BIOL1030 FINAL

where is genetic information stored?

the genes

what does genetic information encode for?

proteins that provide structure and do much of the work of the cell

what are nucleotides?

building blocks of nucleic acids
purines → adenine, guanine
pyridamines → thymine, cytosine

what is a phosphodiester bond?

the C-O-P-O-C linkage connecting two nucleotides

what are the benefits of a phosphodiester bond?

the linkage is stable and can withstand changes in pH and temperature that would break weaker bonds

how many hydrogen bonds hold together A-T and G-C?

A-T → two hydrogen bonds
C-G → three hydrogen bonds

what happens to the two strands of the parental molecule in DNA replication?

they separate, each parental strand serves as a template for the synthesis of a new daughter strand

what occurs after conservative DNA replication?

the new DNA duplex consists of two newly synthesized daughter strands, leaving the parental duplex intact

what occurs after semiconservative DNA replication?

the new DNA duplex is made of one old strand (parental) and one new strand (daughter)

what occurs in DNA replication nucleotide wise?

1. incoming nucleotides are accepted if they correctly base pair with the template

2. the 3’ -OH of the growing strand attacks the high-energy phosphate bond of the incoming nucleotide to initiate the synthesis reaction

what are okazaki fragments?

short pieces of DNA nucleotides that result from the parental strand being unwound and new pieces being elongated

how is the leading strand synthesized (continous replication)?

3’ end in pointing towards the replication fork, it is synthesized as one long continuous polymer as the parental strand is unwound

how is the lagging strand synthesized (discontinuous replication)?

3’ end pointing away from the replication fork, it is synthesized in short, discontinuous pieces

what is the result of discontinuous replication?

all new DNA strands have a short stretch of RNA at their 5’ end, with the lagging strand have one RNA piece on each fragment

how does DNA proofreading work?

1. new nucleotides come into line and are temporarily held in place by hydrogen bonds between the base in the new nucleotide and the base across in the template strand

2. if improper hydrogen bonds form, DNA polymerase can detect the mispairing

3. if an error is detected, DNA polymerase activates a cleavage function, removing the incorrect nucleotide and inserting the correct one in its place

what is the rate DNA replication occurs in eukaryotes?

50 nucleotides/second

what is the origin of replication?

each point where DNA replication is initiated (happens in many places at once)

what is a replication bubble?

the opening of the double helix at each origin of replication with a replication fork on each side

what is the path of replication?

replication starts at the origin and moves around the circular chromosome in both directions

how do RNA primers work on the leading strand?

1. only one primer is required to start synthesis

2. replication continues to the end

3. strand is replaced by DNA when the last fragment of the lagging strand at the opposite fork of the replication bubbles catch up to it

how do RNA primers work on the lagging strand?

1. multiple RNA primers are required

2. the final primer is added about 100 nucleotides from the 3’ end of the template

3. when it is removed, the new daughter strand is shortened by about 100 nucleotides

what is a telomere?

a repeating sequence that caps each end of a eukaryotic chromosome

what is the function of a telomere?

a mechanism to solve the problem of shortened ends

what does the telomere consist of in humans?

5’-TTAGGG-3’, repeated roughly 1500-3000 times

what is telomerase?

an enzyme that replaces missing nucleotides (fully active in germ cells, almost inactive in adult somatic cells)

what are the three components of the cell theory?

1. all living things are made up of cells

2. a cell is the basic unit of structure for living organisms

3. all cells come from pre-existing cells

how do prokaryotes an eukaryotes differ structurally?

prokaryotes → small, simple, no membrane-bound organelles, circular DNA

eukaryotes → large, complex, nucleus and other membrane-bound organelles, linear and circular DNA

what is cell division?

the process by which cells make more cells

why does cell division occur?

1. growth

2. cell replacement

3. healing

4. reproduction

what are the three types of cell division?

1. prokaryotes → binary fission

2. eukaryotes → mitosis

3. eukaryotic gametes → meiosis

what are the two stages of cell division for eukaryotes?

1. M phase → mitosis, parent cell divides into two daughter cells

2. interphase → 10-14 hours between two successive M phases

what are karyotypes?

portrait formed by the number and shapes of chromosomes representative of a species

what are homologous chromosomes?

chromosomes that carry the same set of genes. one from the mother and one from the father

what two things are mitotic cell divisions (followed by cytokinesis) the basis for?

1. asexual reproduction in single-celled eukaryotes

2. development and maintenance of cells, tissues, and organs in multi-cellular eukaryotes

what are centrosomes?

microtubule-organizing centers for animal cells

what is the mitotic spindle?

made of mostly microtubules that pull the chromosomes apart into separate daughter cells

what occurs during mitotic prophase?

1. chromosomes condense

2. centrosomes radiate microtubules and migrate to opposite poles

3. outside the nucleus, the cell assembles the mitotic spindle

what occurs during mitotic prometaphase?

1. nuclear membrane beaks down

2. microtubules of the mitotic spindle attach to the chromosomes

3. microtubules grow and shrink to explore the region that was once the nucleus

4. ends of microtubules encounter chromosomes and attatch at their centromeres

what occurs during mitotic metaphase?

1. chromosomes align in the center of the cell (roughly equidistant from both of the spindle poles)

what occurs during mitotic anaphase?

1. sister chromatids separate and travel to opposite poles

2. the centromere holding a pair together divides, allowing the two sister chromatids to separate from each other

3. sister chromatids become individual chromosomes

what occurs during mitotic telophase?

1. a complete set of chromosomes arrive at a spindle pole

2. cystolic changes occur in preparation for the cells division

3. the microtubules of the mitotic spindle break down and disappear

4. the nuclear envelope begins to re-form around each set of chromosomes, creating two new nuclei

5. once nuclear envelope is re-formed, the chromosomes decondense and become less visible

6. mitosis is over

what occurs during mitotic cytokinesis?

the parent cell divides into two daughter cells

what occurs during mitotic cytokinesis in animal cells?

1. a ring of actin filaments (contractile rings) forms against the inner face of the cell membrane

2. the ring contracts, pinching the cytoplasm of the cell and dividing it in two

what occurs during mitotic cytokinesis in plant cells?

1. during telophase, the plant cells form a structure called the phragmoplast in the middle of the cell

2. phragmoplast consists of overlapping microtubules that guide vesicles containing cell-wall components to the middle of the cell

3. vesicles fuse to form a new cell wall, called the cell plate, in the middle of the dividing cell

4. once the cell plate is large enough, it fuses with the original cell wall at the perimeter of the cell and cytokinesis is complete

what are kinetochores?

two protein complexes with one on each side of the centromere

what is the function of kinetochores?

1. form the site of attachment for one of the two sister chromatids and a single microtubule

2. this arrangement ensures that each sister chromatid is attached to a microtubule radiating from one of the poles of the cell

what does the central dogma state?

1. DNA is transcribed into RNA and that RNA is translated into protein

2. DNA is the template for RNA

where do transcription and translation occur in prokaryotes vs eukaryotes?

prokaryotes → both t&t in the cytoplasm

eukaryotes → transcription in nucleus, translation in the cytoplasm

what occurs during the (conceptual) transcription process?

1. a region of DNA unwinds, one strand is used as a template for the RNA transcript, the other is the non-template

2. the adenines in the template pair with uracil instead of thymine

3. RNA polymerase in the catalyst enzyme

4. the new strand grows in the 5’-3’ direction, meaning the template DNA strand is in the 3’-5’ direction

what are the stages of the transcription process?

1. initiation

2. elongation

3. termination

what occurs during stage one of transcription?

1. RNA polymerase and associated proteins bind to the DNA duplex at promoter sequences

2. the DNA strands are separated

3. transcription actually begins

what occurs during stage two of transcription?

1. successive nucleotides are added to the 3’ end of the growing RNA transcript

2. RNA polymerase moves along the template strand in the 3’-5’ direction

what occurs during stage three of transcription?

1. RNA polymerase encounters a sequence (terminator) in the template strand that causes transcription to stop

2. the RNA transcript is released

how big is the transcription bubble?

14 base pairs in length

what occurs during the polymerization reaction?

1. incoming ribonucleotides are accepted if they correctly base pair with the template DNA

2. the 3’ -OH of the growing strand attacks the high-energy phosphate bond of the incoming ribonucleotide, providing the energy to drive the reaction

3. the two phosphates of the incoming ribonucleotide are released as pyrophosphate

what are the four differences between DNA and RNA?

DNA → deoxyribose sugar, thymine, molecules are usually double stranded, molecules are typically very long

RNA → ribose sugar, uracil, molecules are usually single stranded, molecules are typically much shorter

what are the functions of RNA polymerase in prokaryotes?

1. able to separate DNA

2. allows an RNA-DNA duplex to form

3. elongate the transcript nucleotide by nucleotide

4. release the finished transcript

5. restores the original DNA double helix

what is the barrier between transcription and translation in eukaryotic primary transcript?

the nuclear membrane

what two types of chemical modifications occur before mRNA is translated in eukaryotic primary transcript?

1. the addition of a 5’ cap consisting of 7-methylguanosine to the 5’ end of the primary transcript (ribosome would not recognize mRNA without this)

2. the addition of 250 consecutive adenines to the 3’ end of the mRNA, called the poly(A) tail (helps stabilize the RNA transcript)

what occurs during RNA splicing?

the excision of certain sequences known as introns, leaving the exons intact

what occurs during alternative splicing?

primary transcripts from the same gene can be sliced in different ways to yield mRNAs and ultimately different protein products

what is the full RNA splicing process?

1. specific sequences near the ends of the intron undergo base pairing with RNA molecules in the spliceosome and are brought to close proximity

2. the spliceosome enables a reaction that cuts one end of the intron and connects it to a nucleotide near the other, forming a loop (lariat)

3. the exon one one end of the intron is brought close to the exon at the other end

4. the exons are joined, the introns are released, and the lariat is broken down

what are digestive enzymes and their purpose?

lipase, pepsin → help in food by catabolizing nutriens into monomeric units

what are transport proteins and their purpose?

hemoglobin, albumin → carry substances in the blood or lymph throughout the body

what are structural proteins and their purpose?

actin, tubulin, keratin → construct structures like the cytoskeleton

what are hormone proteins and their purpose?

insulin, thyroxine → coordinate different body systems activties

what are defense proteins and their purpose?

immunoglobins → protect body from foreign pathogens

what are contractile proteins and their purpose?

myosin, actin → effect muscle contraction

what are storage proteins and thier purpose?

legume storage proteins → provide nourishment in early embryo and seedling development

what is an R group?

functional group or molecule that is attached to a core structure (usually carbon chain or ring)

what characteristics are amino acids in R groups grouped by?

1. how they interact with water (hydrophilic or hydrophobic)

2. basic or acidic

3. polar or nonpolar

how do hydrophobic amino acids operate (alanine, valine)?

1. R groups aggregate together away from the water

2. bonds are stabilized by weak van der waals forces, which create temporary charges

3. hydrophobic R groups are attracted to each other

4. tend to be buried in the interior of folded proteins

how do hydrophilic amino acids operate (asparagine, glutamine)?

1. polar molecules contain electronegative elements (N and or O)

2. unequal charge allows the R groups to interact with each other or with water molecules via hydrogen bonding

3. basic +, acidic -

4. charged groups can form ionic bonds

5. interactions between polar R groups cause the protein to fold in such a way that they are located toward the outside of the protein

how does the special amino acid glycine operate?

1. R group is hydrogen, central carbon atom is bonded to two H atoms

2. nonpolar and small, small size of H side chain allows for freer rotation around C-N bond

3. increases the flexibility of the polypeptide backbone

how does the special amino acid cysteine operate?

1. contains a -SH group

2. two cysteines together can form S-S disulfide bonds

3. the resulting cross-bridges can connect different parts of the same protein or different proteins

where do covalent bonds form and what are they called?

between amino acid monomers, called peptide bonds

how do polypeptides form?

1. the carboxyl group of one amino acid reacts with the amnio group of another amino acid

2. a molecule of water is released via a dehydration synthesis reaction

3. the free amino group is at the amino end of the peptide, and the carboxyl group is at the carboxyl end

4. this results in a polymer of amino acids connected by peptide bonds (a polypeptide/protein)

what is a primary structure?

the sequence of amino acids

what is a secondary structure?

results from interactions of nearby amino acids, specifically a result of hydrogen bonding in polypeptide backbone

what is a tertiary structure?

3D shape of a polypeptide (usually made of several secondary structure elements)

what are tertiary structures determined by?

1. the spatial distribution of the hydrophilic and hydrophobic R groups along the molecule

2. the chemical bonds and interactions that form between the R groups

what do tertiary structures determine?

1. proteins function

2. contours and distributions of charge on the outside of the molecule

3. presence of pockets that might bind with smaller molecules on the inside

what is a quaternary structure?

consists of two identical polypeptide subunits resulting from their interactions

what subunits does hemoglobin contain?

four subunits, two alpha, two beta

what does a protein lose if it loses its structure?

function

what are the four main protein functions?

1. structural support

2. membrane channels

3. enzymes

4. signaling

what are ribosomes?

protein factories where translocation takes place

what is the structure of ribosomes and what do they consist of?

1. complex structure of RNA and protein that bond with mRNA

2. consist of a small subunit and a large subunit

3. the large subunit includes three binding sites for tRNA, A (aminoacyl), P (peptidyl), and E (exit) sites

4. eukaryotic ribosomes are larger than prokaryotic ones

what are codons?

each group of three adjacent nucleotides coding for a single amino acid

what is a reading frame?

where the ribosome begins reading the sequence of nucleotides

what does the ribosome determine?

the correct reading frame for the codons

what makes tRNA charged?

if the amino acid is attached, it is charged

what is tRNA synthetases?

1. enzymes called aminoacyl tRNA synthetases connect specific amino acids to specific tRNA molecules

2. very accurate, rarely attach to the wrong amino acid

3. enzyme attaches the amino acid to the 3’ end of the tRNA

how do codon-anticodon interactions work?

1. the first base in the codon in mRNA pairs with the last base in the anticodon because they must be antiparallel

2. most codons specify an amino acid according to a genetic code

3. the codon that initiates the process of translation is AUG, which corresponds to the amino acid methionine

what are the three stop codons?

UAA, UAG, UGA

how does initiation work in eukaryotes?

initiation factors bind to the 5’ cap of the mRNA, so the 5’ cap initiates translation

how does initiation work in prokaryotes?

1. shine-delgaro sequence, since there is no 5’ cap

2. initiation factors recruit the small ribosomal subunit and tRNA and scan the mRNA for an AUG code

3. when the complex reaches an AUG, the large ribosomal subunit joins and initation factors are released

what is the translation process summary?

1. initiation → the initiator AUG codon is recognized and Met is established as the first amino acid in the new polypeptide chain

2. elongation → amino acids are added to the growing chain

3. termination → the addition of amino acid stops, and the polypeptide chain is released from the ribosome

what is a mutation?

any heritable change in the genetic material

what does ‘heritable’ mean in terms of a mutation?

mutation is stable/not detrimental and therefore is passed on through cell division