Biochem - Exam 1 and 2 Flashcards
What are the main types of chemical bonding?
Covalent
Non-Covalent:
- Ionic
- Hydrogen
- Van der Waals attractions
- Hydrophobic Interactions, i.e. protein folding
What are the four main molecule types in living things (list both monomers and the polymers they form)?
Sugars = polysaccharides AAs = protein FAs = fats, lipids, membranes Nucleotides = nucleic acidss
What is the structure of a….
- Hydroxyl
- Carboxyl
- Ketone
- Methyl
- Amino
- Aldehyde
- Sulfhydryl
- Disulfide
- Phosphate
- Hydroxyl = -OH
- Carboxyl = -COOH
- Ketone = =O
- Methyl = -CH3
- Amino = -NH2
- Aldehyde = =O + H
- Sulfhydryl = -SH
- Disulfide = -S-S-
- Phosphate = PO4 (one =)
How many cells do we have and how big are they?
Humans have around 10^14 cells with varying sizes.
Most cells in an organism have a diameter less than 30μm.
White blood cells =±3μm long and nerve cells up to 1m.
Why does the number of cells in an organism increase as the organism gets larger, but not the size of individual cells?
Maintenance of SA:V
To allow adequate exchange of nutrients, ions, waste, gases etc
What are the defining features of Prokaryotes?
- No nucleus
- No membrane bound organelles
- cell division by fission (not mitosis) – rapid growth and reproduction
- Size range: 1-10μm
What are the defining features of Eukaryotes?
- Nucleus and nucleolus
- Membrane-bound organelles
- Cell division by mitosis or meiosis
- Bigger than prokaryotes
- Many are multicellular (i.e. animals and plants)
What are the defining features of viruses?
- These are not cells.
- The nucleocapsid is comprised of an outer protein coat (capsid) and an inner core of nucleic acids
- Tail
- End Plate
- Tail Fibers
What type of reaction often forms polymers?
condensation reactions (opposite of hydrolysis where water is added).
What are the main chemical features of carbs?
Monomer – monosaccharides
Basic unit – CnH2nOn, where n is between 3-8.
Polority – Polar, therefore water soluble
Main Functional Groups – Aldehyde, Ketone
Bonds - glycosdic
What are Glycosidic bonds and in what macromolecule are they relevant?
Glycosidic bonds are covalent bonds forms between monosaccharides from a condensation reaction. I.e. glucose. An O atom bonds to carbons on each monosaccharide.
What molecules are used for storage?
Starch – plant cell and seed storage
Cellulose – structural sugar in plants
Glycogen – animal cell storage – 1000s of glucose monomers
What causes lactose intolerance?
Lack of lactase – the enzyme that breaks down lactose into glucose and galactose. Bacteria multiply in the undigested milk sugar in the gut which results in gas, cramps, bloating.
Can be seen in children after one month if they pull legs up in pain after 1-2 hours after feeding screaming.
Primary Lactose Intolerance – remove lactose from diet
Secondary lactose intolerance – following bad GI infection, can last months.
What are the chemical properties of lipids?
Monomer – fatty acids
Polority – non-polar, therefore not water soluble
Bonds – ester bonds
What are the main types of lipids?
3 main types: Fats & oils & waxes, phospholipids, steroids.
What is a triaglyceride?
Triaglyceroles = glycerol + 3xfatty acids
Saturated has higher mpt.
Formed when three fatty acids join to a glycerol linked by ester bonds.
What is a phospholipid?
Contain N and P as well as C,H,O.
One fatty acid is replaced by phosphate, which is polar and therefore water soluble. Phospholipids are therefore amphipathic.
Often the phosphate group is attached to another functional N-containing group.
What are steroids?
Regulatory molecules composed of interconnected rings.
Non-polar, therefore hydrophobic
Examples – vitamins, hormones, cholesterol
What is rickets?
Disorder involving lipids (cholesterol and Vitamin D (cholecalciferol). At age one year, will be underweight with soft, pliable bones (inadequate calcification). Receive vitamin D treatment.
In adults – osteomalacia.
What are the chemical properties of proteins?
Bonds – peptide bonds
Formation - condensation
20 Amino acids
Central carbon attached to an H, amino group, carbocylic acid
They are chiral with L and D forms. Our proteins are L.
Always write from amino terminal to carboxyl.
What are the ionic forms of proteins?
- In acidic pH: Cation (NH3+)
- In neutral pH: Zwitterion (NH3+ and COO-)
- In Basic pH: Anion (COO-)
What is a peptide bond?
- C(=O) - N(H) -
What are the structures of gly, ala, phe and tyr?
Glycine - R = H
Alanine - R = CH3
Phenylalanine - R = CH2-@
Tyrosine - R = CH2-@-OH
What are the structure levels of protein?
Primary - AA sequence
Secondary - repeating patterns - helixes, pleated sheets and random coil.
Tertiary - Overall confirmation - Driven by hydrophobic forces and disulfide bonds.
Quaternary - Interaction of subunits
What are the effects of a change in AA sequence on protein?
A change in it’s primary structure can have: -
- no effect (genetic variation within species),
- little effect (interspecies variation), or
- enormous effect (i.e. disease causing mutation such as sickle cell anaemia which only has a single amino acid change).
What is a simple protein?
A protein containing only AA’s and no other chemical groups
What is a conjugated protein?
A protein containing AA’s AND other chemical components. The non-AA part is called a prosthetic group.
Examples of prosthetic groups:
Lipoproteins (contain lipids)
Metalloproteins (contain a specific metal, such as myoglobin which contains iron).
Glycoproteins (contain sugar groups)
What is a denatured protein?
“Native” proteins are stabilized in 3D by secondary, tertiary and quaternary structures. If it’s conformation is altered/destroyed, the protein is denatured and won’t function normally. Denaturing does not alter the primary structure, and can sometimes be reversible.
What are some of the main functional proteins?
- Transport protein
- Nutrient and Storage Proteins
- Movement (motile) proteins
- Defense proteins
- Regulatory Proteins
- Structural Proteins – support cell and organ shape
- Enzymes
- Others – i.e. anti freeze proteins.
What are the main components/features of a cell membrane?
- Phospholipid bilayer with peripheral proteins (attached loosely) and integral proteins (tansmembrane proteins).
- ‘Fluid mosaic’ – lipid (and some protein) molecules can move laterally.
- Selectively Permeable. H20, O2 and CO2 cross freely, while ions and other polar molecules must move through selective pores.
What effects do saturated or unsaturated fatty acids have on the cell membrane?
Unsaturated fats kink at the double bond, and have greater fluidity. Whereas Saturday fatty acids give close packing.
Cholesterol enhances order and rigidity, and stabilizes the straight chain arrangement of saturated fatty acids.
What is the nucleus and it’s main characteristics?
Location of main genome, site of most DNA/RNA synthesis. It is surrounded by a double membrane – the nuclear envelope, which is continuous with the ER and is perforated by nuclear pores.
- Also selectively permeable
- Usually contains nucleoli – which is the site of rRNA synthesis and assembly of ribosomal subunits.
What is the cytoskeleton and it’s main characteristics?
It gives and maintains structure and shape of the cell, and governs its internal organization. It is essential in cell division.
It’s comprised of:
a) microtubules
b) microfilaments.
What are ribosomes and their main characteristics?
- Ribosomes are the site of protein synthesis.
- They may be free in the cytosol of attach to ER
- They are NOT organelles
What is mitochondria and it’s main characteristics?
- Site of energy-yielding oxidation reactions – cellular respiration.
- It has its own DNA
- Inner membrane is folded into cristae
What is the endoplasmic reticulum and it’s main characteristics?
- Continuous membrane throughout cell
- Network of sacs (cisternae)
- Rough ER is where polypeptides are synthesized
- Smooth ER lacks ribosomes, and is where lipids are synthesized
- materials are shuffled from one part of cell to another
- It involves biosynthesis, packaging and secretion.
What is the golgi apparatus and it’s main characteristics?
Series of flattened membranes (stacks of cisternae) involved in protein secretion & sugar linkage.
What are Lysosomes and their main characteristics?
- Membrane bound organelles containing hydrolytic enzymes
- They digest unwanted materials in the cytoplasm
What are Peroxisomes?
Contain enzymes for H2O2 metabolism
What are endosomes?
Contains endocytosed substances
How do enzymes work?
Every chemical has a certain amount of Gibbs free energy, and chemical reactions involve a change of free energy (which is the energy available to do work). Exergonic (release E) vs endergonic (use E).
Enzymes enhance rate at which a reaction occurs by lowering Ea. Enzymes stabilize the transition state by binding it with greater affinity than the substrate.
But they speed up reactions in BOTH directions. When S binds to active site, molecules are distorted to have a confirmation that approaches that of the transition state.
Enzymes are highly specific for the reactions they catalyse, and substrate needs to be in a specific orientation.
What factors affect enzyme activity?
a) Temperature – rate of reaction will increase, but after a certain temp the protein will be denatured.
b) pH - most have max activity between 6-8. Some AA side chains of enzyme need to be protonated/deprotonated for substrate binding or catalysis (pH above or below average), but extremes of pH disrupt h-bonds and destabilize protein.
c) Cofactors
d) Substrate concentration, but saturation kinetics
How is energy released from our foods?
Our main fuels (carbs, fats, proteins) contain lots of reduced bonds, which are electrons not shared with O (i.e. C-H, C-C etc). We oxidize the food we eat by adding O, and we get the energy out of it by breaking the reduced bonds. Therefore, oxidation of sugars and fats releases energy.
This energy can be stored in other molecules that are used to perform work, i.e. ATP, NADH. FADH2, acetyl CoA. Energy can also be stored in ion gradients and other high energy phosphate bonds.
What is ATP and how does it work?
ATP: adenosine triphosphate. ATP hydrolyses to ADP (exergonic reaction).
ATP – ADP + P. ADP can have a P added to it to get ATP again but requires energy. ATP hydrolysis yields 29.3 kJ/mol, so energetically unfavorable reactions can be driven by ATP hydrolysis.
What is redox potential?
Redox: OIL RIG
E’ = redox potential. More negative E’ more readily donated electron. When electron passes from a compound with negative E’ to positive, energy is released.
NADH is an electron carrier, and is the cellular currency of reductive potential energy produced during respiration. FADH2 is also an electron carrier.
Define exon, intron, promoter and codon
Exon – Coding part of a gene
Intron – Non-coding part
Promoter – a site on DNA to which the enzyme RNA polymerase can bind to initiate the transcription of DNA into RNA
Codons – a sequence of three nucleotides which together form a unit of genetic code in a DNA or RNA molecule.
What is a Polyadenylation Signal?
Polyadenylation the addition of a poly(A) tail to a messenger RNA. In eukaryotes, polyadenylation is part of the process that produces mature messenger RNA (mRNA) for translation. The signal is required for transcription termination.
Define a gene and genome.
Gene – Fundamental physical and functional unit of heredity, carries info from 1 generation to next. It’s a segment of DNA composed of a transcribed region and regulatory sequences.
Genome – entire complement of genetic material in a chromosome set. An organism’s unique and complete set of genetic info (DNA).
What are the features of DNA?
- A-T and G-C = Adenine, Thymine, Guanine, Cytosine
- 2 strands
- Double Helix
- Sugar: Deoxyribose
- Polymer of nucleotides
What are the features of RNA?
- A-U, G-C - Uracil
- Single strand
- Can form complex secondary structures
- Sugar: ribose
- Polymer of ribonucleotides
What are the features of nucleotides?
Nucleotide = Nitrogenous base + pentose monosaccharide + phosphate: (If it doesn’t have a phosphate group then its a nucleoside). It links to others by dehydration reaction causing glycosidic bond.
Nucleotide is negative because of phosphate group, which is why it interacts with positive amino acids.
What is the difference between DNA and RNA?
The difference between DNA and RNA is that Ribose has an OH- group where deoxyribose just has an H.
What are the nitrogenous bases for DNA and RNA?
- Purines (2 rings)
- G – Guanine
- A - Adenine - Pyrimidines (1 ring)
- C – Cytosine
- T – Thymine (DNA only)
- U – Uracil (RNA only)
A purine always couples with a Pyrimidine – large with small so the radius stays the same. A=T and C=-G. G and C form 3 H-bonds instead of 2.
What are the terminals of DNA?
The base joins the 1’ carbon, and phosphate to the 5’. DNA has 5’ and 3’ terminus. The primary structure (sequence of nucleotides) goes from 5’ to 3’. The secondary structure involves two strands of DNA running ANTIPARALLEL.
H-bonds between complementary bases keeps them together and keeps P’s facing outwards.
How does replication take place?
To begin, the strands are separated at A=T rich areas (only 2 H-bonds, not 3) with the aid of initiator proteins. The DNA helix then unwinds and separates into templates. Separation and therefore replication occurs at multiple points on DNA strand.
Replication requires replication of ALL DNA – new cells need all info from parents.
The process is semiconservative because the old DNA strands are incorporated into two new ones.
P (at 5’) of incoming nucleotide joins 3’ C of nucleotide on growing strand on DNA, catalyzed by DNA polymerase. Replication is always 5’ to 3’ (of new strand).
What is the leading/lagging strand?
Out of the two parent strands, one complementary strand (leading strand – parent is orientated 5’ to 3’, and new nucleotides are laid down 5’ to 3’ in opposite direction, i.e. towards rest of coiled DNA) is made continuously, and one (lagging strand) in fragments. Synthesis is always in 5’-3’ direction of complementary strand. The strand made towards rest of uncoiled DNA is the leading strand.
What are the steps in lagging strand synthesis?
Lagging strand synthesis is discontinuous:
- Short RNA Primers are synthesized by Primase, copied from DNA
- DNA polymerase III elongates RNA primers with new DNA
- DNA polymerase I removes RNA and fills in gaps
- DNA ligase connects adjacent fragments (seals strands)
BUT once last primer is removed, you get one shortened chromosome, so need DNA polymerase to add back nucleotides lost = telomeres.
DNA polymerase has proof reading activity, so if incorrect nt is inserted, it can remove and correct it
What is the central dogma?
DNA is transcribed into mRNA, which is translated in a polypeptide (protein).
What are the main types of RNA in the process?
Main types of RNA to make a protein:
- mRNA (messenger) – code
- tRNA (transfer) – one for each amino acid
- rRNA (ribosomal) – part of ribosomes
How is RNA transcribed?
Transcription is always 5’ to 3’ of RNA, and only one DNA strand is used = template strand (or antisense). The other strand is the coding strand (or sense) as the mRNA mimics this strand, except T becomes U and nucleotides are ribinucleotides. RNA and template strand are antiparallel.
How is the promoter used?
Promoter – upstream at 5’ side of CODING strand of DNA. It’s involved in the initiation of transcription. Enzyme that transcribes RNA (RNA Polymerase) binds here with the help of Transcription Factors (other proteins that need to beat promoter first). RNA synthesis starts on promoter side, which is actually 3’ of template strand and therefore RNA goes 5’ to 3’.
What are the start and stop codons?
Start codon: Met (AUG)
Stop Codons: Stop (UAA, UAG and UGA)
What are transcription factors?
Transcription Factors are accessory proteins and have a role in all aspects of transcription. They are ‘general’ or ‘cell-specific’. The latter allows for unique genes to be expressed.
What is mature mRNA?
The entire gene sequence is transcribed into mRNA (‘pre-RNA’, about same length as DNA), and then non-coding introns are spliced out and the exons are spliced together to make the mature mRNA. Other modification, i.e. adding chemical groups, are also made.
How is mRNA translated?
mRNA must be transported through pores in nuclear envelope into cytosol before it can be translated.
tRNA (transfer) binds AA’s to form aminoacyl-tRNA and delivers them to mRNA. Binds to tRNA anticodon, which is complementary to mRNA codon. rRNA (ribosomal) combines with protein to make ribosome.
How is the code read?
Triplets of nucleotides = codons, each of which specifies one of the 20 amino acids in our proteins. 64 codons.
Initiation codon = AUG = methionine (met). Met is always the first AA made during translation.
Stop codons – there are 3: UAA, UAG and UGA.
Almost every AA is encoded by more than 1 codon. Sequence of triplets is read from 5’ to 3’ as an uninterrupted reading frame. Translated into a N-terminus to C terminus polypeptide.
What are the staged of protein synthesis?
Protein is synthesized in four stages:
- amino acid activation – need E input, then it binds to tRNA. Need enzymes to catalyze reactions.
- Initiation – everything comes together, activated AA-tRNA, ribosomes, mRNA.
- elongation
- termination
Many ribosomes may translate one mRNA molecule simultaneously – structure known as polysome.
What are regulatory sequences?
Regulatory sequences are binding sites for gene regulatory proteins. Can be near or far from promoter, or within introns.
What is the difference between centrosomes, centrioles and centromeres?
Centrosomes – main place where microtubules get organized, regulates cell division cycle. It’s a pair of centrioles at right angles to each other. Only have one per cell until cell prepares to divide.
Centrioles – Small set of microtubules arranged in a specific way. Two at right angles are a centrosome.
Centromere – middle bit that links sister chromatids. Kinetochore is a part of the centromere where spindles attach during mitosis.
Which protein keeps sister chromatids together?
Cohesin
