Lecture 1: Foundations Of Biology Flashcards
Scientific method
Making observations, developing explanations and testing those explanations
What must a hypothesis be
Falsifiable and testable (falsifiable meaning the ability to be proven false)
Failure to falsify a hypothesis means the hypothesis is true
Wrong - there still must be data to prove its validity
Variables in an experiment
Independent- changed by scientist
Dependent- response to changes in independent variables
Controlled- remains constant
Experimental vs Observational science
Observational- infer a pattern and cause for collected data, and use statistical techniques
Experiment: data collected through controlled experiments
Organization of matter (matter, element, and compound)
matter- has mass and occupies space (Consisting of pure elements)
Element- cant be broken down to other substances by chemical reactions
Compound- two or more elements in a fixed ratio
Which elements make up 96% of the matter in living organisms
- Carbon
- Oxygen
- Hydrogen
- Nitrogen
The ratios make living organisms different
Isotopes
- same number of p+, different number of neutrons therefore different atomic mass but same atomic number
Radioisotopes
Unstable isotopes that decay and release energy, rate of their decay is constant
Radioactive tracers
- substance containing a radioisotope that’s used to measure the speed of chemical processes or the movement of a substance
ex. used in imaging tests
Inert
- elements with full valence shells
- unreactive
- ex. Neon
Don’t form chemical bonds
Unequal sharing of electrons forms
a polar covalent bond, if hydrogen is one of the atoms= hydrogen bonding
Hydrogen bonding
- partial positive H attracted to partial negative charge of nearby atoms
- weaker than covalent and ionic bonds
Van der Waals forces
- weaker than hydrogen bonds
- develop between non polar molecules
- constant motion of electrons causes them to accumulate creating zones of positive and negative charges (temporary)
- polar molecules
ORDERING THE STRENGTH OF BOND TYPES
Ionic (strongest)
Covalent
Hydrogen
LDF
Inter vs intra
Inter- between
Intra- within
Hydrogen bonds and water
More dense- liquid form: dynamic (movement) can be used in living cells
Less dense- solid form: ice
- stable, rigid lattice structure prevent it from being used in cells
- ice rigid lattice structures expand and form crystals that can puncture and disrupt cell membranes
Characteristics of water
- high specific heat capacity allows water to stay liquid between 0-100 degrees Celsius
- attraction between water molecules cause cohesion
Why is cohesion important for plants
- keeps water molecules connected, allowing them to move agains the force of gravity easily
- whenever water evaporates, stomata pull water to stems from roots
Hydration shell
- water molecules surround polar molecules and ions
- allows for the separation of molecules until it reaches a saturation point
Buffers
- controls pH, allowing it to stay neutral
- absorbs or releases protons
IN OUR BLOOD:
- kidneys regulate pH by excreting acids in urine
- produce and regulate Bicarbonate to increase pH
Living matter are composed of carbon compounds
Making them organic
Synthesis of a polymer
synthesis of a polymer:
- dehydration synthesis reaction
- remove water
- form a bond
Breakdown of a polymer
hydrolysis reaction:
- add water
- break a bond
- split water molecules
carbohydrates
- sugars and the polymers of sugars
- fuel for cells
- building material (build various cellular components)
monosaccharides
- multiples of CH2O (1:2:1)
isomers of monosaccharides
- same chemical formula
- different molecules structure, different function
mirror imaged isomers
Enantiomers
- structural isomers
- different position of carbonyl group
Disaccharides
- two monosaccharides
- form a covalent bond: GLYCOSIDIC LINKAGE
Glucose+Glucose=Maltose
Glucose+Fructose=Sucrose
Glucose+Galactose=Lactose
Polysaccharides
Branched: alpha glucose (from glycogen and starch)
Unbranched: beta glucose (building)
- form different glycosidic linkages: H bonds and N groups
Proteins
MADE UP OF POLYPEPTIDES
- various structures, various functions
- structural support, storage, transport, etc.
- 100 000 different human proteins (transcription and translation are the blueprint to build these proteins)
polypeptides
polymers of amino acids
how many different types of amino acids
- 20 different amino acids made unique based on their R group
central carbon= alpha carbon
N terminus (amino group)
C terminus (carboxyl group)
also have a functional group attached
What are the non polar amino acids
Glycine (Gly, G)
Alanine (Ala, A)
Valine (Val, V)
Leucine (Leu, L)
Isoleucine (Ile, I)
Methionine (Met, M)
Proline (Pro, P)
Cysteine (Cys, C) *pH of environment can affect its polarity**
Phenylalanine (Phe, F)
Tryptophan (Trp, W)
GREAT ARTISTS VALUE LIFE, IN MY PRETTY CRAZY PAINTING TIME
What are the uncharged polar amino acids (partial charge)
Serine (Ser, S)
Threonine (Thr, T)
Asparagine (Asn, N)
Glutamine (Gln, Q)
Tyrosine (Tyr, Y)
STAG-T
Acidic (negative charge) polar amino acids
Aspartic acid (Asp, D)
Glutamic acid (Glu, E)
AG (2 letters=even, think opposite so odd=negative)
Basic (positive charge) polar amino acids
Lysine (Lys, K)
Arginine (Arg, R)
Histidine (His, H)
LAH (3 letters=odd, think opposite so even=positive)
Peptides
- covalent bond
- formed by dehydration synthesis
- amino acid added only to carboxyl end
= Peptide Bond, connect together in a polypeptide bond
amino acids are joined by peptide bonds to form PEPTIDES (by linking carboxyl ends)
then they will form POLYPEPTIDE CHAINS through peptide bonds which are the building block of protein structure
Primary Protein Structure
1)- linear sequence of amino acids
tells us nothing about its structure
N-terminus …. Amino acid sequence…. C-terminus
Secondary Protein Structure
H bonds between amino acids as part of backbone to connect both strands
- O and H of backbone folds
- forms either an alpha helix or Beta pleated sheet
Primary and secondary protein structures only
involve bonds between amino and carboxyl groups
Tertiary protein structure
- all types of bonds between R groups
- will form chemical bonds with each other
- 3D Shape
- Function
- no bond formation and non polar behaviour leads to hydrophobic interactions
Quaternary Protein structure
less than or equal to 2 polypeptides
- all types of bonds
Hemoglobin For Example needs 4 polypeptides
Prosthetic groups
- part of quaternary protein structure
- non-protein molecules/compounds added to protein after to allow for function
ex. Heme
Heme as a prosthetic group
- helps hemoglobin bind and deliver O2
- iron core
- essential for the function of hemoglobin
Nucleic acids
- polymers of nucleotides
- genetic information=inheritance
1) DNA
2) RNA
a) mRNA (messenger)
b) tRNA (transfer)
c) rRNA (ribosomal)
nucleotides
3 parts (covalent bonds)
1) nitrogenous base
2) pentose sugar
3) 1-3 phosphate groups
difference between DNA and RNA
- if carbon 2 in the nucleotides contain OH or H
OH-RNA
H- DNA
A) Which nucleotide is only found in RNA
B) Which nucleotide is only found in DNA
C) Which nucleotide are used in energy transfer
a) URACIL
b) THYMINE
c) ADENINE AND GUANINE
Pyrimidines vs Purines
Pyrimidines- 1 carbon ring
Purine- 2 carbon rings
DNA and RNA structure
- 2 nucleotide chains
- sugar phosphate backbone
- phosphodiester bonds (building nucleic acids)
- nitrogenous bases inside
- H bonds
How is DNA read
from 5 to 3
DNA structure
- PO4 and sugar backbone
- Nitrogenous bases are NOT part of backbone
- Use nitrogenous bases to form H bonds between 2 strands of polynucleotides to form double strands
Anti parallel strands
5-3
3-5
complementary strands that run in opposite direction
+ knowing the sequence of one DNA strand means you can predict the other
3 C-G
2 A-T
RNA structure
- Single stranded
- no hydrogen bond formation between nitrogenous bases
Lipids
- non polar molecule: hydrocarbon backbone
- not a true macromolecule=no defined monomer subunit
- biological lipids: fat, phospholipids, steroids
Fatty acids
Saturated:
- maximum number of hydrogen atoms
- linear: no double bonds
- increased density: can be packed in
- room temp=solid
ex. butter, stearic acid
Unsaturated:
- one or more double bonds
- room temperature=liquid
- decreased density, pockets of air
- ex. oleic acid
triglycerides= 3 fatty acid chain
- formed through dehydration synthesis
What has more energy: 1g of starch or 1g of fat
1g of fat: holds more energy in fatty acid chains C-H bonds store more energy
phospholipids
- major lipid found in membranes
- amphipathic: polar and non polar components
steroids
- form of lipid: isoprene backbone
- 4 carbon ring
- dual solubility: np and p ends
cells
composed of major macromolecules
- structural organization will impact function
All macromolecules
- proteins
- nucleic acids
- carbs
- lipids
differentiate between
nitrogenous bases
nucleic acids
and nucleotides with regards to the formation of DNA
Nitrogenous bases (a,c,t,g) pair via hydrogen bonds to stabilize the double helix structure of DNA, while nucleotides (sugar, PO4, and base) link together through phosphodiester bonds to form the sugar-phosphate backbone of nucleic acids (DNA, RNA)
