Biology 1A: module 1 + module 2

Midterm 1

structure and function

2 ways of defining life

What are the 7 conditions that classify things as living?

movement, respiration, sensitivity, nutrition, excretion, reproduction and growth

cell theory

1. All living organisms are composed of one or more cells.
2. The cell is the basic unit of structure and organization in organisms.
3. Cells arise from pre-existing cells.
4. Hereditary info is passed from cell to cel
5. Energy flow occurs within cells
6. All cells have the same basic chemical composition

taxonomy

scientific study of naming defining classifying groups of biological organisms base on shared characteristics

prokaryotic cell characteristics

no membrane bound nucleus, usually smaller + singled celled, membrane bound organelles are rare (simple bag)

eukaryotic cell characteristics

membrane bound nucleus, usually bigger, membrane bound organelles common

cell membrane

outer layer made of lipids and proteins that regulates what enters and leaves a cell that all cells possess

3 domains of life

Bacteria, Archaea, Eukarya

macromolecule

A very large organic molecule composed of many smaller molecules. They're polymers built from monomers
proteins, lipids, carbohydrates, DNA/RNA

why has carbon evolved to be the backbone of life

It has 4 unpaired valence electrons in its outer shell that can form 4 covalent bonds w/ other atoms to build complex structures

isomer

same molecular formula but different structures

monomer

small unit that can join together with other small units to form polymers

polymer

A long molecule consisting of covalently linked monomers.
ex: carbohydrates and glucose, proteins and amino acid, nucleic acids and nucleotides

dehydration

reaction used to synthesize monomers to form a polymer

hydrolysis

breaks a bond (monomer seperates from the polymer)

condensation reaction

2 molecules are covalently bonded to each other with the loss of a small molecule

carbohydrate

sugars and polymers of sugars

monomers and polymers of carbohydrates

monosaccaride, disaccaride, polysaccharide

monosaccharide

simplest carbohydrate - have molecular formulas that are usually multiples of CH2O and have a carbonyl group (oxygen double bonded to carbon) and multiple hydroxyl groups (OH groups)

aldehyde sugars

carbohydrates where the carbonyl group is at the end of the chain

ketones

carbohydrates where the carbonyl is within the body of the carbon chain

disaccarhide (+ how they form)

forms when a dehydration reaction joins 2 monosaccharides

glycosidic linkage

covalent bond b/w 2 monosaccharides

sucrose

dissarcharide that is glucose +fructose

polysaccharide

polymers with a few hundred to a few thousand monosaccarhide

amylose

linear unbranched substance in starch joined by 1-4 linkages

amylopectin

somewhat branched substance of starch - branching comes from 1-6 linkages but has mainly 1-4 linkages

starch

stored energy - composed of amylose and amylopectin

glycogen

extensively branched polymer of glucose

• extensive branched structure fits the function as more branching has more free ends that are available for breakdown

cellulose

polysaccharide that a major component of tough cells walls

• has 1-4 linkages like starch but monomers are bonded in B config that allow glucose monomers to hydrogen bond and allow it to be tough and be used for structural support

lipids

diverse group of hydrophobic molecules - most important are fats, phospholipids and steroids

monomer, polymer of lipid

fatty acids, lipids

fats

lipid composed of a glycerol (3 carbons with oh groups attached - leaves during dehydration reaction to join to fatty acid) joined to 3 fatty acids

• major function is energy storage (gains lots of energy from hydrocarbon chain)

ester linkage

bond between a hydroxyl group and a carboxyl group

saturated fat

fat that has lots of hydrogens

unsaturated fat

less hydrogens and has double bond that prevent it from packing together tightly to be a solid @room temp

phospholipid

composed of a glycerol joined to 2 fatty acids and a phosphate group

• phosphate group confers properties to it - hydrophobic tail from hydrocarbon tails and hydrophilic head from phosphate group

steroid

lipids characterized by a carbon skeleton consisting of four fused rings

nucleic acids

store, transmit, and help express hereditary information

monomer, polymer of nucleic acids

nucleotide, polynucleotide

what are the 3 parts of a nucleotide

phosphate group, sugar and nitrogenous base

nucleic acids differ in

sugar base and nitrogenous base

• dna lacks a hydroxyl group on 5 ringed sugar

• thymine in dna and uracil in rna

DNA

stores hereditary information

RNA

various functions in gene expression, including carrying instructions from DNA to ribosomes

Chargaff’s Rule

in DNA, there is always equality in quantity between the bases A and T and between G and C

synthesis of dna

2 phosphate groups are removed to create sugar phosphate backbone (condensation reaction)

polypeptide

polymer of amino acids

structure of amino acid

amino, carbonyl group and functional group that gives properties

proteins

A biologically functional molecule consisting of one or more polypeptides folded and coiled into a specific three-dimensional structure

monomer, polymer of proteins

amino acid, dipeptide, polypeptide

peptide bonds

covalent bonds that links amino acids

primary structure

amino acid sequence

secondary structure

coils and folds of polypeptides

regions stabilized by hydrogen bonds between atoms of the polypeptide backbone

tertiary structure

r group interactions

• interactions include hydrogen bonding, hydrophobic interactions and van der Waals interaction

disulfide bridge

strong covalent bonds that may reinforce protein structure

quaternary structure

2 or more different polypeptide chains form one molecule (not present in all proteins)

3 ideas of central dogma

1. Genetic information generally flows in a single direction from DNA to RNA to protein

2. DNA is used as a template to synthesize RNA in a process known as transcription

3. RNA is used as a template to synthesize proteins in a process known as translation

transcription

RNA polymerase synthesizes a new mRNA strand from the template strand of DNA in the 5' to 3' direction

translation

Ribosomes and tRNA molecules use mRNA template to synthesize proteins

dna template strand

provides the template for sequences of nucleotides in rna transcription

coding strand

strand identical to rna transcript

3 phases of translation

initiation: 2 subunits of a ribosome and tRNA form complex at mRNA start site

elongation: amino acids are added one by one to the C terminus of the growing peptide chain

termination: translation ends when a stop codon in the mRNA reaches the A site

anticodon

part of trna that is complimentary to aug to initiate translation

gene

sequence of nucleotides that are transcribed into RNA

parts of a gene

promoter, intron and exon

promoter

region located most proximal to the start site; signals the start of transcription

exon

sequence of nucleotides in a gene that is included or expressed as part of a functional protein; coding sequence

intron

sequence of nucleotides in a gene that interrupts the sequence of amino acids that are not included or expressed as part of a functional protein; non coding sequence s

spliceosome

processes the pre-mRNA into mature RNA

point mutation

change in the DNA sequence that affects a single base and by extension a single codon and maybe an amino acid

silent mutation

when there is no change in the amino acid sequence

missense mutation

sequence change results in a different codon

nonsense mutation

changes a normal codon into a stop codon

frameshift mutation

involves the insertion or deletion of a nucleotide in the DNA sequence

base pair insertion/ deletion

frameshift causing extensive missense

3 nucleotide insertion/deletion

extra/ missing amino acids - later amino acids are still the same

loss of function

results in an inactive or less active protein

gain of function

results in a more active protein

major difference in plant and animal cells

plants cells have: cell wall and chloroplasts & vacuole.

plasma membrane

phospholipid bilayer that acts as a selective bilayer

nucleus

houses genetic instructions

ribosome

Makes proteins and carries out genetic instructions

ribsomes synthesize proteins

In the cytosol (free ribosomes)
On the outside of the endoplasmic reticulum or the nuclear envelope (bound ribosomes)

smooth ER

synthesizes lipids, detoxifies drugs and posisons, and store calcium ions

rough ER

aids in synthesis of secretory and other proteins on bound ribosomes; adds carbohydrates to proteins to make glycoproteins; produces new membrane

golgi apparatus

system of membranes that modifies products of the ER, sorts and packages proteins for export by the cell into transport votes "the packaging unit"

vacuole

large membrane-bound vesicle that is important for digestion, storage, and waste disposal

lysosome

membranous sac of hydrolytic enzymes, which the cell uses to digest unwanted materials and macromolecules - eats other proteins and organelles

peroxisomes

specialized metabolic compartments that contain oxidation enzymes- changes hydrogen peroxide into water

mitochondria

sites of cellular respiration, the metabolic process that uses oxygen to generate ATP

central vacuole

major role in the growth of plants - contains sap and is a main repository of inorganic molecules

chloroplast

performs photosynthesis and has cholorphyll

photosynthesis

process by which plants and some other organisms use light energy to convert water and carbon dioxide into oxygen and high-energy carbohydrates such as sugars and starches

photoautotroph

Organisms that use light as a source of energy to synthesize organic substances from CO2

heterotroph

Dependent on photoautotrophs for food, either directly or indirectly

chemotroph

Use energy of inorganic molecules to make organic molecules from CO2

what bonds are present in cellulose

1-4 beta

what bonds are present in starch

1-4 and 1-6 alpha

what bonds are present in glycogen

1-6

alpha helix

a coil in the secondary structure of an protein held by H-bond every 4th amino acid