Cellular perspectives in bio test #3

nucleic acids

polymers in nucleotides

• the sugar = ribose in ribonucleotides

• =the deoxyrides in deoxyribonucleotides

nucleotides

composed of a phosphate group, a sugar, and a nitrogenous base

nucleic acid- primary structure

• A polymer of nucleotides, often referred to as a sugar-phosphate backbone

• The monomers are linked together by covalent bonds called phosphodiester bonds

2 groups of nitrogenous bases

• purines ( adenine, guanine)

• pyrimidines (cytosine, uracil, and thymine)

nature of DNA

Erwin Chargaff established 2 empirical rules for DNA.

1. the total number of purines and pyrimines is the same

2. The number of A’s and T’s is equal to the number of C’s and G’s are equal

sequence

the nucleic acid’s primary structure

DNA structure

• 2 strands wound together to form double helix

• strands held together by hydrogen bonds

• bonds are between complementary bases

• strands can be seperated when appropriate

RNA structure

• primary structure = a sugar-phosphate backbone formed by phosphodiester linkages

• extending from that backbone, a sequence of 4 types of nitrogenous bases

primary structure of RNA differs from DNA is 3 ways

1. RNA contains uracil instead of thymine

2. RNA contains ribose instead of deoxyribose

• the presence of the -OH group on ribose makes RNA much more reactive and less stable than DNA

RNA secondary structure

• results from complementary base pairing

• the bases of RNA typically form hydrogen bonds with complementary bases on the same strand

• the RNA strand folds over, forming a hairpin structure: the bases on one side of the fold align with an antiparallel RNA segment on the other side of the fold

• RNA molecules can have tertiary and quaternary structures

DNA is a better genetic info keeper bc its more stables:

• ribose more reactive

• RNA not stable in alkaline condits

• ds RNA easy for enzymes to attack

• less energy to breakdown RNA

Eukaryotic cell cycle (3 stages)

1. Interphase: the cell grows and performs normal housekeeping functions

2. M phase: division of the nucleus

3. cytokinesis division of the cytoplasm

the cell cycle

an ordered sequence of events for cell division

enzymatic proteins

• function: selective acceleration of the chemical reaction

• ex: the digestive system catalyzes the hydrolysis of bonds in food molecules

defensive proteins

• function: protect against disease

• ex: antibodies inactivate and help destroy viruses and bacteri

storage proteins

• Function: storage of amino acids

• Example: casein, a protein of milk, is a major source of amino acids for baby mammals. Plants have storage proteins in their seeds. Ovalbumin is the protein of egg white used as an amino acid source for the developing embryo

transport protein

• function: transport of substances

• ex: hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body. Other proteins transport molecules across cell membranes.

hormonal proteins

• function: coordination of an organism's activities

• ex: insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration

contractile and motor proteins

• function: movement

• ex: motor proteins are responsible for the undulations of the cilia and flagella. Action and myosin proteins are responsible for the contraction of muscles

receptor proteins

• function: response of a cell to chemical stimuli

• example: receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells

structural proteins

• function: support

• ex: keratin is the protein of hair, horns, feathers, and other skin appendages. Insects and spiders use silk fibers to make their cocoons and webs, respectively. Collagen and elastin proteins provide a fibrous framework in animal connective tissue

Amino acids

building blocks of protein

Each amino acids includes a central C atom that bonds to…

1. NH2 - the amino functional group

2. COOH - the carboxyl group

3. H - a hydrogen

4. An “R” group - an atom or group of atoms called a side chain(differs in size, shape, etc)

• 20 unique amino acid building blocks

nonpolar R-groups

hydrophobic; do not form H-bonds, coalesce in water

polar R-groups

hydrophilic; form H-bonds, readily dissolve in water

the peptide bond

condensation reactions bond the carboxyl group of one amino acid to the amino group of another to form a peptide bond

polypeptide

a chain of amino acids

oligopeptides

polypeptides containing < 50 amino acids

proteins

polypeptides containing > 50 amino acids

polypeptide “backbone”

1. R-group orientation: side chains can interact with each other or water

2. Directionality: the free amino group is called the N-terminus. Free carboxyl group is called the C-terminus

3. flexibility: single bonds on either side of the peptide bond can rotate, making the entire structure flexible

protein structure

• primary structure (1 degree) = unique sequence of amino acids

• The R-groups affect a polypeptide's properties and function, so just a single amino acid change can radically alter protein function

secondary structure

• hydrogen bonds between the carboxyl groups of one amino acid and the amino group of another

• depends on the primary structure

• a large number of H-bonds in secondary structure increases its stability

teriatary structure

• Interactions: R-groups to R-groups or R-groups to the peptide backbone

• cause the backbone to bend and fold and contribute to the distinctive 3D shape

quaternary structyre

• Many proteins contain several distinct polypeptide subunits that interact to form a single structure

• the bonding of 2 or more subunits produces quaternary structure (4 degree)

protein structure is hierarchical

• 4 degree is based on 3 degree structure, which is based in part 2 degree structure

• all 3 of the higher-level structures are based on a 1-degree structure

folding and function

• protein folding is often spontaneous, because the H-bonds and Van Der Waals interactions make the folded molecule more energetically stable than the unfolded molecule

• a denatured protein is unable to function normally

gene

a stretch of DA that codes for a functional strand of RNA, be it mRNA, rRNA or tRNA

central dogma of modern bio

• The presence and action of proteins determine the phenotype of an organism

• one gene → one polypeptide hypothesis recognizes that some proteins are composed of multiple polypeptides

phenotype

the physical or functional characters of an organism which are determined by the interaction of its genetic makeup and envirenment

a gene consist of:

• promoter region

• start point

• downstream

• upstream

• transcription unit

• termination region

1st stage: intuition

• RNA polymerase(binds to promoter region and unwinds the helix, transcription starts)

• Initiation completes in eukaryotes

• Sigma factor and RNA polymerase=holoenzyme

2nd stage: elongation

• RNA nucleotides are added to the chain at the 3’ end

• direction of RNA synthesis is 5’ to 3’ (same as DNA)

3rd stage: Termination

• RNA polymerase reaches a terminator sequence and detaches from the template

Post-transcriptional modification

• Eukaryotic RNA must be processed before leaving the nucleus

• mRNA must be stabilized to exist outside the nucleus

• cap added 5’ end: single backwards methyl-guanine

• cap added 3’ end: poly-A-tail of 50-250 A’s

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introns

eukaryotic mRNA interrupting sequences

exons

seperating the eukaryotic mRNA coding regions

RNA splicing

removal of introns and joining of exons to produce a continuous coding sequence

ribosomes build polypeptides

• Translation occurs on the surface of the ribosomes

• Ribosomes have 2 subunits: small and large

• mRNA 1st binds to small subunit

• Ribosomal subunits come together during translation

genetic info in codons translated to amino acid sequences

polypeptide construction requires a conversion of a nucleotide sequence to amino acid sequence

transcription

DNA code into RNA, using the same nucleotide “language”

nucleotide “word”

Each “word” is a codon consisting of 3 nucleotides

translation

switching from the nucleotide “language” to amino acid “language'“

universal genetic code

• Each codon is unambiguous and stands for only one amino acid

• Most amino acids are specified by more than one codon

• stop codons do not specify any amino acids at all

• note special start codons also codes from an amino acid

1st stage: initiation

• mRNA binds to the small ribosomal subunit, and the 1st tRNA binds to the mRNA at the start codon

• The start codon reads AUG and codes for methionine

• The 1st tRNA has the anticodon UAC

• a large ribosomal subunit joins the small subunit

• the 1st tRNA occupies the P site, which will hold the growing peptide clan

• the A site is available to receive the next tRNA

2nd stage: elongation: 1 amino acid at a time

• Each cycle has 3 steps

1. codon recognition: the next tRNA binds to the mRNA at the A site

2. peptide bond formation: the amino acid on the tRNA at the P site is attached by a covalent bond to the amino acid on the tRNA at the A site

3. translocation: tRNA is released from the P site into the E site, and the ribosome shifts down, moving the tRNA from the A site into the P site

Stage 3: termination

• transfer RNA molecules match amino acids to their corresponding mRNA codons

• tRNA structure allows it to convert one language to the other

tRNA structure

• an amino acid attachment site allows each tRNA to carry a specific amino acid

• An anticodon allows the tRNA to bind to a specific mRNA codon, complementary in sequence

• A pairs with U, G pairs with C