diffusion – movement of small or lipophilic molecules
Osmosis – movement of water molecules
Facilitated diffusion – movement of large or charged molecules via membrane proteins
L27: 3 types of active and what they do
Primary active transport: "pump" directly uses ATP [low]-->[high] (against gradient) type of carrier 2 kinds (uniport and cotransport)
secondary active transport: gradients
move 2 molecules at once(antiport, symport)
electron driven transport:
L27: 3Na+/2K+ Pump and steps
- 3 na+ bind to intracellular die of pump
- ATP add phosphate to pump
- Conformational shift (flip to outside/other side)
- 3 Na+ go outside
- 2 K+ bind to extracellular side of pump
- phosphate removed
- conformational shift (flip to inside)
- 2 K+ go inside
- repeat
L28: Difference between endocytosis and exocytosis
endo: into cell
exo: out of cell
L28: 4 different types of vesicle transport
phagocytosis: eat cell
pinocytosis: drink cell
receptor mediated endocytosis: picky eater in cell
receptor= bind specific molecule
exocytosis: exit/out cell
L29: 3 stages of cell signaling
reception, transduction, response
L29: 5 types of cell signaling and their characteristics
gap function: direction connection of 2 cell cytoplasm
very short range
very specific
cell to cell: direct contact of 2 cells
very short range and very specific
synaptic transmission: neuron releasing signal onto another cell
short/ long range
specific
paracrine: signaling to nearby cells
medium range
general
endocrine: signaling to cell far away using the blood stream
long range
general
L29: What does a Kd tell you about a ligand receptor interaction?
how tightly ligand binds to receptor
L29: Why do only certain cells respond to a signal?
a cell has to have the right receptor for that signal
