Bio U1

Gene Mutation Definition

Structural changes in genes at the molecular level, the nucleotide base sequence of a gene is changed

Frameshift Mutation

Insertions and deletions shift the reading frame in translation, usually results in non-functioning proteins because all the codons downstream are changed

Point mutation

A single nucleotide is added, deleted, or changed

Amino acid structure

NH2CRHCOOH

CRISPR-Cas 9 3

Precisely cuts DNA at desired sequences, causes mutations in specific genes.

Allows new sequences to be inserted, the natural DNA repair processes take over

eg first human embryo editing experiment in the US corrects gene for heart condition

Polypeptide examples 3

Lysozyme: antimicrobial enzyme produced by animals, found in tears and saliva

Myoglobin: Iron and oxygen binding protein found in cardiac and skeletal muscle tissue

Glucagon: A hormone that increases blood glucose concentration

Water as a medium for metabolism 3

1. Water is a universal solvent, a wide range of hydrophilic molecules dissolve in water, usually charged or polar

2. Cytoplasm is aqueous/water based, most enzymes involved in cell metabolism are dissolved in the cytoplasm, most catalyze reactions in aqueous solutions

3. Cells also rely on hydrophobic molecules that are insolube in water, eg hydrophobic portions of the cell membrane helps maintain cell structure, some membrane proteins contain hydrophobic regions to stay anchored in the membrane.

Insulin 4

Hormone secreted by pancreas, binds to cell receptors to promote glucose uptake, globular protein, soluble in water so can travel through the bloodstream to reach target cells.

mRNA Modification: splicing 3

removal of introns and the splicing together of exons, introns are non-coding DNA sequences within a gene transcribed into RNA, exons are coding DNA sequences within a gene transcribed into RNA

Glycogen 3

Storage molecule in animals, insoluble due to large molecular size, polymer of a-glucose similar to amylopectin but has shorted a-1,4 chains and more cross-links. More branched

Enzyme Catalysis 4

Substrate collides into the active site, enzyme-substrate complex forms due to induced fit binding, enzyme catalyzes reaction (catabolic or anabolic), product released enzyme available for the next reaction

Transcription key features 5

RNA polymerase separates the DNA strands along a gene by breaking hydrogen bonds, RNA nucleotides form complementary base pairs with DNA nucleotides of 1 strand by hydrogen bonding, RNA polymerase moves along the gene 5’ to 3’ and bonds the RNA nucleotides into a single strand, at the end of the gene RNA polymerase releases the RNA, DNA returns to its double-helix structure, DNA is very stable and is unaffected by transcription.

Leading vs lagging strand

Leading strand: DNA polymerase III moves towards the replication fork, continuous.

Lagging strand: DNA polymerase III moves away from the replication fork, discontinuous. DNA polymerase III must return to the replication fork every time to synthesize the lagging strand. Synthesized in fragments called Okazaki fragments, each with a primer. DNA polymerase I replaces primers with DNA nucleotides. DNA ligase joins Okazaki fragments together with phosphodiester bonds.

Translation: Initiation 4

Small subunit of ribosome binds to 5’ end of mRNA, slides 5’ to 3’ to the start codon, initiator tRNA binds to the start codon, large subunit attaches to the small subunit

Translation: Translocation 4

Ribosome moves 5’ to 3’ one codon, tRNA in the P site now has the polypeptide, tRNA in the E site has no amino acid and exits the ribosome, new tRNA enters the A site with an amino acid

Translation: Elongation 2

tRNA enter the A site with an amino acid, peptide bond forms between the amino acids of tRNAs in the A site and P site.

Noncompetitive inhibition 4

Inhibitor binds to an allosteric site of the enzyme, causes active site conformational change and prevents the formation of the enzyme-substrate complex, reversible binding, does not directly compete with substrates so increasing substrate concentration has no effect.

Generation of heat

Energy transfer is not 100% efficient in metabolic reactions, heat energy is generated as a result, animals such as mammals and birds rely on this production of heat to maintain homeostasis.

Glycoproteins 4

Composed of carbohydrate and a protein, participates in cell-cell recognition, acts as markers on the surface of cells, eg diff blood types have different glycoproteins on the surface on their red blood cells.

Polypeptide modification: insulin

pre-proinsulin is synthesized in the rER, contains 4 sections: signal peptide, A chain, B chain, and C peptide, signal peptide is removed by the rER, disulfide bridge forms between the A chain and B chain, now called proinsulin. Proinsulin is transported to the golgi apparatus where the C peptide is removed to produce insulin.

Polysaccharide can act as: 2

Energy storage compounds, starch in plants, glycogen in animals. Because it is relatively easy to add or remove monomers of a-glucose to build or mobilize energy stores. Insoluble due to large molecular size.

Structural compounds, cellulose, straight chains of B-glucose can be grouped in bundles.

Water is polar:

Contains intramolecular polar covalent bonds, O is more electronegative than H, unequal sharing of electrons, regions of partial charge.

Forms intermolecular hydrogen bonds.

Immobilized enzymes

large substrate molecules can be immobilized, enzymes can be immobilized by embedding into a membrane, industrial enzymes can be immobilized onto a surface to improve the efficiency, stability, and reusability of enzymes.

Properties and uses of glucose

Isomers of glucose play an important role in the formation of different structures of polysaccharide,

Glucose is soluble, the presense of many OH groups cause the molecule to be polar, the O in the ring is also slightly negative, the formation of hydrogen bonds between OH and water causes the molecule to dissolve in water, so can be transported in the bloodstream or fluids between cells.

Glucose is stable, due to the cyclic structure, the polysaccharides it forms are also stable, the bonds within glucose are stable covalent bonds

Yields a lot of chemical energy when the covalent bonds are hydrolyzed.

mRNA modification: caps and tails

5’ methyl caps and 3’ poly-A tails are added post-transcription to provide stability against mRNA degradation

Primary structure of proteins

The sequence of amino acids, will affect the folding of protein structure.

Non-conjugated and conjugated proteins

Non-conjugated proteins contain only polypeptide units, conjugated proteins contain both polypeptide and non-polypeptide subunits, eg hemoglobin contains 4 polypeptide chains and a heme group that allows oxygen to bind.

Four major themes of bio

continuity and change, interaction and interdependence, form and function, unity and diversity

Cohesion and adhesion

Cohesion is the attraction between like molecules, adhesion is the attraction between unlike molecules, surface of water resists external force due to cohesion, capillary action, water travelling through a narrow space against an opposing force due to adhesion

Water as a medium for transport

The plasma portion of blood contains water, able to dissolve polar molecules and transport them in the bloodstream, non-polar molecules are insoluble and need to bind to another polar molecule in order to be transported. Plants contain phloem sap to help transport minerals, sucrose, and salt

Non-coding DNA

DNA sequences that do not code for a specific protein but perform other functions. 1. Regulatory regions: Enhancer and silencer regions where activator and repressor proteins bind to help or hinder initiation. 2. introns removed during splicing 3. Promoter and terminator regions 4. Telomeres 5. Gene for tRNA and rRNA

Metabolism

A complex network of interdependent and interacting chemical reactions, occur in living organisms, controlled and catalyzed by enzymes, can be catabolic (digestion) or anabolic (photosynthesis), can be linear pathway (glycolysis) or cyclical pathway (Krebs cycle)

Gel Electrophoresis

Separates DNA fragments based on size, DNA is negatively charged, moves from negative to positive electrode, shorter and smaller move shorter and slower, vice versa

Transcription, initiation

Promoter region: DNA sequence upstream of coding sequence where RNA polymerase binds

Transcription factors: Proteins that help guide RNA polymerase to the promoter

Mechanism based inihibition

Irreversible binding of inhibitor to the active site, active site is chemically changed, permanent loss of enzyme function. eg transpeptidase is an enzyme that joins chains to form the cell wall in bacteria. Penicillin permanently inhibits this enzyme, causes cell wall to weaken and bacteria cell eventually bursts.

Diversity of carbon

can form up to 4 single covalent bonds, can be a combination of single and double bonds with other carbon atoms or non-metallic elements. This is more than most other elements, allows carbon to form diverse compounds upon which life is based. eg unbranched chain, branched chain, ring/cyclic

Polymerase chain reaction

amplifies small amounts of DNA relying on DNA replicationImpo, each cycle doubles the amount of DNA, performed in labs under specific conditions.

Heat, separates the DNA strands by denaturing, Cool, allows primers to anneal, Warm, optimal temperature for heat resistant DNA polymerase called taq to synthesize new strands starting from the primers.

Importance of Complementary base pairing

nucleotide selectivity of DNA polymerase, a high degree of accuracy to maintain genetic integrity, allows for genetic continuity

Water as medium of life

First cells probably originated in water, the survival of cells required a series of chemical reactions called metabolism that occur in water based solutions, water is the medium in which most processes of life take place, found in cytoplasm, blood, tissue fluid

Golgi apparatus structure

stacks of long, membrane-bound sacs called cisternae and vesicles. proteins from ER enters the cis face, travels through cisternae, and exits from trans face. Site of protein processing and secretion, proteins are sorted modified and tagged for their destination to lysosome, plasma membrane, secretion out of the cell.

Infinite varieties of polypeptides

Polypeptides can vary in length, number of amino acids, and order of amino acids. 20 amino acids are used.

Vesicles functions

Store and transport substances. Secretory vesicles, transport out of the cell, transport vesicles, transport within the cell, vacuole, store water in plant cells to provide osmotic pressure, lysosomes and peroxisomes, break down substances.

Structure of ribosomes

Large subunit and small subunit, three internal sites APE, composed of rRNA and proteins. free ribosomes in the cytoplasm synthesize proteins to be used within the cell, bound ribosomes on the rER synthesize proteins to the secreted out of the cell.

Base substituition example

Sickle cell disease, gene for hemoglobin from GAG to GUG, Glu to Val, hemoglobin from globular to fibrous, red blood cell from round to sickle shaped

protein structure basics

polypeptides, polymers of amino acids, peptide bonds hold amino acids together

Globular protein SPADES

round/spherical, functional, irregular amino acid sequence, more sensitive to changes in pH and temp, hemoglobin and insulin, generally soluble in water

Fibrous Protein SPADES

long and narrow, structural, repetitive amino acid sequence, less sensitive to changes in pH and temp, fibrin and collagen, generally insoluble in water.

Chargaff’s data

Falsified the tetranucleotide hypothesis. Not %A=%T=%C=%G, instead %A=%T, %C=%G, but %AT does not equal to %CG

Enzymes lower activation energy how

Binding of substrate and active site weakens the bonds in the substrate, lower the energy required for a reaction to occur.

Initial, final, and energy released are unchanged.

Proteome

The totality of proteins expressed within a cell, organism, or tissue at a certain time. Proteins are constantly being produced and broken down. Unneeded and damaged proteins are broken down by proteasomes, the amino acids are reused in new proteins.

Examples of carbohydrates

monosaccharides: glucose, fructose

Disaccharides: lactose, maltose

polysaccharides: starch, glycogen

Nuclear membrane in cell division

during cell division, nuclear membrane breaks off into vesicles that are free in the cytoplasm, at the end of cell division, the vesicles bind to chromosomes, then fuse together to reform the nuclear membrane around the chromosomes

Cellulose

polymers of B-glucose with B-1,4 glycosidic bonds, B-conformation inverts successive monosaccharides so that a straight chain is formed, parallel polysaccharide chains are cross-linked by hydrogen bonds, this prevents access to water which makes cellulose resistant to hydrolysis, making it an excellent structural compound

Feedback inhibition

the end product of a metabolic pathway will non-competitively inhibit an enzyme in the first few steps of the pathway, this regulates metabolic pathways and occurs when sufficient amounts of end product is produced. Isoleucine is an enzyme found in plants and bacteria, excess isoleucine will non-competitively inhibit an enzyme that converts threonine into the first intermediate

Secondary structure

initial folding of polypeptides into a-helixes and B-pleated sheets. Occurs due to hydrogen bonding between the carboxyl and amine groups of various amino acids. occur in regular positions for stability

Membrane material

the membrane of vesicles is composed of the same material (called lipid bilayer) as cell membrane, golgi apparatus, and endoplasmic reticulum. this allows the forming of vesicles from a membrane, and the fusing of vesicles to a membrane. endocytosis is the uptake of material in vesicles, exocytosis is the release of material in vesicles.

Starch

energy storage molecule in plant, insoluble due to large molecular size, consists two polymers of a-glucose, amylose and amylopectin. amylose contains only a-1,4 glycosidic bonds, amylopectin contains a-1,4 chains that are cross-linked by a-1,6 glycosidic bonds. branched compound

Anabolism vs catabolism

anabolism is the forming of macromolecules, endergonic, condensation reactions, eg protein synthesis, photosynthesis. catabolism is the breaking down of macromolecules, exogonic, hydrolysis reactions, eg glycolysis, digestion

Enzyme substrate specificity

one enzyme catalyzes only one or a few chemical reactions, many different enzymes are required by living organisms, control over metabolism can be exerted through the regulation of enzymes.

Translation: termination

elongation of polypeptide and the translocation of the ribosome continue until the stop codon is reached, then a release factor binds, ribsome disassembles, tRNA, mRNA, and polypeptide are released

Induced fit binding

both the active site and the substrate change shape when binding occurs, this causes the bonds in the substrate to weaken, which lowers the activation energy, the active site returns to its original shape after the reaction

Organelles

discrete subunit structures within cells that perform specific functions.

compartmentalized except ribosomes, which allows organelles to perform specialized functions, concentrate enzymes and metabolites within compartments, separates incompatible biochemical processes, not cytoskeleton, cytoplasm, cell wall

formation of a dipeptide

NH2CRHCONHCRHCOOH + H2O

Causes of mutation

Mutagens: an agent that causes genetic mutation, chemical: mustard gas, dioxin, radiation: UV, x-ray

Errors: replication and repair errors contribute to genetic mutations

Mutation is random

mutation is random and can occur anywhere in the genome, some nucleotide bases are more prone to mutations, eg cytosine can convert to uracil spontaneously and require repair. cells have no deliberate mechanisms for mutating their dna, organisms have different mutation rate due to variation in replication and repair enzymes. environments can affect mutation rates due to different levels of mutagens.

dna as a information molecule

the sequence of nucleotide bases can be copied to produce an identical dna molecule, using complementary base pairing, a shorter sequence of dna called a gene can be transcribed to produce rna which can be translated to produce proteins to carry out specific functions.

DNA can vary in length and sequence across organisms, but the genetic code, or how it is used is consistent across all organisms. DNA can store immense amounts of information very efficiently.

mRNA and tRNA

mRNA contains the code for building a specific protein. mRNA codons, three-nucleotide sequence that corresponds to a specific tRNA and amino acid.

tRNA brings amino acids to ribosomes. tRNA anticodons, three-nucleotide sequence that base pair with a specific mRNA codon

alternative splicing

exons can be spliced together in a number of ways, so that one gene can be used to produce multiple different proteins.

Quatenary structure

interaction between two or more polypeptide chains to form a functional protein. eg collagen has 3, insulin has 2

Genetic material and exceptions

all living things have dna as their genetic material, genetic material is the material that contains information for creating life and is used to pass on such information to the next generation, except virus, which is not considered a living organism, some viruses have rna instead of dna as their genetic material

advantages of compartments in cytoplasm

allows organelles to carry out specialized functions, increase efficiency and effectiveness of chemical reations, allow for control over concentration of metabolites and enzymes, separate incompatible biochemical processes, eg lysosomes enzyme used to digest substances, require low pH, compartmentalized so that healthy organelles aren’t broke down, mitochondria inner membrane highly folded, which leads to high surface area to volume ratio, allows for efficient synthesis of ATP

Evolutionary stable genes

conserved genes: identical or similar DNA sequences across species or groups of species

highly conseved genes: identical or similar DNA sequences across species or groups of species over long periods of evolution

this occured randomly, not likely. the proteins of these genes are so fundamental to life that variations or mutations dont survive and persist

these genes have had low mutation rates

enzymes in DNA replication

DNA helicase: separates the DNA strands by breaking hydrogen bonds, creates the replication fork

DNA primase: adds primers to the strands to indicate starting points for DNA polymerase III

DNA polymerase III: attaches 5’ ends of DNA nucleotides to 3’ ends of the new strands, detects bases that are mispaired and uses 3’ to 5’ exonuclease activity to remove the incorrect

DNA polymerase I: replaces primers with dna nucleotides

DNA ligase: joins Okazaki fragments together with phosphodiseter bonds

hershey and chase experiment

identified dna as the genetic material instead of proteins, radioactive phosphorus found within the bacteria cell, meaning that DNA entered the cell. Radioactive sulfur found outside of the bacteria cell, meaning that proteins did not enter the bacteria.

mutations and genetic variations

mutation is a source of genetic variation in species, mostly harmful or neutral, but can be beneficial, creates variation in individuals within species, this genetic variation is essential for the evolution of the species by natural selection

the genetic code

identifies the corresponding amino acid for each mRNA codon, 64 possible codons, 20 amino acids are used. degeneracy: many codons can code for the same amino acid. Universality: same code used by almost all organisms.

competitive inhibition

inhibitor has similar chemical properties and conformation as the substrate, can bind to and occupy the active site, preventing the formation of enzyme-substrate complex. reversible binding. directly competes with substrate so increasing substrate concentration decreases the effects of the inhibitor

increasing substrate concentration and inhibitor

increasing substrate concentration increases the collision frequency of substrate and active site, increases the reaction rate and enzyme activity, after a certain substrate concentration, all the active sites are fully saturated, reaching a maximum reaction rate.

statins

a drug used to reduce cholesterol levels, competitively inhibits an enzyme used in the cholesterol synthesis pathway

denaturation

denaturation decreases enzyme activity and function, shape of active site is determined during folding of protein, proteins denature at high temp and non-optimal pH, enzyme denatures, protein unfolds, shape of active site changes, substrate cannot bind, loss of enzyme function and activity

enzyme active site

where the substrate binds, composed of only a few amino acids, interactions between amino acids ensure that the active site has the necessary properties for catalysis, has a specific shape and chemical properties that fit a specific substrate

increasing temp and collision

increasing temp increases molecular motion, increases collision frequency and enzyme activity and function, enzyme denatures past the optimal temp

enzymes

globular proteins, biological catalysts that increase the reaction rate of chemical reactions by decreasing the activation energy, not consumed in the reaction, can be reused

structure of nuclear membrane

double membrane, two layers of lipids (lipid bilayer) interspersed with proteins, contains nuclear pores that control the diffusion of mRNA and proteins, outer membrane continuous with ER and sometimes embedded with ribosomes to efficiently synthesize proteins

Clathrin

assembles as a hexagonal lattice, forms a protein coat around budding vesicles during endocytosis, aids in the formation of vesicles by pulling, shaping, and pinching off membrane, provides structure and shape for round vesicles during transport within the cytoplasm, disassembles when the target membrane is reached to allow the vesicle to fuse to target membrane, can be reused

base pairs

purines pair with pyrimidines, purines are adenine and guanine, pyrimidines are cytosine, thymine, and uracil, purines are bigger, provides stability due to equal length of base pairs

Gene knockout

a technique that makes a gene inoperative, learn about its function by its absence. there is a library of genetically engineered gene knockout mice that exist to act as model organisms for research purposes

monosaccharides

single sugar units, source of energy for cells

mutations in somatic cells vs germ cells

somatic cells are all cells in the body except germ cells, mutations in somatic cells can cause various diseases, not passed on to offspring. germ cells are cells that give rise to eggs and sperm, mutation in germ cells can lead to mutations in gametes, can be passed on to offsprings. inherited mutations can have various effects on the offspring

DNA profiling

used in criminal investigation and paternity testing, match suspect profile to dna evidence. individuals have unique genetic markers that contain varying numbers of short tandem repeats. PCR to amplify initial dna sample, enzymes used to cut dna at specific dna markers to create dna fragments, gel electrophoresis to separate the fragments by mass/size to create dna profile

centrifugation and cell fractionation

a technique that spins solutions at high speed to separate components by density. separation of cell components, allowed for the study of functions of individual organelles. centrifuge, ultracentrifuge, cell fractionation

collagen

most abundant protein in body, found in hair, bones, connective tissues. fibrous protein, insoluble in water so can provide structural strength, support, and stability

non-polar and polar amino acids

non-polar amino acids are hydrophobic, bond with other non-polar amino acids, fold towards the interior of polypeptide to avoid polar molecules. polar amino acids are hydrophilic, bond with other polar amino acids, orient towards to exterior of the polypeptide. polarity of amino acids affect the tertiary structure of proteins

process of dna replication

process of creating identical copies of dna molecules, semi-conservative, relies on complementary pairing

intracellular reactions and extracellular

intracellular: occur within the cell, controlled and catalyzed by enzymes synthesized by free ribosomes, eg glycolysis, krebs sycle. extracellular: occur outside of cell, controlled and catalyzed by enzymes synthesized by bound ribosomes, eg digestion in stomach and small intestine

nucleosomes

dna wrapped around histone proteins, 8 histone proteins in core, octamer. one linker histone attached to linker dna, condenses dna to fit into nuclei, found in eukaryotic cells, not prokaryotic

tertiary structure

further folding of polypeptides into 3D conformation, due to interaction between the R groups of various amino acids. disulfide bridge between a pair of cysteins, ionic bonds between carboxylic and amine groups, covalent bonds, hydrophobic reactions

cytoskeleton

microtubules and microfilaments, provide structure to the cell

plasma membrane

selectively permeable, controls transport in and out

cell wall

protects cell and provides structure