Molecular and Cellular Biology Flashcards
Atomic Structure
protons, neutrons, electrons (valence shell)
Chemical Bonding
ionic (cation and anion) and covalent
Organic vs Inorganic
organic: C&H, held by covalent bonds
inorganic: ionic bonds, metal and nonmetals
Molecular Structure
covalent bonds bw H20 (polar bonds)
oxygen attracts more strongly, carries partial neg
hydrogen bonds bw O and H
Macromolecules
covalent bonds bw subunits, one loses OH and other loses H, this is dehydration synthesis
proteins (amino acids)
carbs (polymers of C,H,O atoms), store energy
lipids (from fatty acids and glycerol, energy storage/ structure of cells)
nucleic acids- store genetic info
Chemical and Physical Gradients
diff in conc. of protons inside and outside of a cell gives membrane electrical charge -this makes potential gradient
this if for cell signaling and cell to cell communication
Thermodynamics
study of energy and its transformations
1st law- energy can change from one for to another but cannot be created or destroyed, total amt of energy is constant
2nd law- direction energy flows/changes
energy flows /changes till reaches equilibrium
entropy inc
Anabolic and Catabolic Rxns
metabolic rxns
enzymes catalyze both
Anabolism- use energy to build complex from simpler molecules
Catabolism- releases energy, degradation rxn (hydrolysis)-add h20 to break covalent bonds
bonds of molecules broken
Oxidation Reduction rxns
cell needs energy so chemical bonds broken and electrons harvested, ATP is made and stored
ATP is degraded and energy released
electrons lost (oxidized) and accepted by another which is reduced
oxidation number: how many electrons atoms can gain/lose
Active Site Structure and Substrate Binding
specificity
induced fit- site changes shape when substrate bound
pH and temp influence
Rxn Kinetics
pH and temp alter enzyme activity
pH alters shape and charge
inc in temp weakens bonds, enzyme unfold or denature
Regulation
Cooperative binding: enzymes bind more than one substrate
substrate bound to one affects another
Positive cooperativity: Inc in affinity of sites for substrate
Negative cooperativity: dec affinity of sites
Feedback inhibition: product of enzymatic rxn can bind to enzyme and repress action of enzyme
product blocks active site therefore repressor is competitive inhibitor
product binds to enzyme not at active site but forces shape change and substrate cant bind (noncompetitive inhibitor
Cellular locations of biochemical pathways
energy for cellular work from the sun maintains membranes, builds proteins, and cell division
plants, algae, photosynthetic bacteria etc use light to convert to chemical
chemical rns occur when bonds forms/breaks
These pathways drive metabolism: photosynthesis, cell resp, and chemosynthesis
Photosynthesis 6CO2+6H2O–C6H12O6+6O2
- light penetrates mesophyll cells filled with chloroplasts
- within chloroplast thylakoids are chlorophyll (light absorbing pigments)
- proteins anchor chlorophyll to thylakoid membrane to form photosystems– light dependent rnxs occur
- cell captures photons of energy in photosystem 2
- electrons become excited and this energy is passed bw cholorophyll molecules
- excited electrons released and go to electron transport
- electrons lost, and rxn splits water to form O2
- in electron transport electrons goes thru series of protein carriers in thylakoid membrane
- energy of electrons pumps protons into thylakoid space
- protons inc and flow down conc. gradient
- they go out of thylakoid space and thru ATP synthase to make ATP
- electron transport transfer e- from photosystem 2 to photosystem 1
- NADPH is produced
- ATP and NADPH enter calvin cycle (in stroma)
- energy of ATP and H atoms make carbs
C3 Photosynthesis (Calvin Cycle) -carbon from CO2 fixed to make glucose
C4 Photosynthesis- malate made in mesophyll then bundle sheath, malate degraded, and CO2 released
Cellular Respiration
-glucose oxidized, electrons harvested, ATP produced
-1st stage: anaerobic (glycolysis)
Glycolysis: in cytoplasm, transform glucose to 2 pyruvate
-2 ATP made and 2 NAD+ reduced
-pyruvate reduced by fermentation
-NAD+ recycled
2nd stage: aerobic (Krebs Cycle)
Krebs Cycle: within mitochondria
-pyruvate oxidized to 6CO2
-2 ATP & 10NADH & 2 FADH2
electron transport: series of oxidation reduction rxns
electrons transferred from NADH and FADH2 to carrier molecules
movement of e- drives formation of H+ gradient
these protons move back across ATP synthase to make ATP
Chemosynthesis
devoid of sunlight
used by organisms within deep sea hydrothermal vents
vents release hydrogen sulfide (H2S)
bacteria and other microbes oxidize H2S and other inorganic molecules to use e- to reduce CO2 to make organic molecules
these molecules serve as base of food chain for deep sea animals
Cell size
smallest unit of life
organelles (for specific fns)- mainly in eukaryotes
Membrane bound organelles
nucleus golgi- collect, packs and ditrib proteins ER- location of some ribosomes mitochondria- metabolism lysosome- degrading enzymes chloroplast vacoules- carry water, collect metabolic waste plastid- make and store sugars
Cell walls
prokaryotes (peptidoglycan) and certain eukaroytes like plant (cellulose) cells
animal cells lack
Plant vs Animal Cells
eukaroytes
have nucleus, mitochondria, golgi bodies, ER, ribosomes
cell membranes around cytoplasm plants have cell wall of cellulose plant cells (rectangular) animal cells (circular mostly) animals have lysosomes plants (choloroplasts) and large central vacoule animal cells (flagella) plants (autotrophs) animals (heterotrophs)
Cell membranes
prokaryotes or eukaryotes
cytoplasm around cell membrane
-2 layers of phospholipids
phospholipid molecules:
- polar head
- chemical group with phosphate attached to 2 nonpolar hydrophobic fatty acids tails (C and H)
- tails on inside, heads on outside
cell membrane has proteins (selective permeability)
cell membrane is semipermeable phospholipid bilayer
-forms channels and bridges
Cytoskeleton
attached to proteins and within plasma membrane
gives cell shape (animals)
certain enzymes and organelles found here
built from 3 types of protein fibers
- intermediate filaments: thick fibers of proteins, gives cell strength and prevent stretching
- microtubules: hollow tubes, made from tubulin, aids in separating chromosomes, and component in flagells
- microfilaments: long thin fibers of actin, cell shape and movement
Selective Permeability
- transmembrane proteins regulate movement of molecules in and out of cell
- acquire nutrients and rid of waste
diffusion: movment down conc gradient
- high to low
- equilibrium
- passive (no energy)
- movment same rate in as out
Active and Passive Transport
passive diffusion: simple and facilitates
simple-small and or hydrophobic down conc. gradient and thru bilayer
facilitated: large and or charged or hydrophilic, via carrier or channel protein
active transport- molecule pushed up or against conc gradient to high conc
-driven by oxidation or hydrolysis of ATP
Example: Na+ K+ pump
- Na+ outside of cell is higher and K+ higher inside cell
- driven by ATP hydrolysis
- ATP phosphorylates pump and incuces conformational change in this protein
- one cycle leads to 3 Na+ outside and 2K+ inside
Water Movement
osmosis- passive diffusion of water from high water (low solute) to low water (high solute)
aquaporins- channels that mediate this
water is polar and reacts with solutes like polar molecules, sugars, and proteins so solute conc. or osmolarity impacts water mvmnt
as solute conc inc. water potential (free water molecules in solution and tendency for them to move into a solution decreses)
solution is hypotonic: if cell is placed in solution with greater water potential than the water potential of the cell and is no movement of water into the cell
-cell will expand and burst (plasmoptysis)
solution is hypertonic: cell placed in solution with less water potential than water potenial of the cell, and is no net movement of water out of the cell
-then cell will shrink (plasmolysis)
Endocytosis and Exocytosis
using ATP bring large materials (organic) and excrete waste via these processes
large particle binds to surface receptors on cell surface and plasma membrane forms around it and engulfs it in vesicle within the cell
Phagocytosis: cell ingests large particles
pinocytosis: ingested material is liquid or macromolecules in dissolved in liquid
Exocytosis: molecules released are carried to the cell surface in a secretory vesicle
-the vesicle fuses with cell membrane and forms a pore thru which molecules are released
Cell surface proteins and cell communication
must respond to other cells and environmental changes
medicated by cell surface proteins or receptors
allow cells to communicate with molecules, tissues, cells outside plasma membrane
homeostasis (allows cell to fn properly) must be regulated which is done by feedback mechanisms which detect changes and respond by inc or dec variable
negative feedback: variable inc and response is to dec, example: temp, hormones
positive feedback: more common, ex: blood clotting
signaling molecules released and recognized which is mediated at cell membrane where signaling molecules binds to cell surface receptor
the binding of this molecules triggers signal transduction cascade that leads to change in target molecule, rxn, or process
Hormone action and feedback
inc in body temp leads to release of neurotransmitters
this message reaches brain and activates sweat glands
Cell cycle Stages
cell division: pass genetic info from parent to daughter cells
prokaryotes: DNA is copied, parent cell splits into 2 daughter cells (binary fission)
eukaryotes: DNA wrapped around histones and packed into chromosomes and housed in nucleus
DNA of eukaryotes divides by mitosis (non reproductive cells) or meiosis (reproductive)
Interphase- first stage
-G1: growing, genes into mRNA and then to protein
-S: 2 copies of each chr made
-G2: chr condense, mitochondria replicate, microtubules made
M: prophase, metaphase, anaphase, telophase
cytokinesis: final stage
Mitosis
Mitosis
- chr replicate in interphase and are made of 2 genetically identical sister chromatids
- in mitosis they are divided to form 2 daughter cells
- parent cell diploid and therefore so is each daughter
- meiosis -4 haploid cells within one set of chr
prophase: chr coil and thicken, become shorter (condensation)
- nuclear envelope starts to degrade
- in animal cells 2 centrosomes (each have 2 centrioles) migrate to oppo sides and this forms mitotic spindle (network of microtubules)
- 2 sister chromatids- attached by centromere (2 kinetochores)
metaphase: microtubules from one centriole attach to kinetochore of 1 sister chromatid and fibers from other centriole attach to other one
- fibers draw chromosomes to middle and align them along cell plate
anaphase; spindle pull sister chromatids apart and to oppo poles of the cell
telophase: mitotic spindle degrades and each set of chromosomes become surrounded by nuclear envelope, chromosomes decondense (uncoil)
cytokinesis: in animal cell actin filaments contract to form cleavage furrow, pinches inward till cytoplasm divides and cell is cleaved into 2 daughter cells
Meiosis
formation of gametes and fusion to form zygote
egg or sperm (1n) and zygote (2n)
interphase precedes just like in mitosis
prophase 1: chromosomes adhere to form homologous pairs (tetrads) and non sister chromatids exchnage info in crossing over
metaphase 1: tetrads migrate metaphase plate and spindle fibers attach to centromeres of each chr
anaphase 1: homologous chr are pulled apart and to oppo poles
telophase 1: cytokinesis occurs and 2 daughter cells form
prophase 2: new spindle forms
metaphase 2: new microtubules fibers attach to centromeres, and make chr align in center of cell
anaphase 2: sister chromatids divided
telophase 2: nucleur envelopes reform to enclose 4 sets of daughter chromosomes
cytokinesis: division of cytoplasm results in 4 haploid gamete cells
Cell cycle checkpoints
ensure cell division occurs under favorable conditions
G1 checkpoint: cell commits to division or not, will not enter S phase if not large enough, limited nutrients, too crowded by others, lacks environmental signals, DNA damage
after G1 checkpoint begins replication of DNA
G2 checkpoint: if DNA damaged or not completely copied repair will be done, if repaired will go to mitosis, if not cell will self destruct
Sugar Phosphate Backbone
single or 2 ringed organic molecule with
nitrogen
sugar w/ 5 carbons
phosphate group
nucleotides joined by dehydration rxns that bind sugar molecule of one nucleotide to the phosphate group of another nucleic acid
nitrogenous bases extend from backbone
backbone on outside an bases on inside
DNA vs RNA
RNA single strand
DNA double helix
RNA -AUCG
DNA- ATCG
Comp. Base Pairing
A-T and C-G and also A-U
Chromosome Structure
DNA coild around histones
nucleosome: 150-200 nucleotides around 8 histones
telomere- at ends of chromosomes, repeated DNA seq
chromosomes easily packaged into nucleus not strands
centromere: center of chromosomes, sister chromatids joined by this
DNA Replication
applies to prokaryotes and eukaryotes
DNA formed from 2 comp strands
phosphate group at 5’ end and 5 carbon sugar at 3’ end
Steps:
- helicase separates 2 strands and forms replication fork
- leading strand (3 to 5)and lagging strand (5 to 3)
- enzyme attaches a primer to leading strand
- DNA polymerase catalyzes addition of nucleotides to leading strand in comp pairing, works toward fork
- strand grown in 5 to 3 direction
- as DNA molecule is unzipped by helicase the lagging strand is built in segments
- primer is attached to lagging strand at fork and comp strand is made in 5 to 3 direction moving away from fork
- DNA ligase joins segments
RNA Transcription
in cytoplasm for prokaryotes and nucleus for eukaryotes
3 steps
Initiation: RNA polymerase binds to promoter and pulls strands apart and begins to make strand of RNA comp to template strand of DNA
Elongation: growth of mRNA, RNA polymerase adds comp. RNA nucleotides to growing single strand of mRNA in 5 to 3
- the oppo strand of original gene is coding strand
- mRNA will have same nucleotides as this strand except uracil
Termination: RNA polymerase reaches sequence of DNA that makes enzyme release itself and stop transcribing
mRNA Processing
exons: coding
introns: noncoding
Steps:
- cap added to 5 prime end of RNA (methylated guanosine triphosphate)
- adenine nucleotides added to 3 prime end
- enzyme called poly(A) polymerase catalyzes addition of the poly A tail (polyadenylation)
- 5 prime cap and poly A tail protect RNA from degrading
- introns removed
- exons joined
Translation
synthesis of amino acids called a polypeptide
takes place in cytoplasm of prokaryotes and eukaryotes
mRNA processed in nucleus of eukaryotes first then transported across nuclear envelope
ribosomes join amino acids into polypeptide chain
ribosomes are made of protein and rRNA
each ribosome has small and large subunit
Steps:
- mRNA transcript binds to short piece of rRNA on small subunit
- next to this are A, P, and E sites that binds tRNA
- tRNA carries anticodon which is comp to codon of mRNA
- anticodon read via enzymes which attach amino acid to proper tRNA
- start at AUG codon
- tRNA has UAC anticondon that carrier methionine which binds and starts initiation
- in elongation tRNAs bind to comp mRNA codonds
- new tRNA anticodon binds at A site
- at P site each new amino acid is joined by peptide bond
- tRNAs released at E site
- translocation refers to process by which mRNA advances on the ribosome by revealing next codon and letting tRNA bind and add its amino acid
- termination is when machinery reaches stop codon
- translation stops and chain is released from tRNA
- ribosome splits into subunits and leaves mRNA
Promoters
where transciption starts on the operon
where RNA polymerase binds
activators bind to turn transcription ON
operator is next to promoter
repressors bind to operator and block RNA polymerase from binding from reaching promoter and therefore turn transcription OFF
Enhancers
transcription factors bind to activate transcription in a sequence of DNA nucleotides called an enhancer
located far from promoter
Transcription Factors
proteins that bind DNA and influence whether RNA polymerase binds a promoter and transcribes gene
Operons
a collection of genes transcribed and translated in a cluster
Environmental Influences
epigenetics: study of gene regulation and changes in an organism that result from this regulation (gene expression/)
modifying gene expression can lead to phenotypic variations, not caused by mutations or changes in sequence of DNA nucleotides
Differential gene expression
only a small number of the genes carried by a cell are expressed by that cell
unspecialized into specialized cell
signals control this
could be external (chemical) or internal (transcription factor)
Stem cells
differentiate into specialized cells
adult vs embryonic
adult: found in specific organ or tissue and gives rise to cells of that organ or tissue
stem cell can be described by its potency
- totipotent: into all cells and therefore can produce all structures, tissues, and organs
- pluripotent: any cell except those with placenta
- multipotent: into several cell types
- oligopotent: only a few cell types
- unipotent: only one cell type
Causes of mutations
mistakes during DNA replication
chemicals or radiation (mutagens)- small scale
recombination- large scale
translocation (type of recombination): segment of DNA moves from one position to another on same chr
Type of mutations
Point mutation- single base change, happen thru single base sub, insertion, or deletion
base substitution can lead to
- missense mutation: one amino acid is substituted for another
- nonsense: substitution causes codon to be changed to stop codon
- silent: changes in non coding region so no change
insertion- base added
deletion: base lost
frame shift: adding or removing nucleotides changes total amt of DNA
chromosome inversion: a break occurs and fragment breaks away and flips around then reattaches
Somatic vs germline mutations
germline: mutations in a cell that will become a gamete and these can be passed on
somatic: body cell and cannot be passed on
Gel electrophoresis
used to separate and learn size of proteins, RNA or DNA
- gel placed in salt solution
- fragments loaded at top of gel
- electrical field applied
- salt solution conduct electricity and draws DNA to bottom of gel
- DNA and RNA are neg charged so are drawn to positive charge at bottom
- shorter fragments make it thru gel more quickly
- fragments separated by size
Microscopy
optical microscope (light)- focuses visible light or UV thru series of magnification lenses to view specimen
electron microscope: magnify even smaller cells, structures, or particles
- use beam of electrons which are passed over surface of cell or structure
- electrons reflected back and used to capture 3D image
Spectrophotometry
study of how much light molecule absorbs
tendency of molecules to be light absorbing or transmitting can be used to learn
use spectrophotometer- passed stream of photons thru sample, some will be absorbed and reduce intensity of the light so conc of molecule is the diff in the intensity of light before passing thru sample and after
light transmitted by spectrophotometer is of a certain wavelength
electromagnetic spectrum - describes various wavelengths of electromagnetic radiation
DNA Sequencing and PCR
to identify order of A, T, C, and G
before DNA can be sequenced has to be amplified
amplification: make copies of DNA and PCR used to amplify
3 Steps of PCR
- segment of DNA is denatured with heat
- short segments of comp DNA primers anneal to separated DNA strands
- DNA polymerase makes new double stranded DNA
Gene therapy
the process of transferring a functional gene into the cells of a patient to treat or prevent a disease by replacing defective gene
can also be used to silence or knock out a gene or introduce new gene into the cells to fend off disease
Cloning
take a cell, cell product or entire organism and make genetically identical copies of the original
gene cloning: to clone and analyze segment of DNA the fragment is ligated to a cloning vector–a plasmid, and then inserted into a host, as vector replicates inside host the DNA is replicated
reproductive cloning: organism in cloned and nucleus of adult is removed from that cell and inserted into enucleated egg cell, the cell is stimulated to form embryo which becomes blastocyst which will be implanted into mother, the offspring will be a reproductive clone
therapeutic cloning: follows above process until blastocyst, then embryonic stem cells are extracted, grown, and induced to differentiate into specific cell type
Transgenic and genetically engineered cells
manipulate genetic info of cell or organism
involved taking gene or sequence from one organisms and introducing this foreign DNA into another
the splicing of the DNA and reinsertion is done via restriction enzyme
the enzymes recognize short symmetrical specific seq of DNA and cut at those sites
-cuts result in blunt ends which terminates the base pair and cannot easily join other DNA
-or sticky ends in which can be joined to another segment of DNA with comp sticky ends
genetic engineering confers new property of an organisms and passes it on, this is called transgenesis
