Bio 161 Exam #2

Carbohydrate monomers

Monosachharides

Carbohydrates

Saccharides

Mono, di, oligo, poly-saccharide

Mono-a simple sugar monomer

Di-two linked monosaccharides

Oligo-multiple linked monosaccharides

Poly-many monosaccharides, linked by covalent bonds into a polymer

Sugar bonds

Glycosidic linkages

-A covalent bond between a monosaccharide and another sugar or another molecule

Linking carbohydrates

-Linking carbohydrate monomers to for a polymer occurs through a condensation (dehydration) reaction, broken by hydrolysis reactions

Energy storage: carbohydrates

-Gylcogen (animals) and the starch called amylpectin (plants) are branched polymers of glucose, used to store energy

-When energy is needed, hydrolysis can release glucose molecules to be broken down during metabolism

Structural support: carbohydrates

-Cellulose is an unbranched polymer of glucose, used for structural support, for example in cell walls

-The orientation of the glycosidic linkages creates a straight polymer and allows many opportunities for H-bonding between different polymers of cellulose, creating a stable fiber

Carbohydrates can be modified to alter function

-Occurs when functional groups are attached to a monomer, in these examples, a phosphate group (or two) is attached to a monosaccharide

Enzyme ending

Ase

Sugar ending

Ose

Macromolecules

-Proteins, carbohydrates, lipids and nucleic acids

-A macromolecule’s shape determines its biological function

-Many macromolecules are polymers, long “chains” of repeating molecular units

Protein functions

-Protection

-Hormonal

-Contractile

-Receptor

-Structural

-Storage

-Enzyme

-Transport

Amino Acid Regions

Nonvariable: amino group, central carbon, carboxylic (acidic) group

Variable: R-group/side chain

Amino acids in aqueous (water)

-At neutral ph, amine group acts as a base and becomes NH3+ and carboxyl group acts as an acid and becomes COO-

Different amino acid side groups

-Charged

-Polar

-Nonpolar

-”Special cases" - H, ch2-sh

Protein ends

-N terminus and C terminus

Polymers formed by.. broken by..

Condensation/dehydration, hydrolysis

Protein primary structure

-the order or amino acids in the polypeptide formed by covalent bonds between amino acids

Protein secondary structure

-formed by hydrogen bonds between the non-variable parts of non-adjacent amino acids

Protein tertiary structure

determined by

-interactions and bonds between side chains (R groups) of different amino acids within one polypeptide

-interactions and bonds between side chains and the environment

Cysteine/disulfide bridge

-two cysteines can form a strong covalent S-S bond, called a “disulfide bridge”

Protein quaternary structure

-determined by interactions and bonds between side chains (R groups) of different amino acids in different polypeptides

-the individual polypeptide chains are called subunits, and often the multi-subunit protein complex only functions once the subunits come together

Protein are..

dynamic, not rigid

Enzymes

-enzymes are usually proteins

-speed up reactions

-within enzyme’s shape, there is a region called the active site, where reactants (substrates) bind

-the folding of the protein and the R-groups in the active sit allow it to bind to a specific substrate

-once substrates are bound, the enzyme catalyzes the reaction and turns substrates into products

-they are catalysts, substances that speed chemical reactions without being consumed in the reaction

Induced fit

-Induced fit model of enzyme-substrate binding

-once an enzyme binds to substrate it undergoes a shape change that leads to a more optimal binding, for efficient catalysis

-most enzymes change shape upon binding their substrates, this induced fit then allows the reaction to proceed

Enzymes can help substrates (reagents) interact

-orient two substrates next to each other so they can interact

-place the substrate under physical strain, weakening its covalent bonds

-temporarily transfer an electrical charge to the substrate, promoting a reaction

Nucleotides

-monomers of nucleic acids

-phosphate, base, sugar

-ribose in RNA, deoxyribose in DNA (lacking oxygen @ C2)

-essential for signaling and energy

Bonds for nucleic acids

-phosphodiester bonds

Bonds for amino acids

peptide bonds

Two nucleic acid strands can..

base pair to become double-stranded and anti-parallel

Bond between polymers of nucleic acid

-hydrogen bonds form between two polymers

DNA strands base pair, forming

a double helix

Lipids

-primarily hydrocarbons

-mostly hydrophobic

Fats

-fatty acids are a “building block” - mono-, di- and triglycerides polar fats

Steroids

-include 4 fused hydrocarbon rings

Fatty acids

-lipids with a hydrocarbon chain and a terminal carboxyl group

Fatty acids are an example of

amphipathic molecule: hydrophilic at one end and hydrophobic at the other

Fatty acids joined to one glycerol molecule via

covalent ester linkages

Transcription general

-one nucleic acid strand contains all of the information needed to build the complementary strand

-all polymerase enzymes that synthesize new strands of DNA or RNA follow the same pattern: they can only add nucleotides onto 3 prime ends

Nucleic acid synthesis

-new nucleic acid polymer (strand) is made using another polymer (strand) as a template

-the new strand will be antiparallel and complementary to the template strand

-nucleic acid synthesis requires a free 3 prime hydroxyl group (OH) on the end of the growing strand

Nucleic acid steps

1. during synthesis the 3 prime OH group of the last nucleotide on the strand will bond to the “inner” phosphate of the incoming NTP or dNTP

2. two phosphates are cleaved off

3. a phosphodiester bond is formed between the nucleotides..

4. …and phosphate ions are released

nucleic acid synthesis rules

1. two strands of nucleic acid must be anti-parallel in order to base pair

2. new nucleotides can only be added to a 3 prime OH group, thus we say that DNA and RNA are built in the 5 prime to 3 prime direction

3. the enzyme making the new strand of DNA or RNA determines which nucleotide to insert by reading the existing template strand, thus the strands are complementary to each other

Flow of genetic information/central dogma

DNA

sequence of nucleotides in DNA of a gene

to

RNA

sequence of nucleotides complementary to the gene’s DNA code

to

Protein

sequence of amino acids, determines a protein’s identity, structure, and function

Genome

-all the DNA of an organism

Chromosome

-long DNA molecule coiled around proteins and compacted

Gene

-segment of DNA that codes for a product

-genes are sequences of DNA nucleotides that encode RNAS

mRNA

-serve the function of coding for a protein

Non-coding RNAS

-serve their function as RNAS and are not made into protein

Transcription

-creates an RNA whose nucleotides are complementary to the DNA template strand of a gene

-occurs in the nucleus of eukaryotes

-carried out by the enzyme RNA polymerase

Parts of a gene

1. promoter: DNA region where RNA polymerase initially binds. NOT copied into RNA

2. initiation site: where transcription begins, the first DNA nucleotide copied into RNA

3. transcribed region: DNA region with nucleotides that are copied RNA

4. termination site: where transcription ends, the signal for RNA polymerase to cease copying the DNA

Transcription Initiation

-transcription initiates when the RNA polymerase protein complex binds to the promoter DNA region in front of a gene

-the RNA polymerase complex contains a helicase that breaks the hydrogen bonds between DNA strands, to expose the template strand, a “transcription bubble” forms

-RNA polymerase begins to synthesize an RNA that is complementary (and anti-parallel) to the DNA template strand

-transcription will begin at the transcription initiation site

Transcription elongation

-RNA polymerase moves along the template DNA strand, synthesizing a complementary RNA strand, using ribonucleotide triphosphates)

-the 5 prime end of the RNA is produced first; new nucleotides are added onto the 3 prime OH of the preceeding nucleotide as RNA polymerase catalyzes the formation of phosphodiester bonds

Transcription termination

-when RNA polymerase reaches the termination site, it falls off the DNA and the new RNA is released

-in eukaryotes, that RNA will then be processed in the nucleus before being exported to the cytoplasm

-another RNA polymerase molecule can begin transcribing the same gene before the first RNA polymerase finishes. thus, many RNA transcripts are produced from a single gene

Transcription: synthesizing RNA

1. two strands of nucleic acid must be anti-parallel in order to base pair

2. new nucleotides can only be added to a 3 prime oh group. the new rna is synthesized from its 5 prime end to its 3 prime end last

3. RNA polymerase determines which nucleotide to insert by reading the existing DNA template strand, moving from its 3 prime end to its 5 prime end. thus, the strands are complementary to each other

Transcript processing in eukaryotes

-the pre-mRNA undergoes processing to become mature mRNA

-5 prime cap is added

-3 prime tail of many adenine nucleotides is added

-splicing removes introns

the 5 prime cap and 3 prime tail

-stabilize the mRNA

-facilitate mRNA export from nucleus

RNA splicing

-sequences at exon/intron boundaries are bound by snRNPS

-snRNP (small nuclear ribonucleoprotein) particles are complexes of proteins + snRNAS (an example of a non-coding RNA)

-several snRNPS form the splicesome

-the splicesome removes introns, which are degraded

-exons are ligated together by splicesome

Transcription occurs in the

nucleus

Mature mRNA is exported from the..

nucleus to the cytoplasm, through nuclear pores

Translation (mRNA to protein) occurs in

cytoplasm within the ribosome, a huge complex of proteins and ribosomal RNAs

Translation requires

-mRNA

-tRNAS that have the appropriate amino acid attached

-ribosomes

-release factor proteins

Codon

-three mRNA nucleotides code for one amino acids

-the ribosome reads codons one at a time, in a non-overlapping way

Reading frame

-ribosome “chooses” the reading frame by scanning the transcript from the 5 prime end until it finds the first start codon, 5 prime AUG-3 prime. it begins translation with that codon, which sets the reading frame

start/stop codons

-within the mRNA, there are translation start and stop codons, that don’t have anything to do with transcription. the only complex that recognizes them is the ribosome (RNA polymerase does not recognize these sequences in DNA)

-mRNAs have 5 prime and 3 prime untranslated regions: parts that are transcribed but not translated

-the first AUG codon is the start codon and specifies adding methionine to the protein. other AUGS are treated as normal codons, and proteins can have multiple methionines within them

-the stop codons do not encode amino acids; they tell the ribosome to release the polypetide

tRNA

-transfer RNAS translate between the language of codons and the languae of amino acids

-each tRNA carries an amino acid at one end, and binds to MRNA at its other end

Translation: initiation

-small ribosomal subunit attaches to the 5 prime cap of mRNA

-small subunit scans mRNA base-by-base for the first AUG

-once the tRNA and mRNA base pair, the large subunit binds and the reading frame is set

Translation: elongation

-cytoplasm contains a pool of every possible tRNA

-after the ribosome fully assembles, charged tRNAS drift in and out of the A site of the ribosome until the correct tRNA stably bonds with the mRNA by H-bonding between complementary base pairs

-peptide bonds form between amino acids

-the new peptide bond is formed by the ribosome’s peptidyl transferase activity

-the ribosome catalyzes a condensation reaction

-after formation of peptide bond, first tRNA releases its amino acid

-ribosome translocates along the mRNA: the first tRNA is shifted from the P site to the E site and disassociates from the ribiosome

-the second tRNA is shifted from the A site to the P site

-a charged, tRNA, complementary to the next codon, enters the A site

-peptide bond is formed, ribosome transolactes

-process repeats for each amino acid to the polypetide chain

Translation: termination

-stop codons do not encode amino acids

-instead, a release factor binds

tRNA binding sites

-A site (aminoacyl tRNA): charged tRNA anticodon binds mRNA

-P site (peptidyl tRNA) RNA adds amino acid to the polypetide chain

E site (exit site): tRNA (without amino acid) binds before being released from ribosome