Unit 1 Flashcards
Living Organisms
Composed of common set of chemical components and similar structures
-depend on interactions among structurally complex parts to maintain the living state
-genetic information
-convert molecules
-extract energy from enviroment and use it for life
-replicate genetic information
-fundamental set of genes with structural similarities
-evolve through gradual genetic changes
Three domains of life
Bacteria, archaea, eukarya= Luca(last universal common ancestor)
Inductive biotic theory
Relate to mitchoandria and chloroplasts
Inductive logic/reasoning:
Used to form hypothesis, specific to general
Deductive logic/reasoning
Used to create testable predictions assuming hypothesis is supported, general to specific predictions
In metabolism the action of going from subunits to macro units is called what?
Anabolism( ATP to ADP)
Isotopes
Different number of neutrons, same number of protons
Radioisotope:
Unstable and spontaneously breakdown going off energy, short life
Unequal sharing of electrons happens when:
The two atoms are different elements- electronegativity difference
Non polar bond
Electrons shared equally
Polar bond
Electrons are pulled closer to the nucleus of the more electronegative atom
A large difference in electronegativity results in what type of bond? Smaller difference?
Bigger= ionic, smaller= polar covalent
In metabolism the action of going from macro units to subunits is called what
Catabolism (ADP to ATP)
Ionic bonds tend to form what and that makes for what arrangement?
Crystals, anions and cation
A characteristic of life is what
The ability to acquire and transform ENERGY from one form to another
In general an anabolic reaction is what
Simple to complex molecules, energy INPUT is required(stored in chemical bonds)
In general a catabolic reaction is:
Complex to simple, energy is released from chemical bonds
Define Metabolism
The sum total of all chemical reactions occurring in a biological system at a given time
Chemical reactions:
Involve energy changes, the energy in covalent bonds differed between the reactant and product.
Any chemical reaction means there is a
Change in energy= transformation
Energy
The capacity to do work
Potentional energy
Energy stored in chemical bonds, concentration gradient, charge imbalance, etc.
Kinetic energy
The energy of movement
Types of energy in biology
Chemical(stored in bonds), electrical(separation of charges), heat(transfer due to temp. Difference) , light(electromagnetic radiation stored as photons), mechanical(energy of motion)
1st law of thermodynamics
Energy is neither created or destroyed, it can be converted
Second law of thermodynamics
When energy is converted from one form to another some of that energy become unavailable to do work (an example if heat)
Entropy definition
Some energy is converted to a non usable form associated with disorder and randomness- overall increasing in universe
The second law tells us:
A change that would decrease in entropy will not happen spontaneously- it will only happen is energy is added to system (ex: heating up water)
In a closed system the amount of usable energy will what with every transformation
Decrease
Total energy=
Usable(free) energy + unusable energy(entropy)
Only what type of energy can be used for cellular work
Free energy
Enthalpy(H)= free energy (G) + entropy(s)
A chemical reaction occurs when
Atoms combine or change their bonding partners
The ending -lysis means what
Breaking down something
If G is negative the reaction releases energy which is called what
Exergonic
If G is positive the reaction requires energy to occur which is called what
Endergonic
Chemical transformation require additional energy to initate the reaction is what
Activation Energy
Ea is required in what type of reactions
Endergonic and exergonic because covalent bonds in reactants must be broken first
Reaction rate is influenced by what
Activation energy, tempature, and concentration
Equilibrium
Rate of forward and reverse reaction are equal- relative concentrations of reactants and products will no longer change
Exergonic reactions:
Catabolic reations(complex to similar), complexity decreases and generates disorder, can occur spontaneously
Endergonic reactions
Consume free energy, include anabolic reactions(simple to complex), complexity(order) increases, localized decrease in entropy, not spontaneous
What bond in water makes it naturally cohesive
H bonding
The greater number of H bonds in liquid water gives it ? Specific heat
Higher
All hydrophilic (ionic, polar) molecules are?
Soluble (able to dissolve) in water
When acids dissolve in water they ? With H+
Release
A strong acid? A weak acid?
Dissociated completely in water, I complete dissociation
A buffer
Helps maintain constant pH by absorbing or releasing H+ ions, is a weak acid and is corresponding base
Hydroxyl group
R-OH, polar, h bonds with water to help dissolve molecules, enables linkage to other molecules by condensation(opposite of hydrolysis)
Aldehyde Group
R-C=O and that C is C-H, the C=O group is very reactive. Important in building molecules and in energy-releasing reactions.
Keto Group
R-C(this C is also C=O)-R, the C=O is important in carbohydrates and in energy reactions
Carboxyl Group
R-C=O(and the C is C-OH) this is acidic. Ionizes in living tissues from -COO^-, and H+ Enters into condensation reaction by giving up -OH some carboxylic acids important in energy releasing reactions
Amino Group
R-N-H(N is bonded to another H) Basic, accepts H+ in living issues to form -NH3+, enters into condemnation reactions by giving up H+
Phosphate Group
R-O,P=O,O,O (P is in middle with one double bond to O and the rest single bonds) acidic, enters into condensation reations giving up OH, when bonded to another phosphate, hydrolysis release much energy
Sulfhyrdryl Group
R-SH by giving up H two -SH groups can reaction to form a disulfide bridge, stabilizing protein structure
When attached to a larger molecule, funcational groups give properties to larger molecule
Phosphate groups are highly polar, tend to interact with water. Addition of phosphate group can turn a hydrophobic, non polar molecule into a hydrophilic polar one
Macro molecules are Polymers- polymers are
Long chains of smaller molecules called monomers joined by covalent bonds
Different polymer types are defined by the functional group that attaches to the
Carbon skeleton
Amino acids
Proteins
Nucleotides
Nucleic acid
Sugar
Polysaccharide (carbohydrates)
Phospholipid
Membrane (NOT A POLYMER- NOT Covalent bonds, but VAN DER Walls bonds)
Make a polymer by
Condensation (water out, energy in) AKA dehydration synthesis
Carbohydrates
-each carbon is being hydrated
General formula for carbohydrates
Cn(H2O)n
Types of carbohydrates/polysaccharides
-Monosaccharides
-disaccharides
-oligosacchrides
-polysaccharides
Monosaccharide
Smaller sugars- 3 to 6 carbons
Disaccharides
Two monosaccharides linked by covalent bonds
Oligosacchrides
3-20 monosaccharide’s
Polysaccharides
Hundreds or thousands of monosaccharide’s- starches, glycogen, cellulose
Glucose
Aldehyde groups at carbon 1
Alpha carbon ring
H on top of carbon 1
Beta Carbon ring/ glucose
H on Bottom
How to count Carbons
C1 is at the center of the C hole
Be able to name and identify Alpha, Beta, Glucose, Fructose, and Sucrose and others on slide 8 of lecture 4
Linear, branched, and highly branched examples
Cellulose, Strachey, glycogen
Highly branched molecules will have what type of energy
A lot of stored energy
Functions of Carbohydrates
-Cell energy: immediate- glucose adn other monosaccharide’s
- Cell energy: stored energy source- starch, glycogen
-Carbon Skeltons for many other molecules : sugar component of nucleotides- ribose, deoxyribose
-Cell recognition signals: attached to proteins or lipids on cell surface
-extracellular structures: cell walls (bacteria, plants, fungi), exoskeletons, cartilage
Nucleic acids: building block and function
Building block: nucleotides, the acids carry genetic information
DNA to DNA
Replication
DNA to RNA
Transcription
RNA to Polypeptide(protein)
Translation (think poLypeptide and transLation)
Neculeotides
The monomer, can be joined in chains or reversible attached to ther types of cell molecules (proteins)
Nucleic acids
Polymers of nucleotides, DNA= deoxyribonucleic acid, RNA= ribonucleic acid
Nucleic acid bases
Pyrimidines and Purines
Purines have
A and G, PURe As Gold
nucleotides=
Pentode sugar + phosphate group + nitrogenous base
Pyrimidines
C, T, U. (Think pyramids CUT)
The difference in the base of RNA and DNA is
DNA does not have OH at carbon 2, RNA does have OH at carbon 2
The bases interact at carbons:
carbon 3 of molecule one interacts with carbon 5 of molecule 2
When base paring in DNA and RNA the stands should be….
Going opposite ways (one is 3-5 carbons and the other 5-3 carbon) Unparallel
A goes with and G goes with
T and C (think AT and G and C make Great Complements)
Nucleotides are joined by what type of bond
Strong covalent bonds
Paired chains are bonded by what type of bond
Hydrogen Bond
A and T have how many H bonds
2 H bonds
G and C have how many hydrogen bonds
3 (think G and C are Great Complements- longer phrase= more hydrogen bonds)
RNA folds
A strand of RNA can also from intramolecular base pair bonds with itself folding to make a more complex double stranded shapes
DNA is always Double stands
Functions of DNA
-carries information for all of an organism’s structures and functions, held in specific sequence of base pairs
-can reproduce itself (replication using complementary base pairing)
-can copy specific segments of the information into RNA (transscRiption)
RNA can specify. Sequence of amino acids in a polypeptide
Structural and functional characteristics of cells
Functions for nucleotides
ATP- energy transducer in biochemical reactions (can go to ADP and AMP)
GTP- energy source in protein synthesis
cyclic AMP- essential to the action of hormones and transmission of information in the nervous system
Types of proteins
Enzymes, structural, defensive, signaling, receptor, membrane transporters, storage, transportation, gene regulation
Amino Acids are what type of bond, called what
Covalent bond, called peptide bond, joined amino acids are polypeptides
Know the generic amino acid structure
C in middle, a R bond (side chain), H bond to C, COO- (carboxyl group) bonded to C and H3N+ (amino group) bonded to C
Charged amino acids
The charges side interacts with water or with ions of opposite charge- positive charge will have a + in the R group. Negative will have a - in the R group
Hyrophilic amino acids with polar but un charges side chains form hydrogen bonds
All have CH2 or CH3
Amino acids with non polar hydrophobic side chains all have
CH3, or CH2
Special Cases
Cysteine, Glycine, Proline
Cysteine
Can for a s-s bridge with another Cys
Glycine
Can fit through tight corners in a folded protein
Proline
Can cause a kink or turn in a folded protein- R group also bonded to H2N+ group
Proteins 4 levels of structure
Primary- linear sequence
Secondary- regular, repeated pattern in different regions of the Aa chain that arise from H bonding between AA
Tertiary- 3D shape arises from interactions (ionic, H bonds, or hyrodphobic) between R groups
Quaternary- association of two ro more polypeptides to form the functional proteins
The secondary term has what shapes
Beta pleated sheet and alpha helix
Tertiary level has what type of bonds
H bonds, disulfide bridges, van der waals interaction, and ionic bonds
This is when it starts forming specific shapes
Disulfide bridges
The terminal SH group of cysteine can react with another cysteine side chain to for a -s-s bond (VERY IMPORTANT IN PROTEIN FOLDING)
Enzymes are
Catalytic molecules
Tertiary structure
If a protein is heated the secondary and tertiary structure is broken down to the protein is said to be denatured- when cooled returns to normal tertiary structure, demonstrating that the information to specific protein shape is contained in its primary structure
Non covalent interactions between proteins
Environmental factors can destabilize a protein structure
-pH changes disrupt ionic bonds
- heat or high concentrations of polar molecule disrupts h bonds
-non polar substances- can disrupt folding of proteins that have many hydrophobic interactions
- high concentration of polar solutes can disrupt h bonding
How to read the P20 measurements
Top- 10s
Middle- 1s
Bottom- .1s
How to read P200 measurements
Top- 100s
Middle- 10s
Bottom- 1s
How to read P1000 measurements
Top- 1000s
Middle- 100s
Bottom- 10s
Be able to calculate a serial dilution and explain it
It is when the first tube gets a 1:1 ratio of solution and water then the second tube gets a 1:1 ratio of tube 1’s solution and water, and so on
Hypothesis vs theory-
Hypothesis: educated guess, can be tested (can never be proven true
Theory: backed up by an idea, can be changed/revised
Homeostasis
Maintain consistent conditions in the cell
Dry lab 1 observations with salt water and leaf
When the leaf was with regular water it had chloroplasts all throughout the cell, when in salt water the chloroplasts collected, the membranes made a “line” , there was salt water inside the cell in the “open” area.
When cell membranes move away from the cell wall that shows what
Hypertonic
The outside of the cell with salt water is hypertonic to the cytoplasm therfore
Water wants to move out
The fresh water and cell was hypotonic to the outside in freshwater to cytoplasm
The cytoplasm was hypertonic to water
Plasmolysis:
The movement of water from the cell into the environment causing the plasma membrane to pull away from the cell wall. In hypertonic conditions the cell is prevented from bursting due to presence of elastic but rigid cell walls.
Osmosis
The movement of water from LOW solute concentration (hypotonic) to HIGH concentration (hypertonic) via permeable membrane (plasma membrane)
Hypertonic
High concentration solution
Hypotonic
Low concentration solution
Isotonic
The balance of concentration solutions (equal)
Negative control
Should have no change from adding something, control for false positives
Positive control
Expected outcome/desired outcome- adding something you know works. Controls for false negatives
Dependent vs independent variables
Dependent- variable being measured in output
Independent- variable the gets manipulated
Polymers
Most macromolecules are made of this, they are long chains of smaller molecules called monomers, joined covalently
Building blocks of life:
Amino acids- proteins, nucleotides- Nucleic acid, sugar-polysaccharide (all are polymers)
Phospholipid- membrane (not a polymer, not covalently bonded
How to make a polymer
Dehydration synthesis- an H2O group leaves so that the monomer can attach with the other monomer
How to break a polymer
Hydrolysis- (water in, energy out) where a monomer will break with another monomer H2O will go in, the OH attaching to the monomer and the H attaching to the polymer
Carbohydrates/polysaccharides
General formula of C_n(H2)_n, includes small sugars and long polymers of sugars, there are 4 categories: monosaccharide, disaccharide, oligosacchrides, and polysaccharide
Monosaccharides
Smallest sugar- 3C to 6C
Disaccharides
Two monosaccharide’s link by covalent bonding
Oligosacchrides
3-20 monosaccharides
Polysaccharides
Hundreds or thousands of monosaccharides- starch, glycogen, cellulose
