BCMB 230 Exam 1

Covalent bonds

electrons are shared among atoms

polar covalent bonds

unequal sharing, hydrophilic

nonpolar covalent bonds

equal sharing, hydrophobic

electronegativity

the measure of an atom’s ability to attract electrons in a covalent bond

ionic bonds

one or more electrons from one atom are removed and attached to another atom, forming positively charged cations and negatively charged anions

hydrogen bonds

weak bonds between hydrogen and other atoms due to polarity

organic chemicals

compounds containing carbon bonded to hydrogens

fundamental element of life

carbon -- contains 4 atoms in its outer orbital; can form single, double, or triple covalent bonds; can form linear, branched, or ringed molecules

dehydration synthesis

lose water, two amino acids are joined and a peptide bond is created

pH

the measure of hydrogen ion (proton) concentration in a solution

monomer carbohydrate

monosaccharide

polymer carbohydrate

polysaccharide

protein monomer

amino acid

protein polymer

polypeptide

lipid monomer

fatty acid, glycerol

lipid polymer

lipid

nucleic acid monomer

nucleotide

nucleic acid polymer

nucleic acid

lipids are primarily composed of _____ bonds

carbon-hydrogen

lipids are nonpolar or polar and hydrophilic or hydrophobic

nonpolar and hydrophobic

triglycerides

simple fats, glycerol and 3 fatty acids

saturated fatty acids

all carbons are linked by single covalent bonds -- saturated with hydrogen

unsaturated fatty acids

one or more double bonds between carbon atoms -- not saturated with carbon

phospholipids

glycerol, 2 fatty acids, phosphate, and polar head group

amphipathic

major component of cellular membranes

steroids

four interconnected rings of carbon atoms form the skeleton of every steroid

hydrophobic

proteins

predominant molecules in cells monomer--amino acids--20 polymer--polypeptide, protein

primary protein structure

held together by peptide bonds

secondary protein structure

hydrogen bonds between amino acid backbones (form alpha helix or beta strand)

tertiary protein structure

interactions between R groups (hydrogen bonds, ionic bonds, hydrophobic interacts, covalent disulfide bond)

quaternary protein structure

interactions between 2 or more tertiary proteins

nucleic acid

DNA and RNA, nucleotide monomer

DNA

double stranded, TCAG, codes for RNA, found within the nucleus, deoxyribose

RNA

single stranded, UCAG, codes for proteins, found in the cytosol, ribose

function of ATCG

hereditary material ribonucleic acid

function of AUCG

organize protein synthesis

a nucleotide is composed of:

phosphate, pentose sugar, and nitrogenous base

(PHOSPHATE, SUGAR, BASE)

ATP function

transfer and storage of energy (most energy stored between second and third phosphate)

tight junctions

two cells touching each other

gap junctions

channel exists between two adjacent cells so they can share information

desmosomes

cells are close together but not touching; can share information due to their proximity

functions of plasma membranes

\-regulating the passage of substances into and out of cells and between cell organelles and cytosol

\-detecting chemical messengers arriving at the cell surface

\-linking adjacent cells together by membrane junctions

\-anchoring cells to the extracellular matrix

phospholipids

non-polar (hydrophobic) tails: 2 fatty acids

polar (hydrophilic) heads: phosphate group

cholesterol

4 non polar rings; interacts strongly with phospholipid fatty acids

a more saturated fatty acid means:

stronger hydrophobic interactions and more rigid membrane

integral membrane proteins

\-embedded within bilayer

\-can not be extracted without membrane disruption

\-amphipathic

\-usually referred to as transmembrane proteins

peripheral membrane proteins

\-not amphipathic

\-located only on membrane surface

membrane junctions

allow adjacent cells to physically contact along part of their membranes securely

integrins

\-transmembrane proteins that bind to specific proteins in the extracellular matrix

\-link them to membrane proteins on adjacent cells

primary functions of the nucleus

\-storage and transmission of genetic information to next generation of cells

\-info is also used to synthesize proteins

chromatin

\-DNA in association with proteins (histones) forming a fine network of threads

during cell division, chromatin threads become tightly condensed, and form rod-like bodies known as:

chromosomes

nucleolus

\-densely staining filamentous region without a membrane prominent in the nucleus

\-site of ribosomal subunit assembly

ribosomes

\-site of protein assembly

\-two subunits: small and large

ribosomes are found:

free--in cytoplasm for synthesis of normal proteins

bound--on rough ER membrane for synthesis of special proteins

Endoplasmic Reticulum

membranous networks adjacent to nucleus; two types

Rough ER

\-rough due to bound ribosomes to its surface

\-site of membrane protein synthesis, synthesis of secretory proteins, and proteins that require modification for functionality

Smooth ER

\-no ribosomes bound

\-site of most cellular lipid metabolism, degradation of certain toxins, and storage of ions

golgi apparatus

\-membranous sacs

\-site of modifications of newly synthesized proteins and protein processing prior to transport to final location

lysosomes

\-organelle originating from a golgi vesicle

\-contain digestive enzymes--garbage man of the cell

Order of transcription and translation

DNA codes for RNA. RNA leaves the nucleus and travels to the rough ER, where there is a large collection of ribosomes. It binds to a ribosome, where the protein is made. Once complete, the protein undergoes some changes in the ER, then it is sent to the Golgi apparatus. The Golgi packages the protein into a vesicle, which then leaves the cell.

(DNA→RNA→rough ER→Golgi→out of cell)

mitochondria

-site of aerobic cellular respiration to create ATP

-unique structures and composition

cytoskeleton

filamentous network associated with process that maintain and change cell shape and produce cell movements

3 classes of filaments

actin filaments (microfilaments), intermediate filaments, and microtubules

transcription

DNA→RNA (product is messenger RNA)

translation

RNA→protein

codon

three sequential nucleotides (bases) that specify a dedicated amino acid (61 codons) or a stop (3 codons)

splicing

removal of introns

introns

non-coding sequence of RNA

exons

sequence encoding amino acids

alternative splicing

process of selecting different combinations of splice sites within a messenger RNA precursor to produce variably spliced mRNAs.

transfer RNA

brings amino acid to ribosome based upon anticodon base-pairing to mRNA

step 1 of DNA replication

DNA helicase unzips DNA

step 2 of DNA replication

DNA polymerase matches complimentary bases and attaches them to the template strand

step 3 of DNA replication

DNA ligase binds the bases together to form a new strand

Okazaki fragments

smaller sections on the lagging strand (3’→5’) which are joined together later with DNA ligase

DNA replication is semi-conservative. What does this mean?

each of the resulting strands of DNA contain one original strand of DNA and one new strand of DNA (one strand is conserved)

initiation step of transcription

DNA helicase binds to the DNA and unzips it

elongation step of transcription

RNA polymerase adds new nucleotides to the RNA to make it longer

termination step of transcription

RNA strand falls off of DNA strand. The DNA re-seals to keep it safe

what happens in translation?

tRNA collects one specific amino acid from the cytoplasm and hold it into place. When the codons (3 amino acids) bind to the mRNA, the amino acids line up in order and a chemical bond forms to bind them together (dehydration synthesis)

ligand

any molecule or ion that is bound to a protein by either:

\-electrical attractions between oppositely charged ionic or polarized groups on the ligand and the protein

\-weaker attractions due to hydrophobic forces between nonpolar regions on the two molecules

bind to protein at the binding site

affinity

strength with which a chemical messenger binds to its receptor

saturation

fraction of total binding sites that are occupied at any given time

allosteric modulation

when protein has two binding sites and the noncovalent binding of a ligand to one of the sites alters the shape of the second binding site

functional/active site

carries out the protein’s physiological function

regulatory site

the site where the ligand allosterically modulates the shape and activity of the site

phosphorylation

covalent addition of a phosphate group, typically via protein kinase phosphatase that removes phosphate

metabolism

sum of all chemical reactions

catabolism

breakdown of organic molecules

anabolism

synthesis of organic molecules

enzymes

typically proteins, biocatalyst (speeds up reactions without being altered), lower activation energy

substrates

enzyme-specific reactants

cofactors

non-protein helpers required for enzyme action

oxidation-reduction reactions

\-movement of electrons from one molecule to another

\-strategy to convert energy stored in nutrients into ATP

oxidation

loss of one or more electrons

reduction

gain of one or more electrons

substrate-level phosphorylation

-enzyme transfers a phosphate group from an unstable or energetic substrate molecule to ADP and ATP is formed

intermediates

molecules that form between initial substrate and the end products

aerobic cellular respiration

utilizing oxygen to extract all energy stored in electrons of nutrients

steps of cellular respiration

glycolysis: 1 glucose in→1 pyruvate out

pyruvate oxidation: 1 pyruvate in→1acetyl coA out

krebs cycle: 1 acetyl co A in → 12 ATP out (CO2 released)

Electron transport chain