APBio unit 1

Nucleic Acids function

stores genetic material like genes and blueprint for building proteins, transfers information like blueprint for new cells

RNA (ribonucleic acid)

nucleic acid with a single strand that preforms a lot of functions including protein synthesis and regulation of gene expression

DNA (deoxyribonucleic acid)

nucleic acid with a double helix that stores info for its own replication and the sequence of amino acids in proteins

monomers of nucleic acids

nucleotides (ACGTU)

Types of bases found in nucleotides

purines and pyrimidines

purines

double ring N base, Adenine (A), and Guanine (G)

pyrimidines

single ring N base, cytosine (c), thymine (t), and Uracil (u)

What is a nucleotide composed of?

A phosphate group and a pentose sugar as the backbone, and a nitrogen-containing (nitrogenous) base (AGTCU)

How are nucleotides joined together?

a series dehydration synthesis reactions to form a linear molecule (strand), or a sequence of nucleotides

RNA is predominately a

single strand molecule

DNA is

a double strand molecule

the 2 strands in DNA are held together by

hydrogen bonds

Adenine (purine) makes hydrogen bonds with...

Thymine (pyrimidine)

Cytosine (pyrimidine) make hydrogen bonds with...

guanine (purine)

complementary base pairing

bonding between nitrogenous bases in DNA

How many hydrogen bonds are between Adenine and Thymine

2 bonds

How many hydrogen bonds are between Guanine and Cytosine

3 bonds, meanings its stronger

Replication

Copying process by which a cell duplicates its DNA

mitosis

cell replication

meiosis

gamete production

Protein monomer

amino acids

how are amino acids linked together in proteins

peptide bonds (a covalent bond between amino acids)

peptides

two or more amino acids joined together

polypeptides

long chains of amino acids joined together

protein

a polypeptide that has folded into a particular shape that determines its functioning

ending in -ase means...

its an enzyme

Functions of proteins

involved in almost everything, including metabolism, support, transport, defense, regulation, motion

polymer of protein

polypeptide

Amino acid structure

central carbon, amino group, carboxyl (acid), R group (side chain)

variable that changes amino acids is the...

R group, which is different for each amino acid and provides each with different chemical properties and functions

Sulfur containing amino acids form...

disulfide bridges, which stabilizes a 3-d structure

peptide bonds

covalent bond between NH2 (amine) of one amino acid and COOH (carboxyl) of another. C-N bond

N-terminus and C-terminus are...

ends of amino acids

N-terminus

NH2 end

C-terminus

COOH end

What happens when a protein loses its proper shape?

it is denatured (change in structure = can't function the same)

Levels of protein structure

primary, secondary, teritary, quaternary

primary structure

sequence of amino acids in a protein, determined by gene and can altar a proteins function

secondary structure

the patterns of coils or folds of a polypeptide chain (protein), created by inteactions between adjacent amino acids like H bonds (weak bonds between R groups)

tertiary structure

The overall, three-dimensional shape of a polypeptide due to interactions between distant amino acids R groups, such as disulfide bonds, hydrophobic interactions, H bonds, or ionic bonds

quaternary structure

more than one polypeptide chain bonded together, finally it becomes a functional protein

Unfolding a protein

conditions like temp, pH, or salinity (salt) can disrupt H bonds, ionic bonds, or disulfide bridges, altering secondary or tertiaty structure and 3-D shape, destorying a proteins functionality

Can proteins reserve being denaturalized

some can return to their functional shape but many cannot

Chaperone proteins

assist in folding other proteins correctly

Matter

anything that has mass and takes up space (solid, liquid, gas, plasma)

Matter is composed of basic substances called...

elements

Element

composed of one atom, a subtance that cant be broken down into substances with different properties,

The 6 elements that make up 95% of the body weight of organisms

(acronym CHNOPS) Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur

The 3 elements all macromolecules have

Carbon, Hydrogen, and Oxygen

Phosphorus is found where?

DNA, RNA, Nucleic Acids

Sulfur is found where?

Occasionally proteins

Atom

smallest part of an element

proton

positive charge, in central nucleus

Neutrons

no charge, in central nucleus

Electrons

Negative charge, very low mass, in electron shells

electron shells

orbiting clouds around nucleus

Atomic number

equal to the number of protons in each atom of an element

mass number/atomic mass

the sum (+) of the number of protons and neutrons in the nucleus of an atom

Periods (periodic table)

Horizontal rows, elements in the same row have the same number of shells

Groups

Vertical columns on the periodic table, elements in the same group have the same valence and similar chemical properties

Atoms in the periodic table being electrically neutral means..

the atomic number tells you the number of electrons and protons

Isotopes

atoms that are the same (same element) but have different atomic masses

Radioactive Isotopes

give off energy in the form of rays and subatomic particles, ex Carbon 14 (used to examine photosynthesis reactions)

Four elements that make up 96% of living matter

carbon, hydrogen, oxygen, nitrogen

Four elements that make up remaining 4% of living matter

phosphorus, calcium, sulfur, potassium

Valence shell

outermost energy shell of an atom, determines many of an atoms chemical properties

octet rule

states that the outermost shell is most stable when it has 8 electrons

excpetion to the octet rule

if an atom only has one shell, the outermost valence shell us complete when it had two electrons, (Hydrogen, only has 1 shell)

atoms that have their valence shells filled with electrons tend to be...

chemically stable

atoms that do not have their valence shells filled with electrons tend to be...

chemically reactive

Effect of electrons on atom

they determine its chemical behaviors using the number of electrons in the atoms outermost shell (valence shell), like if it will share electrons with another atom

What tendency drives chemical reactions and creates bonds?

Atoms tendency to either complete a partially filled valence shell or empty a partially filled valence shell

Hydrogen bond

weak, attraction between + and -

Hydrophobic bonds

weak, no charge (non polar), repels/doesnt mix with water

Hydrophilic bonds

weak, polar (- or + charge), reacts/mixes with water

Covalent bonds

Strong, very stavke bonds formed by sharing electron pairs so there are 8 between them, forms molecules. ex. hydrogen gas

The more electrons shared in a covalent bond...

the stronger it gets

Nonpolar covalent bond

pair of electrons shared equally by 2 atoms (ex methane)

Polar covalent bond

electrons are shared unequally, ex water

electronegativity

the ability of an atom ot attract electrons towards itself in a chemical bond

Why are the bonds in water polar?

because the oxygen atom is more electronegative than the hydrogen atoms

Is water polar or non polar?

polar

Hydrogen bond

weak attraction between a slightly positive hydrogen atom and a slightly negative atom, weak on its own, strong with multiple

What makes hydrogen bonding possible in water?

the shape of the molecule and its polarity

Why does DNA have hydrogen bonds?

So it is weaker and able to break to replicate

OH stands for

Hydroxl

What kind of bonds do H2O molecules form with eachother?

H-bonds, where +H is attracted to -O and it creates a sticky molecule

Cohesion

ability of water molecules to cling to each other due to hydrogen bonding, surface tension

Adhesion

The ability of water molecules to cling to other polar substances, capillary action (water goes up tree)

Cohesion and adhesion example

Water getting to the tops of trees

What makes H2O a good solvent?

polarily

Solvents

dissolve (water)

Solutes

getting dissolved (salt)

Solution

mixture of solvent and solute (salt water)

Hydrophilic

mixes with water, POLAR

Hydrophobic

DOESNT mix with water, NON-polar

Special thing about ice

Water is LESS dense as a solid (rare) so ice floats

WHY is water less dense as a solid?

Water is made up of hydrogen bonds, and at temps below 4C, hydrogen bonds between water molecules become more rigid but also more open

Why is ice floating important?

oceans and lakes don't freeze solid over winter because the surface ice can insulate the water below

water having a high specific heat capacity means what?

allowed by hydrogen bonds, water is able to absorb large amounts of thermal energy, which allows it to it resist big changes in temperature