What are the four macromolecules found in cells?

      Carbohydrates

      Lipids and Fats

      Proteins

      Nucleic Acids

     In general, how are macromolecules synthesized?

      Polymerization

      Condensation reaction: a molecule of water is released, an addition of a subunit to an end and a covalent bond is formed

      Condensation reactions are catalyzed by specific enzymes

     What determines the shape of a particular macromolecule?

      Noncovalent bonds specify the shape of the macromolecule

      Single covalent bonds between subunits allow for rotation of atoms

      Non-covalent bonds that form between different parts of the polymer constrain rotation

     What is the general structure of each type of macromolecule?

      Subunits = monomers (sugars, amino acids, and nucleotides)

      Subunits join together through covalent bonds to create macromolecules

      Macromolecules can join together through non-covalent bonds to form a macromolecule complex

     What are the chemical properties of each of the macromolecules?

Monosaccharides

      Monosaccharides – (CH₂O)_n where n = 3, 4, 5, or 6, 2 or more hydroxyl groups, and an aldehyde or ketone

     What is the primary function of each type of macromolecule?

      Carbohydrates – energy source, energy storage for cells, mechanical support, cell surface markers

      Lipids and Fats – food reserve in cells, form cell membrane to enclose cell organelles, aid in cell signaling, turn on expression of specific types of genes in male development or female development

      Nucleotides – chemical energy, coenzymes (carrier group to take to a specific region of the cell, can enhance reaction rates), signaling molecules, building blocks of nucleic acids (DNA and RNA)

      Proteins – many functions!, building and repair of body tissues, nutrient transport, muscle contraction, source of energy, maintains overall good health

     Identify and explain the levels of protein structure

      Primary Structure – amino acid sequence

      Secondary Structure – small region of polypeptide chain starts folding, α helix forms from amino acids that are right next to each other in the polypeptide sequence, β-sheet. α helix and β-sheet are the result of hydrogen bonds formed between NH & COOH groups in the backbone of a polypeptide

      Tertiary Structure – 3-D structure of a polypeptide chain. Includes alpha helices, beta sheets, loops, random coils, and random folds.

      Quartenary Structure – complete structure of a protein that has more than one polypeptide chain, polypeptide chains bonded through noncovalent bonds

     What is specificity and how does it relate to proteins and protein binding?

      The correct ligand binds to the specific protein

      Specificity is determined by protein shape and side chains

      Binding site: the correct must bind to the binding site of the protein to activate the protein

      Regulatory site: other binding sites that cause a conformational change when ligand binds to it and causes the protein to activate or deactivate

      If the wrong ligand binds to the wrong protein it aggregates the cell and can cause damage to the cell

      The correct binding of a ligand to a protein initiates different functions the proteins need to carry out

      Some proteins sole purpose is to bind to a ligand (ex. actin and antibody’s)

     How are proteins controlled?

      Most proteins and enzymes do not work continuously in the cell so they must be controlled somehow

      Ways proteins are controlled…

      Switching protein activity on or off – enzyme activity changes in response to other specific molecules it encounters, causes change in protein conformation (fast)

      Localizing proteins into specific compartments

      Gene expression – DNA regulates how much transcript is made or destroyed (slow)

     What is allosteric binding, phosphorylation, GTP binding, & ATP binding? How can each be used to regulate a protein?

      Allosteric binding – an allosteric molecule binds at a site other than the active site which induces a conformational change which can induce a change in enzyme activity. Can have positive regulation if it turns on the enzyme or negative regulation if it turns off the enzyme.

      Phosphorylation – the addition of a phosphate group (negative) to serine, threonine, or tyrosine. This causes a conformational change which either turns the protein on or off.

      GTP binding – GTP proteins can hydrolyze GTP into GDP and cause a slight conformational change turning the protein off. When GTP binds to protein it is turned on again

      ATP binding – hydrolysis of ATP bound to a motor protein such as myosin or kinesin induces a slight conformational change of the motor protein

     Give a general overview of the process of DNA synthesis

      What is the template used?

      What is the product produced?

     Why does DNA replication have to be so accurate?

      DNA replication has to be very accurate because if incorrect base pairs are formed and allowed to remain, they would kill the cell through an accumulation of mutations

     What is meant by saying that transcription is a process where there is successive amplification of genetic material?

      From one piece of DNA, many copies of RNA can be produced

     Give a general overview of the process of transcription

     What is the general process of transcription?

     Where does transcription occur?

      Cytosol in prokaryotes

      Nucleus of eukaryotes

     What is the template used?

      The noncoding strand

     What is the product produced?

      RNA

     What is a coding strand?

      The DNA strand which has the same base sequence as the RNA transcript produced. This strand contains the codons. The nontemplate strand for transcription which has a sequence equivalent to the transcript.

     What is the non-coding strand?

      The strand of DNA that does not contain the genetic information necessary to make proteins. It is the template for transcription and it has a complementary sequence to the transcript (RNA) produced

     What is a promoter?

      A promoter is a specific sequence of nucleotides that indicates the start of transcription

      RNA polymerase binds tightly to DNA at the promoter due to the recognition by its subunit, the sigma factor

      Both prokaryotes and eukaryotes require a promoter

     What is a terminator?

      A terminator is a specific sequence of nucleotides that indicates the stop of transcription

      RNA polymerase halts and releases the DNA template and newly synthesized stand of RNA at the terminator

      Both prokaryotes and eukaryotes require a terminator

     Give an overview of the process of translation.

     What is the process of translation?

      Decode mRNA to produce a protein

     Where does translation occur?

     What is the template used?

      RNA

     What is the product produced?

      A protein

     What is meant by the term genetic code?

      The set of rules specifying the correspondence between nucleotide codons in DNA or RNA and amino acids in proteins

     What are codons, anticodons, tRNA (aminoacyl tRNA, peptidyl tRNA), and ribosomes?

      Codons – sequence of 3 nucleotides in a DNA or mRNA molecule that represent the instructions for the incorporation of a specific amino acid into a growing polypeptide chain. The start codon AUG codes for an amino acid, methionine. The 3 stop codons, UAA, UAG, UGA, are not recognized by tRNA and do not specify an amino acid, but they instead signal to the ribosome to stop translation

      Anticodons- sequence of 3 nucleotides in a tRNA molecule that is complementary to the 3 nucleotide codon on a mRNA molecule; each anticodon is matched to a specific amino acid covalently attached elsewhere on the tRNA molecule

      tRNA – a set of small RNA molecules used in protein synthesis as an interface between mRNA and amino acids (binding partner = specific amino acid)

      aminoacyl tRNA  – site where aminoacyl tRNA enters ribsome and binds to codon in mRNA

      peptidyl tRNA – site where growing polypeptide chain is attached to tRNA

      ribosomes – particle composed of ribosomal RNA’s and ribosomal proteins that associates with mRNA and catalyzes the synthesis of a protein. Has 2 subunits, the large subunit which catalyzes the formation of peptide bonds and the small subunit which matches tRNA codons to mRNA.

     Which amino acid is translated first?

      Methionine, the start codon

     Is a newly synthesized polypeptide always a functional protein? Explain.

      No, sometimes proteins require further attention before they are useful to the cell. For example, covalent modification (like phosphorylation), the binding of small-molecule cofactors, or the association with other protein subunits may be needed to activate a newly synthesized protein.

     Compare and contrast replication, transcription, and translation in eukaryotes and prokaryotes.

      Eukaryotes

      DNA à Transcription à5’ Capping, RNA splicing, 3’ Polyadenylation à  mRNA àExport of mRNA to cytoplasm à Translation (initiation, elongation, termination) à Protein!

Compare and contrast replication, transcription, and translation in eukaryotes and prokaryotes.

- Prokaryotes

      DNA à Transcription à mRNA àTranslation (initiation, elongation, termination) à Protein!

     If given a sequence of DNA, you should be able to determine the unprocessed mRNA sequence, the mature (processed) mRNA sequence, and the amino acid sequence of the protein produced from this sequence. 

     What is gene expression?

      The process by which information from a gene is used to produce a functional gene product (protein or RNA) with a characteristic activity

     At what stage can gene expression be controlled?

      Transcriptional control – change rate at which transcription initiates

      RNA processing – addition of poly-A tail and 5’ cap

      Splicing – splice different ways to make different transcripts which makes different proteins

      Degradation – change rate

      Translation – control initiation

      Protein Activity – presence of kinase or phosphotase

     Which stage is most commonly regulated to control gene expressions?

      Transcriptional control – doesn’t waste energy making RNA or protein

     What are DNA regulatory sites and how can they be used to regulate transcription?

      Transcription regulators bind to the regulatory DNA sequence which acts as a switch to control transcription. The regulatory sites influence the rate of transcription and determine what regulatory protein binds

      You can add an additional transcription regulator that can bind to the regulatory sequences of each gene which combine for efficient initiation of transcription, and the genes will be switched on as a set.

      Cells may want to do this to create different cell types

     What are some post-transcriptional controls used to contribute to gene expression?

   Alternative Splicing – allows different forms of a protein to be made in different tissues

      Riboswitches – short sequences of RNA that change their conformation when bound to small molecules. Each riboswitch recognize a specific small molecule. The conformational change that is driven by the binding of that molecule can regulate gene expression.

      Untranslated regions of mRNA control initiation of translation – repressors inhibit translation initiation by binding to specific RNA sequences in the 5’ untranslated region of the mRNA and keeping the ribosome from finding the first AUG.

      miRNA’s black translation of genes – controls gene expression by base-pairing with specific mRNAs and controlling their stability and translation. Forms complex with RISC proteins.

      Fatty Acids 

      Amino acids